core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.source.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T01:44:18.723947 core.init: command: /Users/suzukikazushi/Desktop/rosetta_src_2018.33.60351_bundle/main/source/bin/rosetta_scripts.macosclangrelease @design.options -parser:protocol design.xml -out:suffix _design -scorefile design.fasc core.init: 'RNG device' seed mode, using '/dev/urandom', seed=183039112 seed_offset=0 real_seed=183039112 core.init.random: RandomGenerator:init: Normal mode, seed=183039112 RG_type=mt19937 core.init: Resolved executable path: /Users/suzukikazushi/Desktop/rosetta_src_2018.33.60351_bundle/main/source/bin/rosetta_scripts.macosclangrelease core.init: Looking for database based on location of executable: /Users/suzukikazushi/Desktop/rosetta_src_2018.33.60351_bundle/main/database/ protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 3rh8_renum.pdb nstruct indices 1 - 2 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 3rh8_renum.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.579719 seconds. core.import_pose.import_pose: File '3rh8_renum.pdb' automatically determined to be of type PDB core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 140 core.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 6 atom name CG core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Users/suzukikazushi/Desktop/rosetta_src_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Users/suzukikazushi/Desktop/rosetta_src_2018.33.60351_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.187338 seconds to load from binary core.pack.pack_rotamers: built 13 rotamers at 1 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 2920 bytes protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=design.xml protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ifcl" of type InitializeFromCommandline protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "rrf" of type ReadResfile core.pack.task.xml_util: Object design reading the following task_operations: Adding the following task operations ifcl rrf protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "design" of type PackRotamersMover protocols.analysis.InterfaceAnalyzerMover: Fixed chains are: A, these will be moved together. protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "analyze" of type InterfaceAnalyzerMover protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "design" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "analyze" with filter "true_filter" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy 3rh8_renum.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - design======================= core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 29442 rotamers at 62 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 15592112 bytes protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER InterfaceAnalyzerMover - analyze======================= protocols.analysis.InterfaceAnalyzerMover: Using explicit constructor protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/core/conformation/Conformation.hh:499 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1. protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job 3rh8_renum_design_0001 File: src/core/conformation/Conformation.hh:499 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1. protocols.jd2.JobDistributor: [ ERROR ] protocols.jd2.JobDistributor: [ WARNING ] 3rh8_renum_design_0001 reported failure and will NOT retry protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy 3rh8_renum.pdb protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy 3rh8_renum.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - design======================= core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 29442 rotamers at 62 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 15592112 bytes protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER InterfaceAnalyzerMover - analyze======================= protocols.analysis.InterfaceAnalyzerMover: Using explicit constructor protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/core/conformation/Conformation.hh:499 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1. protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job 3rh8_renum_design_0002 File: src/core/conformation/Conformation.hh:499 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1. protocols.jd2.JobDistributor: [ ERROR ] protocols.jd2.JobDistributor: [ WARNING ] 3rh8_renum_design_0002 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 2 jobs considered, 2 jobs attempted in 446 seconds Error: [ ERROR ] Exception caught by rosetta_scripts application: File: src/protocols/jd2/JobDistributor.cc:329 2 jobs failed; check output for error messages Error: [ ERROR ]