core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.binary.linux.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-21T14:46:08.581859 core.init: (0) command: /opt/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/antibody_designer.mpi.linuxgccrelease -s complex_3.pdb -primary_cdrs H1 -graft_design_cdrs H1 -do_dock -nstruct 1 -overwrite -constant_seed basic.random.init_random_generator: (0) Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.init: (0) Resolved executable path: /opt/rosetta_bin_linux_2020.08.61146_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/8/mpi/antibody_designer.mpi.linuxgccrelease core.init: (0) Looking for database based on location of executable: /opt/rosetta_bin_linux_2020.08.61146_bundle/main/database/ protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (0) pushed complex_3.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (0) filling pose from PDB complex_3.pdb core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 982 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.22 seconds. core.import_pose.import_pose: (0) File 'complex_3.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: (0) [ WARNING ] discarding 1 atoms at position 123 in file complex_3.pdb. Best match rsd_type: PWB:NtermProteinFull core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue SER:CtermProteinFull 122 core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 238 core.conformation.Conformation: (0) Found disulfide between residues 33 103 core.conformation.Conformation: (0) current variant for 33 CYS core.conformation.Conformation: (0) current variant for 103 CYS core.conformation.Conformation: (0) current variant for 33 CYD core.conformation.Conformation: (0) current variant for 103 CYD core.conformation.Conformation: (0) Found disulfide between residues 145 218 core.conformation.Conformation: (0) current variant for 145 CYS core.conformation.Conformation: (0) current variant for 218 CYS core.conformation.Conformation: (0) current variant for 145 CYD core.conformation.Conformation: (0) current variant for 218 CYD core.io.pose_from_sfr.PoseFromSFRBuilder: (0) [ WARNING ] can't find pose atom for file-residue 123 atom OE (trying to store temperature in PDBInfo) basic.io.database: (0) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (0) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (0) Antibody CDR definition read successfully antibody.AntibodyInfo: (0) Successfully finished the CDR definition antibody.AntibodyInfo: (0) Could not setup Vl Vh Packing angle for camelid antibody antibody.AntibodyInfo: (0) AC Detecting Camelid CDR H3 Stem Type antibody.AntibodyInfo: (0) AC Finished Detecting Camelid CDR H3 Stem Type: NEUTRAL antibody.AntibodyInfo: (0) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (0) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 10 Omega: TTTTCTTTTT protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] *** No known cluster of CDR length 10 omega of TTTTCTTTTT found. *** protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] *** Consider using the command-line option -allow_omega_mismatches_for_north_clusters to find the closest cluster! *** protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] antibody.AntibodyInfo: (0) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 15 Omega: TTTTTTTTTTTTTTT //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Info /// /// /// /// Antibody Type: Camelid Antibody /// Light Chain Type: unknown /// Predict H3 Cterminus Base: NEUTRAL /// /// H1 info: /// length: 13 /// sequence: AASGYAYTSDCMG /// north_cluster: H1-13-1 /// loop_info: LOOP start: 23 stop: 35 cut: 29 size: 13 skip rate: 0 extended?: False /// H2 info: /// length: 10 /// sequence: LIYTPGNSTN /// north_cluster: NA /// loop_info: LOOP start: 50 stop: 59 cut: 55 size: 10 skip rate: 0 extended?: False /// H3 info: /// length: 15 /// sequence: AARRGACSLRLPFFY /// north_cluster: H3-15-2 /// loop_info: LOOP start: 97 stop: 111 cut: 98 size: 15 skip rate: 0 extended?: False //////////////////////////////////////////////////////////////////////////////// core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.etable: (0) Starting energy table calculation 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: (0) Finished calculating energy tables. basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (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 basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (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: (0) SCOREFUNCTION: ref2015 core.scoring.CartesianBondedEnergy: (0) Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80 basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: (0) Read 759 bb-independent lengths. basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: (0) Read 1434 bb-independent angles. basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.scoring.CartesianBondedEnergy: (0) Read 1 bb-independent torsions. basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt core.scoring.CartesianBondedEnergy: (0) Read 2202 bb-independent improper tors. antibody.AntibodyInfo: (0) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (0) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 10 Omega: TTTTCTTTTT protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] *** No known cluster of CDR length 10 omega of TTTTCTTTTT found. *** protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] *** Consider using the command-line option -allow_omega_mismatches_for_north_clusters to find the closest cluster! *** protocols.antibody.cluster.CDRClusterMatcher: (0) [ WARNING ] antibody.AntibodyInfo: (0) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 15 Omega: TTTTTTTTTTTTTTT protocols.antibody.clusters.CDRClusterSet: (0) Adding cacheable cluster data to pose protocols.antibody.design.util: (0) Reading CDRSetOptions from: /sampling/antibodies/design/default_instructions.txt protocols.antibody.design.util: (0) Reading CDRGraftDesignOptions from: /sampling/antibodies/design/default_instructions.txt protocols.antibody.design.util: (0) Reading CDRSeqDesignOptions from: /sampling/antibodies/design/default_instructions.txt core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 basic.io.database: (0) Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine 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: (0) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (0) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 basic.io.database: (0) [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db antibody.database.AntibodyDatabaseManager: (0) Reading from: /opt/rosetta_bin_linux_2020.08.61146_bundle/main/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db antibody.database.AntibodyDatabaseManager: (0) Checking loadable structures antibody.database.AntibodyDatabaseManager: (0) Skipping 12 structures from reading core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 antibody.database.AntibodyDatabaseManager: (0) Total H1 in CDRSet: 258 LOADED 12e8H_H1_0001 LOADED 1axsB_H1_0001 LOADED 1axtH_H1_0001 LOADED 1bfoB_H1_0001 LOADED 1bj1H_H1_0001 LOADED 1cz8H_H1_0001 LOADED 1dbmH_H1_0001 LOADED 1dfbH_H1_0001 LOADED 1dqlH_H1_0001 LOADED 1f3dH_H1_0001 LOADED 1f8tH_H1_0001 LOADED 1fl5H_H1_0001 LOADED 1fvcB_H1_0001 LOADED 1i8kB_H1_0001 LOADED 1ibgH_H1_0001 LOADED 1kb5H_H1_0001 LOADED 1kegH_H1_0001 LOADED 1l7iH_H1_0001 LOADED 1lo2H_H1_0001 LOADED 1mreH_H1_0001 LOADED 1n4xI_H1_0001 LOADED 1nakH_H1_0001 LOADED 1nbyB_H1_0001 LOADED 1ol0A_H1_0001 LOADED 1op3H_H1_0001 LOADED 