[mpiexec@mu03] Launch arguments: /opt/intel/2020/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin//hydra_bstrap_proxy --upstream-host mu03 --upstream-port 34259 --pgid 0 --launcher ssh --launcher-number 0 --base-path /opt/intel/2020/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin/ --tree-width 16 --tree-level 1 --time-left -1 --collective-launch 1 --debug --proxy-id 0 --node-id 0 --subtree-size 1 --upstream-fd 7 /opt/intel/2020/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin//hydra_pmi_proxy --usize -1 --auto-cleanup 0 --abort-signal 9 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=init pmi_version=1 pmi_subversion=1 [proxy:0:0@mu03] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0 [proxy:0:0@mu03] pmi cmd from fd 9: cmd=init pmi_version=1 pmi_subversion=1 [proxy:0:0@mu03] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=get_maxes [proxy:0:0@mu03] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=4096 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=init pmi_version=1 pmi_subversion=1 [proxy:0:0@mu03] PMI response: cmd=response_to_init pmi_version=1 pmi_subversion=1 rc=0 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=get_appnum [proxy:0:0@mu03] PMI response: cmd=appnum appnum=0 [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get_maxes [proxy:0:0@mu03] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=4096 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=get_my_kvsname [proxy:0:0@mu03] PMI response: cmd=my_kvsname kvsname=kvs_1023514_0 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get_maxes [proxy:0:0@mu03] PMI response: cmd=maxes kvsname_max=256 keylen_max=64 vallen_max=4096 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=get kvsname=kvs_1023514_0 key=PMI_process_mapping [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=(vector,(0,1,3)) [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get_appnum [proxy:0:0@mu03] PMI response: cmd=appnum appnum=0 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get_appnum [proxy:0:0@mu03] PMI response: cmd=appnum appnum=0 [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get_my_kvsname [proxy:0:0@mu03] PMI response: cmd=my_kvsname kvsname=kvs_1023514_0 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get_my_kvsname [proxy:0:0@mu03] PMI response: cmd=my_kvsname kvsname=kvs_1023514_0 [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get kvsname=kvs_1023514_0 key=PMI_process_mapping [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=(vector,(0,1,3)) [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get kvsname=kvs_1023514_0 key=PMI_process_mapping [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=(vector,(0,1,3)) [proxy:0:0@mu03] pmi cmd from fd 10: cmd=barrier_in [proxy:0:0@mu03] pmi cmd from fd 6: cmd=put kvsname=kvs_1023514_0 key=-bcast-1-0 value=2F6465762F73686D2F496E74656C5F4D50495F557168695930 [proxy:0:0@mu03] PMI response: cmd=put_result rc=0 msg=success [proxy:0:0@mu03] pmi cmd from fd 9: cmd=barrier_in [proxy:0:0@mu03] pmi cmd from fd 6: cmd=barrier_in [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get kvsname=kvs_1023514_0 key=-bcast-1-0 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=2F6465762F73686D2F496E74656C5F4D50495F557168695930 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get kvsname=kvs_1023514_0 key=-bcast-1-0 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=2F6465762F73686D2F496E74656C5F4D50495F557168695930 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=put kvsname=kvs_1023514_0 key=bc-0 value=mpi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proxy:0:0@mu03] PMI response: cmd=put_result rc=0 msg=success [proxy:0:0@mu03] pmi cmd from fd 10: cmd=put kvsname=kvs_1023514_0 key=bc-2 value=mpi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proxy:0:0@mu03] PMI response: cmd=put_result rc=0 msg=success [proxy:0:0@mu03] pmi cmd from fd 6: cmd=put kvsname=kvs_1023514_0 key=-bcast-2-0 value=2F6465762F73686D2F496E74656C5F4D50495F634653417131 [proxy:0:0@mu03] PMI response: cmd=put_result rc=0 msg=success [proxy:0:0@mu03] pmi cmd from fd 10: cmd=barrier_in [proxy:0:0@mu03] pmi cmd from fd 6: cmd=barrier_in [proxy:0:0@mu03] pmi cmd from fd 9: cmd=put kvsname=kvs_1023514_0 key=bc-1 value=mpi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proxy:0:0@mu03] PMI response: cmd=put_result rc=0 msg=success [proxy:0:0@mu03] pmi cmd from fd 9: cmd=barrier_in [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] PMI response: cmd=barrier_out [proxy:0:0@mu03] pmi cmd from fd 9: cmd=get kvsname=kvs_1023514_0 key=-bcast-2-0 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=2F6465762F73686D2F496E74656C5F4D50495F634653417131 [proxy:0:0@mu03] pmi cmd from fd 10: cmd=get kvsname=kvs_1023514_0 key=-bcast-2-0 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=2F6465762F73686D2F496E74656C5F4D50495F634653417131 [proxy:0:0@mu03] pmi cmd from fd 6: cmd=get kvsname=kvs_1023514_0 key=bc-0 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=mpi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proxy:0:0@mu03] pmi cmd from fd 9: cmd=get kvsname=kvs_1023514_0 key=bc-1 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=mpi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proxy:0:0@mu03] pmi cmd from fd 10: cmd=get kvsname=kvs_1023514_0 key=bc-2 [proxy:0:0@mu03] PMI response: cmd=get_result rc=0 msg=success value=mpi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core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (1) Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) Checking for fconfig files in pwd and ./rosetta/flags 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: (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: (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=1534393666 seed_offset=0 real_seed=1534393666 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1534393666 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=-1312669421 seed_offset=0 real_seed=1534393667 basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=1534393667 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=-821995375 seed_offset=0 real_seed=1534393668 basic.random.init_random_generator: (2) RandomGenerator:init: Normal mode, seed=1534393668 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: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (2) SCOREFUNCTION: ref2015 core.scoring.etable: (2) Starting energy table calculation core.scoring.etable: (1) Starting energy table calculation core.scoring.etable: (0) 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: (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: (2) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (1) smooth_etable: spline smoothing solvation etables (max_dis = 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: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (2) Finished calculating energy tables. basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv core.scoring.etable: (1) Finished calculating energy tables. basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (2) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv core.scoring.etable: (0) Finished calculating energy tables. 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/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: (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/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/DonStrength.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.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.chemical.GlobalResidueTypeSet: (2) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 0.923412 seconds. core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 0.921045 seconds. core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 986 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.923671 seconds. basic.io.database: (2) Database file opened: scoring/score_functions/rama/fd/all.ramaProb 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/all.ramaProb basic.io.database: (1) 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: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb 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: (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/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 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: (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 basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt 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: (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 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 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 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... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 1 to node 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: 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.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 2 to node 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 2 from master. 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.PDBJobInputter: (1) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (1) filling pose from PDB /test/playground/5T35.ppdock/5T35.pdb protocols.jd2.PDBJobInputter: (2) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (2) 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.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: (2) [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 111 core.conformation.Conformation: (2) [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 451 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: (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 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: (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: (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: (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.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: (2) Finished initializing centroid residue type set. Created 71 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 0.025378 seconds. core.chemical.GlobalResidueTypeSet: (1) Finished initializing centroid residue type set. Created 71 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 0.024424 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.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: (2) sliding into contact protocols.docking.DockingInitialPerturbation: (2) Moving away protocols.docking.DockingInitialPerturbation: (2) Moving together protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -13.8346 -46.1836 5.46103 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -13.4699 -45.2623 5.32631 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -13.4699 -45.2623 5.32631 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -13.1053 -44.3409 5.19159 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 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -10.7066 -47.7677 14.9603 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -10.4137 -46.8603 14.6592 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -13.1053 -44.3409 5.19159 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.7407 -43.4195 5.05687 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -10.4137 -46.8603 14.6592 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -10.1209 -45.9528 14.358 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.7407 -43.4195 5.05687 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.3761 -42.4982 4.92215 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -10.1209 -45.9528 14.358 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.828 -45.0453 14.0569 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.3761 -42.4982 4.92215 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.0115 -41.5768 4.78744 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.828 -45.0453 14.0569 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.53514 -44.1378 13.7557 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -12.0115 -41.5768 4.78744 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -11.6469 -40.6555 4.65272 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.53514 -44.1378 13.7557 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.24227 -43.2303 13.4546 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -11.6469 -40.6555 4.65272 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -11.2823 -39.7341 4.518 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -9.24227 -43.2303 13.4546 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.9494 -42.3228 13.1535 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -11.2823 -39.7341 4.518 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.9177 -38.8127 4.38328 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.9494 -42.3228 13.1535 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.65653 -41.4153 12.8523 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.65653 -41.4153 12.8523 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.36366 -40.5078 12.5512 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.9177 -38.8127 4.38328 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.5531 -37.8914 4.24856 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.36366 -40.5078 12.5512 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.0708 -39.6003 12.2501 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.5531 -37.8914 4.24856 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.1885 -36.97 4.11385 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -8.0708 -39.6003 12.2501 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.77793 -38.6928 11.9489 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.1885 -36.97 4.11385 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -9.82385 -36.0486 3.97913 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.77793 -38.6928 11.9489 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.48506 -37.7853 11.6478 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -9.82385 -36.0486 3.97913 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.378196 0.923829 0.0592239 -0.627062 0.208592 0.750522 0.681 -0.320981 0.658187 -10.1885 -36.97 4.11385 protocols.docking.DockingProtocol: (2) finished initial perturbation protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.48506 -37.7853 11.6478 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.19219 -36.8778 11.3467 protocols.docking.DockingLowRes: (2) in DockingLowRes.apply protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.19219 -36.8778 11.3467 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -6.89933 -35.9703 11.0455 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -6.89933 -35.9703 11.0455 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.360736 0.930311 0.0662648 -0.448481 0.110729 0.886907 0.817762 -0.349658 0.45717 -7.19219 -36.8778 11.3467 protocols.docking.DockingProtocol: (1) finished initial perturbation protocols.docking.DockingLowRes: (1) 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.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 (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: 0.02 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.05 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.26 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: 0.08 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.645 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.2805 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.04 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: 0.14 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.65721 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: (2) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.39148 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.1 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.39148 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 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.14 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.15234 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (2) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.16 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.271194 protocols.docking.DockingLowRes: (1) Rotation magnitude: 1.9371 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.02 protocols.docking.DockingProtocol: (2) Scoretype: interchain_contact score: -6.5, cutoff: 9.99 protocols.docking.DockingProtocol: (2) Scoretype: interchain_vdw score: 1.32365, cutoff: 1 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Mark current job for repetition, id 2 protocols.jd2.JobDistributor: (2) [ WARNING ] 5T35_pose_0002 reported failure and will retry protocols.jd2.MPIWorkPoolJobDistributor: (2) Job 2 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 2 from node 2. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Repeating job id 2 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: (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 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -10.2039 -46.0466 8.57231 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.92451 -45.1097 8.3623 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.92451 -45.1097 8.3623 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.64515 -44.1727 8.1523 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.64515 -44.1727 8.1523 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.3658 -43.2358 7.94229 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.3658 -43.2358 7.94229 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.08644 -42.2988 7.73228 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -9.08644 -42.2988 7.73228 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.80708 -41.3619 7.52227 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.80708 -41.3619 7.52227 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.52772 -40.425 7.31226 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.52772 -40.425 7.31226 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.24836 -39.488 7.10225 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -8.24836 -39.488 7.10225 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.96901 -38.5511 6.89224 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.96901 -38.5511 6.89224 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.68965 -37.6141 6.68223 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.68965 -37.6141 6.68223 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.41029 -36.6772 6.47222 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.41029 -36.6772 6.47222 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.13093 -35.7403 6.26221 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -7.13093 -35.7403 6.26221 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -6.85157 -34.8033 6.0522 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -6.85157 -34.8033 6.0522 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -6.57221 -33.8664 5.8422 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -6.57221 -33.8664 5.8422 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.629602 0.766266 0.128211 -0.627791 0.404559 0.664989 0.45769 -0.499168 0.735766 -6.85157 -34.8033 6.0522 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() 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'. protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.16 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (2) Rotation magnitude: 4.5 core.pack.dunbrack.RotamerLibrary: (1) Dunbrack 2010 library took 0.170032 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 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: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (2) Rotation magnitude: 3.645 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG0 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 core.pack.pack_rotamers: (1) built 10189 rotamers at 434 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph protocols.docking.DockingLowRes: (2) Acceptance rate is: 0 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0.04 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.65721 protocols.docking.DockingLowRes: (2) Acceptance rate is: 0 protocols.docking.DockingLowRes: (2) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (2) Rotation magnitude: 2.39148 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 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: (2) Acceptance rate is: 0 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'. core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.17429 seconds to load from binary 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.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (2) built 10599 rotamers at 434 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: (1) Score before repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2591.419 -2591.419 fa_rep 0.550 9715.613 5343.587 fa_sol 1.000 1541.457 1541.457 fa_intra_rep 0.005 660.894 3.304 fa_intra_sol_xover4 1.000 93.464 93.464 lk_ball_wtd 1.000 -50.472 -50.472 fa_elec 1.000 -615.211 -615.211 pro_close 1.250 50.090 62.613 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -86.715 -86.715 hbond_bb_sc 1.000 -46.700 -46.700 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: 4592.398 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (1) built 5660 rotamers at 452 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: (1) Score after repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2564.300 -2564.300 fa_rep 0.550 3208.755 1764.815 fa_sol 1.000 1498.769 1498.769 fa_intra_rep 0.005 804.617 4.023 fa_intra_sol_xover4 1.000 90.011 90.011 lk_ball_wtd 1.000 -57.253 -57.253 fa_elec 1.000 -647.178 -647.178 pro_close 1.250 30.913 38.642 hbond_sr_bb 1.000 -87.874 -87.874 hbond_lr_bb 1.000 -86.715 -86.715 hbond_bb_sc 1.000 -49.152 -49.152 hbond_sc 1.000 -61.347 -61.347 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 932.563 652.794 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: 680.997 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 protocols.docking.DockingProtocol: (2) Score before repack: protocols.docking.DockingProtocol: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2598.568 -2598.568 fa_rep 0.550 7064.090 3885.249 fa_sol 1.000 1555.704 1555.704 fa_intra_rep 0.005 660.894 3.304 fa_intra_sol_xover4 1.000 93.464 93.464 lk_ball_wtd 1.000 -51.326 -51.326 fa_elec 1.000 -595.291 -595.291 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: 3161.738 core.pack.