SetSeed InfilePrefix // Note: the training atoms are needed for patching up chain breaks // when reading in conformations. InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/ ReadTrainingAtoms dunbrack-2191.atoms ReadRotamerLibrary dunbrack-2191.rot InFilePrefix /projects/compbio/experiments/undertaker/spots/ ReadAtomType exp-pdb.types ReadClashTable exp-pdb-2191-2symm.clash SetClashDefinition exp-pdb-2191-2symm CreateBurialCost near_backbone near-backbone-center.spot smoothed-near-backbone-2spot.hist near-backbone-count.spot CreateBurialCost way_back way-back-center.spot smoothed-way-back-2spot.hist way-back-count.spot CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist CreateAlphaCost alpha dunbrack-2191-alpha.hist CreateAlphaCost alpha_prev dunbrack-2191-alpha-1.hist -1 Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0295.blank.pdb ReadTargetSeq T0295.a2m 1 NameTarget T0295 PopConform InFilePrefix /projects/compbio/lib/alphabet/ ReadAlphabet alpha.alphabet InFilePrefix include try5.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Switch to the following (commenting out the TryAllAlign) // to polish existing models InfilePrefix decoys/ ReadConformPDB T0295.try1-opt1-scwrl.pdb.gz ReadConformPDB T0295.try1-opt1.pdb.gz ReadConformPDB T0295.try1-opt2.gromacs0.pdb.gz ReadConformPDB T0295.try1-opt2.pdb.gz ReadConformPDB T0295.try1-opt2.repack-nonPC.pdb.gz ReadConformPDB T0295.try2-opt1-scwrl.pdb.gz ReadConformPDB T0295.try2-opt1.pdb.gz ReadConformPDB T0295.try2-opt2.gromacs0.pdb.gz ReadConformPDB T0295.try2-opt2.pdb.gz ReadConformPDB T0295.try2-opt2.repack-nonPC.pdb.gz ReadConformPDB T0295.try4-opt1-scwrl.pdb.gz ReadConformPDB T0295.try4-opt1.pdb.gz ReadConformPDB T0295.try4-opt2.gromacs0.pdb.gz ReadConformPDB T0295.try4-opt2.pdb.gz ReadConformPDB T0295.try4-opt2.repack-nonPC.pdb.gz InfilePrefix decoys/servers/ ReadConformPDB 3D-JIGSAW_POPULUS_TS1.pdb NameConform 3D-JIGSAW_POPULUS_TS1 SCWRLconform NameConform 3D-JIGSAW_POPULUS_TS1-scwrl ReadConformPDB 3D-JIGSAW_POPULUS_TS2.pdb NameConform 3D-JIGSAW_POPULUS_TS2 SCWRLconform NameConform 3D-JIGSAW_POPULUS_TS2-scwrl ReadConformPDB 3D-JIGSAW_POPULUS_TS3.pdb NameConform 3D-JIGSAW_POPULUS_TS3 SCWRLconform NameConform 3D-JIGSAW_POPULUS_TS3-scwrl ReadConformPDB 3D-JIGSAW_POPULUS_TS4.pdb NameConform 3D-JIGSAW_POPULUS_TS4 SCWRLconform NameConform 3D-JIGSAW_POPULUS_TS4-scwrl ReadConformPDB 3D-JIGSAW_POPULUS_TS5.pdb NameConform 3D-JIGSAW_POPULUS_TS5 SCWRLconform NameConform 3D-JIGSAW_POPULUS_TS5-scwrl ReadConformPDB 3D-JIGSAW_RECOM_TS1.pdb NameConform 3D-JIGSAW_RECOM_TS1 SCWRLconform NameConform 3D-JIGSAW_RECOM_TS1-scwrl ReadConformPDB 3D-JIGSAW_RECOM_TS2.pdb NameConform 3D-JIGSAW_RECOM_TS2 