core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373 core.init: command: /software/repo/moleculardynamics/rosetta/3.9/main/source/bin/fixbb.static.linuxgccrelease -s 2fad.pdb -use_input_sc -nstruct 1 -extra_res_fa OCT.params -resfile ncaa_resfile.txt -score:weights mm_std -database /software/repo/moleculardynamics/rosetta/3.9/main/database -ex1 -ex2 -overwrite -minimize_sidechains core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1969604488 seed_offset=0 real_seed=1969604488 core.init.random: RandomGenerator:init: Normal mode, seed=1969604488 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: mm_std 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. core.mm.MMLJLibrary: MM lj sets added: 105 core.mm.MMTorsionLibrary: MM torsion sets added fully assigned: 1028; wildcard: 48 and 1 virtual parameter. 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 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed 2fad.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...  protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB 2fad.pdb 
 ERROR: Only the third ICOOR atom in a topology file should list itself as its own dihedral atom, from file OCT.params ERROR:: Exit from: src/core/chemical/residue_io.cc line: 1221 BACKTRACE: [0x58c76f8] [0x5320747] [0x5323cdd] [0x52bcfb1] [0x52a5d14] [0x52a8637] [0x52a760c] [0x52a78a8] [0x51ce4ee] [0x3f2ab5d] [0x36972a0] [0x3697446] [0x35d34cf] [0x35ab0e0] [0x35ad0d1] [0x364fc48] [0x411249] [0x5e0d454] [0x61601d] Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job '2fad_0001' Error: [ ERROR ]  
 File: src/core/chemical/residue_io.cc:1221 [ ERROR ] UtilityExitException ERROR: Only the third ICOOR atom in a topology file should list itself as its own dihedral atom, from file OCT.params 
 
 Error: [ ERROR ]  Error: [ ERROR ] Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 2fad_0001 protocols.jd2.JobDistributor: no more batches to process...  protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 6 seconds caught exception  
 File: src/protocols/jd2/JobDistributor.cc:329 1 jobs failed; check output for error messages