core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) Checking for fconfig files in pwd and ./rosetta/flags core.init: (1) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (0) command: /opt/rosetta/3.13/main/source/bin/docking_protocol.mpi.linuxiccrelease @/test/playground/5T35.ppdock/docking.flag core.init: (2) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (2) command: /opt/rosetta/3.13/main/source/bin/docking_protocol.mpi.linuxiccrelease @/test/playground/5T35.ppdock/docking.flag core.init: (1) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (1) command: /opt/rosetta/3.13/main/source/bin/docking_protocol.mpi.linuxiccrelease @/test/playground/5T35.ppdock/docking.flag basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-1894040954 seed_offset=0 real_seed=-1894040954 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-1894040954 RG_type=mt19937 core.init: (0) Resolved executable path: /opt/rosetta/3.13/main/source/build/src/release/linux/4.18/64/x86/icc/19.1/mpi/docking_protocol.mpi.linuxiccrelease core.init: (0) Looking for database based on location of executable: /opt/rosetta/3.13/main/database/ basic.random.init_random_generator: (1) 'RNG device' seed mode, using '/dev/urandom', seed=1614983385 seed_offset=0 real_seed=-1894040953 basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=-1894040953 RG_type=mt19937 core.init: (1) Resolved executable path: /opt/rosetta/3.13/main/source/build/src/release/linux/4.18/64/x86/icc/19.1/mpi/docking_protocol.mpi.linuxiccrelease core.init: (1) Looking for database based on location of executable: /opt/rosetta/3.13/main/database/ basic.random.init_random_generator: (2) 'RNG device' seed mode, using '/dev/urandom', seed=814137867 seed_offset=0 real_seed=-1894040952 basic.random.init_random_generator: (2) RandomGenerator:init: Normal mode, seed=-1894040952 RG_type=mt19937 core.init: (2) Resolved executable path: /opt/rosetta/3.13/main/source/build/src/release/linux/4.18/64/x86/icc/19.1/mpi/docking_protocol.mpi.linuxiccrelease core.init: (2) Looking for database based on location of executable: /opt/rosetta/3.13/main/database/ basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (2) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (2) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (2) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (2) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (2) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: (2) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.etable: (2) Starting energy table calculation core.scoring.etable: (0) Starting energy table calculation core.scoring.etable: (1) Starting energy table calculation core.scoring.etable: (2) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (2) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (2) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (1) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (1) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (1) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (0) Finished calculating energy tables. basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv core.scoring.etable: (2) Finished calculating energy tables. basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.etable: (1) Finished calculating energy tables. basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: (2) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 0.945812 seconds. core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.945599 seconds. basic.io.database: (2) Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 0.958261 seconds. basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (2) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (2) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (2) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (2) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (2) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: (2) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (2) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (2) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (2) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (1) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (0) Reading options... core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (0) pushed /test/playground/5T35.ppdock/5T35.pdb nstruct indices 1 - 3 protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 1 of 3 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (2) Reading options... core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 protocols.jd2.PDBJobInputter: (2) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (2) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (2) pushed /test/playground/5T35.ppdock/5T35.pdb nstruct indices 1 - 3 protocols.evaluation.ChiWellRmsdEvaluatorCreator: (2) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 1 to node 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 1 from master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 2 of 3 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.PDBJobInputter: (2) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (2) filling pose from PDB /test/playground/5T35.ppdock/5T35.pdb core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (1) Reading options... core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.jd2.PDBJobInputter: (1) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (1) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (1) pushed /test/playground/5T35.ppdock/5T35.pdb nstruct indices 1 - 3 protocols.evaluation.ChiWellRmsdEvaluatorCreator: (1) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 2 to node 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 3 of 3 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 2 from master. protocols.jd2.PDBJobInputter: (1) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (1) filling pose from PDB /test/playground/5T35.ppdock/5T35.pdb core.import_pose.import_pose: (2) File '/test/playground/5T35.ppdock/5T35.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (1) File '/test/playground/5T35.ppdock/5T35.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: (2) Adding undetected upper terminus type to residue 111, 459 E core.io.pose_from_sfr.PoseFromSFRBuilder: (2) Adding undetected upper terminus type to residue 451, 207 H core.conformation.Conformation: (2) [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 111 core.conformation.Conformation: (2) [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 451 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (2) Reading options... core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 protocols.docking.DockingProtocol: (2) Danger Will Robinson! Native is an impostor! protocols.docking.DockingProtocol: (2) Setting docking foldtree protocols.docking.DockingProtocol: (2) old fold tree: FOLD_TREE EDGE 1 111 -1 EDGE 1 112 1 EDGE 1 113 2 EDGE 113 216 -1 EDGE 1 217 3 EDGE 217 304 -1 EDGE 1 305 4 EDGE 305 451 -1 EDGE 1 452 5 protocols.docking.DockingProtocol: (2) new fold tree: FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (2) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (2) /// /// protocols.docking.DockingProtocol: (2) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (2) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// core.io.pose_from_sfr.PoseFromSFRBuilder: (1) Adding undetected upper terminus type to residue 111, 459 E core.io.pose_from_sfr.PoseFromSFRBuilder: (1) Adding undetected upper terminus type to residue 451, 207 H core.chemical.GlobalResidueTypeSet: (2) Finished initializing centroid residue type set. Created 71 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 0.027265 seconds. core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 111 core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 451 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (1) Reading options... core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.docking.DockingProtocol: (1) Danger Will Robinson! Native is an impostor! protocols.docking.DockingProtocol: (1) Setting docking foldtree protocols.docking.DockingProtocol: (1) old fold tree: FOLD_TREE EDGE 1 111 -1 EDGE 1 112 1 EDGE 1 113 2 EDGE 113 216 -1 EDGE 1 217 3 EDGE 217 304 -1 EDGE 1 305 4 EDGE 305 451 -1 EDGE 1 452 5 protocols.docking.DockingProtocol: (1) new fold tree: FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (1) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (1) /// /// protocols.docking.DockingProtocol: (1) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (1) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// core.chemical.GlobalResidueTypeSet: (1) Finished initializing centroid residue type set. Created 71 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 0.025602 seconds. protocols.docking.DockingProtocol: (2) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (2) dock_pert: true protocols.docking.DockingInitialPerturbation: (2) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (2) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (2) sliding into contact protocols.docking.DockingInitialPerturbation: (2) Moving away protocols.docking.DockingInitialPerturbation: (2) Moving together protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -11.1843 -42.0525 1.32253 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.8534 -41.1115 1.25138 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.8534 -41.1115 1.25138 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.5225 -40.1706 1.18022 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.5225 -40.1706 1.18022 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.1916 -39.2296 1.10906 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -10.1916 -39.2296 1.10906 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.86067 -38.2886 1.0379 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.86067 -38.2886 1.0379 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.52976 -37.3476 0.966747 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.52976 -37.3476 0.966747 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.19884 -36.4067 0.895589 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.19884 -36.4067 0.895589 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -8.86792 -35.4657 0.824432 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -8.86792 -35.4657 0.824432 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.385585 0.899593 0.205076 -0.801186 0.216201 0.557995 0.457631 -0.379459 0.804105 -9.19884 -36.4067 0.895589 protocols.docking.DockingProtocol: (2) finished initial perturbation protocols.docking.DockingLowRes: (2) in DockingLowRes.apply protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (2) /// /// protocols.docking.DockingLowRes: (2) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (2) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (2) /// Scorefunction: /// protocols.docking.DockingLowRes: (2) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (2) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (2) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (2) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (2) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (2) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (2) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (2) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (2) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (2) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (2) Rotation magnitude: 5 protocols.docking.DockingProtocol: (1) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (1) dock_pert: true protocols.docking.DockingInitialPerturbation: (1) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (1) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (1) sliding into contact protocols.docking.DockingInitialPerturbation: (1) Moving away protocols.docking.DockingInitialPerturbation: (1) Moving together protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -9.54666 -47.3387 12.0045 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -9.27075 -46.4129 11.7462 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -9.27075 -46.4129 11.7462 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.99484 -45.4871 11.4879 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.99484 -45.4871 11.4879 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.71893 -44.5612 11.2297 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.71893 -44.5612 11.2297 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.44302 -43.6354 10.9714 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.44302 -43.6354 10.9714 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.16711 -42.7096 10.7131 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -8.16711 -42.7096 10.7131 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.8912 -41.7837 10.4548 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.8912 -41.7837 10.4548 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.6153 -40.8579 10.1965 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.6153 -40.8579 10.1965 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.33939 -39.9321 9.93818 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.33939 -39.9321 9.93818 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.06348 -39.0063 9.67988 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -7.06348 -39.0063 9.67988 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.78757 -38.0804 9.42159 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.78757 -38.0804 9.42159 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.51166 -37.1546 9.16329 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.51166 -37.1546 9.16329 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.23575 -36.2288 8.905 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.23575 -36.2288 8.905 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -5.95984 -35.3029 8.6467 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -5.95984 -35.3029 8.6467 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.502946 0.86409 -0.0198411 -0.503916 0.311802 0.805511 0.702221 -0.395131 0.592248 -6.23575 -36.2288 8.905 protocols.docking.DockingProtocol: (1) finished initial perturbation protocols.docking.DockingLowRes: (1) in DockingLowRes.apply protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (1) /// /// protocols.docking.DockingLowRes: (1) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (1) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (1) /// Scorefunction: /// protocols.docking.DockingLowRes: (1) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (1) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (1) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (1) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (1) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (1) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (1) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (1) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (1) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (1) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (1) Rotation magnitude: 5 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.2 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.28 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.05 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.24 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.05 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.645 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.16 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.645 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.08 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (2) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.18 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (1) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0 protocols.docking.DockingProtocol: (2) Scoretype: interchain_contact score: -9.5, cutoff: 9.99 protocols.docking.DockingProtocol: (2) Scoretype: interchain_vdw score: 3.43861, cutoff: 1 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Mark current job for repetition, id 1 protocols.jd2.JobDistributor: (2) [ WARNING ] 5T35_pose_0001 reported failure and will retry protocols.jd2.MPIWorkPoolJobDistributor: (2) Job 1 failed! Slave process 2 transmitting failure to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 40 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master node: Received job failure message for job id 1 from node 2. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 1 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Repeating job id 1 protocols.jd2.PDBJobInputter: (2) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (2) filling pose from saved copy /test/playground/5T35.ppdock/5T35.pdb protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (2) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (2) /// /// protocols.docking.DockingProtocol: (2) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (2) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.18 protocols.docking.DockingProtocol: (1) Scoretype: interchain_contact score: -7, cutoff: 9.99 protocols.docking.DockingProtocol: (1) Scoretype: interchain_vdw score: 2.05017, cutoff: 1 protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Mark current job for repetition, id 2 protocols.jd2.JobDistributor: (1) [ WARNING ] 5T35_pose_0002 reported failure and will retry protocols.jd2.MPIWorkPoolJobDistributor: (1) Job 2 failed! Slave process 1 transmitting failure to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 40 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master node: Received job failure message for job id 2 from node 1. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Repeating job id 2 protocols.jd2.PDBJobInputter: (1) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (1) filling pose from saved copy /test/playground/5T35.ppdock/5T35.pdb protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (1) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (1) /// /// protocols.docking.DockingProtocol: (1) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (1) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (2) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (2) dock_pert: true protocols.docking.DockingInitialPerturbation: (2) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (2) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (2) sliding into contact protocols.docking.DockingInitialPerturbation: (2) Moving away protocols.docking.DockingInitialPerturbation: (2) Moving together protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -10.3327 -46.1034 1.85861 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -10.0229 -45.1534 1.81728 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -10.0229 -45.1534 1.81728 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.7132 -44.2035 1.77595 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.7132 -44.2035 1.77595 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.40348 -43.2536 1.73461 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.40348 -43.2536 1.73461 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.09376 -42.3037 1.69328 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -9.09376 -42.3037 1.69328 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.78403 -41.3537 1.65195 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.78403 -41.3537 1.65195 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.47431 -40.4038 1.61061 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.47431 -40.4038 1.61061 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.16458 -39.4539 1.56928 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -8.16458 -39.4539 1.56928 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -7.85486 -38.5039 1.52795 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -7.85486 -38.5039 1.52795 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -7.54513 -37.554 1.48662 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -7.54513 -37.554 1.48662 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.280016 0.948967 0.145094 -0.331998 -0.046088 0.942153 0.90076 -0.311989 0.30215 -7.85486 -38.5039 1.52795 protocols.docking.DockingProtocol: (2) finished initial perturbation protocols.docking.DockingLowRes: (2) in DockingLowRes.apply protocols.docking.DockingProtocol: (1) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (1) dock_pert: true protocols.docking.DockingInitialPerturbation: (1) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (1) sliding into contact for centroid mode protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (2) /// /// protocols.docking.DockingLowRes: (2) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (2) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (2) /// Scorefunction: /// protocols.docking.DockingLowRes: (2) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (2) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (2) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (2) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (2) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (2) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (2) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (2) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (2) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (2) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (2) Rotation magnitude: 5 protocols.docking.DockingInitialPerturbation: (1) sliding into contact protocols.docking.DockingInitialPerturbation: (1) Moving away protocols.docking.DockingInitialPerturbation: (1) Moving together protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -13.8667 -42.9036 6.05107 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -13.4895 -41.9907 5.89494 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -13.4895 -41.9907 5.89494 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -13.1122 -41.0778 5.73881 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -13.1122 -41.0778 5.73881 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -12.735 -40.165 5.58268 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -12.735 -40.165 5.58268 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -12.3578 -39.2521 5.42656 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -12.3578 -39.2521 5.42656 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.9806 -38.3392 5.27043 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.9806 -38.3392 5.27043 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.6034 -37.4264 5.1143 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.6034 -37.4264 5.1143 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.2261 -36.5135 4.95817 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.2261 -36.5135 4.95817 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.442908 0.859179 0.256209 -0.551689 0.0359119 0.833277 0.706733 -0.510413 0.489905 -11.6034 -37.4264 5.1143 protocols.docking.DockingProtocol: (1) finished initial perturbation protocols.docking.DockingLowRes: (1) in DockingLowRes.apply protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (1) /// /// protocols.docking.DockingLowRes: (1) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (1) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (1) /// Scorefunction: /// protocols.docking.DockingLowRes: (1) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (1) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (1) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (1) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (1) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (1) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (1) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (1) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (1) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (1) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (1) Rotation magnitude: 5 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.46 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.14 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.16 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.05 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.08 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.05 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.14 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.645 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.645 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.12 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.24 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.12 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (2) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.3 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (1) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0 protocols.docking.DockingProtocol: (1) Scoretype: interchain_contact score: -4.5, cutoff: 9.99 protocols.docking.DockingProtocol: (1) Scoretype: interchain_vdw score: 1.78542, cutoff: 1 protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Mark current job for repetition, id 2 protocols.jd2.JobDistributor: (1) [ WARNING ] 5T35_pose_0002 reported failure and will retry protocols.jd2.MPIWorkPoolJobDistributor: (1) Job 2 failed! Slave process 1 transmitting failure to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 40 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master node: Received job failure message for job id 2 from node 1. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Repeating job id 2 protocols.jd2.PDBJobInputter: (1) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (1) filling pose from saved copy /test/playground/5T35.ppdock/5T35.pdb protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (1) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (1) /// /// protocols.docking.DockingProtocol: (1) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (1) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_missing_sidechains: (2) packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 2 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 3 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 4 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 5 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 6 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 7 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 8 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 9 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 12 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 13 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 14 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 15 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 16 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 17 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 18 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 19 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 20 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 21 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 22 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 23 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 24 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 25 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 26 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 27 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 28 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 29 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 30 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 31 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 32 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 33 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 34 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 35 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 36 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 37 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 39 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 40 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 41 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 42 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 43 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 44 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 45 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 46 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 47 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 48 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 49 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 50 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 51 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 52 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 53 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 54 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 55 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 56 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 57 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 58 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 59 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 60 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 61 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 62 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 63 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 64 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 65 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 66 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 67 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 68 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 69 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 70 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 72 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 73 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 74 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 75 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 76 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 77 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 78 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 79 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 80 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 81 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 82 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 83 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 84 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 85 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 86 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 87 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 88 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 89 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 90 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 91 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 92 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 93 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 94 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 95 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 96 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 97 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 98 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 99 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 100 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 101 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 102 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 103 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 104 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 105 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 106 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 107 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 108 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 109 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 110 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 111 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 112 because of missing atom number 1 atom name CBX core.pack.pack_missing_sidechains: (2) packing residue number 113 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 114 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 115 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 116 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 117 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 118 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 119 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 120 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 121 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 122 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 123 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 124 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 125 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 126 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 127 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 128 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 129 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 130 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 131 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 132 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 133 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 134 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 135 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 136 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 137 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 138 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 139 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 140 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 141 