SCWRLconform NameConform 3D-JIGSAW_RECOM_TS2-scwrl ReadConformPDB 3D-JIGSAW_RECOM_TS3.pdb NameConform 3D-JIGSAW_RECOM_TS3 SCWRLconform NameConform 3D-JIGSAW_RECOM_TS3-scwrl ReadConformPDB 3D-JIGSAW_RECOM_TS4.pdb NameConform 3D-JIGSAW_RECOM_TS4 SCWRLconform NameConform 3D-JIGSAW_RECOM_TS4-scwrl ReadConformPDB 3D-JIGSAW_RECOM_TS5.pdb NameConform 3D-JIGSAW_RECOM_TS5 SCWRLconform NameConform 3D-JIGSAW_RECOM_TS5-scwrl ReadConformPDB 3D-JIGSAW_TS1.pdb NameConform 3D-JIGSAW_TS1 SCWRLconform NameConform 3D-JIGSAW_TS1-scwrl ReadConformPDB 3D-JIGSAW_TS2.pdb NameConform 3D-JIGSAW_TS2 SCWRLconform NameConform 3D-JIGSAW_TS2-scwrl ReadConformPDB 3Dpro_TS1.pdb NameConform 3Dpro_TS1 SCWRLconform NameConform 3Dpro_TS1-scwrl ReadConformPDB 3Dpro_TS2.pdb NameConform 3Dpro_TS2 SCWRLconform NameConform 3Dpro_TS2-scwrl ReadConformPDB BayesHH_TS1.pdb NameConform BayesHH_TS1 SCWRLconform NameConform BayesHH_TS1-scwrl ReadConformPDB Bilab-ENABLE_TS1.pdb NameConform Bilab-ENABLE_TS1 SCWRLconform NameConform Bilab-ENABLE_TS1-scwrl ReadConformPDB Bilab-ENABLE_TS2.pdb NameConform Bilab-ENABLE_TS2 SCWRLconform NameConform Bilab-ENABLE_TS2-scwrl ReadConformPDB Bilab-ENABLE_TS3.pdb NameConform Bilab-ENABLE_TS3 SCWRLconform NameConform Bilab-ENABLE_TS3-scwrl ReadConformPDB Bilab-ENABLE_TS4.pdb NameConform Bilab-ENABLE_TS4 SCWRLconform NameConform Bilab-ENABLE_TS4-scwrl ReadConformPDB CIRCLE_TS1.pdb NameConform CIRCLE_TS1 SCWRLconform NameConform CIRCLE_TS1-scwrl ReadConformPDB CIRCLE_TS2.pdb NameConform CIRCLE_TS2 SCWRLconform NameConform CIRCLE_TS2-scwrl ReadConformPDB CIRCLE_TS3.pdb NameConform CIRCLE_TS3 SCWRLconform NameConform CIRCLE_TS3-scwrl ReadConformPDB CIRCLE_TS4.pdb NameConform CIRCLE_TS4 SCWRLconform NameConform CIRCLE_TS4-scwrl ReadConformPDB CIRCLE_TS5.pdb NameConform CIRCLE_TS5 SCWRLconform NameConform CIRCLE_TS5-scwrl ReadConformPDB CPHmodels_TS1.pdb NameConform CPHmodels_TS1 SCWRLconform NameConform CPHmodels_TS1-scwrl ReadConformPDB CaspIta-FOX_TS1.pdb NameConform CaspIta-FOX_TS1 SCWRLconform NameConform CaspIta-FOX_TS1-scwrl ReadConformPDB FAMSD_TS1.pdb NameConform FAMSD_TS1 SCWRLconform NameConform FAMSD_TS1-scwrl ReadConformPDB FAMSD_TS2.pdb NameConform FAMSD_TS2 SCWRLconform NameConform FAMSD_TS2-scwrl ReadConformPDB FAMSD_TS3.pdb NameConform FAMSD_TS3 SCWRLconform NameConform FAMSD_TS3-scwrl ReadConformPDB FAMSD_TS4.pdb NameConform FAMSD_TS4 SCWRLconform NameConform FAMSD_TS4-scwrl ReadConformPDB FAMS_TS2.pdb NameConform FAMS_TS2 SCWRLconform NameConform FAMS_TS2-scwrl ReadConformPDB FAMS_TS3.pdb NameConform FAMS_TS3 SCWRLconform NameConform FAMS_TS3-scwrl ReadConformPDB FAMS_TS4.pdb NameConform FAMS_TS4 SCWRLconform NameConform FAMS_TS4-scwrl ReadConformPDB