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG1 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 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.rotamer_set.RotamerSet_: (2) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (1) built 966 rotamers at 31 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.pack_rotamers: (2) built 5686 rotamers at 452 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() protocols.docking.DockingProtocol: (2) Score after repack: protocols.docking.DockingProtocol: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2567.144 -2567.144 fa_rep 0.550 904.915 497.703 fa_sol 1.000 1513.092 1513.092 fa_intra_rep 0.005 828.319 4.142 fa_intra_sol_xover4 1.000 97.052 97.052 lk_ball_wtd 1.000 -58.534 -58.534 fa_elec 1.000 -632.224 -632.224 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 -45.767 -45.767 hbond_sc 1.000 -62.845 -62.845 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 931.999 652.400 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: -551.027 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 core.pack.task: (1) 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() 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.pack.task: (1) Packer task: initialize from command line() 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 1542 rotamers at 39 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() 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 477 rotamers at 21 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: (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() core.pack.pack_rotamers: (1) built 403 rotamers at 17 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: (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 784 rotamers at 24 positions. core.pack.interaction_graph.interaction_graph_factory: (2) 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.pack_rotamers: (1) built 352 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: (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() 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: (1) built 352 rotamers at 16 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.pack_rotamers: (2) built 701 rotamers at 22 positions. core.pack.interaction_graph.interaction_graph_factory: (2) 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.pack_rotamers: (1) built 397 rotamers at 19 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.pack_rotamers: (2) built 633 rotamers at 18 positions. core.pack.interaction_graph.interaction_graph_factory: (2) 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() protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.304789 0.882547 0.35807 -0.868807 0.103595 0.484193 0.390229 -0.45867 0.798338 -14.7305 -30.4861 9.33449 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.304789 0.882547 0.35807 -0.868807 0.103595 0.484193 0.390229 -0.45867 0.798338 -498.75 -853.017 307.945 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2505.764 -2505.764 fa_rep 0.550 340.371 187.204 fa_sol 1.000 1454.103 1454.103 fa_intra_rep 0.005 808.089 4.040 fa_intra_sol_xover4 1.000 89.960 89.960 lk_ball_wtd 1.000 -58.414 -58.414 fa_elec 1.000 -634.758 -634.758 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 -49.152 -49.152 hbond_sc 1.000 -62.052 -62.052 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 921.077 644.754 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: -878.978 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2525.379 -2525.379 fa_rep 0.550 344.233 189.328 fa_sol 1.000 1474.066 1474.066 fa_intra_rep 0.005 808.089 4.040 fa_intra_sol_xover4 1.000 89.960 89.960 lk_ball_wtd 1.000 -58.059 -58.059 fa_elec 1.000 -649.493 -649.493 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 -51.608 -51.608 hbond_sc 1.000 -64.352 -64.352 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 921.077 644.754 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: -895.643 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -878.978 protocols.docking.DockingProtocol.metrics: (1) bound energy: -895.643 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -16.6645 protocols.docking.DockingProtocol.metrics: (1) rb_jump: 1 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.304789 0.882547 0.35807 -0.868807 0.103595 0.484193 0.390229 -0.45867 0.798338 -14.7305 -30.4861 9.33449 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.304789 0.882547 0.35807 -0.868807 0.103595 0.484193 0.390229 -0.45867 0.798338 -498.75 -853.017 307.945 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2505.764 -2505.764 fa_rep 0.550 340.371 187.204 fa_sol 1.000 1454.103 1454.103 fa_intra_rep 0.005 808.089 4.040 fa_intra_sol_xover4 1.000 89.960 89.960 lk_ball_wtd 1.000 -58.414 -58.414 fa_elec 1.000 -634.758 -634.758 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 -49.152 -49.152 hbond_sc 1.000 -62.052 -62.052 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 921.077 644.754 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: -878.978 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2525.379 -2525.379 fa_rep 0.550 344.233 189.328 fa_sol 1.000 1474.066 1474.066 fa_intra_rep 0.005 808.089 4.040 fa_intra_sol_xover4 1.000 89.960 89.960 lk_ball_wtd 1.000 -58.059 -58.059 fa_elec 1.000 -649.493 -649.493 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 -51.608 -51.608 hbond_sc 1.000 -64.352 -64.352 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 921.077 644.754 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: -895.643 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -878.978 