1op9A_H1_0001 LOADED 1q9oB_H1_0001 LOADED 1rz7H_H1_0001 LOADED 1sm3H_H1_0001 LOADED 1sy6H_H1_0001 LOADED 1t66H_H1_0001 LOADED 1uweH_H1_0001 LOADED 1uywM_H1_0001 LOADED 1uz8H_H1_0001 LOADED 1v7mH_H1_0001 LOADED 1w72H_H1_0001 LOADED 1xgyH_H1_0001 LOADED 1xiwD_H1_0001 LOADED 1y0lH_H1_0001 LOADED 1yy8D_H1_0001 LOADED 2a6iB_H1_0001 LOADED 2aabH_H1_0001 LOADED 2aepH_H1_0001 LOADED 2ajvH_H1_0001 LOADED 2b2xH_H1_0001 LOADED 2brrY_H1_0001 LOADED 2dqfB_H1_0001 LOADED 2eh7H_H1_0001 LOADED 2f5bH_H1_0001 LOADED 2fd6H_H1_0001 LOADED 2fjfV_H1_0001 LOADED 2fx7H_H1_0001 LOADED 2g5bH_H1_0001 LOADED 2g75A_H1_0001 LOADED 2ghwB_H1_0001 LOADED 2gk0H_H1_0001 LOADED 2h32H_H1_0001 LOADED 2hffH_H1_0001 LOADED 2ipuG_H1_0001 LOADED 2iq9H_H1_0001 LOADED 2j88H_H1_0001 LOADED 2ny2D_H1_0001 LOADED 2ok0H_H1_0001 LOADED 2oslH_H1_0001 LOADED 2otuF_H1_0001 LOADED 2p4aD_H1_0001 LOADED 2pcpB_H1_0001 LOADED 2qhrH_H1_0001 LOADED 2v7nH_H1_0001 LOADED 2vdrH_H1_0001 LOADED 2vl5A_H1_0001 LOADED 3b2uH_H1_0001 LOADED 3b9vC_H1_0001 LOADED 3baeH_H1_0001 LOADED 3bz4D_H1_0001 LOADED 3c2aH_H1_0001 LOADED 3cfbB_H1_0001 LOADED 3difD_H1_0001 LOADED 43c9D_H1_0001 antibody.database.AntibodyDatabaseManager: (0) 258 Cached antibody.database.AntibodyDatabaseManager: (0) cdrs loaded from database. protocols.antibody.design.AntibodyDesignMover: (0) ///// Total CDRs in set ///// protocols.antibody.design.AntibodyDesignMover: (0) /// H1 258 protocols.antibody.design.AntibodyDesignMover: (0) Total possible CDR combinations: 258 //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Design Settings /// /// /// // Design Protocol: even_cluster_monte_carlo // Outer Cycles: 25 // Inner Cycles: 1 // Dock? true ///////////////////////////////////// H1 /////////////////////////////////////// /// Weight: 1 /// /// Graft? true /// SeqDesign? false /// /// Min Neighbors: [H2, H3] /// Current Clusters only? false /// Center Clusters only? false //// ////// Length Types: //// /// 1 true /// 2 true /// 3 true //// ////// Lengths: //// /// Min 1 /// Max 25 /// ////// Include Only: ////// Exclude: /////////////////////////////////////////////////////////////////////////////////////////////////////////////// basic.io.database: (0) Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: (0) Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: (0) Binary rotamer library selected: /opt/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file '/opt/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: (0) Dunbrack 2010 library took 0.22 seconds to load from binary core.scoring.ScoreFunction: (0) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -1348.159 -1348.159 fa_rep 0.550 9209.452 5065.199 fa_sol 1.000 772.300 772.300 fa_intra_rep 0.005 438.881 2.194 fa_intra_sol_xover4 1.000 36.498 36.498 lk_ball_wtd 1.000 -18.496 -18.496 fa_elec 1.000 -326.181 -326.181 pro_close 1.250 23.625 29.531 hbond_sr_bb 1.000 -23.117 -23.117 hbond_lr_bb 1.000 -110.557 -110.557 hbond_bb_sc 1.000 -34.388 -34.388 hbond_sc 1.000 -15.702 -15.702 dslf_fa13 1.250 29.282 36.602 atom_pair_constraint 0.010 621.727 6.217 omega 0.400 126.882 50.753 fa_dun 0.700 492.373 344.661 p_aa_pp 0.600 -62.244 -37.347 yhh_planarity 0.625 0.000 0.000 ref 1.000 106.695 106.695 rama_prepro 0.450 18.799 8.459 --------------------------------------------------- Total weighted score: 4545.165 protocols.antibody.design.AntibodyDesignMover: (0) Running basic monte carlo algorithm protocols.antibody.design.AntibodyDesignMover: (0) Outer round: 1 protocols.antibody.design.AntibodyDesignMover: (0) Grafting CDR from cluster H1-16-1 fragment 1qd0A_H1_0001 protocols.grafting.CCDEndsGraftMover: (0) Start: 22 End: 36 NterO: 3 CterO: 3 protocols.grafting.util: (0) Superimposing overhang residues core.chemical.AtomICoor: (0) [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: (0) [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: (0) [ WARNING ] --> generating it using idealized coordinates. core.conformation.Residue: (0) [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1 core.conformation.Residue: (0) [ WARNING ] ResConnID info stored on the connected residue (residue 2) is now out of date! core.conformation.Residue: (0) [ WARNING ] Connection atom name (in src): C protocols.grafting.util: (0) Deleting 13 residues from 23 to 35 core.conformation.Conformation: (0) Reverting out-of-date disulfide to thiol type at resid 90 core.conformation.Conformation: (0) Found disulfide between residues 132 205 core.conformation.Conformation: (0) current variant for 132 CYD core.conformation.Conformation: (0) current variant for 205 CYD core.conformation.Conformation: (0) current variant for 132 CYD core.conformation.Conformation: (0) current variant for 205 CYD protocols.grafting.util: (0) insert_point 22 protocols.grafting.util: (0) insert_start 23 protocols.grafting.util: (0) insert_end 38 protocols.grafting.util: (0) insert_length 16 protocols.grafting.util: (0) FOLD_TREE EDGE 1 22 -1 EDGE 22 23 1 EDGE 23 225 -1 protocols.grafting.GraftMoverBase: (0) Insertion complete. protocols.grafting.AnchoredGraftMover: (0) Setting default movemap protocols.grafting.CCDEndsGraftMover: (0) Start: 22 protocols.grafting.CCDEndsGraftMover: (0) Original End: 36 protocols.grafting.CCDEndsGraftMover: (0) End: 39 protocols.grafting.CCDEndsGraftMover: (0) Insert Length: 16 basic.io.database: (0) Database file opened: scoring/score_functions/centroid_smooth/cen_smooth_params.txt core.scoring.ramachandran: (0) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: (0) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.grafting.CCDEndsGraftMover: (0) LOOP start: 21 stop: 24 cut: 22 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: (0) protocols.grafting.CCDEndsGraftMover: (0) LOOP start: 37 stop: 40 cut: 38 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: (0) protocols.loops.FoldTreeFromLoopsWrapper: (0) old foldtree FOLD_TREE EDGE 1 22 -1 EDGE 22 39 1 EDGE 39 241 -1 EDGE 22 23 -2 C N EDGE 23 24 -2 C N EDGE 24 25 -2 C N EDGE 25 26 -2 C N EDGE 26 27 -2 C N EDGE 27 28 -2 C N EDGE 28 29 -2 C N EDGE 29 30 -2 C N EDGE 30 31 -2 C N EDGE 31 32 -2 C N EDGE 32 33 -2 C N EDGE 33 34 -2 C N EDGE 34 35 -2 C N EDGE 35 36 -2 C N EDGE 36 37 -2 C N EDGE 37 38 -2 C N New foldtree FOLD_TREE EDGE 1 20 -1 EDGE 20 22 -1 EDGE 20 25 1 EDGE 25 23 -1 EDGE 25 36 -1 EDGE 36 38 -1 EDGE 36 41 2 EDGE 41 39 -1 EDGE 41 241 -1 protocols.grafting.util: (0) Loop: 1 protocols.grafting.util: (0) Add variant to: 22 protocols.grafting.util: (0) Loop: 2 protocols.grafting.util: (0) Add variant to: 38 protocols.grafting.util: (0) idealized 21 protocols.grafting.util: (0) idealized 22 protocols.grafting.util: (0) ideal 23 protocols.grafting.util: (0) ideal 38 protocols.grafting.util: (0) idealized 39 protocols.grafting.util: (0) idealized 40 core.chemical.GlobalResidueTypeSet: (0) Finished initializing centroid residue type set. Created 64 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.04 seconds. basic.io.database: (0) Database file opened: scoring/score_functions/disulfides/centroid_distance_score basic.io.database: (0) Database file opened: scoring/score_functions/disulfides/centroid_CaCbCb_angle_score basic.io.database: (0) Database file opened: scoring/score_functions/disulfides/centroid_CaCbCbCa_dihedral_score basic.io.database: (0) Database file opened: scoring/score_functions/disulfides/centroid_backbone_dihedral_score protocols.grafting.CCDEndsGraftMover: (0) start 610.866 protocols.grafting.CCDEndsGraftMover: (0) round 1 Segmentation fault AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.