core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/dancebean/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.linuxgccrelease @ /mnt/hgfs/Cheng/test/LC/in/flags core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /mnt/hgfs/Cheng/test/LC/in/aaC226S_LC03_05.200_v1_3 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 127200 protocols.loops.loops_main: Fragment libraries: 3 42400 protocols.loops.loops_main: Fragment libraries: 9 41200 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: current variant for 134 CYS core.conformation.Conformation: current variant for 194 CYS core.conformation.Conformation: current variant for 134 CYD core.conformation.Conformation: current variant for 194 CYD core.pack.task: Packer task: initialize from command line() protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.comparative_modeling.threading: skipping atom,position HG ,23 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,88 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,134 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,194 because template doesn't have atom HG . protocols.comparative_modeling.util: No unaligned residues, no loops found. protocols.threading: loops to be rebuilt are: protocols.threading: 0xb81c200 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 protocols.looprelax: ==== Loop protocol: ================================================= protocols.looprelax: remodel quick_ccd protocols.looprelax: intermedrelax no protocols.looprelax: refine refine_ccd protocols.looprelax: relax no protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.comparative_modeling.util: No chainbreaks found, so not picking any loops! protocols.comparative_modeling.util: No unaligned residues, no loops found. core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types protocols.looprelax: ==================================================================================== protocols.looprelax: === protocols.looprelax: === Initial Building protocols.looprelax: === protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: ALL_LOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: SELECTEDLOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: protocols::checkpoint: Deleting checkpoints of InitialBuild protocols.looprelax: Buildtime: 0 protocols.looprelax: FOLD_TREE EDGE 1 214 -1 protocols.looprelax: protocols.looprelax: ==================================================================================== protocols.looprelax: === protocols.looprelax: === Fullatom protocols.looprelax: === protocols.looprelax: Annotated sequence before fa switch: D[ASP:NtermProteinFull]IQMTQSPSSLSASVGDRVTITCKASQNVRTVVAWYQQKPGKAPKTLIYLASNRHTGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCLQHWSYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC[CYS:CtermProteinFull] protocols.looprelax: Repacking required protocols.looprelax: Detecting disulfides protocols.looprelax: Annotated sequence before repack: D[ASP:NtermProteinFull]IQMTQSPSSLSASVGDRVTITCKASQNVRTVVAWYQQKPGKAPKTLIYLASNRHTGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCLQHWSYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC[CYS:CtermProteinFull] core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: current variant for 134 CYS core.conformation.Conformation: current variant for 194 CYS core.conformation.Conformation: current variant for 134 CYD core.conformation.Conformation: current variant for 194 CYD core.pack.task: Packer task: initialize from command line() protocols.looprelax: 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000disabling minimization on disulfide residue 23 protocols.looprelax: disabling minimization on disulfide residue 88 protocols.looprelax: disabling minimization on disulfide residue 134 protocols.looprelax: disabling minimization on disulfide residue 194 core.pack.dunbrack: Dunbrack 2010 library took 0.645507 seconds to load from binary core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 197 rotamers at 19 positions. core.pack.pack_rotamers: IG: 45144 bytes protocols.looprelax: -259.503 -734.580 86.189 415.884 1.481 -83.887 0.761 -16.622