core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: loopmodel.linuxgccdebug @flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-791386380 seed_offset=0 real_seed=-791386380 core.init.random: RandomGenerator:init: Normal mode, seed=-791386380 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /usr/local/rosetta/main/database protocols.loop_build.LoopBuild: ==== Loop protocol: ================================================= protocols.loop_build.LoopBuild: remodel no protocols.loop_build.LoopBuild: intermedrelax no protocols.loop_build.LoopBuild: refine refine_kic_with_fragments protocols.loop_build.LoopBuild: relax no protocols.loops.loops_main: Frag libraries debug ./input/a3h2.frag9 9 core.io.fragments: reading fragments from file: ./input/a3h2.frag9 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file ./input/a3h2.frag9 protocols.loops.loops_main: Frag libraries debug ./input/a3h2.frag3 3 core.io.fragments: reading fragments from file: ./input/a3h2.frag3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ./input/a3h2.frag3 protocols.loops.loops_main: Frag libraries debug none 1 protocols.loops.loops_main: Set up 1-mer library from 3-mer library protocols.loops.loops_main: Fragment libraries: 1 108000 protocols.loops.loops_main: Fragment libraries: 3 36000 protocols.loops.loops_main: Fragment libraries: 9 34800 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 basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 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/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp core.scoring.ScoreFunctionFactory: The -auto_setup_metals flag was used with no atom_pair_constraint weight set in the weights file. Setting to 1.0. core.scoring.ScoreFunctionFactory: The -auto_setup_metals flag was used with no angle_constraint weight set in the weights file. Setting to 1.0. protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed ./input/a3h-v0.1.9_input_newZ.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB ./input/a3h-v0.1.9_input_newZ.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 785 residue types core.io.pdb.file_data: ZN 183 was added by a jump, with base residue 85 core.pack.task: Packer task: initialize from command line() core.util.metalloproteins_util: Automatically setting covalent bonds between metal ions and metal-binding residues. core.util.metalloproteins_util: Adding covalent linkage between residue 54's ND1 atom and residue 183's ZN atom. core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.pack.dunbrack: Dunbrack 2010 library took 0.926516 seconds to load from binary core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:CtermProteinFull core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:NtermProteinFull core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:CtermProteinFull:NtermProteinFull core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:protein_cutpoint_upper core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:CtermProteinFull:protein_cutpoint_upper core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:protein_cutpoint_lower core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:NtermProteinFull:protein_cutpoint_lower core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:protein_cutpoint_upper:protein_cutpoint_lower core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:MethylatedCtermProteinFull core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:AcetylatedNtermProteinFull core.chemical.ResidueProperties: Rosetta does not recognize the variant: ND1_CONNECT; has it been added to variant_types.list? core.chemical.ResidueProperties: Adding the custom variant ND1_CONNECT to HISND1_connect:MethylatedCtermProteinFull:AcetylatedNtermProteinFull core.util.metalloproteins_util: Adding covalent linkage between residue 85's SG atom and residue 183's ZN atom. core.chemical.ResidueProperties: Adding the custom variant ZN_CONNECT2 to ZNZN_connectZN_connect2 core.util.metalloproteins_util: Adding covalent linkage between residue 88's SG atom and residue 183's ZN atom. core.chemical.ResidueProperties: Adding the custom variant ZN_CONNECT3 to ZNZN_connectZN_connect2ZN_connect3 core.util.metalloproteins_util: Automatically setting up constraints between metal ions and metal-binding residues. protocols.loops.loops_main: set_secstruct for pose: LLLLLHHHHEEELLLLLLLLLLLLLLLEEEEEEEEELLLLLLLLLEEELLLLLLHHHHHHHHLLLLLLLLLLEEEEEEEEELLLHHHHHHHHHHHHHHLLLEEEEEEEEELLLLLLHHHHHHHHHHHHLLLLEEELLHHHHHHHHHHHEELLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHL protocols.loops.loops_main: set pose secstruct from psipred_ss2 file succesfully protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.loop_build.LoopBuildMover: Annotated sequence of pose: M[MET:NtermProteinFull]ALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCH[HISND1_connect]AEICFINEIKSMGLDETQCYQVTCYLTWSPC[CYSSG_connect]SSC[CYSSG_connect]AWELVDFIKAHDH[HIS_D]LNLGIFASRLYYH[HIS_D]WCKPQQKGLRLLCGSQVPVEVMGFPKFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLERIKS[SER:CtermProteinFull]Z[ZNZN_connectZN_connect2ZN_connect3] protocols.looprelax: ==== Loop protocol: ================================================= protocols.looprelax: remodel no protocols.looprelax: intermedrelax no protocols.looprelax: refine refine_kic_with_fragments protocols.looprelax: relax no protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1042 residue types MALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPKFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLERIKSZ can not find a residue type that matches the residue HISND1_connectat position 54 ERROR: core::util::switch_to_residue_type_set fails ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 323 loopmodel.linuxgccdebug(print_backtrace()+0x20) [0x40310d] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x1a4) [0x7f608a0e7cd5] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libcore.4.so(core::util::switch_to_residue_type_set(core::pose::Pose&, std::string const&, bool)+0x1f8a) [0x7f608f84d33d] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols_g.4.so(protocols::comparative_modeling::LoopRelaxMover::apply(core::pose::Pose&)+0xcca) [0x7f609688ce98] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols_b.5.so(protocols::loop_build::LoopBuildMover::apply(core::pose::Pose&)+0x6de) [0x7f6097bdfe98] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(boost::shared_ptr&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xd2e) [0x7f6090cfd8a0] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(boost::shared_ptr)+0xab) [0x7f6090cfc061] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(boost::shared_ptr)+0x46) [0x7f6090cd9304] /usr/local/rosetta/main/source/build/src/debug/linux/3.19/64/x86/gcc/4.9/default/libprotocols_b.5.so(protocols::loop_build::LoopBuild_main(bool)+0x4e6) [0x7f6097bd2496] loopmodel.linuxgccdebug() [0x402a6c] loopmodel.linuxgccdebug() [0x40352d] loopmodel.linuxgccdebug() [0x402b47] /lib64/libc.so.6(__libc_start_main+0xf0) [0x7f6088140790] loopmodel.linuxgccdebug() [0x402989] protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job a3h2_v0.3.0-a3h-v0.1.9_input_newZ_0001 [ERROR] EXCN_utility_exit has been thrown from: src/core/util/SwitchResidueTypeSet.cc line: 323 ERROR: core::util::switch_to_residue_type_set fails protocols.jd2.JobDistributor: a3h2_v0.3.0-a3h-v0.1.9_input_newZ_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 8 seconds caught exception 1 jobs failed; check output for error messages