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 142 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 143 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 144 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 146 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 147 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 148 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 149 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 150 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 151 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 152 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 153 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 154 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 155 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 156 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 157 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 158 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 159 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 160 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 161 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 162 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 163 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 164 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 165 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 167 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 168 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 169 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 171 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 172 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 174 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 175 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 176 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 177 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 178 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 179 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 180 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 181 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 182 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 183 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 184 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 185 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 186 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 187 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 189 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 190 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 191 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 192 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 193 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 194 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 195 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 197 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 198 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 199 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 200 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 201 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 202 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 203 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 204 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 205 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 206 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 207 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 208 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 209 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 210 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 211 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 212 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 213 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 214 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 215 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 216 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 217 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 218 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 219 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 220 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 221 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 222 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 223 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 224 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 225 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 226 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 228 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 229 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 230 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 231 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 232 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 233 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 234 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 235 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 236 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 237 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 238 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 240 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 242 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 243 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 244 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 245 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 246 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 247 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 248 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 250 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 251 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 252 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 253 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 254 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 255 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 256 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 257 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 258 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 260 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 261 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 262 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 263 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 264 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 265 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 266 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 267 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 268 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 269 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 270 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 271 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 272 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 273 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 274 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 275 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 276 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 277 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 278 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 279 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 280 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 281 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 282 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 283 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 284 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 285 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 286 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 287 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 288 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 289 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 290 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 291 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 292 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 293 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 294 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 295 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 296 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 297 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 298 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 299 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 300 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 301 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 302 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 303 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 304 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 305 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 306 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 307 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 308 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 309 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 310 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 311 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 312 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 313 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 314 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 315 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 316 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 317 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 318 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 319 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 320 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 321 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 322 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 323 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 324 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 325 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 326 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 327 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 328 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 329 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 330 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 331 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 332 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 333 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 334 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 335 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 336 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 338 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 339 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 340 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 341 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 342 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 343 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 344 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 345 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 346 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 347 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 349 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 351 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 352 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 353 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 354 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 355 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 356 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 357 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 359 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 360 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 361 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 362 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 363 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 364 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 365 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 366 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 368 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 369 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 370 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 372 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 373 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 374 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 375 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 376 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 377 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 378 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 379 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 380 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 381 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 382 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 383 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 384 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 385 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 386 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 387 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 389 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 390 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 391 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 392 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 393 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 394 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 395 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 396 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 397 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 398 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 399 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 400 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 401 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 402 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 403 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 404 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 405 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 406 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 407 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 408 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 409 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 410 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 411 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 412 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 413 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 414 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 415 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 416 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 417 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 418 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 419 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 420 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 421 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 422 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 423 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 424 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 425 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 426 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 427 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 428 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 429 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 430 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 431 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 432 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 433 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 434 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 435 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 436 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 437 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 438 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 439 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 440 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 441 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 442 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 443 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 444 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 445 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 446 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 447 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 448 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 449 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 450 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 451 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 452 because of missing