core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.linuxgccrelease @/mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/comparative_model.options -database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-502704320 seed_offset=0 real_seed=-502704320 core.init.random: RandomGenerator:init: Normal mode, seed=-502704320 RG_type=mt19937 protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA09_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/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA03_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/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA03_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 81600 protocols.loops.loops_main: Fragment libraries: 3 27200 protocols.loops.loops_main: Fragment libraries: 9 26000 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue PRO:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue PRO:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ILE:CtermProteinFull 147 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG 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/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 core.pack.dunbrack: Dunbrack 2010 library took 2.20747 seconds to load from binary core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1 rotamers at 1 positions. core.pack.pack_rotamers: IG: 792 bytes protocols.comparative_modeling.ThreadingJobInputter: Warning: no template pdb provided for alignment protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 0 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: no jobs were attempted, did you forget to pass -overwrite?