protocols.docking.DockingProtocol.metrics: (1) bound energy: -895.643 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -16.6645 protocols.docking.DockingProtocol.metrics: (1) rb_jump: 1 core.pack.task: (2) Packer task: initialize from command line() 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 1 from node 1 blocking till output is done protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received output confirmation from master. Writing output. core.pack.task: (2) Packer task: initialize from command line() protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Finished writing output in 0.16578 seconds. Sending message to master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job output finish message for job id 1 from node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 1 as completed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... 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 3 to node 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: No more jobs to assign, setting next job id to zero protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 3 from master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Finished handing out jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs 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.task: (2) Packer task: initialize from command line() 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 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.51063 -44.4988 7.57248 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.34849 -43.531 7.37998 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.34849 -43.531 7.37998 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.18636 -42.5631 7.18748 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.18636 -42.5631 7.18748 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.02423 -41.5953 6.99499 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -3.02423 -41.5953 6.99499 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.8621 -40.6275 6.80249 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.8621 -40.6275 6.80249 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.69997 -39.6597 6.60999 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.69997 -39.6597 6.60999 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.53784 -38.6919 6.41749 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.53784 -38.6919 6.41749 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.3757 -37.7241 6.22499 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.3757 -37.7241 6.22499 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.525572 0.833136 0.172218 -0.484385 0.12663 0.865642 0.69939 -0.538377 0.470111 -2.53784 -38.6919 6.41749 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.task: (2) Packer task: initialize from command line() protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.44 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.63 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.5 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.567 protocols.docking.DockingLowRes: (1) Rotation magnitude: 4.05 core.pack.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 657 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: (2) Instantiating DensePDInteractionGraph protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.08 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.5103 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.645 core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.08 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.45927 protocols.docking.DockingLowRes: (1) Rotation magnitude: 3.2805 core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.06 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.413343 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.95245 protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.26 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.372009 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.65721 core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.08 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.334808 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.39148 core.pack.task: (2) Packer task: initialize from command line() protocols.docking.DockingLowRes: (1) Acceptance rate is: 0.2 protocols.docking.DockingLowRes: (1) Translation magnitude: 0.301327 protocols.docking.DockingLowRes: (1) Rotation magnitude: 2.15234 core.pack.task: (2) Packer task: initialize from command line() 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: 0.14 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.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 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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 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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 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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 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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 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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 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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 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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 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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 core.pack.task: (2) Packer task: initialize from command line() 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.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (2) built 654 rotamers at 18 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.task: (2) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 10090 rotamers at 434 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() protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.571049 0.543983 -0.614806 0.611502 0.217787 0.76068 0.547693 -0.81034 -0.20828 6.95291 -38.1078 24.2011 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.571049 0.543983 -0.614806 0.611502 0.217787 0.76068 0.547693 -0.81034 -0.20828 29.4197 -885.02 555.458 protocols.docking.DockingProtocol.metrics: (2) unbound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2505.496 -2505.496 fa_rep 0.550 340.952 187.523 fa_sol 1.000 1461.140 1461.140 fa_intra_rep 0.005 808.328 4.042 fa_intra_sol_xover4 1.000 93.394 93.394 lk_ball_wtd 1.000 -55.601 -55.601 fa_elec 1.000 -644.077 -644.077 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 -50.992 -50.992 hbond_sc 1.000 -65.731 -65.731 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 919.132 643.393 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: -881.308 protocols.docking.DockingProtocol.metrics: (2) bound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2519.633 -2519.633 fa_rep 0.550 343.326 188.829 fa_sol 1.000 1476.711 1476.711 fa_intra_rep 0.005 808.328 4.042 fa_intra_sol_xover4 1.000 93.394 93.394 lk_ball_wtd 1.000 -53.638 -53.638 fa_elec 1.000 -660.164 -660.164 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 -50.992 -50.992 hbond_sc 1.000 -68.128 -68.128 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 919.132 643.393 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: -895.088 protocols.docking.DockingProtocol.metrics: (2) unbound energy: -881.308 protocols.docking.DockingProtocol.metrics: (2) bound energy: -895.088 protocols.docking.DockingProtocol.metrics: (2) interaction energy: -13.7803 protocols.docking.DockingProtocol.metrics: (2) rb_jump: 1 protocols.moves.RigidBodyMover: (2) Translate: Jump (before): RT 0.571049 0.543983 -0.614806 0.611502 0.217787 0.76068 0.547693 -0.81034 -0.20828 6.95291 -38.1078 24.2011 protocols.moves.RigidBodyMover: (2) Translate: Jump (after): RT 0.571049 0.543983 -0.614806 0.611502 0.217787 0.76068 0.547693 -0.81034 -0.20828 29.4197 -885.02 555.458 protocols.docking.DockingProtocol.metrics: (2) unbound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2505.496 -2505.496 fa_rep 0.550 340.952 187.523 fa_sol 1.000 1461.140 1461.140 fa_intra_rep 0.005 808.328 4.042 fa_intra_sol_xover4 1.000 93.394 93.394 lk_ball_wtd 1.000 -55.601 -55.601 fa_elec 1.000 -644.077 -644.077 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 -50.992 -50.992 hbond_sc 1.000 -65.731 -65.731 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 919.132 643.393 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: -881.308 protocols.docking.DockingProtocol.metrics: (2) bound pose: protocols.docking.DockingProtocol.metrics: (2) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2519.633 -2519.633 fa_rep 0.550 343.326 188.829 fa_sol 1.000 1476.711 1476.711 fa_intra_rep 0.005 808.328 4.042 fa_intra_sol_xover4 1.000 93.394 93.394 lk_ball_wtd 1.000 -53.638 -53.638 fa_elec 1.000 -660.164 -660.164 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 -50.992 -50.992 hbond_sc 1.000 -68.128 -68.128 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 919.132 643.393 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: -895.088 protocols.docking.DockingProtocol.metrics: (2) unbound energy: -881.308 protocols.docking.DockingProtocol.metrics: (2) bound energy: -895.088 protocols.docking.DockingProtocol.metrics: (2) interaction energy: -13.7803 protocols.docking.DockingProtocol.metrics: (2) rb_jump: 1 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 2 from node 2 blocking till output is done protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received output confirmation from master. Writing output. protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Finished writing output in 0.168362 seconds. Sending message to master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job output finish message for job id 2 from node 2 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: (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 spin down signal to node 2 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 1 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 0 from master. protocols.jd2.JobDistributor: (2) no more batches to process... protocols.jd2.JobDistributor: (2) 3 jobs considered, 2 jobs attempted in 53 seconds protocols.docking.DockingProtocol: (1) Score before repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2549.235 -2549.235 fa_rep 0.550 4756.831 2616.257 fa_sol 1.000 1513.863 1513.863 fa_intra_rep 0.005 660.894 3.304 fa_intra_sol_xover4 1.000 93.464 93.464 lk_ball_wtd 1.000 -52.912 -52.912 fa_elec 1.000 -603.943 -603.943 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: 1889.999 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG1 core.pack.rotamer_set.RotamerSet_: (1) Using simple Rotamer generation logic for LG0 core.pack.pack_rotamers: (1) built 5668 rotamers at 452 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph protocols.docking.DockingProtocol: (1) Score after repack: protocols.docking.DockingProtocol: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2518.790 -2518.790 fa_rep 0.550 424.444 233.444 fa_sol 1.000 1470.555 1470.555 fa_intra_rep 0.005 799.720 3.999 fa_intra_sol_xover4 1.000 89.662 89.662 lk_ball_wtd 1.000 -56.424 -56.424 fa_elec 1.000 -636.882 -636.882 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 -51.887 -51.887 hbond_sc 1.000 -65.582 -65.582 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 907.352 635.146 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: -845.662 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.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 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 513 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 374 rotamers at 13 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.pack_rotamers: (1) built 186 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: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() core.pack.pack_rotamers: (1) built 170 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.pack_rotamers: (1) built 171 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.task: (1) 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() core.pack.pack_rotamers: (1) built 171 rotamers at 9 positions. core.pack.interaction_graph.interaction_graph_factory: (1) Instantiating DensePDInteractionGraph core.pack.task: (1) 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() core.pack.task: (1) Packer task: initialize from command line() core.pack.task: (1) Packer task: initialize from command line() protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.186262 0.966481 -0.176692 -0.338392 0.231943 0.911972 0.922387 -0.110075 0.370252 1.13224 -37.9545 8.91313 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.186262 0.966481 -0.176692 -0.338392 0.231943 0.911972 0.922387 -0.110075 0.370252 -116.442 -1005.77 231.411 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2502.141 -2502.141 fa_rep 0.550 339.645 186.804 fa_sol 1.000 1455.827 1455.827 fa_intra_rep 0.005 801.143 4.006 fa_intra_sol_xover4 1.000 89.735 89.735 lk_ball_wtd 1.000 -55.681 -55.681 fa_elec 1.000 -635.335 -635.335 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 -65.582 -65.582 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 905.260 633.682 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: -888.118 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2508.654 -2508.654 fa_rep 0.550 340.127 187.070 fa_sol 1.000 1463.678 1463.678 fa_intra_rep 0.005 801.143 4.006 fa_intra_sol_xover4 1.000 89.735 89.735 lk_ball_wtd 1.000 -55.883 -55.883 fa_elec 1.000 -639.151 -639.151 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 -51.682 -51.682 hbond_sc 1.000 -65.582 -65.582 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 905.260 633.682 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: -891.682 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -888.118 protocols.docking.DockingProtocol.metrics: (1) bound energy: -891.682 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -3.56418 protocols.docking.DockingProtocol.metrics: (1) rb_jump: 1 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.186262 0.966481 -0.176692 -0.338392 0.231943 0.911972 0.922387 -0.110075 0.370252 1.13224 -37.9545 8.91313 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.186262 0.966481 -0.176692 -0.338392 0.231943 0.911972 0.922387 -0.110075 0.370252 -116.442 -1005.77 231.411 protocols.docking.DockingProtocol.metrics: (1) unbound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2502.141 -2502.141 fa_rep 0.550 339.645 186.804 fa_sol 1.000 1455.827 1455.827 fa_intra_rep 0.005 801.143 4.006 fa_intra_sol_xover4 1.000 89.735 89.735 lk_ball_wtd 1.000 -55.681 -55.681 fa_elec 1.000 -635.335 -635.335 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 -65.582 -65.582 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 905.260 633.682 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: -888.118 protocols.docking.DockingProtocol.metrics: (1) bound pose: protocols.docking.DockingProtocol.metrics: (1) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -2508.654 -2508.654 fa_rep 0.550 340.127 187.070 fa_sol 1.000 1463.678 1463.678 fa_intra_rep 0.005 801.143 4.006 fa_intra_sol_xover4 1.000 89.735 89.735 lk_ball_wtd 1.000 -55.883 -55.883 fa_elec 1.000 -639.151 -639.151 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 -51.682 -51.682 hbond_sc 1.000 -65.582 -65.582 dslf_fa13 1.250 0.000 0.000 omega 0.400 300.329 120.132 fa_dun 0.700 905.260 633.682 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: -891.682 protocols.docking.DockingProtocol.metrics: (1) unbound energy: -888.118 protocols.docking.DockingProtocol.metrics: (1) bound energy: -891.682 protocols.docking.DockingProtocol.metrics: (1) interaction energy: -3.56418 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 3 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 0.178487 seconds. Sending message to master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received job output finish message for job id 3 from node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 3 as completed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 1 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: Finished sending spin down signals to slaves 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, 2 jobs attempted in 82 seconds =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 0 PID 1023534 RUNNING AT mu03 = KILLED BY SIGNAL: 15 (Terminated) =================================================================================== =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 1 PID 1023535 RUNNING AT mu03 = KILLED BY SIGNAL: 15 (Terminated) =================================================================================== [mpiexec@mu03] Exit codes: [mu03] 15,15,65280