# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0302/ # command:# Making conformation for sequence T0302 numbered 1 through 132 Created new target T0302 from T0302.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0302/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fqiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fqiA expands to /projects/compbio/data/pdb/1fqi.pdb.gz 1fqiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1fqiA/merged-good-all-a2m # 1fqiA read from 1fqiA/merged-good-all-a2m # adding 1fqiA to template set # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK # choosing archetypes in rotamer library T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 1fqiA read from 1fqiA/merged-good-all-a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 1fqiA read from 1fqiA/merged-good-all-a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLKY T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 338 :GDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y3nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y3nA expands to /projects/compbio/data/pdb/1y3n.pdb.gz 1y3nA:# T0302 read from 1y3nA/merged-good-all-a2m # 1y3nA read from 1y3nA/merged-good-all-a2m # adding 1y3nA to template set # found chain 1y3nA in template set T0302 27 :AFTRF 1y3nA 79 :KFIRY T0302 32 :LKTEFSEENIEFWIACEDF 1y3nA 95 :LIDQNAPNLKAFFKTHPEV T0302 51 :KKSKGPQ 1y3nA 396 :ERQWTND T0302 62 :KAKAIYEKFIQTDAP 1y3nA 403 :VALQGIDMYIKNKYV T0302 77 :KEVNLDFHTKEVITNSITQPTLHSFDAAQSRVY 1y3nA 422 :TGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVM T0302 121 :LKSDIYLDLMEG 1y3nA 461 :KTWNDYQQQLKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=12 Number of alignments=4 # 1y3nA read from 1y3nA/merged-good-all-a2m # found chain 1y3nA in template set T0302 2 :MVSPEEAVKWGESFDKLLS 1y3nA 90 :IPLNKLIDQNAPNLKAFFK T0302 21 :HRDGLEAF 1y3nA 110 :HPEVQRAI T0302 52 :KSKGPQ 1y3nA 397 :RQWTND T0302 62 :KAKAIYEKFIQTDA 1y3nA 403 :VALQGIDMYIKNKY T0302 76 :PKEVNLDFHTKEVITNSI 1y3nA 421 :FTGVNLTVEEREIYDKYW T0302 98 :LHSFDAAQSRVYQLMEQD 1y3nA 439 :PDVKTYMFEMGQSWVMGT T0302 117 :YTRFLKSDIYLDLMEG 1y3nA 457 :KDPEKTWNDYQQQLKN Number of specific fragments extracted= 7 number of extra gaps= 0 total=19 Number of alignments=5 # 1y3nA read from 1y3nA/merged-good-all-a2m # found chain 1y3nA in template set T0302 2 :MVSPEEAVKWGESFDKLLS 1y3nA 90 :IPLNKLIDQNAPNLKAFFK T0302 54 :KGPQ 1y3nA 109 :THPE T0302 58 :QIHL 1y3nA 394 :EYER T0302 62 :KAKAIYEKFIQTDA 1y3nA 403 :VALQGIDMYIKNKY T0302 76 :PKEVNLDFHTKEVITNSI 1y3nA 421 :FTGVNLTVEEREIYDKYW T0302 98 :LHSFDAAQSRVYQLM 1y3nA 439 :PDVKTYMFEMGQSWV T0302 113 :E 1y3nA 460 :E T0302 121 :LKSDIYLDLME 1y3nA 461 :KTWNDYQQQLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=27 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1agrH/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1agrH expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrH:# T0302 read from 1agrH/merged-good-all-a2m # 1agrH read from 1agrH/merged-good-all-a2m # adding 1agrH to template set # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 Number of alignments=7 # 1agrH read from 1agrH/merged-good-all-a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=29 Number of alignments=8 # 1agrH read from 1agrH/merged-good-all-a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=30 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2crpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/2crpA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2crpA/merged-good-all-a2m.gz for input Trying 2crpA/merged-good-all-a2m Error: Couldn't open file 2crpA/merged-good-all-a2m or 2crpA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2af0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/2af0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2af0A/merged-good-all-a2m.gz for input Trying 2af0A/merged-good-all-a2m Error: Couldn't open file 2af0A/merged-good-all-a2m or 2af0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ngnA expands to /projects/compbio/data/pdb/1ngn.pdb.gz 1ngnA:Skipped atom 495, because occupancy 0.5 <= existing 0.500 in 1ngnA Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1ngnA # T0302 read from 1ngnA/merged-good-all-a2m # 1ngnA read from 1ngnA/merged-good-all-a2m # adding 1ngnA to template set # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENI 1ngnA 446 :KMAIPVLWEFLEKYPSAEVA T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSIT 1ngnA 511 :IGKYGNDSYRIFCV T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=35 Number of alignments=10 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENIE 1ngnA 446 :KMAIPVLWEFLEKYPSAEVAR T0302 44 :WIACEDF 1ngnA 470 :WRDVSEL T0302 51 :KKSKGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 478 :KPLGLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNS 1ngnA 511 :IGKYGNDSYRIF T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=40 Number of alignments=11 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set T0302 21 :HRDGLEAFTRFLKTEFSEEN 1ngnA 445 :GKMAIPVLWEFLEKYPSAEV T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSITQ 1ngnA 511 :IGKYGNDSYRIFCVN T0302 96 :PTLHSFDAAQSRVYQLMEQ 1ngnA 532 :PEDHKLNKYHDWLWENHEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=45 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eh2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eh2 expands to /projects/compbio/data/pdb/1eh2.pdb.gz 1eh2:Warning: there is no chain 1eh2 will retry with 1eh2A # T0302 read from 1eh2/merged-good-all-a2m # 1eh2 read from 1eh2/merged-good-all-a2m # adding 1eh2 to template set # found chain 1eh2 in template set T0302 46 :ACEDFKKS 1eh2 13 :DKAKYDAI T0302 54 :KGPQQIHLKAK 1eh2 31 :LSGDKVKPVLL T0302 72 :QT 1eh2 42 :NS T0302 80 :NLDFHTKEVITNSI 1eh2 44 :KLPVDILGRVWELS T0302 94 :TQ 1eh2 62 :DG T0302 96 :PTLHSFDAAQSRVYQLMEQDSYT 1eh2 65 :LDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 6 number of extra gaps= 0 total=51 Number of