core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-231 r231 2019.35+release.767c1ea 767c1ea25c572fbc078db45ad65dddb507240ad3 https://www.rosettacommons.org 2019-08-30T12:04:30.133343 core.init: command: /data1/Rosetta/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/FlexPepDocking.static.linuxgccrelease -database /data1/Rosetta/rosetta_bin_linux_2019.35.60890_bundle/main/database -overwrite -in:file:s test.pdb -constraints:cst_fa_file constraints.cst -extra_res_fa LIN_LYS.params BGL.params -ignore_zero_occupancy false -out:prefix refined_ -out:no_nstruct_label -pep_refine basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1999146820 seed_offset=0 real_seed=1999146820 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1999146820 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 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/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 core.chemical: [ WARNING ] Residue LIN claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning. core.chemical: [ WARNING ] Residue BGL claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning. core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.81 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt 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 core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop 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 core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed test.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB test.pdb core.import_pose.import_pose: File 'test.pdb' automatically determined to be of type PDB core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinFull implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinFull implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinMethylated implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinMethylated implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch AcetylatedNtermProteinFull implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch AcetylatedNtermProteinFull implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch hbs_pre implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch hbs_pre implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch a3b_hbs_pre implies it can apply to residue type BGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch a3b_hbs_pre implies it can apply to residue type DBGL, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch CtermProteinFull implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinFull implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinFull implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinMethylated implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch NtermProteinMethylated implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch AcetylatedNtermProteinFull implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch AcetylatedNtermProteinFull implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch DimethylatedCtermProteinFull implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch hbs_pre implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch hbs_pre implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch a3b_hbs_pre implies it can apply to residue type LIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.chemical.Patch: [ WARNING ] Patch a3b_hbs_pre implies it can apply to residue type DLIN, but actually applying it fails. core.chemical.Patch: [ WARNING ] You may want to check your patch definitions. core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 2 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 3 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 4 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 5 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 6 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 7 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 8 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 9 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 10 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 11 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 12 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 13 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 14 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 15 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 16 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 17 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 18 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 19 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 20 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 21 in file test.pdb. Best match rsd_type: TRP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 22 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 23 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 24 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 25 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 26 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 27 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 28 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 29 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 30 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 31 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 32 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 33 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 34 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 35 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 36 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 37 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 38 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 39 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 40 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 41 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 42 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 43 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 44 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 45 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 46 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 47 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 48 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 49 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 50 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 51 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 52 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 53 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 54 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 55 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 56 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 57 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 58 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 59 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 60 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 61 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 62 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 63 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 64 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 65 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 66 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 67 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 68 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 69 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 70 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 71 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 72 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 73 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 74 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 75 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 76 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 77 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 78 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 79 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 80 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 81 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 82 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 83 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 84 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 85 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 86 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 87 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 88 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 89 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 90 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 91 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 92 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 93 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 94 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 95 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 96 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 97 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 98 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 99 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 100 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 101 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 102 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 103 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 104 in file test.pdb. Best match rsd_type: TRP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 105 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 106 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 107 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 108 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 109 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 110 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 111 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 112 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 113 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 114 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 115 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 116 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 117 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 118 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 119 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 120 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 121 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 122 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 123 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 124 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 125 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 126 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 127 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 128 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 129 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 130 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 131 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 132 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 133 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 134 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 135 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 136 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 137 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 138 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 139 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 6 atoms at position 140 in file test.pdb. Best match rsd_type: ILE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 141 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 142 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 143 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 144 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 145 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 146 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 147 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 148 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 149 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 150 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 151 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 152 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 153 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 154 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 155 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 156 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 157 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 158 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 159 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 160 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 161 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 162 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 163 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 164 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 165 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 166 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 167 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 168 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 169 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 170 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 171 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 172 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 173 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 174 in file test.pdb. Best match rsd_type: GLN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 175 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 176 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 177 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 178 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 179 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 180 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 181 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 182 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 183 in file test.pdb. Best match rsd_type: PHE core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 184 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 185 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 186 in file test.pdb. Best match rsd_type: LEU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 187 in file test.pdb. Best match rsd_type: HIS_D core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 188 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 189 in file test.pdb. Best match rsd_type: PRO core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 190 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 191 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 192 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 193 in file test.pdb. Best match rsd_type: CYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 194 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 195 in file test.pdb. Best match rsd_type: PRO:CtermProteinFull core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 196 in file test.pdb. Best match rsd_type: LYS:NtermProteinFull core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 197 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 198 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 199 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 200 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 201 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 202 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 203 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 204 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 205 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 206 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 207 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 208 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 209 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 210 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 211 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 212 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 213 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 214 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 215 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 216 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 217 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 218 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 219 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 220 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 221 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 222 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 223 in file test.pdb. Best match rsd_type: GLY core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 224 in file test.pdb. Best match rsd_type: ASN core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 225 in file test.pdb. Best match rsd_type: VAL core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 226 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 227 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 228 in file test.pdb. Best match rsd_type: ARG core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 229 in file test.pdb. Best match rsd_type: THR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 230 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 231 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 232 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 5 atoms at position 233 in file test.pdb. Best match rsd_type: LYS core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 234 in file test.pdb. Best match rsd_type: ALA core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 235 in file test.pdb. Best match rsd_type: GLU core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 236 in file test.pdb. Best match rsd_type: ASP core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 3 atoms at position 237 in file test.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 238 in file test.pdb. Best match rsd_type: HIS_D core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 2 atoms at position 239 in file test.pdb. Best match rsd_type: TYR core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 8 atoms at position 240 in file test.pdb. Best match rsd_type: LYS:CtermProteinFull core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 26 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 70 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 78 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 86 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 102 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 136 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue ILE 140 core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue PRO:CtermProteinFull 195 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue PRO:CtermProteinFull 195 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 240 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 242 with connection point 1 core.conformation.Conformation: Found disulfide between residues 4 29 core.conformation.Conformation: current variant for 4 CYS core.conformation.Conformation: current variant for 29 CYS core.conformation.Conformation: current variant for 4 CYD core.conformation.Conformation: current variant for 29 CYD core.conformation.Conformation: Found disulfide between residues 47 100 core.conformation.Conformation: current variant for 47 CYS core.conformation.Conformation: current variant for 100 CYS core.conformation.Conformation: current variant for 47 CYD core.conformation.Conformation: current variant for 100 CYD core.conformation.Conformation: Found disulfide between residues 59 193 core.conformation.Conformation: current variant for 59 CYS core.conformation.Conformation: current variant for 193 CYS core.conformation.Conformation: current variant for 59 CYD core.conformation.Conformation: current variant for 193 CYD core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 26 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 70 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 78 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 86 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 102 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 136 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 140 atom CD (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 195 atom OT1 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 195 atom OT2 (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 240 atom 1H (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 240 atom 2H (trying to store temperature in PDBInfo) core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] can't find pose atom for file-residue 240 atom NT (trying to store temperature in PDBInfo) core.pack.pack_missing_sidechains: packing residue number 26 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 70 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 78 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 86 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 102 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 136 because of missing atom number 8 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 140 because of missing atom number 8 atom name CD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /data1/Rosetta/rosetta_bin_linux_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/data1/Rosetta/rosetta_bin_linux_2019.35.60890_bundle/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.13 seconds to load from binary