atom number 1 atom name NBM basic.io.database: (2) Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: (2) Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: (2) shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: (2) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: (2) Binary rotamer library selected: /opt/rosetta/3.13/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: (2) Using Dunbrack library binary file '/opt/rosetta/3.13/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. protocols.docking.DockingProtocol: (1) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (1) dock_pert: true protocols.docking.DockingInitialPerturbation: (1) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (1) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (1) sliding into contact protocols.docking.DockingInitialPerturbation: (1) Moving away protocols.docking.DockingInitialPerturbation: (1) Moving together protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -12.4887 -52.3512 6.31375 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -12.2 -51.4047 6.16982 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -12.2 -51.4047 6.16982 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.9112 -50.4581 6.02589 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.9112 -50.4581 6.02589 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.6225 -49.5116 5.88196 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.6225 -49.5116 5.88196 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.3337 -48.5651 5.73803 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.3337 -48.5651 5.73803 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.045 -47.6186 5.59409 core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.170279 seconds to load from binary protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -11.045 -47.6186 5.59409 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.7563 -46.672 5.45016 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.7563 -46.672 5.45016 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.4675 -45.7255 5.30623 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.4675 -45.7255 5.30623 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.1788 -44.779 5.1623 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -10.1788 -44.779 5.1623 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.89008 -43.8324 5.01837 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.89008 -43.8324 5.01837 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.60135 -42.8859 4.87444 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.60135 -42.8859 4.87444 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.31262 -41.9394 4.73051 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.31262 -41.9394 4.73051 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.02388 -40.9929 4.58658 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -9.02388 -40.9929 4.58658 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -8.73515 -40.0463 4.44265 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -8.73515 -40.0463 4.44265 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -8.44642 -39.0998 4.29872 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -8.44642 -39.0998 4.29872 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.780823 0.615999 0.104219 -0.378451 0.333638 0.8634 0.497082 -0.713604 0.493638 -8.73515 -40.0463 4.44265 protocols.docking.DockingProtocol: (1) finished initial perturbation protocols.docking.DockingLowRes: (1) in DockingLowRes.apply protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (1) /// /// protocols.docking.DockingLowRes: (1) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (1) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (1) /// Scorefunction: /// protocols.docking.DockingLowRes: (1) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (1) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (1) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (1) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (1) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (1) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (1) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (1) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (1) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (1) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (1) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (1) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (1) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (1) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (1) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (1) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (1) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) protocols.docking.DockingLowRes: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (1) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (1) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (1) Rotation magnitude: 5 core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (2) [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 112 LG1 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.24 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.1 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.05 core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG0 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.645 core.pack.pack_rotamers: (2) built 10168 rotamers at 434 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph protocols.docking.DockingLowRes: (1) Acceptance rate is: 0 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.28 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.12 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (1) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_missing_sidechains: (1) packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 2 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 3 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 4 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 5 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 6 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 7 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 8 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 9 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 12 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 13 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 14 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 15 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 16 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 17 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 18 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 19 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 20 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 21 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 22 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 23 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 24 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 25 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 26 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 27 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 28 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 29 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 30 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 31 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 32 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 33 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 34 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 35 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 36 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 37 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 39 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 40 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 41 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 42 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 43 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 44 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 45 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 46 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 47 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 48 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 49 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 50 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 51 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 52 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 53 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 54 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 55 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 56 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 57 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 58 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 59 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 60 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 61 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 62 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 63 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 64 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 65 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 66 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 67 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 68 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 69 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 70 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 72 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 73 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 74 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 75 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 76 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 77 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 78 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 79 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 80 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 81 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 82 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 83 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 84 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 85 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 86 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 87 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 88 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 89 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 90 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 91 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 92 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 93 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 94 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 95 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 96 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 97 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 98 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 99 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 100 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 101 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 102 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 103 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 104 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 105 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 106 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 107 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 108 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 109 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 110 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 111 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 112 because of missing atom number 1 atom name CBX core.pack.pack_missing_sidechains: (1) packing residue number 113 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 114 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 115 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 116 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 117 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 118 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 119 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 120 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 121 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 122 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 123 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 124 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 125 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 126 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 127 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 128 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 129 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 130 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 131 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 132 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 133 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 134 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 135 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 136 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 137 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 138 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 139 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 140 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 141 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 142 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 143 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 144 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 146 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 147 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 148 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 149 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 150 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 151 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 152 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 153 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 154 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 155 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 156 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 157 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 158 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 159 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 160 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 161 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 162 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 163 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 164 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 165 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 167 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 168 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 169 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 171 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 172 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 174 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 175 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 176 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 177 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 178 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 179 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 180 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 181 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 182 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 183 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 184 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 185 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 186 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 187 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 189 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 190 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 191 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 192 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 193 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 194 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 195 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 197 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 198 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 199 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 200 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 201 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 202 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 203 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 204 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 