alignments=13 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0302 56 :PQQIHLKAKAIY 1eh2 10 :KPEDKAKYDAIF T0302 68 :EKFIQTD 1eh2 37 :KPVLLNS T0302 80 :NLDFHTKEVITNSI 1eh2 44 :KLPVDILGRVWELS T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYT 1eh2 63 :GMLDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Number of alignments=14 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0302 56 :PQQIHLKAKAIY 1eh2 10 :KPEDKAKYDAIF T0302 68 :EKFIQTDA 1eh2 37 :KPVLLNSK T0302 81 :LDFHTKEVITNSI 1eh2 45 :LPVDILGRVWELS T0302 96 :PTLHSFDAAQSRVYQLMEQDSYT 1eh2 65 :LDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b64/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b64 expands to /projects/compbio/data/pdb/1b64.pdb.gz 1b64:Warning: there is no chain 1b64 will retry with 1b64A # T0302 read from 1b64/merged-good-all-a2m # 1b64 read from 1b64/merged-good-all-a2m # adding 1b64 to template set # found chain 1b64 in template set T0302 86 :KEVITNSITQPTLH 1b64 21 :MAKLEECVRSIQAD T0302 101 :FDAAQSRV 1b64 66 :TDMLEEQI Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=16 # 1b64 read from 1b64/merged-good-all-a2m # found chain 1b64 in template set T0302 55 :GP 1b64 20 :DM T0302 83 :FHTKEVITNSI 1b64 22 :AKLEECVRSIQ T0302 94 :T 1b64 34 :D T0302 95 :QPTLHS 1b64 63 :KVGTDM T0302 104 :AQSRV 1b64 69 :LEEQI Number of specific fragments extracted= 5 number of extra gaps= 0 total=66 Number of alignments=17 # 1b64 read from 1b64/merged-good-all-a2m # found chain 1b64 in template set T0302 55 :GPQQIHLKAKA 1b64 20 :DMAKLEECVRS Number of specific fragments extracted= 1 number of extra gaps= 0 total=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1omwA expands to /projects/compbio/data/pdb/1omw.pdb.gz 1omwA:# T0302 read from 1omwA/merged-good-all-a2m # 1omwA read from 1omwA/merged-good-all-a2m # adding 1omwA to template set # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQ 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIM T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=72 Number of alignments=18 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDA 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKEL T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=77 Number of alignments=19 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 10 :KWGESFDKLLSHRDGLEAFTRFLKTEFS 1omwA 50 :RGEVTFEKIFSQKLGYLLFRDFCLKHLE T0302 38 :EENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQT 1omwA 80 :KPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMK T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSITQ 1omwA 126 :KSAIEHVQGHLVK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 141 :VPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=82 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eztA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eztA expands to /projects/compbio/data/pdb/1ezt.pdb.gz 1eztA:# T0302 read from 1eztA/merged-good-all-a2m # 1eztA read from 1eztA/merged-good-all-a2m # adding 1eztA to template set # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=83 Number of alignments=21 # 1eztA read from 1eztA/merged-good-all-a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=84 Number of alignments=22 # 1eztA read from 1eztA/merged-good-all-a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDL Number of specific fragments extracted= 1 number of extra gaps= 0 total=85 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2es0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/2es0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2es0A/merged-good-all-a2m.gz for input Trying 2es0A/merged-good-all-a2m Error: Couldn't open file 2es0A/merged-good-all-a2m or 2es0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bt2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bt2A expands to /projects/compbio/data/pdb/2bt2.pdb.gz 2bt2A:Skipped atom 45, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 49, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 542, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 548, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 641, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 645, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 647, because occupancy 0.400 <= existing 0.600 in 2bt2A # T0302 read from 2bt2A/merged-good-all-a2m # 2bt2A read from 2bt2A/merged-good-all-a2m # adding 2bt2A to template set # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=86 Number of alignments=24 # 2bt2A read from 2bt2A/merged-good-all-a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=87 Number of alignments=25 # 2bt2A read from 2bt2A/merged-good-all-a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=88 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2acxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/2acxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2acxA/merged-good-all-a2m.gz for input Trying 2acxA/merged-good-all-a2m Error: Couldn't open file 2acxA/merged-good-all-a2m or 2acxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iapA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iapA expands to /projects/compbio/data/pdb/1iap.pdb.gz 1iapA:# T0302 read from 1iapA/merged-good-all-a2m # 1iapA read from 1iapA/merged-good-all-a2m # adding 1iapA to template set # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 Number of alignments=27 # 1iapA read from 1iapA/merged-good-all-a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTR T0302 94 :TQPTLHSFDAAQSRVYQLME 1iapA 128 :DLISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Number of alignments=28 # 1iapA read from 1iapA/merged-good-all-a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1emuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/1emuA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1emuA/merged-good-all-a2m.gz for input Trying 1emuA/merged-good-all-a2m Error: Couldn't open file 1emuA/merged-good-all-a2m or 