FAMS_TS5.pdb NameConform FAMS_TS5 SCWRLconform NameConform FAMS_TS5-scwrl ReadConformPDB FOLDpro_TS1.pdb NameConform FOLDpro_TS1 SCWRLconform NameConform FOLDpro_TS1-scwrl ReadConformPDB FOLDpro_TS2.pdb NameConform FOLDpro_TS2 SCWRLconform NameConform FOLDpro_TS2-scwrl ReadConformPDB FUGMOD_TS1.pdb NameConform FUGMOD_TS1 SCWRLconform NameConform FUGMOD_TS1-scwrl ReadConformPDB FUNCTION_TS1.pdb NameConform FUNCTION_TS1 SCWRLconform NameConform FUNCTION_TS1-scwrl ReadConformPDB FUNCTION_TS2.pdb NameConform FUNCTION_TS2 SCWRLconform NameConform FUNCTION_TS2-scwrl ReadConformPDB FUNCTION_TS3.pdb NameConform FUNCTION_TS3 SCWRLconform NameConform FUNCTION_TS3-scwrl ReadConformPDB FUNCTION_TS5.pdb NameConform FUNCTION_TS5 SCWRLconform NameConform FUNCTION_TS5-scwrl ReadConformPDB GeneSilicoMetaServer_TS1.pdb NameConform GeneSilicoMetaServer_TS1 SCWRLconform NameConform GeneSilicoMetaServer_TS1-scwrl ReadConformPDB GeneSilicoMetaServer_TS2.pdb NameConform GeneSilicoMetaServer_TS2 SCWRLconform NameConform GeneSilicoMetaServer_TS2-scwrl ReadConformPDB GeneSilicoMetaServer_TS3.pdb NameConform GeneSilicoMetaServer_TS3 SCWRLconform NameConform GeneSilicoMetaServer_TS3-scwrl ReadConformPDB GeneSilicoMetaServer_TS4.pdb NameConform GeneSilicoMetaServer_TS4 SCWRLconform NameConform GeneSilicoMetaServer_TS4-scwrl ReadConformPDB GeneSilicoMetaServer_TS5.pdb NameConform GeneSilicoMetaServer_TS5 SCWRLconform NameConform GeneSilicoMetaServer_TS5-scwrl ReadConformPDB HHpred1_TS1.pdb NameConform HHpred1_TS1 SCWRLconform NameConform HHpred1_TS1-scwrl ReadConformPDB HHpred2_TS1.pdb NameConform HHpred2_TS1 SCWRLconform NameConform HHpred2_TS1-scwrl ReadConformPDB HHpred3_TS1.pdb NameConform HHpred3_TS1 SCWRLconform NameConform HHpred3_TS1-scwrl ReadConformPDB LOOPP_TS1.pdb NameConform LOOPP_TS1 SCWRLconform NameConform LOOPP_TS1-scwrl ReadConformPDB Ma-OPUS-server_TS1.pdb NameConform Ma-OPUS-server_TS1 SCWRLconform NameConform Ma-OPUS-server_TS1-scwrl ReadConformPDB Ma-OPUS-server_TS2.pdb NameConform Ma-OPUS-server_TS2 SCWRLconform NameConform Ma-OPUS-server_TS2-scwrl ReadConformPDB PROTINFO-AB_TS1.pdb NameConform PROTINFO-AB_TS1 SCWRLconform NameConform PROTINFO-AB_TS1-scwrl ReadConformPDB PROTINFO-AB_TS2.pdb NameConform PROTINFO-AB_TS2 SCWRLconform NameConform PROTINFO-AB_TS2-scwrl ReadConformPDB PROTINFO-AB_TS3.pdb NameConform PROTINFO-AB_TS3 SCWRLconform NameConform PROTINFO-AB_TS3-scwrl ReadConformPDB PROTINFO-AB_TS4.pdb NameConform PROTINFO-AB_TS4 SCWRLconform NameConform PROTINFO-AB_TS4-scwrl ReadConformPDB PROTINFO-AB_TS5.pdb NameConform PROTINFO-AB_TS5 SCWRLconform NameConform PROTINFO-AB_TS5-scwrl ReadConformPDB PROTINFO_TS1.pdb NameConform PROTINFO_TS1 SCWRLconform NameConform PROTINFO_TS1-scwrl ReadConformPDB PROTINFO_TS2.pdb NameConform PROTINFO_TS2 SCWRLconform NameConform PROTINFO_TS2-scwrl ReadConformPDB PROTINFO_TS3.pdb NameConform PROTINFO_TS3 SCWRLconform NameConform PROTINFO_TS3-scwrl ReadConformPDB PROTINFO_TS4.pdb NameConform PROTINFO_TS4 SCWRLconform NameConform PROTINFO_TS4-scwrl ReadConformPDB PROTINFO_TS5.pdb NameConform PROTINFO_TS5 SCWRLconform NameConform PROTINFO_TS5-scwrl ReadConformPDB Pcons6_TS1.pdb NameConform Pcons6_TS1 SCWRLconform NameConform Pcons6_TS1-scwrl ReadConformPDB Pcons6_TS2.pdb NameConform Pcons6_TS2 SCWRLconform NameConform Pcons6_TS2-scwrl ReadConformPDB Pcons6_TS3.pdb NameConform Pcons6_TS3 SCWRLconform NameConform Pcons6_TS3-scwrl ReadConformPDB Pcons6_TS4.pdb NameConform Pcons6_TS4 SCWRLconform NameConform Pcons6_TS4-scwrl ReadConformPDB Pcons6_TS5.pdb NameConform Pcons6_TS5 SCWRLconform NameConform Pcons6_TS5-scwrl ReadConformPDB Phyre-1_TS1.pdb NameConform Phyre-1_TS1 SCWRLconform NameConform Phyre-1_TS1-scwrl ReadConformPDB Phyre-2_TS1.pdb NameConform Phyre-2_TS1 SCWRLconform NameConform Phyre-2_TS1-scwrl ReadConformPDB Phyre-2_TS2.pdb NameConform Phyre-2_TS2 SCWRLconform NameConform Phyre-2_TS2-scwrl ReadConformPDB Phyre-2_TS3.pdb NameConform Phyre-2_TS3 SCWRLconform NameConform Phyre-2_TS3-scwrl ReadConformPDB Phyre-2_TS4.pdb NameConform Phyre-2_TS4 SCWRLconform NameConform Phyre-2_TS4-scwrl ReadConformPDB Phyre-2_TS5.pdb NameConform Phyre-2_TS5 SCWRLconform NameConform Phyre-2_TS5-scwrl ReadConformPDB Pmodeller6_TS1.pdb NameConform Pmodeller6_TS1 SCWRLconform NameConform Pmodeller6_TS1-scwrl ReadConformPDB Pmodeller6_TS2.pdb NameConform Pmodeller6_TS2 SCWRLconform NameConform Pmodeller6_TS2-scwrl ReadConformPDB Pmodeller6_TS3.pdb NameConform Pmodeller6_TS3 SCWRLconform NameConform Pmodeller6_TS3-scwrl ReadConformPDB Pmodeller6_TS4.pdb NameConform Pmodeller6_TS4 SCWRLconform NameConform Pmodeller6_TS4-scwrl ReadConformPDB Pmodeller6_TS5.pdb NameConform Pmodeller6_TS5 SCWRLconform NameConform Pmodeller6_TS5-scwrl ReadConformPDB RAPTOR-ACE_TS1.pdb NameConform RAPTOR-ACE_TS1 SCWRLconform NameConform RAPTOR-ACE_TS1-scwrl ReadConformPDB RAPTOR-ACE_TS2.pdb NameConform RAPTOR-ACE_TS2 SCWRLconform NameConform RAPTOR-ACE_TS2-scwrl ReadConformPDB RAPTOR-ACE_TS3.pdb NameConform RAPTOR-ACE_TS3 SCWRLconform NameConform RAPTOR-ACE_TS3-scwrl ReadConformPDB RAPTOR-ACE_TS4.pdb NameConform RAPTOR-ACE_TS4 SCWRLconform NameConform RAPTOR-ACE_TS4-scwrl ReadConformPDB RAPTOR-ACE_TS5.pdb NameConform RAPTOR-ACE_TS5 SCWRLconform NameConform RAPTOR-ACE_TS5-scwrl ReadConformPDB RAPTORESS_TS1.pdb NameConform RAPTORESS_TS1 SCWRLconform NameConform RAPTORESS_TS1-scwrl ReadConformPDB RAPTORESS_TS2.pdb NameConform RAPTORESS_TS2 SCWRLconform NameConform RAPTORESS_TS2-scwrl ReadConformPDB RAPTORESS_TS3.pdb NameConform RAPTORESS_TS3 SCWRLconform NameConform RAPTORESS_TS3-scwrl ReadConformPDB RAPTORESS_TS4.pdb NameConform RAPTORESS_TS4 SCWRLconform NameConform RAPTORESS_TS4-scwrl ReadConformPDB RAPTORESS_TS5.pdb NameConform RAPTORESS_TS5 SCWRLconform NameConform RAPTORESS_TS5-scwrl ReadConformPDB RAPTOR_TS1.pdb NameConform RAPTOR_TS1 SCWRLconform NameConform RAPTOR_TS1-scwrl ReadConformPDB RAPTOR_TS2.pdb NameConform RAPTOR_TS2 SCWRLconform NameConform RAPTOR_TS2-scwrl ReadConformPDB ROBETTA_TS1.pdb NameConform ROBETTA_TS1 SCWRLconform NameConform ROBETTA_TS1-scwrl ReadConformPDB ROBETTA_TS2.pdb NameConform ROBETTA_TS2 SCWRLconform NameConform ROBETTA_TS2-scwrl ReadConformPDB ROBETTA_TS3.pdb NameConform ROBETTA_TS3 SCWRLconform NameConform ROBETTA_TS3-scwrl ReadConformPDB ROBETTA_TS4.pdb NameConform ROBETTA_TS4 SCWRLconform NameConform ROBETTA_TS4-scwrl ReadConformPDB ROBETTA_TS5.pdb NameConform ROBETTA_TS5 SCWRLconform NameConform ROBETTA_TS5-scwrl ReadConformPDB ROKKY_TS1.pdb NameConform ROKKY_TS1 SCWRLconform NameConform ROKKY_TS1-scwrl ReadConformPDB SAM-T99_AL1.pdb NameConform SAM-T99_AL1 SCWRLconform NameConform SAM-T99_AL1-scwrl ReadConformPDB SAM-T99_AL2.pdb NameConform SAM-T99_AL2 SCWRLconform NameConform SAM-T99_AL2-scwrl ReadConformPDB SAM_T06_server_TS1.pdb NameConform SAM_T06_server_TS1 SCWRLconform NameConform SAM_T06_server_TS1-scwrl ReadConformPDB SP3_TS1.pdb NameConform SP3_TS1 SCWRLconform NameConform SP3_TS1-scwrl ReadConformPDB SP4_TS1.pdb NameConform SP4_TS1 SCWRLconform NameConform SP4_TS1-scwrl ReadConformPDB SPARKS2_TS1.pdb NameConform SPARKS2_TS1 SCWRLconform NameConform SPARKS2_TS1-scwrl ReadConformPDB UNI-EID_bnmx_TS1.pdb NameConform UNI-EID_bnmx_TS1 SCWRLconform NameConform UNI-EID_bnmx_TS1-scwrl ReadConformPDB UNI-EID_sfst_AL1.pdb NameConform UNI-EID_sfst_AL1 SCWRLconform NameConform UNI-EID_sfst_AL1-scwrl ReadConformPDB Zhang-Server_TS1.pdb NameConform Zhang-Server_TS1 SCWRLconform NameConform Zhang-Server_TS1-scwrl ReadConformPDB Zhang-Server_TS2.pdb NameConform Zhang-Server_TS2 SCWRLconform NameConform Zhang-Server_TS2-scwrl ReadConformPDB Zhang-Server_TS4.pdb NameConform Zhang-Server_TS4 SCWRLconform NameConform Zhang-Server_TS4-scwrl ReadConformPDB Zhang-Server_TS5.pdb NameConform Zhang-Server_TS5 SCWRLconform NameConform Zhang-Server_TS5-scwrl ReadConformPDB keasar-server_TS1.pdb NameConform keasar-server_TS1 SCWRLconform NameConform keasar-server_TS1-scwrl ReadConformPDB keasar-server_TS2.pdb NameConform keasar-server_TS2 SCWRLconform NameConform keasar-server_TS2-scwrl ReadConformPDB keasar-server_TS3.pdb