205 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 206 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 207 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 208 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 209 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 210 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 211 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 212 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 213 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 214 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 215 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 216 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 217 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 218 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 219 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 220 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 221 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 222 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 223 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 224 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 225 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 226 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 228 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 229 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 230 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 231 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 232 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 233 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 234 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 235 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 236 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 237 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 238 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 240 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 242 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 243 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 244 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 245 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 246 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 247 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 248 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 250 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 251 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 252 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 253 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 254 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 255 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 256 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 257 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 258 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 260 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 261 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 262 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 263 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 264 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 265 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 266 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 267 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 268 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 269 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 270 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 271 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 272 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 273 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 274 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 275 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 276 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 277 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 278 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 279 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 280 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 281 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 282 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 283 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 284 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 285 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 286 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 287 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 288 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 289 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 290 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 291 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 292 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 293 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 294 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 295 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 296 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 297 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 298 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 299 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 300 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 301 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 302 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 303 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 304 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 305 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 306 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 307 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 308 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 309 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 310 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 311 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 312 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 313 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 314 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 315 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 316 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 317 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 318 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 319 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 320 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 321 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 322 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 323 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 324 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 325 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 326 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 327 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 328 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 329 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 330 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 331 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 332 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 333 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 334 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 335 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 336 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 338 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 339 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 340 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 341 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 342 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 343 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 344 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 345 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 346 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 347 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 349 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 351 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 352 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 353 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 354 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 355 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 356 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 357 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 359 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 360 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 361 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 362 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 363 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 364 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 365 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 366 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 368 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 369 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 370 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 372 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 373 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 374 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 375 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 376 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 377 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 378 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 379 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 380 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 381 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 382 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 383 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 384 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 385 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 386 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 387 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 389 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 390 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 391 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 392 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 393 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 394 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 395 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 396 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 397 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 398 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 399 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 400 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 401 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 402 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 403 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 404 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 405 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 406 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 407 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 408 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 409 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 410 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 411 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 412 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 413 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 414 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 415 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 416 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 417 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 418 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 419 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 420 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 421 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 422 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 423 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 424 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 425 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 426 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 427 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 428 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 429 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 430 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 431 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 432 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 433 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 434 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 435 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 436 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 437 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 438 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 439 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 440 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 441 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 442 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 443 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 444 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 445 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 446 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 447 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 448 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 449 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 450 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 451 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (1) packing residue number 452 because of missing atom number 1 atom name NBM basic.io.database: (1) Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: (1) Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: (1) Binary rotamer library selected: /opt/rosetta/3.13/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: (1) Using Dunbrack library binary file '/opt/rosetta/3.13/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: (1) Dunbrack 2010 library took 0.165865 seconds to load from binary core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (1) [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 112 LG1 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (1) built 10216 rotamers at 434 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: (2) Score before repack: protocols.docking.DockingProtocol: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2543.900 -2543.900 fa_rep 0.550 2113.518 1162.435 fa_sol 1.000 1511.986 1511.986 fa_intra_rep 0.005 660.894 3.304 fa_intra_sol_xover4 1.000 93.464 93.464 lk_ball_wtd 1.000 -51.968 -51.968 fa_elec 1.000 -603.281 -603.281 pro_close 1.250 50.090 62.613 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -46.471 -46.471 hbond_sc 1.000 -61.410 -61.410 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 1288.578 902.005 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.115 0.072 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: 441.242 core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (2) built 5683 rotamers at 452 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: (2) Score after repack: protocols.docking.DockingProtocol: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2521.036 -2521.036 fa_rep 0.550 492.540 270.897 fa_sol 1.000 1475.240 1475.240 fa_intra_rep 0.005 805.798 4.029 fa_intra_sol_xover4 1.000 92.253 92.253 lk_ball_wtd 1.000 -58.268 -58.268 fa_elec 1.000 -640.062 -640.062 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -50.533 -50.533 hbond_sc 1.000 -65.597 -65.597 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 919.712 643.798 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -798.180 protocols.docking.DockMCMProtocol: (2) in DockMCMProtocol.apply protocols.docking.DockMCMProtocol: (2) Using the DockingTaskFactory. core.pack.rotamer_set.UnboundRotamersOperation: (2) Adding 'unbound' rotamers from /test/playground/5T35.ppdock/5T35.pdb protocols.docking.DockingProtocol: (1) Score before repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2573.813 -2573.813 fa_rep 0.550 7888.487 4338.668 fa_sol 1.000 1528.250 1528.250 fa_intra_rep 0.005 660.894 3.304 fa_intra_sol_xover4 1.000 93.464 93.464 lk_ball_wtd 1.000 -52.922 -52.922 fa_elec 1.000 -612.191 -612.191 pro_close 1.250 50.090 62.613 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -86.398 -86.398 hbond_bb_sc 1.000 -47.354 -47.354 hbond_sc 1.000 -61.410 -61.410 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 1288.578 902.005 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.115 0.072 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: 3592.112 core.io.pose_from_sfr.PoseFromSFRBuilder: (2) Adding undetected upper terminus type to residue 111, 459 E core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG1 core.io.pose_from_sfr.PoseFromSFRBuilder: (2) Adding undetected upper terminus type to residue 451, 207 H core.conformation.Conformation: (2) [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 111 core.conformation.Conformation: (2) [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 451 protocols.docking.DockMCMCycle: (2) Setting up defaults for DockMCMCycle: protocols.docking.DockMCMCycle: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockMCMCycle: (2) /// Dockable Jumps: 1 /// protocols.docking.DockMCMCycle: (2) /// Translation: 0.1 /// protocols.docking.DockMCMCycle: (2) /// Rotation: 5 /// protocols.docking.DockMCMCycle: (2) /// Scorefunction: /// protocols.docking.DockMCMCycle: (2) ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_intra_res_protein: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: (2) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_intra_res_protein_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_hb_env_dep: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: (2) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: (2) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: (2) HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: (2) protocols.docking.DockMCMCycle: (2) protocols.docking.DockMCMCycle: (2) /// Packing scorefunction: /// protocols.docking.DockMCMCycle: (2) ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: exclude_intra_res_protein: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: (2) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: (2) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_intra_res_protein_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_hb_env_dep: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: (2) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: (2) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: (2) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: (2) HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: (2) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: (2) HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: (2) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: (2) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: (2) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: (2) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: (2) protocols.docking.DockMCMCycle: (2) protocols.docking.DockMCMCycle: (2) //////////////////////////////////////////////////////////////////////////////// core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 507 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (1) built 5672 rotamers at 452 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockingProtocol: (1) Score after repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2549.466 -2549.466 fa_rep 0.550 2657.578 1461.668 fa_sol 1.000 1496.953 1496.953 fa_intra_rep 0.005 814.513 4.073 fa_intra_sol_xover4 1.000 92.070 92.070 lk_ball_wtd 1.000 -53.068 -53.068 fa_elec 1.000 -642.002 -642.002 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -86.398 -86.398 hbond_bb_sc 1.000 -50.128 -50.128 hbond_sc 1.000 -60.577 -60.577 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 912.923 639.046 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: 388.702 protocols.docking.DockMCMProtocol: (1) in DockMCMProtocol.apply protocols.docking.DockMCMProtocol: (1) Using the DockingTaskFactory. core.pack.rotamer_set.UnboundRotamersOperation: (1) Adding 'unbound' rotamers from /test/playground/5T35.ppdock/5T35.pdb core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 230 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.io.pose_from_sfr.PoseFromSFRBuilder: (1) Adding undetected upper terminus type to residue 111, 459 E core.io.pose_from_sfr.PoseFromSFRBuilder: (1) Adding undetected upper terminus type to residue 451, 207 H core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 111 core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 451 core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockMCMCycle: (1) Setting up defaults for DockMCMCycle: protocols.docking.DockMCMCycle: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockMCMCycle: (1) /// Dockable Jumps: 1 /// protocols.docking.DockMCMCycle: (1) /// Translation: 0.1 /// protocols.docking.DockMCMCycle: (1) /// Rotation: 5 /// protocols.docking.DockMCMCycle: (1) /// Scorefunction: /// protocols.docking.DockMCMCycle: (1) ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_intra_res_protein: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: (1) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_intra_res_protein_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_hb_env_dep: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: (1) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: (1) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: (1) HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: (1) protocols.docking.DockMCMCycle: (1) protocols.docking.DockMCMCycle: (1) /// Packing scorefunction: /// protocols.docking.DockMCMCycle: (1) ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: exclude_intra_res_protein: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockMCMCycle: (1) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockMCMCycle: (1) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_intra_res_protein_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_hb_env_dep: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockMCMCycle: (1) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockMCMCycle: (1) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockMCMCycle: (1) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockMCMCycle: (1) HBondOptions::show: fade_energy_: 1 protocols.docking.DockMCMCycle: (1) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: Mbhbond: false protocols.docking.DockMCMCycle: (1) HbondOptions::show: mphbond: false protocols.docking.DockMCMCycle: (1) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockMCMCycle: (1) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockMCMCycle: (1) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockMCMCycle: (1) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockMCMCycle: (1) protocols.docking.DockMCMCycle: (1) protocols.docking.DockMCMCycle: (1) //////////////////////////////////////////////////////////////////////////////// core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 834 rotamers at 26 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 240 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 319 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 358 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 334 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 204 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 373 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 201 rotamers at 10 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.170548 0.97565 0.137917 -0.253156 -0.0918834 0.963052 0.952274 -0.199161 0.231321 -7.63359 -37.6606 -3.3607 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.170548 0.97565 0.137917 -0.253156 -0.0918834 0.963052 0.952274 -0.199161 0.231321 -328.931 -979.185 -104.849 protocols.docking.DockingProtocol.metrics: (2) unbound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2508.448 -2508.448 fa_rep 0.550 347.078 190.893 fa_sol 1.000 1458.613 1458.613 fa_intra_rep 0.005 806.623 4.033 fa_intra_sol_xover4 1.000 91.552 91.552 lk_ball_wtd 1.000 -56.350 -56.350 fa_elec 1.000 -641.853 -641.853 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -51.631 -51.631 hbond_sc 1.000 -65.182 -65.182 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 916.551 641.586 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -885.689 protocols.docking.DockingProtocol.metrics: (2) bound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2519.127 -2519.127 fa_rep 0.550 348.257 191.541 fa_sol 1.000 1475.701 1475.701 fa_intra_rep 0.005 806.623 4.033 fa_intra_sol_xover4 1.000 91.552 91.552 lk_ball_wtd 1.000 -54.805 -54.805 fa_elec 1.000 -659.128 -659.128 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -53.077 -53.077 hbond_sc 1.000 -66.239 -66.239 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 916.551 641.586 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -896.864 protocols.docking.DockingProtocol.metrics: (2) unbound energy: -885.689 protocols.docking.DockingProtocol.metrics: (2) bound energy: -896.864 protocols.docking.DockingProtocol.metrics: (2) interaction energy: -11.1753 protocols.docking.DockingProtocol.metrics: (2) rb_jump: 1 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.170548 0.97565 0.137917 -0.253156 -0.0918834 0.963052 0.952274 -0.199161 0.231321 -7.63359 -37.6606 -3.3607 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.170548 0.97565 0.137917 -0.253156 -0.0918834 0.963052 0.952274 -0.199161 0.231321 -328.931 -979.185 -104.849 protocols.docking.DockingProtocol.metrics: (2) unbound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2508.448 -2508.448 fa_rep 0.550 347.078 190.893 fa_sol 1.000 1458.613 1458.613 fa_intra_rep 0.005 806.623 4.033 fa_intra_sol_xover4 1.000 91.552 91.552 lk_ball_wtd 1.000 -56.350 -56.350 fa_elec 1.000 -641.853 -641.853 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -51.631 -51.631 hbond_sc 1.000 -65.182 -65.182 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 916.551 641.586 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -885.689 protocols.docking.DockingProtocol.metrics: (2) bound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2519.127 -2519.127 fa_rep 0.550 348.257 191.541 fa_sol 1.000 1475.701 1475.701 fa_intra_rep 0.005 806.623 4.033 fa_intra_sol_xover4 1.000 91.552 91.552 lk_ball_wtd 1.000 -54.805 -54.805 fa_elec 1.000 -659.128 -659.128 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -53.077 -53.077 hbond_sc 1.000 -66.239 -66.239 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 916.551 641.586 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -896.864 protocols.docking.DockingProtocol.metrics: (2) unbound energy: -885.689 protocols.docking.DockingProtocol.metrics: (2) bound energy: -896.864 protocols.docking.DockingProtocol.metrics: (2) interaction energy: -11.1753 protocols.docking.DockingProtocol.metrics: (2) rb_jump: 1 core.pack.task: (1) Packer task: initialize from command line() protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Finished job successfully! Sending output request to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 30 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job success message for job id 1 from node 2 blocking till output is done protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received output confirmation from master. Writing output. core.pack.task: (1) Packer task: initialize from command line() protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Finished writing output in 0.171743 seconds. Sending message to master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job output finish message for job id 1 from node 2 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 1 as completed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 3 to node 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: No more jobs to assign, setting next job id to zero protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Finished handing out jobs protocols.jd2.MPIWorkPoolJobDistributorprotocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 3 from master. : (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.PDBJobInputter: (2) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (2) filling pose from saved copy /test/playground/5T35.ppdock/5T35.pdb protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (2) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (2) /// /// protocols.docking.DockingProtocol: (2) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (2) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (2) /// Low Resolution Filter: on /// protocols.docking.DockingProtocol: (2) /// High Resolution Filter: on /// protocols.docking.DockingProtocol: (2) //////////////////////////////////////////////////////////////////////////////// core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 290 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingProtocol: (2) FOLD_TREE EDGE 1 74 -1 EDGE 74 112 -1 EDGE 74 285 1 EDGE 285 217 -1 EDGE 285 304 -1 EDGE 217 216 3 EDGE 304 305 2 EDGE 216 113 -1 EDGE 305 452 -1 protocols.docking.DockingInitialPerturbation: (2) dock_pert: true protocols.docking.DockingInitialPerturbation: (2) option[ docking::dock_pert ]()8 3 protocols.docking.DockingInitialPerturbation: (2) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (2) sliding into contact protocols.docking.DockingInitialPerturbation: (2) Moving away protocols.docking.DockingInitialPerturbation: (2) Moving together protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -7.46898 -43.3681 8.6116 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -7.23105 -42.4235 8.38552 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -7.23105 -42.4235 8.38552 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.99312 -41.4789 8.15944 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.99312 -41.4789 8.15944 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.75519 -40.5342 7.93336 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.75519 -40.5342 7.93336 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.51727 -39.5896 7.70729 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.51727 -39.5896 7.70729 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.27934 -38.645 7.48121 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.27934 -38.645 7.48121 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.484254 0.845322 0.225673 -0.763059 0.281851 0.581636 0.428064 -0.453861 0.781519 -6.51727 -39.5896 7.70729 protocols.docking.DockingProtocol: (2) finished initial perturbation protocols.docking.DockingLowRes: (2) in DockingLowRes.apply protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) /// Docking Low Res Protocol /// protocols.docking.DockingLowRes: (2) /// /// protocols.docking.DockingLowRes: (2) /// Centroid Inner Cycles: 50 /// protocols.docking.DockingLowRes: (2) /// Centroid Outer Cycles: 10 /// protocols.docking.DockingLowRes: (2) /// Scorefunction: /// protocols.docking.DockingLowRes: (2) ScoreFunction::show(): weights: (interchain_pair 1) (interchain_vdw 1) (interchain_env 1) (interchain_contact 2) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: mhc_epitope_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: netcharge_setup_files: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: aspartimide_penalty_value: 25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: covalent_labeling_fa_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hrf_dynamics_input: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_monomer_fa_elec: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_max_dis: 5.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_min_dis: 1.6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_die: 10 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_no_dis_dep_die: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_die: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D: 80 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_D0: 6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: smooth_fa_elec: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_type: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param1: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_param2: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_fade_hbond: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grp_cpfxn: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: grpelec_context_dependent: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_polarization: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: use_gen_kirkwood: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: protein_dielectric: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: water_dielectric: 78.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: exclude_intra_res_protein: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_hybrid: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: count_pair_full: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: put_intra_into_total: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: eval_intrares_elec_ST_only: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: envsmooth_zero_negatives: false protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_bound_tag: bound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: pb_unbound_tag: unbound protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_wat_penalty: 1.221 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_ref_seq_length_: 9 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_term_length_: 3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_scorecut_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_aa_matrix_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_list_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: nmer_svm_rank_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: hbnet_max_network_size_: 0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: target_clash_pdb_: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_prefix_: traj protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_gz_: FALSE protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: dump_trajectory_stride_: 1 protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_central_atoms_to_score: protocols.docking.DockingLowRes: (2) EnergyMethodOptions::show: bond_angle_residue_type_param_set: none protocols.docking.DockingLowRes: (2) HBondOptions::show: hb_max_energy: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_DNA_DNA: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_protein_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_intra_res_RNA_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: put_intra_into_total_: false protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_self_hbonds: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: use_hb_env_dep_DNA: true protocols.docking.DockingLowRes: (2) HBondOptions::show: smooth_hb_env_dep: true protocols.docking.DockingLowRes: (2) HBondOptions::show: bb_donor_acceptor_check: true protocols.docking.DockingLowRes: (2) HBondOptions::show: decompose_bb_hb_into_pair_energies: false protocols.docking.DockingLowRes: (2) HBondOptions::show: params_database_tag_: ref2015_params protocols.docking.DockingLowRes: (2) HBondOptions::show: use_sp2_chi_penalty_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_BAH180_rise_: 0.75 protocols.docking.DockingLowRes: (2) HBondOptions::show: sp2_outer_width_: 0.357 protocols.docking.DockingLowRes: (2) HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true protocols.docking.DockingLowRes: (2) HBondOptions::show: fade_energy_: 1 protocols.docking.DockingLowRes: (2) HBondOptions::show: exclude_ether_oxygens_: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: Mbhbond: false protocols.docking.DockingLowRes: (2) HbondOptions::show: mphbond: false protocols.docking.DockingLowRes: (2) HBondOptions::show: hbond_energy_shift: 0 protocols.docking.DockingLowRes: (2) HBondOptions::show: water_hybrid_sf: false protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson protocols.docking.DockingLowRes: (2) RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_suite_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_2HOprime_bonus: -0.5 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_sugar_bonus: -1 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: pack_phosphate_penalty: 0.25 protocols.docking.DockingLowRes: (2) FreeDOF_Options::show: free_side_chain_bonus: -0.5 protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) protocols.docking.DockingLowRes: (2) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingLowRes: (2) ::::::::::::::::::Centroid Adaptive::::::::::::::::::: protocols.docking.DockingLowRes: (2) Translation magnitude: 0.7 protocols.docking.DockingLowRes: (2) Rotation magnitude: 5 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.1 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.5 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.2 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.05 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.645 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.1 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.16 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.65721 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.39148 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.15234 core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 326 rotamers at 15 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (2) Rotation magnitude: 1.9371 core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.06 core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_missing_sidechains: (2) packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 2 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 3 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 4 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 5 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 6 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 7 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 8 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 9 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 10 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 12 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 13 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 14 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 15 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 16 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 17 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 18 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 19 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 20 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 21 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 22 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 23 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 24 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 25 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 26 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 27 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 28 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 29 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 30 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 31 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 32 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 33 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 34 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 35 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 36 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 37 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 39 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 40 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 41 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 42 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 43 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 44 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 45 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 46 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 47 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 48 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 49 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 50 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 51 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 52 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 53 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 54 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 55 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 56 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 57 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 58 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 59 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 60 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 61 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 62 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 63 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 64 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 65 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 66 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 67 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 68 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 69 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 70 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 72 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 73 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 74 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 75 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 76 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 77 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 78 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 79 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 80 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 81 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 82 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 83 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 84 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 85 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 86 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 87 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 88 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 89 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 90 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 91 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 92 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 93 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 94 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 95 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 96 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 97 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 98 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 99 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 100 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 101 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 102 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 103 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 104 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 105 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 106 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 107 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 108 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 109 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 110 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 111 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 112 because of missing atom number 1 atom name CBX core.pack.pack_missing_sidechains: (2) packing residue number 113 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 114 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 115 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 116 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 117 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 118 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 119 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 120 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 121 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 122 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 123 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 124 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 125 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 126 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 127 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 128 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 129 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 130 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 131 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 132 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 133 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 134 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 135 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 136 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 137 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 138 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 139 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 140 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 141 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 142 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 143 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 144 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 146 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 147 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 148 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 149 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 150 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 151 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 152 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 153 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 154 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 155 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 156 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 157 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 158 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 159 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 160 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 161 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 162 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 163 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 164 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 165 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 167 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 168 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 169 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 171 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 172 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 174 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 175 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 176 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 177 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 178 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 179 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 180 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 181 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 182 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 183 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 184 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 185 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 186 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 187 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 189 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 190 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 191 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 192 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 193 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 194 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 195 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 197 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 198 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 199 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 200 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 201 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 202 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 203 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 204 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 205 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 206 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 207 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 208 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 209 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 210 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 211 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 212 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 213 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 214 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 215 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 216 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 217 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 218 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 219 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 220 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 221 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 222 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 223 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 224 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 225 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 226 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 228 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 229 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 230 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 231 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 232 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 233 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 234 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 235 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 236 