~/linux_program/rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_program/rosetta/main/database/ -ignore_zero_occupancy false -ignore_unrecognized_res -use_input_sc -s 1cz8-2.pdb -ex1 -ex2 -parser:protocol InverseRotamers.xml core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: /home/ali-linux/linux_program/rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -database /home/ali-linux/linux_program/rosetta/main/database/ -ignore_zero_occupancy false -ignore_unrecognized_res -use_input_sc -s 1cz8-2.pdb -ex1 -ex2 -parser:protocol InverseRotamers.xml core.init: 'RNG device' seed mode, using '/dev/urandom', seed=473822867 seed_offset=0 real_seed=473822867 core.init.random: RandomGenerator:init: Normal mode, seed=473822867 RG_type=mt19937 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 1cz8-2.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.JobDistributor: Parser is present. Input mover will be overwritten with whatever the parser creates. protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 1cz8-2.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.480394 seconds. core.import_pose.import_pose: File '1cz8-2.pdb' automatically determined to be of type PDB core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 96 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 144 200 core.conformation.Conformation: current variant for 144 CYS core.conformation.Conformation: current variant for 200 CYS core.conformation.Conformation: current variant for 144 CYD core.conformation.Conformation: current variant for 200 CYD core.conformation.Conformation: Found disulfide between residues 231 273 core.conformation.Conformation: current variant for 231 CYS core.conformation.Conformation: current variant for 273 CYS core.conformation.Conformation: current variant for 231 CYD core.conformation.Conformation: current variant for 273 CYD core.conformation.Conformation: Found disulfide between residues 262 307 core.conformation.Conformation: current variant for 262 CYS core.conformation.Conformation: current variant for 307 CYS core.conformation.Conformation: current variant for 262 CYD core.conformation.Conformation: current variant for 307 CYD core.conformation.Conformation: Found disulfide between residues 266 309 core.conformation.Conformation: current variant for 266 CYS core.conformation.Conformation: current variant for 309 CYS core.conformation.Conformation: current variant for 266 CYD core.conformation.Conformation: current variant for 309 CYD protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=InverseRotamers.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: talaris2014 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/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 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 basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction. 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/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 protocols.simple_filters.EnergyPerResidueFilter: EnergyPerResidueFilter for residue 102 of score_type total_score with cutoff 0 protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "energy" of type EnergyPerResidue protocols.simple_filters.DdgFilter: ddg filter with threshold -1 repeats=1 and scorefxn commandline over jump 1extreme_value_removal: 0 and repack 1 protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg protocols.protein_interface_design.movers.TryRotamers: Using shove atomtype for 102H TryRotamers was instantiated using scorefxn=commandline, jump_number=1, solo_res=0, clash_check=0, include_current=1, and explosion=0 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "try" of type TryRotamers protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "try" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "energy" protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "ddg" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy 1cz8-2.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER TryRotamers - try======================= protocols.protein_interface_design.movers.TryRotamers: current fold-tree: FOLD_TREE EDGE 1 218 -1 EDGE 1 219 1 EDGE 219 312 -1 protocols.protein_interface_design.movers.TryRotamers: New foldtree: FOLD_TREE EDGE 1 54 -1 EDGE 54 218 -1 JEDGE 54 219 1 C CG1 END core.conformation.Conformation: Error in assigning a FoldTree to a Conformation - size mismatch. core.conformation.Conformation: Conformation of length 312: E[GLU:NtermProteinFull]VQLVESGGGLVQPGGSLRLSC[CYS:disulfide]AASGYDFTHYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYC[CYS:disulfide]AKYPYYYGTSHWYFDVWGQGTLVTVSSASTKGPSVFPLAPSGTAALGC[CYS:disulfide]LVKDYFPEPVTVSWNSGALTSGVH[HIS_D]TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC[CYS:disulfide]NVNHKPSNTKVDKKVEPK[LYS:CtermProteinFull]V[VAL:NtermProteinFull]VKFMDVYQRSYC[CYS:disulfide]H[HIS_D]PIETLVDIFQEYPDEIEYIFKPSCVPLMRC[CYS:disulfide]GGCC[CYS:disulfide]NDEGLEC[CYS:disulfide]VPTEESNITMQIMRIKPHQGQH[HIS_D]IGEMSFLQHNKC[CYS:disulfide]EC[CYS:disulfide]RPK[LYS:CtermProteinFull] core.conformation.Conformation: FoldTree of length 219: FOLD_TREE EDGE 1 54 -1 EDGE 54 218 -1 JEDGE 54 219 1 C CG1 END ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 312 fold_tree nres: 219 ERROR:: Exit from: src/core/conformation/Conformation.cc line: 761 /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libutility.so(print_backtrace(char const*)+0x3e) [0x7f8bf438c97e] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libutility.so(utility::exit(std::__cxx11::basic_string, std::allocator > const&, int, std::__cxx11::basic_string, std::allocator > const&, int)+0x19e) [0x7f8bf438bfae] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libcore.2.so(core::conformation::Conformation::fold_tree(core::kinematics::FoldTree const&)+0x206) [0x7f8beeb96ed6] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.6.so(protocols::protein_interface_design::movers::TryRotamers::apply(core::pose::Pose&)+0x214f) [0x7f8becbabb0f] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x208) [0x7f8bf848cbe8] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator > >)+0x3b) [0x7f8bf848edab] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a7) [0x7f8bf848f6c7] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr&, long, std::__cxx11::basic_string, std::allocator >&, std::__cxx11::basic_string, std::allocator >&, unsigned long&, unsigned long&, bool)+0x105e) [0x7f8bf8587ade] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr)+0x18e) [0x7f8bf8589bce] /home/ali-linux/linux_program/rosetta/main/source/build/src/release/linux/4.10/64/x86/gcc/6.3/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr)+0x57) [0x7f8bf8552dc7] /home/ali-linux/linux_program/rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease(+0x6cb3) [0x557fc1560cb3] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1) [0x7f8bf37203f1] /home/ali-linux/linux_program/rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease(+0x6e5a) [0x557fc1560e5a] protocols.rosetta_scripts.ParsedProtocol: Exception while processing procotol: protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job 1cz8-2_0001 [ERROR] EXCN_utility_exit has been thrown from: src/core/conformation/Conformation.cc line: 761 ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 312 fold_tree nres: 219 protocols.jd2.JobDistributor: 1cz8-2_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... ali-linux@alilinux-Lenovo-Y50-70:~/Desktop/peptide_design/1CZ8/inverse_rotamers_1cz8/inverse_rotamers_Y102$ ~/linux_program/rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_program/rosetta/main/database/ -ignore_zero_occupancy false -ignore_unrecognized_res -use_input_sc -s 1cz8-2.pdb -ex1 -ex2 -parser:protocol InverseRotamers.xml rror: