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-40pc-3157.atoms # The rotamer library need not be from the same set of chains as the TrainingAtoms. # It encodes the most probable conformations of sidechain and backbone # for each residue type. ReadRotamerLibrary dunbrack-40pc-3157.rot Time //Need to read in target before specific fragments or alignments can // be read, also before constraints can be defined. InFilePrefix # ReadTargetPDB T0423.blank.pdb ReadTargetSeq T0423.a2m 1 NameTarget T0423 PopConform InFilePrefix include costfcn-init.under include MQA_init.costfcn Time MakeGenericFragmentLibrary Time OutFilePrefix decoys/ InFilePrefix ReadTemplateAtoms Template.atoms // Edit this to include full sets of alignments from any // strongly-predicted superfamily // InfilePrefix 1xxxX/ // include read-alignments-scwrl.under # Include T0423.t04.undertaker-align.under # ReadFragmentAlignment 2otmA/T0423-2otmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.5921e-23 ReadFragmentAlignment 2b33A/T0423-2b33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.7570e-21 ReadFragmentAlignment 1qu9A/T0423-1qu9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.9154e-21 ReadFragmentAlignment 2cvlA/T0423-2cvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.2365e-21 ReadFragmentAlignment 1jd1A/T0423-1jd1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.3132e-21 ReadFragmentAlignment 1qahA/T0423-1qahA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.6360e-21 ReadFragmentAlignment 1oniA/T0423-1oniA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.2847e-21 ReadFragmentAlignment 1qd9A/T0423-1qd9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.7273e-21 ReadFragmentAlignment 1x25A/T0423-1x25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.8489e-21 ReadFragmentAlignment 2ig8A/T0423-2ig8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.0517e-20 ReadFragmentAlignment 2uykA/T0423-2uykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.6818e-20 ReadFragmentAlignment 1pf5A/T0423-1pf5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.5344e-20 ReadFragmentAlignment 2ewcA/T0423-2ewcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.5863e-17 ReadFragmentAlignment 1zl0A/T0423-1zl0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.2465e+01 ReadFragmentAlignment 2ch5A/T0423-2ch5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.2492e+01 ReadFragmentAlignment 1zc6A/T0423-1zc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.2701e+01 ReadFragmentAlignment 1glcG/T0423-1glcG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.9954e+01 ReadFragmentAlignment 1zrsA/T0423-1zrsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.1058e+01 ReadFragmentAlignment 1zcoA/T0423-1zcoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.3237e+01 ReadFragmentAlignment 1sfjA/T0423-1sfjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.0313e+01 TryAllAlign shrink 0 min_keep_length 1 NameConform T0423.try2-al1 # Include T0423.t06.undertaker-align.under # ReadFragmentAlignment 2otmA/T0423-2otmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.7765e-23 ReadFragmentAlignment 1x25A/T0423-1x25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.1387e-21 ReadFragmentAlignment 1qahA/T0423-1qahA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.1508e-21 ReadFragmentAlignment 1pf5A/T0423-1pf5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.2307e-21 ReadFragmentAlignment 1jd1A/T0423-1jd1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.5542e-21 ReadFragmentAlignment 1qd9A/T0423-1qd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.3382e-21 ReadFragmentAlignment 2uykA/T0423-2uykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.7975e-21 ReadFragmentAlignment 1qu9A/T0423-1qu9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.2156e-21 ReadFragmentAlignment 2cvlA/T0423-2cvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.7390e-21 ReadFragmentAlignment 2ig8A/T0423-2ig8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.0199e-20 ReadFragmentAlignment 2ewcA/T0423-2ewcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.9723e-17 ReadFragmentAlignment 1zc6A/T0423-1zc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.4797e+01 ReadFragmentAlignment 1p9eA/T0423-1p9eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.9329e+01 ReadFragmentAlignment 2gmnA/T0423-2gmnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.0356e+01 ReadFragmentAlignment 2r7hA/T0423-2r7hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.8453e+01 ReadFragmentAlignment 2p3rA/T0423-2p3rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.9276e+01 ReadFragmentAlignment 8abpA/T0423-8abpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.9649e+01 ReadFragmentAlignment 3bxpA/T0423-3bxpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.9793e+01 ReadFragmentAlignment 2aioA/T0423-2aioA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.2506e+01 ReadFragmentAlignment 1qxyA/T0423-1qxyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.3825e+01 TryAllAlign shrink 0 min_keep_length 1 NameConform T0423.try2-al1A #Include T0423.t2k.undertaker-align.under # ReadFragmentAlignment 2otmA/T0423-2otmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.9777e-22 ReadFragmentAlignment 1x25A/T0423-1x25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.4174e-19 ReadFragmentAlignment 2uykA/T0423-2uykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.0672e-18 ReadFragmentAlignment 1jd1A/T0423-1jd1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.9193e-18 ReadFragmentAlignment 2b33A/T0423-2b33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.6057e-18 ReadFragmentAlignment 1qahA/T0423-1qahA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.6702e-18 ReadFragmentAlignment 2cvlA/T0423-2cvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.0886e-18 ReadFragmentAlignment 1qu9A/T0423-1qu9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.1533e-17 ReadFragmentAlignment 1oniA/T0423-1oniA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.2209e-17 ReadFragmentAlignment 1qd9A/T0423-1qd9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.2786e-17 ReadFragmentAlignment 1pf5A/T0423-1pf5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.2890e-16 ReadFragmentAlignment 2ewcA/T0423-2ewcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.8243e-15 ReadFragmentAlignment 2ig8A/T0423-2ig8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.0507e-14 ReadFragmentAlignment 1eejA/T0423-1eejA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.4072e+01 ReadFragmentAlignment 2ox1A/T0423-2ox1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.7789e+01 ReadFragmentAlignment 1dbfA/T0423-1dbfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.8159e+01 ReadFragmentAlignment 2a2lA/T0423-2a2lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.1164e+01 ReadFragmentAlignment 2btuA/T0423-2btuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.4922e+01 ReadFragmentAlignment 1qfeA/T0423-1qfeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.5975e+01 ReadFragmentAlignment 1vs1A/T0423-1vs1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.5975e+01 # Include T0423.undertaker-align.under # ReadFragmentAlignment 2otmA/T0423-2otmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 3.1754e-23 ReadFragmentAlignment 1x25A/T0423-1x25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.5675e-21 ReadFragmentAlignment 1jd1A/T0423-1jd1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.8569e-21 ReadFragmentAlignment 1qahA/T0423-1qahA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.9891e-21 ReadFragmentAlignment 1qd9A/T0423-1qd9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.4003e-20 ReadFragmentAlignment 2cvlA/T0423-2cvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.4810e-20 ReadFragmentAlignment 2uykA/T0423-2uykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.5468e-20 ReadFragmentAlignment 1qu9A/T0423-1qu9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.6385e-20 ReadFragmentAlignment 1pf5A/T0423-1pf5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 4.2506e-20 ReadFragmentAlignment 2ig8A/T0423-2ig8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.6359e-19 ReadFragmentAlignment 2ewcA/T0423-2ewcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.0158e-17 ReadFragmentAlignment 2b33A/T0423-2b33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 9.1369e-11 ReadFragmentAlignment 1oniA/T0423-1oniA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 1.5748e-10 ReadFragmentAlignment 1zc6A/T0423-1zc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 2.6748e+01 ReadFragmentAlignment 1zl0A/T0423-1zl0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.2330e+01 ReadFragmentAlignment 2ox1A/T0423-2ox1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 5.7827e+01 ReadFragmentAlignment 2yr1A/T0423-2yr1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.6319e+01 ReadFragmentAlignment 1p9eA/T0423-1p9eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.7933e+01 ReadFragmentAlignment 1sflA/T0423-1sflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 6.8131e+01 ReadFragmentAlignment 2gmnA/T0423-2gmnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m NOFILTER SCWRL force_alignment e_value 7.1094e+01 TryAllAlign shrink 0 min_keep_length 1 NameConform T0423.try2-al2 # ReadFragmentAlignment NOFILTER SCWRL force_alignment all-align.a2m # If disulfides are expected to be important, read the aligment # without SCWRL, since it destroys disulfides. # Also SCWRL is *very* slow, so try to use it less on the server. # ReadFragmentAlignment NOFILTER force_alignment all-align.a2m InfilePrefix Time # ReportCost try2.rdb TryAllAlign shrink 0. min_keep_length 1 NameConform T0423.try2-al3 TryAllAlign shrink 0.2 min_keep_length 1 NameConform T0423.try2-al4 TryAllAlign shrink 0.3 min_keep_length 1 cumulative NameConform T0423.try2-al5 TryAllAlign shrink 0.4 min_keep_length 1 NameConform T0423.try2-al6 TryAllAlign shrink 0.5 min_keep_length 1 cumulative NameConform T0423.try2-al7 TryAllAlign shrink 0. min_keep_length 1 NameConform T0423.try2-al8 SCWRLConform NameConform T0423.try2 OutFilePrefix decoys/ PrintConformPDB T0423.try2-init.pdb // Switch to the following (commenting out the TryAllAlign) // to polish existing models ## InfilePrefix decoys/ ## include read-pdb.under CostConform Time include try2.costfcn CostConform Time // Scale the break and clashe costs down, then gradually back up again ScaleCost break 0.25 soft_clashes 0.04 // The following alignments are not as good as the ones tried above, // so are not used in getting the starting point. InFilePrefix ReadFragmentAlignment fragment_only T0423.t2k.many.frag ReadFragmentAlignment fragment_only T0423.t04.many.frag ReadFragmentAlignment fragment_only T0423.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 \ Backrub 0.5 \ BigBackrub 0.3 \ FixOmega 0.3 \ 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 20 \ InsertFragment 5 \ TwoFragment 5 \ CrossOver 3 \ CrossAndInsert 5 \ ReduceClash 5 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0423.try2-opt1 PrintConformPDB T0423.try2-opt1.pdb SCWRLConform NameConform T0423.try2-opt1-scwrl PrintConformPDB T0423.try2-opt1-scwrl.pdb CostConform Time ScaleCost break 2 soft_clashes 5 CostConform Time InitMethodProbs \ Backrub 2 \ BigBackrub 1 \ FixOmega 1 \ 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 OptConform pool_size 20 num_gen 60 gen_size 100 \ super_iter 1 super_num_gen 100 \ scwrl_each use_all keep_all NameConform T0423.try2-opt2 PrintConformPDB T0423.try2-opt2.pdb CostConform ScaleCost break 2 soft_clashes 5 CostConform Time OptConform pool_size 40 num_gen 60 gen_size 100 \ super_iter 2 super_num_gen 300 use_all NameConform T0423.try2-opt3 PrintConformPDB T0423.try2-opt3.pdb # PrintConformHbonds try2-opt3.all-hbonds # PrintConformHbonds nonhelix backbone try2-opt3.beta-hbonds PrintConformSheets try2-opt3.sheets PrintConformHelices try2-opt3.helices PrintConstraints all try2-opt3.constraints # PrintConformBreaks try2-opt3.breaks CostConform Time quit