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 237 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 238 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 240 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 242 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 243 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 244 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 245 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 246 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 247 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 248 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 250 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 251 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 252 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 253 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 254 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 255 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 256 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 257 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 258 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 260 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 261 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 262 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 263 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 264 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 265 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 266 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 267 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 268 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 269 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 270 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 271 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 272 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 273 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 274 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 275 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 276 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 277 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 278 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 279 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 280 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 281 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 282 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 283 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 284 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 285 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 286 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 287 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 288 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 289 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 290 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 291 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 292 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 293 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 294 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 295 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 296 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 297 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 298 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 299 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 300 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 301 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 302 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 303 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 304 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 305 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 306 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 307 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 308 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 309 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 310 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 311 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 312 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 313 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 314 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 315 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 316 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 317 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 318 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 319 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 320 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 321 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 322 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 323 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 324 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 325 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 326 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 327 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 328 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 329 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 330 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 331 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 332 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 333 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 334 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 335 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 336 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 338 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 339 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 340 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 341 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 342 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 343 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 344 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 345 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 346 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 347 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 349 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 351 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 352 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 353 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 354 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 355 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 356 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 357 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 359 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 360 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 361 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 362 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 363 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 364 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 365 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 366 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 368 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 369 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 370 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 372 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 373 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 374 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 375 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 376 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 377 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 378 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 379 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 380 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 381 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 382 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 383 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 384 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 385 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 386 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 387 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 389 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 390 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 391 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 392 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 393 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 394 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 395 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 396 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 397 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 398 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 399 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 400 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 401 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 402 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 403 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 404 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 405 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 406 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 407 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 408 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 409 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 410 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 411 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 412 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 413 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 414 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 415 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 416 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 417 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 418 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 419 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 420 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 421 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 422 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 423 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 424 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 425 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 426 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 427 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 428 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 429 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 430 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 431 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 432 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 433 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 434 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 435 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 436 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 437 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 438 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 439 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 440 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 441 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 442 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 443 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 444 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 445 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 446 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 447 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 448 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 449 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 450 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 451 because of missing atom number 6 atom name CB core.pack.pack_missing_sidechains: (2) packing residue number 452 because of missing atom number 1 atom name NBM core.pack.task: (1) Packer task: initialize from command line() core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (2) [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 112 LG1 core.pack.task: (1) Packer task: initialize from command line() core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (2) built 10224 rotamers at 434 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.669997 0.738852 0.0721243 -0.693796 0.588638 0.414912 0.264104 -0.32803 0.906998 -7.8258 -31.0212 7.63897 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.669997 0.738852 0.0721243 -0.693796 0.588638 0.414912 0.264104 -0.32803 0.906998 -335.233 -938.694 270.195 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2504.419 -2504.419 fa_rep 0.550 358.474 197.161 fa_sol 1.000 1456.646 1456.646 fa_intra_rep 0.005 816.019 4.080 fa_intra_sol_xover4 1.000 91.918 91.918 lk_ball_wtd 1.000 -54.650 -54.650 fa_elec 1.000 -636.860 -636.860 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -49.364 -49.364 hbond_sc 1.000 -62.848 -62.848 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 906.663 634.664 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -872.573 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2516.724 -2516.724 fa_rep 0.550 360.299 198.164 fa_sol 1.000 1469.566 1469.566 fa_intra_rep 0.005 816.019 4.080 fa_intra_sol_xover4 1.000 91.918 91.918 lk_ball_wtd 1.000 -54.914 -54.914 fa_elec 1.000 -647.656 -647.656 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -49.837 -49.837 hbond_sc 1.000 -64.437 -64.437 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 906.663 634.664 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -884.075 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -872.573 protocols.docking.DockingProtocol.metrics: (1) bound energy: -884.075 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -11.5021 protocols.docking.DockingProtocol.metrics: (1) rb_jump: 1 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.669997 0.738852 0.0721243 -0.693796 0.588638 0.414912 0.264104 -0.32803 0.906998 -7.8258 -31.0212 7.63897 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.669997 0.738852 0.0721243 -0.693796 0.588638 0.414912 0.264104 -0.32803 0.906998 -335.233 -938.694 270.195 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2504.419 -2504.419 fa_rep 0.550 358.474 197.161 fa_sol 1.000 1456.646 1456.646 fa_intra_rep 0.005 816.019 4.080 fa_intra_sol_xover4 1.000 91.918 91.918 lk_ball_wtd 1.000 -54.650 -54.650 fa_elec 1.000 -636.860 -636.860 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -49.364 -49.364 hbond_sc 1.000 -62.848 -62.848 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 906.663 634.664 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -872.573 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2516.724 -2516.724 fa_rep 0.550 360.299 198.164 fa_sol 1.000 1469.566 1469.566 fa_intra_rep 0.005 816.019 4.080 fa_intra_sol_xover4 1.000 91.918 91.918 lk_ball_wtd 1.000 -54.914 -54.914 fa_elec 1.000 -647.656 -647.656 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -85.431 -85.431 hbond_bb_sc 1.000 -49.837 -49.837 hbond_sc 1.000 -64.437 -64.437 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 906.663 634.664 p_aa_pp 0.600 -87.547 -52.528 yhh_planarity 0.625 0.104 0.065 ref 1.000 110.924 110.924 rama_prepro 0.450 15.935 7.171 --------------------------------------------------- Total weighted score: -884.075 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -872.573 protocols.docking.DockingProtocol.metrics: (1) bound energy: -884.075 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -11.5021 protocols.docking.DockingProtocol.metrics: (1) rb_jump: 1 protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Finished job successfully! Sending output request to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 30 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job success message for job id 2 from node 1 blocking till output is done protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received output confirmation from master. Writing output. protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Finished writing output in 0.169498 seconds. Sending message to master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job output finish message for job id 2 from node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as completed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 1 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 0 from master. protocols.jd2.JobDistributor: (1) no more batches to process... protocols.jd2.JobDistributor: (1) 3 jobs considered, 3 jobs attempted in 52 seconds =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 1094200 RUNNING AT mu03 = KILLED BY SIGNAL: 9 (Killed) =================================================================================== =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 2 PID 1094202 RUNNING AT mu03 = KILLED BY SIGNAL: 9 (Killed) ===================================================================================