core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) Rosetta version: rosetta.source.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T01:44:18.723947 core.init: (0) command: antibody_designer.mpi.macosclangrelease -s complex.pdb -light_chain lambda -cdr_instructions cdr_instructions.txt @RabD_flag core.init: (0) 'RNG device' seed mode, using '/dev/urandom', seed=2027995061 seed_offset=0 real_seed=2027995061 core.init.random: (0) RandomGenerator:init: Normal mode, seed=2027995061 RG_type=mt19937 core.init: (0) found database environment variable ROSETTA3_DB: /usr/local/rosetta_src_2018.33.60351_bundle/main/database protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (0) pushed complex.pdb nstruct indices 1 - 500 protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... protocols.antibody.design.AntibodyDesignProtocol: (0) Instructions file: cdr_instructions.txt protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (0) filling pose from PDB complex.pdb core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 617 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 0.716275 seconds. core.import_pose.import_pose: (0) File 'complex.pdb' automatically determined to be of type PDB core.io.pdb.pdb_reader: (0) Parsing 0 .pdb records with unknown format to search for Rosetta-specific comments. core.conformation.Conformation: (0) Found disulfide between residues 13 55 core.conformation.Conformation: (0) current variant for 13 CYS core.conformation.Conformation: (0) current variant for 55 CYS core.conformation.Conformation: (0) current variant for 13 CYD core.conformation.Conformation: (0) current variant for 55 CYD core.conformation.Conformation: (0) Found disulfide between residues 44 89 core.conformation.Conformation: (0) current variant for 44 CYS core.conformation.Conformation: (0) current variant for 89 CYS core.conformation.Conformation: (0) current variant for 44 CYD core.conformation.Conformation: (0) current variant for 89 CYD core.conformation.Conformation: (0) Found disulfide between residues 48 91 core.conformation.Conformation: (0) current variant for 48 CYS core.conformation.Conformation: (0) current variant for 91 CYS core.conformation.Conformation: (0) current variant for 48 CYD core.conformation.Conformation: (0) current variant for 91 CYD core.conformation.Conformation: (0) Found disulfide between residues 107 149 core.conformation.Conformation: (0) current variant for 107 CYS core.conformation.Conformation: (0) current variant for 149 CYS core.conformation.Conformation: (0) current variant for 107 CYD core.conformation.Conformation: (0) current variant for 149 CYD core.conformation.Conformation: (0) Found disulfide between residues 138 183 core.conformation.Conformation: (0) current variant for 138 CYS core.conformation.Conformation: (0) current variant for 183 CYS core.conformation.Conformation: (0) current variant for 138 CYD core.conformation.Conformation: (0) current variant for 183 CYD core.conformation.Conformation: (0) Found disulfide between residues 142 185 core.conformation.Conformation: (0) current variant for 142 CYS core.conformation.Conformation: (0) current variant for 185 CYS core.conformation.Conformation: (0) current variant for 142 CYD core.conformation.Conformation: (0) current variant for 185 CYD protocols.antibody.design.AntibodyDesignProtocol: (0) Instructions file: cdr_instructions.txt 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: TTTTTTTTTT antibody.AntibodyInfo: (0) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 18 Omega: TTTTTTTTTTTTTTTTTT //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Info /// /// /// /// Antibody Type: Camelid Antibody /// Light Chain Type: unknown /// Predict H3 Cterminus Base: NEUTRAL /// /// H1 info: /// length: 13 /// sequence: VSDEFTARHYAIG /// north_cluster: H1-13-5 /// loop_info: LOOP start: 211 stop: 223 cut: 217 size: 13 skip rate: 0 extended?: False /// H2 info: /// length: 10 /// sequence: CIGSSADIQY /// north_cluster: H2-10-2 /// loop_info: LOOP start: 238 stop: 247 cut: 243 size: 10 skip rate: 0 extended?: False /// H3 info: /// length: 18 /// sequence: AAVRSIDIVQHICDPVDS /// north_cluster: H3-18-2 /// loop_info: LOOP start: 285 stop: 302 cut: 286 size: 18 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 protocols.antibody.design.AntibodyDesignMover: (0) Instructions file: cdr_instructions.txt protocols.antibody.design.AntibodyDesignProtocol: (0) Score without constraints: 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: /usr/local/rosetta_src_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: (0) Using Dunbrack library binary file '/usr/local/rosetta_src_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: (0) Dunbrack 2010 library took 0.284898 seconds to load from binary protocols.antibody.design.AntibodyDesignProtocol: (0) ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -1689.326 -1689.326 fa_rep 0.550 526.355 289.495 fa_sol 1.000 965.173 965.173 fa_intra_rep 0.005 666.377 3.332 fa_intra_sol_xover4 1.000 64.478 64.478 lk_ball_wtd 1.000 -34.323 -34.323 fa_elec 1.000 -443.365 -443.365 pro_close 1.250 16.086 20.107 hbond_sr_bb 1.000 -33.074 -33.074 hbond_lr_bb 1.000 -128.403 -128.403 hbond_bb_sc 1.000 -38.041 -38.041 hbond_sc 1.000 -23.362 -23.362 dslf_fa13 1.250 -6.352 -7.940 atom_pair_constraint 0.010 0.000 0.000 omega 0.400 116.382 46.553 fa_dun 0.700 610.947 427.663 p_aa_pp 0.600 -90.988 -54.593 yhh_planarity 0.625 0.000 0.000 ref 1.000 99.159 99.159 rama_prepro 0.450 101.052 45.474 --------------------------------------------------- Total weighted score: -490.994 protocols.antibody.design.AntibodyDesignProtocol: (0) protocols.antibody.design.AntibodyDesignProtocol: (0) /// Run Antibody Designer: true protocols.antibody.design.AntibodyDesignProtocol: (0) // ->Post SnugDock: false protocols.antibody.design.AntibodyDesignProtocol: (0) // ->Post DS Relax: false protocols.antibody.design.AntibodyDesignProtocol: (0) protocols.antibody.design.AntibodyDesignProtocol: (0) Running Graft Design Protocol //////////////////////////////////////////////////////////////////////////////// /// Rosetta Antibody Info /// /// /// /// Antibody Type: Camelid Antibody /// Light Chain Type: unknown /// Predict H3 Cterminus Base: NEUTRAL /// /// H1 info: /// length: 13 /// sequence: VSDEFTARHYAIG /// north_cluster: H1-13-5 /// loop_info: LOOP start: 211 stop: 223 cut: 217 size: 13 skip rate: 0 extended?: False /// H2 info: /// length: 10 /// sequence: CIGSSADIQY /// north_cluster: H2-10-2 /// loop_info: LOOP start: 238 stop: 247 cut: 243 size: 10 skip rate: 0 extended?: False /// H3 info: /// length: 18 /// sequence: AAVRSIDIVQHICDPVDS /// north_cluster: H3-18-2 /// loop_info: LOOP start: 285 stop: 302 cut: 286 size: 18 skip rate: 0 extended?: False //////////////////////////////////////////////////////////////////////////////// core.scoring.CartesianBondedEnergy: (0) Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40 basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: (0) Read 757 bb-independent lengths. basic.io.database: (0) Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: (0) Read 1456 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 2197 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: TTTTTTTTTT antibody.AntibodyInfo: (0) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (0) Length: 18 Omega: TTTTTTTTTTTTTTTTTT protocols.antibody.clusters.CDRClusterSet: (0) Adding cacheable cluster data to pose protocols.antibody.NativeAntibodySeq: (0) Setting full pose sequence protocols.jd2.JobDistributor: (0) [ ERROR ] [ERROR] Exception caught by JobDistributor for job complex_0001 File: src/protocols/antibody/AntibodyInfo.cc:1117 L1 start resnum not found in pose: 24 L Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB. This could also mean missing density in the cdr loop. Loop modeling applications can be used to fill missing residues protocols.jd2.JobDistributor: (0) [ ERROR ] protocols.jd2.JobDistributor: (0) [ WARNING ] complex_0001 reported that its input was bad and will not retry protocols.jd2.FileSystemJobDistributor: (0) job failed, reporting bad input; other jobs of same input will be canceled: complex_0001 protocols.jd2.JobDistributor: (0) no more batches to process... protocols.jd2.JobDistributor: (0) 500 jobs considered, 1 jobs attempted in 4 seconds Error: (0) [ ERROR ] ERROR: Exception caught by antibody_design application: File: src/protocols/jd2/JobDistributor.cc:329 1 jobs failed; check output for error messages Error: (0) [ ERROR ]