1emuA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eca/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1eca/merged-good-all-a2m # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 21 :HRDGLEAFTRFLKT 1eca 2 :SADQISTVQASFDK T0302 36 :FSEENIEFWIACEDF 1eca 16 :VKGDPVGILYAVFKA T0302 51 :KKSKGPQQIHLKAKAIYEKF 1eca 47 :ESIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=108 Number of alignments=30 # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 4 :S 1eca 2 :S T0302 22 :RDGLEAFTRFLKT 1eca 3 :ADQISTVQASFDK T0302 36 :FSEENIEFWIAC 1eca 16 :VKGDPVGILYAV T0302 50 :FK 1eca 28 :FK T0302 52 :KSKGPQQIHLKAKAIYEKF 1eca 48 :SIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 11 number of extra gaps= 1 total=119 Number of alignments=31 # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)V3 because first residue in template chain is (1eca)L1 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEA 1eca 2 :SADQISTVQASFDKVKGDPVGILY T0302 46 :AC 1eca 26 :AV T0302 50 :FK 1eca 28 :FK T0302 54 :KGPQ 1eca 30 :ADPS T0302 58 :QIHLKAKAIYEKFIQ 1eca 54 :PFETHANRIVGFFSK T0302 73 :TDAP 1eca 71 :GELP T0302 80 :NL 1eca 75 :NI T0302 83 :FHTKEVITNSITQ 1eca 77 :EADVNTFVASHKP T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1eca 92 :VTHDQLNNFRAGFVSYMKAHTD Number of specific fragments extracted= 9 number of extra gaps= 0 total=128 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bv1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/2bv1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2bv1A/merged-good-all-a2m.gz for input Trying 2bv1A/merged-good-all-a2m Error: Couldn't open file 2bv1A/merged-good-all-a2m or 2bv1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zv4X/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/1zv4X/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1zv4X/merged-good-all-a2m.gz for input Trying 1zv4X/merged-good-all-a2m Error: Couldn't open file 1zv4X/merged-good-all-a2m or 1zv4X/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dk8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1dk8A/merged-good-all-a2m # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=132 Number of alignments=33 # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSK 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLE T0302 55 :GPQQIHLKAKAIYEKFIQTDA 1dk8A 170 :NEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLME 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=136 Number of alignments=34 # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 2 :MVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 113 :ASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSITQ 1dk8A 197 :TKPATKSFIKGCIMK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYL 1dk8A 214 :IDPAMFDQAQTEIQATMEENTYPSFLKSDIYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=140 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a72A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a72A expands to /projects/compbio/data/pdb/2a72.pdb.gz 2a72A:# T0302 read from 2a72A/merged-good-all-a2m # 2a72A read from 2a72A/merged-good-all-a2m # adding 2a72A to template set # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=142 Number of alignments=36 # 2a72A read from 2a72A/merged-good-all-a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=144 Number of alignments=37 # 2a72A read from 2a72A/merged-good-all-a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=146 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x3kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x3kA expands to /projects/compbio/data/pdb/1x3k.pdb.gz 1x3kA:# T0302 read from 1x3kA/merged-good-all-a2m # 1x3kA read from 1x3kA/merged-good-all-a2m # adding 1x3kA to template set # found chain 1x3kA in template set T0302 2 :MVSPEEAVKWGESFDKLLSH 1x3kA 4 :GLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKT 1x3kA 26 :GTANTVFYNYLKK T0302 35 :EFSEE 1x3kA 41 :SNQDK T0302 51 :KKSKGPQQIHLKAKAIYEKF 1x3kA 55 :DEVKDTANFKLIAGRIFTIF T0302 73 :TD 1x3kA 79 :KN T0302 79 :VNLDFHTKEVITNSI 1x3kA 81 :VGNDKGFQKVIADMS T0302 94 :TQPTLHSFDAAQSRVYQLM 1x3kA 101 :RPITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFLKS 1x3kA 125 :HGAAWNKMMDN T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=155 Number of alignments=39 # 1x3kA read from 1x3kA/merged-good-all-a2m # found chain 1x3kA in template set T0302 2 :MVSPEEAVKWGESFDKLLSH 1x3kA 4 :GLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKT 1x3kA 26 :GTANTVFYNYLKK T0302 35 :EFSEE 1x3kA 41 :SNQDK T0302 52 :KSKGPQQIHLKAKAIYEKF 1x3kA 56 :EVKDTANFKLIAGRIFTIF T0302 73 :TD 1x3kA 79 :KN T0302 79 :VNLDFHTKEVITNSI 1x3kA 81 :VGNDKGFQKVIADMS T0302 94 :TQPTLHSFDAAQSRVYQLM 1x3kA 101 :RPITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFLKS 1x3kA 125 :HGAAWNKMMDN T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=164 Number of alignments=40 # 1x3kA read from 1x3kA/merged-good-all-a2m # found chain 1x3kA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSH 1x3kA 3 :VGLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKTEFS 1x3kA 26 :GTANTVFYNYLKKYPS T0302 50 :FKKSKGPQQIHLKAKAIYEKFIQ 1x3kA 54 :LDEVKDTANFKLIAGRIFTIFDN T0302 80 :NLDFHTKEVITNSITQ 1x3kA 82 :GNDKGFQKVIADMSGP T0302 96 :PTLHSFDAAQSRVYQLM 1x3kA 103 :ITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFL 1x3kA 129 :WNKMMDNFF T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=171 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302/1cmzA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1cmzA/merged-good-all-a2m.gz for input Trying 1cmzA/merged-good-all-a2m Error: Couldn't open file 1cmzA/merged-good-all-a2m or 1cmzA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r89A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1r89A/merged-good-all-a2m # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 4 :SPEEAVK 1r89A 2 :KVEEILE T0302 14 :SFDKLLSH 1r89A 9 :KALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDF 1r89A 31 :LRRRLDEL T0302 57 :QQIHLKAKAIYEKFIQ 1r89A 232 :LDNLARFVHLCREFME T0302 73 :TDAPKEVN 1r89A 256 :PKHPLEIE T0302 82 :DFHTKEVITNSI 1r89A 264 :PERLRKIVEERG T0302 95 :QPTLH 1r89A 287 :DIVDD T0302 100 :SFDAAQSRVYQLMEQDSY 1r89A 296 :QLERASRKIFEFLERENF Number of specific fragments extracted= 9 number of extra gaps= 0 total=180 Number of alignments=42 # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 5 :PEEA 1r89A 3 :VEEI T0302 12 :GESFDKLLSH 1r89A 7 :LEKALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDFK 1r89A 31 :LRRRLDELG T0302 56 :PQQIHLKAKAIYEKFIQ 1r89A 231 :SLDNLARFVHLCREFME T0302 73 :T 1r89A 256 :P T0302 76 :PKEVNLD 1r89A 257 :KHPLEIE T0302 83 :FHTKEVITNS 1r89A 265 :ERLRKIVEER T0302 94 :T 1r89A 275 :G T0302 95 :QPT 1r89A 287 :DIV T0302 98 :LHSFDAAQSRVYQLMEQDSY 1r89A 294 :YPQLERASRKIFEFLERENF Number of specific fragments extracted= 11 number of extra gaps= 0 total=191 Number of alignments=43 # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 5 :PEEAV 1r89A 3 :VEEIL T0302 13 :ESFDKLLS 1r89A 8 :EKALELVI T0302 21 :HRDGLEAFTR 1r89A 17 :DEEEVRKGRE T0302 46 :ACEDFKKSKGPQ 1r89A 27 :AEEELRRRLDEL T0302 58 :QIHLKAKAIYEKFIQT 1r89A 233 :DNLARFVHLCREFMEA T0302 74 :DAPKEVNLDFHTKEVITNSITQ 1r89A 255 :KPKHPLEIEPERLRKIVEERGT T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1r89A 292 :NLYPQLERASRKIFEFLERENF Number of specific fragments extracted= 7 number of extra gaps= 0 total=198 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1htjF/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1htjF expands to /projects/compbio/data/pdb/1htj.pdb.gz 1htjF:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1htjF/merged-good-all-a2m # 1htjF read from 1htjF/merged-good-all-a2m # adding 1htjF to template set # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLMEG 1htjF 417 :HDYRTKRTL Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=45 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0302 8 :AVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1htjF 307 :SDIIFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQA T0302 55 :GPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 353 :SPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLME 1htjF 417 :HDYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=46 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRLRN T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1htjF 396 :DARGVLCEAQEAAMPEIQEQIH T0302 125 :IYLDLME 1htjF 418 :DYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=210 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1agrE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1agrE expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrE:# T0302 read from 1agrE/merged-good-all-a2m # 1agrE read from 1agrE/merged-good-all-a2m # adding 1agrE to template set # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=211 Number of alignments=48 # 1agrE read from 1agrE/merged-good-all-a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=212 Number of alignments=49 # 1agrE read from 1agrE/merged-good-all-a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=213 Number of alignments=50 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/T0302/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/T0302/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0302/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0302/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0302)I71.CB, (T0302)I89.CB) [> 3.5962 = 5.9937 < 7.7918] w=1.0000 to align # Constraint # added constraint: constraint((T0302)E42.CB, (T0302)F70.CB) [> 4.4405 = 7.4008 < 9.6211] w=0.9969 to align # Constraint # added constraint: constraint((T0302)L18.CB, (T0302)F28.CB) [> 3.5166 = 5.8611 < 7.6194] w=0.9666 to align # Constraint # added constraint: constraint((T0302)T29.CB, (T0302)I41.CB) [> 3.4339 = 5.7231 < 7.4401] w=0.9666 to align # Constraint # added constraint: constraint((T0302)L32.CB, (T0302)I41.CB) [> 3.2707 = 5.4512 < 7.0865] w=0.9666 to align # Constraint # added constraint: constraint((T0302)E39.CB, (T0302)F70.CB) [> 3.8949 = 6.4915 < 8.4390] w=0.9666 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)I66.CB) [> 4.4964 = 7.4940 < 9.7422] w=0.9666 to align # Constraint # added constraint: constraint((T0302)A46.CB, (T0302)I66.CB) [> 3.1313 = 5.2189 < 6.7846] w=0.9666 to align # Constraint # added constraint: constraint((T0302)A46.CB, (T0302)F70.CB) [> 4.1435 = 6.9058 < 8.9775] w=0.9666 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)K62.CB) [> 3.3219 = 5.5365 < 7.1975] w=0.9666 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)A63.CB) [> 3.9910 = 6.6517 < 8.6472] w=0.9666 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)I66.CB) [> 3.8289 = 6.3815 < 8.2959] w=0.9666 to align # Constraint # added constraint: constraint((T0302)Y67.CB, (T0302)I89.CB) [> 4.0615 = 6.7692 < 8.7999] w=0.9666 to align # Constraint # added constraint: constraint((T0302)I71.CB, (T0302)L81.CB) [> 4.1975 = 6.9958 < 9.0945] w=0.9648 to align # Constraint # added constraint: constraint((T0302)I89.CB, (T0302)A104.CB) [> 3.5460 = 5.9100 < 7.6830] w=0.9513 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)V108.CB) [> 3.5914 = 5.9856 < 7.7813] w=0.9313 to align # Constraint # added constraint: constraint((T0302)T85.CB, (T0302)R107.CB) [> 3.4764 = 5.7940 < 7.5321] w=0.9201 to align # Constraint # added constraint: constraint((T0302)I71.CB, (T0302)K86.CB) [> 3.7384 = 6.2307 < 8.0999] w=0.9033 to align # Constraint # added constraint: constraint((T0302)K64.CB, (T0302)I93.CB) [> 4.0833 = 6.8054 < 8.8470] w=0.8699 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)I93.CB) [> 3.6124 = 6.0206 < 7.8268] w=0.8699 to align # Constraint # added constraint: constraint((T0302)H60.CB, (T0302)P96.CB) [> 3.2487 = 5.4145 < 7.0388] w=0.8699 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)P96.CB) [> 3.0087 = 5.0145 < 6.5189] w=0.8699 to align # Constraint # added constraint: constraint((T0302)C47.CB, (T0302)I66.CB) [> 4.1809 = 6.9681 < 9.0585] w=0.8699 to align # Constraint # added constraint: constraint((T0302)T85.CB, (T0302)A104.CB) [> 3.3516 = 5.5860 < 7.2618] w=0.8699 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)I59.CB) [> 3.9791 = 6.6319 < 8.6215] w=0.8699 to align # Constraint # added constraint: constraint((T0302)C47.CB, (T0302)Q105.CB) [> 2.7195 = 4.5326 < 5.8924] w=0.8699 to align # Constraint # added constraint: constraint((T0302)I66.CB, (T0302)F101.CB) [> 4.0981 = 6.8302 < 8.8792] w=0.8067 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)F101.CB) [> 4.2906 = 7.1510 < 9.2963] w=0.8067 to align # Constraint # added constraint: constraint((T0302)F31.CB, (T0302)F120.CB) [> 3.0545 = 5.0909 < 6.6181] w=0.8024 to align # Constraint # added constraint: constraint((T0302)F28.CB, (T0302)F120.CB) [> 3.6639 = 6.1065 < 7.9385] w=0.8024 to align # Constraint # added constraint: constraint((T0302)K51.CB, (T0302)L98.CB) [> 3.4257 = 5.7095 < 7.4224] w=0.7900 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)F101.CB) [> 3.6519 = 6.0865 < 7.9125] w=0.7900 to align # Constraint # added constraint: constraint((T0302)F15.CB, (T0302)E113.CB) [> 3.0358 = 5.0597 < 6.5777] w=0.7765 to align # Constraint # added constraint: constraint((T0302)F15.CB, (T0302)M112.CB) [> 4.0470 = 6.7450 < 8.7685] w=0.7733 to align # Constraint # added constraint: constraint((T0302)N40.CB, (T0302)V108.CB) [> 3.0501 = 5.0835 < 6.6086] w=0.7733 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)A104.CB) [> 4.5776 = 7.6293 < 9.9181] w=0.7733 to align # Constraint # added constraint: constraint((T0302)W44.CB, (T0302)Q105.CB) [> 3.6836 = 6.1394 < 7.9812] w=0.7733 to align # Constraint # added constraint: constraint((T0302)W44.CB, (T0302)V108.CB) [> 3.3912 = 5.6519 < 7.3475] w=0.7733 to align # Constraint # added constraint: constraint((T0302)C47.CB, (T0302)F101.CB) [> 2.8122 = 4.6870 < 6.0931] w=0.7733 to align # Constraint # added constraint: constraint((T0302)F28.CB, (T0302)I41.CB) [> 4.0026 = 6.6709 < 8.6722] w=0.7733 to align # Constraint # added constraint: constraint((T0302)D49.CB, (T0302)K62.CB) [> 4.3793 = 7.2989 < 9.4885] w=0.7733 to align # Constraint # added constraint: constraint((T0302)I41.CB, (T0302)M112.CB) [> 4.0917 = 6.8195 < 8.8653] w=0.7733 to align # Constraint # added constraint: constraint((T0302)W44.CB, (T0302)M112.CB) [> 4.1744 = 6.9574 < 9.0446] w=0.7733 to align # Constraint # added constraint: constraint((T0302)E39.CB, (T0302)V79.CB) [> 3.1265 = 5.2108 < 6.7740] w=0.7733 to align # Constraint # added constraint: constraint((T0302)N40.CB, (T0302)V79.CB) [> 3.5474 = 5.9124 < 7.6861] w=0.7733 to align # Constraint # added constraint: constraint((T0302)E42.CB, (T0302)K77.CB) [> 3.8623 = 6.4373 < 8.3684] w=0.7733 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)V79.CB) [> 3.0144 = 5.0240 < 6.5312] w=0.7733 to align # Constraint # added constraint: constraint((T0302)F70.CB, (T0302)V79.CB) [> 3.0346 = 5.0577 < 6.5750] w=0.7733 to align # Constraint # added constraint: constraint((T0302)A46.CB, (T0302)K69.CB) [> 4.5586 = 7.5976 < 9.8769] w=0.7733 to align # Constraint # added constraint: constraint((T0302)F15.CB, (T0302)Y117.CB) [> 3.1463 = 5.2438 < 6.8169] w=0.7475 to align # Constraint # added constraint: constraint((T0302)L32.CB, (T0302)S116.CB) [> 3.7781 = 6.2968 < 8.1859] w=0.7410 to align # Constraint # added constraint: constraint((T0302)F31.CB, (T0302)I125.CB) [> 3.5418 = 5.9030 < 7.6739] w=0.7380 to align # Constraint # added constraint: constraint((T0302)L81.CB, (T0302)V108.CB) [> 4.2284 = 7.0473 < 9.1615] w=0.7267 to align # Constraint # added constraint: constraint((T0302)L19.CB, (T0302)F28.CB) [> 3.9722 = 6.6203 < 8.6064] w=0.6766 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)S100.CB) [> 3.5025 = 5.8375 < 7.5887] w=0.6766 to align # Constraint # added constraint: constraint((T0302)V88.CB, (T0302)A103.CB) [> 3.4370 = 5.7283 < 7.4467] w=0.6766 to align # Constraint # added constraint: constraint((T0302)W11.CB, (T0302)G24.CA) [> 3.5513 = 5.9189 < 7.6946] w=0.6766 to align # Constraint # added constraint: constraint((T0302)W11.CB, (T0302)H21.CB) [> 3.8930 = 6.4883 < 8.4348] w=0.6766 to align # Constraint # added constraint: constraint((T0302)L81.CB, (T0302)R107.CB) [> 3.2618 = 5.4363 < 7.0671] w=0.6766 to align # Constraint # added constraint: constraint((T0302)L81.CB, (T0302)A104.CB) [> 3.4230 = 5.7049 < 7.4164] w=0.6766 to align # Constraint # added constraint: constraint((T0302)Y67.CB, (T0302)T90.CB) [> 4.3387 = 7.2311 < 9.4005] w=0.6766 to align # Constraint # added constraint: constraint((T0302)F15.CB, (T0302)Y109.CB) [> 4.2815 = 7.1359 < 9.2766] w=0.6766 to align # Constraint # added constraint: constraint((T0302)I59.CB, (T0302)L98.CB) [> 4.1707 = 6.9511 < 9.0364] w=0.6766 to align # Constraint # added constraint: constraint((T0302)V79.CB, (T0302)V108.CB) [> 3.6517 = 6.0862 < 7.9120] w=0.6766 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)K77.CB) [> 4.3254 = 7.2090 < 9.3717] w=0.6766 to align # Constraint # added constraint: constraint((T0302)W44.CB, (T0302)Y109.CB) [> 3.7529 = 6.2548 < 8.1313] w=0.6766 to align # Constraint # added constraint: constraint((T0302)S37.CB, (T0302)S116.CB) [> 3.6416 = 6.0694 < 7.8902] w=0.6444 to align # Constraint # added constraint: constraint((T0302)E35.CB, (T0302)R119.CB) [> 4.4815 = 7.4691 < 9.7099] w=0.6444 to align # Constraint # added constraint: constraint((T0302)E35.CB, (T0302)S116.CB) [> 4.0494 = 6.7490 < 8.7736] w=0.6444 to align # Constraint # added constraint: constraint((T0302)F31.CB, (T0302)S116.CB) [> 4.4008 = 7.3347 < 9.5352] w=0.6444 to align # Constraint # added constraint: constraint((T0302)L18.CB, (T0302)Y117.CB) [> 4.3419 = 7.2365 < 9.4075] w=0.6444 to align # Constraint # added constraint: constraint((T0302)N40.CB, (T0302)S116.CB) [> 4.3305 = 7.2175 < 9.3828] w=0.6444 to align # Constraint # added constraint: constraint((T0302)A27.CB, (T0302)I125.CB) [> 3.4404 = 5.7341 < 7.4543] w=0.6414 to align # Constraint # added constraint: constraint((T0302)F31.CB, (T0302)Y126.CB) [> 4.2890 = 7.1483 < 9.2928] w=0.6414 to align # Constraint # added constraint: constraint((T0302)S53.CB, (T0302)K62.CB) [> 3.9995 = 6.6658 < 8.6656] w=0.6289 to align # Constraint # added constraint: constraint((T0302)L18.CB, (T0302)F120.CB) [> 4.6174 = 7.6957 < 10.0044] w=0.5799 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)S92.CB) [> 4.5555 = 7.5925 < 9.8702] w=0.5799 to align # Constraint # added constraint: constraint((T0302)F28.CB, (T0302)S116.CB) [> 4.6533 = 7.7554 < 10.0820] w=0.5799 to align # Constraint # added constraint: constraint((T0302)K51.CB, (T0302)F101.CB) [> 4.4034 = 7.3391 < 9.5408] w=0.5799 to align # Constraint # added constraint: constraint((T0302)L25.CB, (T0302)I45.CB) [> 4.5388 = 7.5646 < 9.8340] w=0.5799 to align # Constraint # added constraint: constraint((T0302)L19.CB, (T0302)W44.CB) [> 4.4367 = 7.3945 < 9.6129] w=0.5799 to align # Constraint # added constraint: constraint((T0302)N40.CB, (T0302)N80.CB) [> 4.5480 = 7.5799 < 9.8539] w=0.5799 to align # Constraint # added constraint: constraint((T0302)N80.CB, (T0302)L111.CB) [> 3.5828 = 5.9714 < 7.7628] w=0.5799 to align # Constraint # added constraint: constraint((T0302)C47.CB, (T0302)V108.CB) [> 4.4739 = 7.4565 < 9.6934] w=0.5754 to align # Constraint # added constraint: constraint((T0302)S37.CB, (T0302)M112.CB) [> 4.5811 = 7.6351 < 9.9257] w=0.5477 to align # Constraint # added constraint: constraint((T0302)L32.CB, (T0302)F120.CB) [> 4.6760 = 7.7933 < 10.1312] w=0.5477 to align # Constraint # added constraint: constraint((T0302)F50.CB, (T0302)S100.CB) [> 4.4952 = 7.4920 < 9.7397] w=0.4833 to align # Constraint # added constraint: constraint((T0302)L32.CB, (T0302)M112.CB) [> 4.5785 = 7.6308 < 9.9201] w=0.4833 to align # Constraint # added constraint: constraint((T0302)A27.CB, (T0302)Y126.CB) [> 4.1883 = 6.9804 < 9.0745] w=0.4833 to align # Constraint # added constraint: constraint((T0302)L25.CB, (T0302)I41.CB) [> 4.2502 = 7.0837 < 9.2088] w=0.4833 to align # Constraint # added constraint: constraint((T0302)W11.CB, (T0302)Y126.CB) [> 4.4112 = 7.3520 < 9.5577] w=0.4833 to align # Constraint # added constraint: constraint((T0302)G12.CA, (T0302)L121.CB) [> 3.4202 = 5.7003 < 7.4103] w=0.4833 to align # Constraint # added constraint: constraint((T0302)V79.CB, (T0302)A104.CB) [> 4.4262 = 7.3771 < 9.5902] w=0.4833 to align # Constraint # added constraint: constraint((T0302)F28.CB, (T0302)Y117.CB) [> 4.5341 = 7.5568 < 9.8239] w=0.4511 to align # Constraint # added constraint: constraint((T0302)A27.CB, (T0302)L129.CB) [> 3.8920 = 6.4867 < 8.4327] w=0.3866 to align # Constraint # added constraint: constraint((T0302)K64.CB, (T0302)P96.CB) [> 4.3967 = 7.3279 < 9.5262] w=0.3866 to align # Constraint # added constraint: constraint((T0302)W11.CB, (T0302)L121.CB) [> 4.4965 = 7.4942 < 9.7425] w=0.3866 to align # Constraint # added constraint: constraint((T0302)V88.CB, (T0302)A104.CB) [> 4.6322 = 7.7204 < 10.0365] w=0.3866 to align # Constraint # added constraint: constraint((T0302)V79.CB, (T0302)L111.CB) [> 4.6583 = 7.7638 < 10.0929] w=0.3866 to align # Constraint # added constraint: constraint((T0302)A8.CB, (T0302)M130.CB) [> 3.1405 = 5.2341 < 6.8043] w=0.3222 to align # Constraint # added constraint: constraint((T0302)E7.CB, (T0302)G24.CA) [> 4.4407 = 7.4012 < 9.6216] w=0.2900 to align # Constraint # added constraint: constraint((T0302)A8.CB, (T0302)L129.CB) [> 3.1249 = 5.2081 < 6.7706] w=0.2900 to align # Constraint # added constraint: constraint((T0302)L19.CB, (T0302)I45.CB) [> 4.4170 = 7.3617 < 9.5702] w=0.2900 to align # Constraint # added constraint: constraint((T0302)Y67.CB, (T0302)F101.CB) [> 4.3225 = 7.2042 < 9.3654] w=0.2267 to align # Constraint # added constraint: constraint((T0302)V3.CB, (T0302)G24.CA) [> 4.6294 = 7.7157 < 10.0304] w=0.1933 to align # Constraint # added constraint: constraint((T0302)V3.CB, (T0302)D23.CB) [> 3.1201 = 5.2002 < 6.7603] w=0.1933 to align # Constraint # added constraint: constraint((T0302)L19.CB, (T0302)I41.CB) [> 4.0459 = 6.7432 < 8.7662] w=0.1933 to align # Constraint # added constraint: constraint((T0302)H60.CB, (T0302)T94.CB) [> 3.2030 = 5.3383 < 6.9398] w=0.1933 to align # Constraint # added constraint: constraint((T0302)V79.CB, (T0302)R107.CB) [> 4.5451 = 7.5752 < 9.8478] w=0.1933 to align # Constraint # added constraint: constraint((T0302)A63.CB, (T0302)T97.CB) [> 3.8150 = 6.3584 < 8.2659] w=0.1933 to align # Constraint # added constraint: constraint((T0302)I71.CB, (T0302)I93.CB) [> 4.4763 = 7.4605 < 9.6986] w=0.1933 to align # Constraint # added constraint: constraint((T0302)G12.CA, (T0302)Y126.CB) [> 4.3586 = 7.2643 < 9.4436] w=0.1933 to align # Constraint # added constraint: constraint((T0302)I71.CB, (T0302)T85.CB) [> 4.6044 = 7.6740 < 9.9762] w=0.1915 to align # Constraint # added constraint: constraint((T0302)F36.CB, (T0302)S116.CB) [> 3.7343 = 6.2238 < 8.0910] w=0.1611 to align # Constraint # added constraint: constraint((T0302)G24.CA, (T0302)L129.CB) [> 3.7856 = 6.3094 < 8.2022] w=0.1581 to align # Constraint # added constraint: constraint((T0302)F36.CB, (T0302)D115.CB) [> 3.3777 = 5.6294 < 7.3183] w=0.1581 to align # Constraint # added constraint: constraint((T0302)L81.CB, (T0302)L111.CB) [> 3.9433 = 6.5722 < 8.5438] w=0.1468 to align # Constraint # added constraint: constraint((T0302)Q72.CB, (T0302)K86.CB) [> 4.4666 = 7.4443 < 9.6776] w=0.1301 to align # Constraint # added constraint: constraint((T0302)L18.CB, (T0302)S116.CB) [> 4.5365 = 7.5609 < 9.8291] w=0.1274 to align # Constraint # added constraint: constraint((T0302)I41.CB, (T0302)A63.CB) [> 3.2602 = 5.4337 < 7.0637] w=0.1221 to align # Constraint # added constraint: constraint((T0302)E39.CB, (T0302)N80.CB) [> 4.6429 = 7.7382 < 10.0596] w=0.0967 to align # Constraint # added constraint: constraint((T0302)E35.CB, (T0302)D115.CB) [> 