NameConform keasar-server_TS3 SCWRLconform NameConform keasar-server_TS3-scwrl ReadConformPDB keasar-server_TS4.pdb NameConform keasar-server_TS4 SCWRLconform NameConform keasar-server_TS4-scwrl CostConform Time // The following alignments are not as good as the ones tried above, // so are not used in getting the starting point. InFilePrefix ReadFragmentAlignment T0295.t2k.many.frag ReadFragmentAlignment T0295.t04.many.frag ReadFragmentAlignment T0295.t06.many.frag // The next 3 lines save the templates in a single file, to avoid having // to reread the PDB files. Note that ReadTemplateAtoms should be called // before any ReadFragmentAlignments to take full advantage of this // cached results. OutFilePrefix # PrintTemplateAtoms Template.atoms OutFilePrefix decoys/ Time InitMethodProbs \ HealPeptide 0.3 \ JiggleSubtree 0.3 \ JiggleSegment 0.3 \ OptSubtree 1 \ OptSegment 1 \ OptAllSegments 0.3 \ ShiftSubtree 0.3 \ ShiftSegment 0.3 \ TweakPhiSubtree 0.3 \ TweakPhiSegment 0.3 \ TweakPsiSubtree 0.3 \ TweakPsiSegment 0.3 \ TweakPsiPhiSubtree 0.3 \ TweakPsiPhiSegment 0.3 \ TweakHbondSubtree 0.3 \ TweakHbondSegment 0.3 \ TweakMultimer 0.3 \ TweakPeptide 0.3 \ OneRotamer 1 \ ClashingRotamer 1 \ ClusteredRotamer 2 \ ReduceBreak 5 \ CloseGap 5 \ HealGap 5 \ MoveGap 5 \ ReduceConstraint 5 \ ImproveSSBond 0 \ InsertSSBond 0 \ InsertAlignment 1 \ InsertSpecificFragment 5 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 3 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 60 \ super_iter 2 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0295.try5-opt1 PrintConformPDB T0295.try5-opt1.pdb SCWRLConform NameConform T0295.try5-opt1-scwrl PrintConformPDB T0295.try5-opt1-scwrl.pdb CostConform Time InitMethodProbs \ OneRotamer 5 \ ClashingRotamer 1 \ ClusteredRotamer 1 \ CrossOver 1 \ CrossAndInsert 1\ CloseGap 1 \ MoveGap 1 \ HealGap 2 \ InsertFragment 1 \ InsertSpecificFragment 2 \ ReduceBreak 2 \ ReduceConstraint 2 \ ReduceClash 1 \ JiggleSegment 1 \ JiggleSubtree 1 \ OptAllSegments 1 \ OptSegment 1 \ OptSubtree 1 \ ShiftSegment 1 \ ShiftSubtree 1 \ TweakHbondSegment 1 \ TweakHbondSubtree 1 \ TweakPhiSegment 1 \ TweakPhiSubtree 1 \ TweakPsiSegment 1 \ TweakPsiSubtree 1 \ TweakPsiPhiSegment 1 \ TweakPsiPhiSubtree 1 CostConform OptConform pool_size 40 num_gen 60 gen_size 50 \ super_iter 2 super_num_gen 200 use_all NameConform T0295.try5-opt2 PrintConformPDB T0295.try5-opt2.pdb # PrintConformHbonds try5-opt2.all-hbonds # PrintConformHbonds nonhelix backbone try5-opt2.beta-hbonds PrintConformSheets try5-opt2.sheets PrintConformHelices try5-opt2.helices PrintConstraints all try5-opt2.constraints # PrintConformBreaks try5-opt2.breaks CostConform Time quit