4.6672 = 7.7786 < 10.1122] w=0.0967 to align # Constraint # added constraint: constraint((T0302)S92.CB, (T0302)D102.CB) [> 4.5162 = 7.5271 < 9.7852] w=0.0967 to align # Constraint # added constraint: constraint((T0302)D16.CB, (T0302)Y109.CB) [> 4.7698 = 7.9497 < 10.3346] w=0.0967 to align # Constraint # added constraint: constraint((T0302)S37.CB, (T0302)V79.CB) [> 4.7268 = 7.8780 < 10.2414] w=0.0967 to align # Constraint # added constraint: constraint((T0302)F15.CB, (T0302)S116.CB) [> 4.0714 = 6.7856 < 8.8213] w=0.0967 to align # Constraint # added constraint: constraint((T0302)S116.CB, (T0302)L127.CB) [> 3.8971 = 6.4952 < 8.4437] w=0.0967 to align # Constraint # added constraint: constraint((T0302)T85.CB, (T0302)S100.CB) [> 3.6359 = 6.0599 < 7.8778] w=0.0967 to align # Constraint # added constraint: constraint((T0302)F36.CB, (T0302)R119.CB) [> 4.3659 = 7.2765 < 9.4594] w=0.0967 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)M112.CB) [> 3.4146 = 5.6911 < 7.3984] w=0.0966 to align # Constraint # added constraint: constraint((T0302)D82.CB, (T0302)L111.CB) [> 2.9694 = 4.9489 < 6.4336] w=0.0966 to align # Constraint # added constraint: constraint((T0302)S100.CB, (T0302)M130.CB) [> 4.2879 = 7.1465 < 9.2904] w=0.0950 to align # Constraint # added constraint: constraint((T0302)C47.CB, (T0302)I59.CB) [> 4.7173 = 7.8621 < 10.2207] w=0.0910 to align # Constraint # added constraint: constraint((T0302)E35.CB, (T0302)C47.CB) [> 4.2416 = 7.0694 < 9.1902] w=0.0910 to align # Constraint # added constraint: constraint((T0302)H84.CB, (T0302)L98.CB) [> 3.1393 = 5.2321 < 6.8017] w=0.0910 to align # Constraint # added constraint: constraint((T0302)E78.CB, (T0302)I89.CB) [> 2.8860 = 4.8099 < 6.2529] w=0.0910 to align # Constraint # added constraint: constraint((T0302)K77.CB, (T0302)I89.CB) [> 4.3057 = 7.1762 < 9.3291] w=0.0910 to align # Constraint # added constraint: constraint((T0302)E48.CB, (T0302)I59.CB) [> 4.1864 = 6.9773 < 9.0705] w=0.0910 to align # Constraint # added constraint: constraint((T0302)D74.CB, (T0302)T85.CB) [> 4.2333 = 7.0556 < 9.1722] w=0.0706 to align # Constraint # added constraint: constraint((T0302)A27.CB, (T0302)M130.CB) [> 3.6503 = 6.0839 < 7.9090] w=0.0644 to align # Constraint # added constraint: constraint((T0302)L25.CB, (T0302)P76.CB) [> 4.1530 = 6.9216 < 8.9981] w=0.0614 to align # Constraint # added constraint: constraint((T0302)F43.CB, (T0302)Y67.CB) [> 3.2819 = 5.4698 < 7.1107] w=0.0614 to align # Constraint # added constraint: constraint((T0302)S14.CB, (T0302)S116.CB) [> 3.9811 = 6.6352 < 8.6258] w=0.0371 to align # Constraint # added constraint: constraint((T0302)A75.CB, (T0302)K86.CB) [> 4.3328 = 7.2213 < 9.3877] w=0.0322 to align # Constraint # added constraint: constraint((T0302)A27.CB, (T0302)E78.CB) [> 3.5430 = 5.9050 < 7.6765] w=0.0317 to align # Constraint # added constraint: constraint((T0302)K17.CB, (T0302)S116.CB) [> 3.3844 = 5.6407 < 7.3330] w=0.0307 to align # Constraint # added constraint: constraint((T0302)W11.CB, (T0302)A75.CB) [> 4.3056 = 7.1761 < 9.3289] w=0.0307 to align # Constraint # added constraint: constraint((T0302)A8.CB, (T0302)P76.CB) [> 4.1640 = 6.9399 < 9.0219] w=0.0307 to align # Constraint # added constraint: constraint((T0302)A8.CB, (T0302)A75.CB) [> 2.8631 = 4.7718 < 6.2034] w=0.0307 to align # Constraint # added constraint: constraint((T0302)E42.CB, (T0302)E68.CB) [> 2.4515 = 4.0858 < 5.3115] w=0.0303 to align # Constraint # added constraint: constraint((T0302)R30.CB, (T0302)E48.CB) [> 3.5049 = 5.8415 < 7.5940] w=0.0302 to align # Constraint # added constraint: constraint((T0302)V3.CB, (T0302)S116.CB) [> 4.0051 = 6.6751 < 8.6777] w=0.0097 to align # Constraint # added constraint: constraint((T0302)Q105.CB, (T0302)L121.CB) [> 3.8319 = 6.3865 < 8.3024] w=0.0097 to align # Constraint # added constraint: constraint((T0302)I93.CB, (T0302)M130.CB) [> 3.7222 = 6.2036 < 8.0647] w=0.0097 to align # Constraint # added constraint: constraint((T0302)I93.CB, (T0302)L129.CB) [> 2.1112 = 3.5186 < 4.5742] w=0.0097 to align # Constraint # added constraint: constraint((T0302)D82.CB, (T0302)S123.CB) [> 4.7482 = 7.9137 < 10.2879] w=0.0064 to align # Constraint # added constraint: constraint((T0302)F36.CB, (T0302)S100.CB) [> 3.2211 = 5.3684 < 6.9790] w=0.0064 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0302/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 57 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 35 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 197, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 197, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 271, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 283, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 270, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 272, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 274, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 290, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz Skipped atom 283, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 57 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0302)T73.O and (T0302)D74.N only 0.000 apart, marking (T0302)D74.N as missing # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0302)L111.O and (T0302)M112.N only 0.000 apart, marking (T0302)M112.N as missing # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0302 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.3424 model score -0.3863 model score -0.5428 model score -0.6788 model score -0.3126 model score -0.5789 model score -0.6473 model score -0.6832 model score -0.6714 model score -0.6596 model score -0.6634 model score -0.6352 model score -0.7114 model score -0.5246 model score -0.4698 model score -0.7631 model score -0.7083 model score 1.1558 model score 1.3165 model score -0.5987 model score 1.3368 model score 1.6202 model score 1.4410 model score 1.0412 model score 1.3486 model score -0.7537 model score -0.7147 model score -0.6736 model score -0.6237 model score -0.6626 model score -0.6567 model score -0.6871 model score -0.6967 model score -0.6632 model score -0.6100 model score -0.6743 model score -0.6245 model score -0.5340 model score -0.6655 model score -0.5951 model score -0.6440 model score -0.7114 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6536 model score -0.6632 model score -0.6442 model score -0.6503 model score -0.5029 model score -0.7433 model score -0.6100 model score -0.6743 model score -0.6742 model score -0.6967 model score -0.7637 model score -0.7278 model score 1.2260 model score -0.6512 model score 1.2383 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8900 model score 2.1116 model score 1.9945 model score 1.9969 model score 2.0547 model score -0.7150 model score -0.7428 model score -0.0331 model score 0.1663 model score 1.7551 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6382 model score -0.6742 model score -0.6366 model score -0.6674 model score -0.7038 model score -0.7359 model score -0.7184 model score -0.7184 model score -0.7249 model score -0.6936 model score -0.5125 model score -0.7215 model score -0.7682 model score -0.7682 model score -0.6652 model score -0.6453 model score -0.7223 model score -0.3975 model score -0.7042 model score -0.6509 model score -0.7169 model score -0.6566 model score -0.4704 model score -0.6956 model score 1.2771 model score -0.6747 model score -0.7181 model score -0.5437 model 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2.2719 USE_META, weight: 0.3945 cost: 1.2771 min: -0.7682 max: 2.2719 USE_META, weight: 0.3945 cost: 1.2771 min: -0.7682 max: 2.2719 USE_META, weight: 0.3945 cost: 1.2771 min: -0.7682 max: 2.2719 USE_META, weight: 0.3945 cost: 1.2771 min: -0.7682 max: 2.2719 USE_META, weight: 0.3945 cost: 1.2771 min: -0.7682 max: 2.2719 USE_META, weight: 0.9278 cost: -0.5244 min: -0.7682 max: 2.2719 USE_META, weight: 0.9766 cost: -0.6893 min: -0.7682 max: 2.2719 USE_META, weight: 0.9145 cost: -0.4794 min: -0.7682 max: 2.2719 USE_META, weight: 0.9857 cost: -0.7199 min: -0.7682 max: 2.2719 USE_META, weight: 0.9773 cost: -0.6914 min: -0.7682 max: 2.2719 USE_META, weight: 0.2333 cost: 1.8216 min: -0.7682 max: 2.2719 USE_META, weight: 0.1000 cost: 2.2719 min: -0.7682 max: 2.2719 USE_META, weight: 0.1215 cost: 2.1994 min: -0.7682 max: 2.2719 USE_META, weight: 0.2490 cost: 1.7688 min: -0.7682 max: 2.2719 USE_META, weight: 0.2341 cost: 1.8190 min: -0.7682 max: 2.2719 USE_META, weight: 0.8877 cost: -0.3890 min: -0.7682 max: 2.2719 USE_META, weight: 0.9849 cost: -0.7173 min: -0.7682 max: 2.2719 USE_META, weight: 0.9303 cost: -0.5329 min: -0.7682 max: 2.2719 USE_META, weight: 0.7924 cost: -0.0670 min: -0.7682 max: 2.2719 USE_META, weight: 0.9199 cost: -0.4977 min: -0.7682 max: 2.2719 USE_META, weight: 0.9638 cost: -0.6459 min: -0.7682 max: 2.2719 USE_META, weight: 0.9766 cost: -0.6892 min: -0.7682 max: 2.2719 USE_META, weight: 0.9489 cost: -0.5955 min: -0.7682 max: 2.2719 USE_META, weight: 0.9723 cost: -0.6748 min: -0.7682 max: 2.2719 USE_META, weight: 0.9511 cost: -0.6032 min: -0.7682 max: 2.2719 USE_META, weight: 0.9864 cost: -0.7223 min: -0.7682 max: 2.2719 USE_META, weight: 0.9864 cost: -0.7223 min: -0.7682 max: 2.2719 USE_META, weight: 0.9264 cost: -0.5197 min: -0.7682 max: 2.2719 USE_META, weight: 0.8790 cost: -0.3596 min: -0.7682 max: 2.2719 USE_META, weight: 0.3402 cost: 1.4605 min: -0.7682 max: 2.2719 USE_META, weight: 0.2704 cost: 1.6964 min: -0.7682 max: 2.2719 USE_META, weight: 0.9540 cost: -0.6129 min: -0.7682 max: 2.2719 USE_META, weight: 0.9788 cost: -0.6966 min: -0.7682 max: 2.2719 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9824 eval: 1.6100 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9824 eval: 1.6100 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9824 eval: 1.6100 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9412 eval: 5.3776 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9412 eval: 5.3776 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9412 eval: 5.3776 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.5188 eval: 44.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.5188 eval: 44.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.5188 eval: 44.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9696 eval: 2.7800 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9696 eval: 2.7800 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9999 eval: 0.0075 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9999 eval: 0.0075 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9999 eval: 0.0075 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9530 eval: 4.2952 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9530 eval: 4.2952 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9530 eval: 4.2952 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.1000 eval: 82.3000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.1000 eval: 82.3000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.1000 eval: 82.3000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9378 eval: 5.6855 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9378 eval: 5.6855 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 0.9378 eval: 5.6855 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0002 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 82.3000 Number of contacts in models: 256 Number of contacts in alignments: 50 NUMB_ALIGNS: 50 Adding 2281 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -196.1715, CN propb: -196.1715 weights: 0.5551 constraints: 165 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 165 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 165 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2116 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2116 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2281 # command: