# 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/T0337/ # command:# Making conformation for sequence T0337 numbered 1 through 151 Created new target T0337 from T0337.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0337/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0337//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0337/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0337//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0337/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0337/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0337/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hw5A expands to /projects/compbio/data/pdb/1hw5.pdb.gz 1hw5A:Skipped atom 179, because occupancy 0.5 <= existing 0.500 in 1hw5A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1hw5A # T0337 read from 1hw5A/merged-good-all-a2m # 1hw5A read from 1hw5A/merged-good-all-a2m # adding 1hw5A to template set # found chain 1hw5A in template set Warning: unaligning (T0337)T36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0337)R37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0337 9 :RVDMQLVKILSENSRL 1hw5A 141 :GRIAQTLLNLAKQPDA # choosing archetypes in rotamer library T0337 25 :TYRELADILNT 1hw5A 168 :TRQEIGQIVGC T0337 38 :QRIARRIDKLKKLGIIR 1hw5A 181 :ETVGRILKMLEDQNLIS Number of specific fragments extracted= 3 number of extra gaps= 1 total=3 Number of alignments=1 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0337)T36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0337)R37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0337 8 :DRVDMQLVKILSENSRL 1hw5A 140 :TGRIAQTLLNLAKQPDA T0337 25 :TYRELADILNT 1hw5A 168 :TRQEIGQIVGC T0337 38 :QRIARRIDKLKKLGIIR 1hw5A 181 :ETVGRILKMLEDQNLIS Number of specific fragments extracted= 3 number of extra gaps= 1 total=6 Number of alignments=2 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0337)T36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0337)R37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0337 24 :LTYRELADILNT 1hw5A 167 :ITRQEIGQIVGC T0337 38 :QRIARRIDKLKKLGIIR 1hw5A 181 :ETVGRILKMLEDQNLIS T0337 65 :LGYMYAI 1hw5A 198 :AHGKTIV Number of specific fragments extracted= 3 number of extra gaps= 1 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jhfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1jhfA/merged-good-all-a2m # 1jhfA read from 1jhfA/merged-good-all-a2m # found chain 1jhfA in training set Warning: unaligning (T0337)R5 because first residue in template chain is (1jhfA)K2 T0337 6 :KLDRVDMQLVKIL 1jhfA 3 :ALTARQQEVFDLI T0337 19 :SENSRLTYRELADILNT 1jhfA 21 :QTGMPPTRAEIAQRLGF T0337 36 :TRQRIARRIDKLKKLGIIR 1jhfA 39 :SPNAAEEHLKALARKGVIE T0337 57 :TIIPDIDKLGY 1jhfA 97 :HYQVDPSLFKP T0337 68 :MYA 1jhfA 109 :ADF T0337 73 :LIKSKV 1jhfA 112 :LLRVSG T0337 79 :PSD 1jhfA 121 :KDI T0337 100 :KGVGR 1jhfA 124 :GIMDG T0337 107 :IIVRLLLPK 1jhfA 129 :DLLAVHKTQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=18 Number of alignments=4 # 1jhfA read from 1jhfA/merged-good-all-a2m # found chain 1jhfA in training set Warning: unaligning (T0337)R5 because first residue in template chain is (1jhfA)K2 T0337 6 :KLDRVDMQLVKIL 1jhfA 3 :ALTARQQEVFDLI T0337 19 :SENSRLTYRELADILNT 1jhfA 21 :QTGMPPTRAEIAQRLGF T0337 36 :TRQRIARRIDKLKKLGIIR 1jhfA 39 :SPNAAEEHLKALARKGVIE T0337 55 :KFTII 1jhfA 65 :GIRLL T0337 60 :PDIDKLGY 1jhfA 100 :VDPSLFKP T0337 68 :MYAI 1jhfA 109 :ADFL T0337 74 :IKSKV 1jhfA 113 :LRVSG T0337 79 :PSD 1jhfA 121 :KDI T0337 91 :DIE 1jhfA 124 :GIM T0337 102 :VG 1jhfA 127 :DG T0337 108 :IVRLLLPKD 1jhfA 130 :LLAVHKTQD T0337 134 :AENVEVILIS 1jhfA 139 :VRNGQVVVAR T0337 144 :EVRKF 1jhfA 156 :KRLKK Number of specific fragments extracted= 13 number of extra gaps= 0 total=31 Number of alignments=5 # 1jhfA read from 1jhfA/merged-good-all-a2m # found chain 1jhfA in training set T0337 6 :KLDRVDMQLVKIL 1jhfA 3 :ALTARQQEVFDLI T0337 19 :SENSRLTYRELADILNT 1jhfA 21 :QTGMPPTRAEIAQRLGF T0337 36 :TRQRIARRIDKLKKLGIIR 1jhfA 39 :SPNAAEEHLKALARKGVIE T0337 55 :KFTII 1jhfA 65 :GIRLL T0337 61 :DIDKLGY 1jhfA 70 :QEEEEGL T0337 72 :VLIKSKVPS 1jhfA 77 :PLVGRVAAD T0337 89 :ISDIEYVKSVEKGV 1jhfA 88 :LLAQQHIEGHYQVD T0337 103 :GRYNIIVRLLL 1jhfA 107 :PNADFLLRVSG T0337 115 :KDI 1jhfA 118 :MSM T0337 130 :RIKNAEN 1jhfA 121 :KDIGIMD T0337 138 :EVILISEVR 1jhfA 128 :GDLLAVHKT Number of specific fragments extracted= 11 number of extra gaps= 0 total=42 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cg4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cg4A expands to /projects/compbio/data/pdb/2cg4.pdb.gz 2cg4A:# T0337 read from 2cg4A/merged-good-all-a2m # 2cg4A read from 2cg4A/merged-good-all-a2m # adding 2cg4A to template set # found chain 2cg4A in template set Warning: unaligning (T0337)R5 because first residue in template chain is (2cg4A)Y4 Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)I6 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 Warning: unaligning (T0337)G101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0337)V102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0337)G103 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 Warning: unaligning (T0337)I131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)D131 Warning: unaligning (T0337)K132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)D131 Warning: unaligning (T0337)E149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)T149 Warning: unaligning (T0337)I150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)T149 Warning: unaligning (T0337)I151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I150 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGY 2cg4A 7 :DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGARIDVSPKQLGY T0337 68 :MYAIVLIKSKVPSDADKVISEISDIEYVKSVEK 2cg4A 68 :VGCFIGIILKSAKDYPSALAKLESLDEVTEAYY T0337 104 :RYNIIVRLLL 2cg4A 104 :HYSIFIKVMC T0337 115 :KDIKDAENLISEFLQR 2cg4A 114 :RSIDALQHVLINKIQT T0337 133 :NAENVEVILISEVRKF 2cg4A 132 :EIQSTETLIVLQNPIM Number of specific fragments extracted= 5 number of extra gaps= 3 total=47 Number of alignments=7 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set Warning: unaligning (T0337)R5 because first residue in template chain is (2cg4A)Y4 Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)I6 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 Warning: unaligning (T0337)G101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0337)V102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0337)G103 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 Warning: unaligning (T0337)I131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)D131 Warning: unaligning (T0337)K132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)D131 Warning: unaligning (T0337)E149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)T149 Warning: unaligning (T0337)I150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)T149 Warning: unaligning (T0337)I151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I150 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGY 2cg4A 7 :DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGARIDVSPKQLGY T0337 68 :MYAIVLIKSKVPSDADKVISEISDIEYVKSVEK 2cg4A 68 :VGCFIGIILKSAKDYPSALAKLESLDEVTEAYY T0337 104 :RYNIIVRLLL 2cg4A 104 :HYSIFIKVMC T0337 115 :KDIKDAENLISEFLQR 2cg4A 114 :RSIDALQHVLINKIQT T0337 133 :NAENVEVILISEVRKF 2cg4A 132 :EIQSTETLIVLQNPIM Number of specific fragments extracted= 5 number of extra gaps= 3 total=52 Number of alignments=8 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)I6 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 Warning: unaligning (T0337)G101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0337)V102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0337)G103 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 Warning: unaligning (T0337)I131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)D131 Warning: unaligning (T0337)K132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)D131 Warning: unaligning (T0337)E149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cg4A)T149 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGYMYAIVLIKSKV 2cg4A 7 :DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGARIDVSPKQLGYDVGCFIGIILK T0337 79 :PSDADKVISEISDIEYVKSVEK 2cg4A 79 :AKDYPSALAKLESLDEVTEAYY T0337 104 :RYNIIVRLLL 2cg4A 104 :HYSIFIKVMC T0337 115 :KDIKDAENLISEFLQR 2cg4A 114 :RSIDALQHVLINKIQT T0337 133 :NAENVEVILISEVRKF 2cg4A 132 :EIQSTETLIVLQNPIM Number of specific fragments extracted= 5 number of extra gaps= 4 total=57 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0337 read from 2a61A/merged-good-all-a2m # 2a61A read from 2a61A/merged-good-all-a2m # adding 2a61A to template set # found chain 2a61A in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 2a61A 31 :GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0337 61 :DIDKLGY 2a61A 83 :DPADRRA T0337 70 :A 2a61A 90 :Y T0337 73 :LIKS 2a61A 91 :FLVI T0337 79 :PSDADKVISEISDI 2a61A 95 :TRKGEEVIEKVIER Number of specific fragments extracted= 5 number of extra gaps= 0 total=62 Number of alignments=10 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 2a61A 31 :GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0337 59 :IPDIDKLGY 2a61A 81 :TPDPADRRA T0337 73 :LIKS 2a61A 91 :FLVI T0337 79 :PSDADKVISEISDIEY 2a61A 95 :TRKGEEVIEKVIERRE T0337 95 :VKSVEK 2a61A 112 :FIEKIT T0337 115 :KDIKDAENLI 2a61A 120 :LGKEKSSKIL T0337 126 :EFLQR 2a61A 130 :DYLKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=69 Number of alignments=11 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 2a61A 31 :GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0337 59 :IPDIDKLGYMYAIV 2a61A 81 :TPDPADRRAYFLVI T0337 79 :PSDADKVISEISDI 2a61A 95 :TRKGEEVIEKVIER T0337 117 :IKDAENLISE 2a61A 109 :RENFIEKITS Number of specific fragments extracted= 4 number of extra gaps= 0 total=73 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1r1tA/merged-good-all-a2m # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0337 8 :DRVDMQLVKILSE 1r1tA 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FT 1r1tA 91 :YR T0337 66 :GY 1r1tA 95 :GR T0337 72 :VLIKSKVPSDADKVISEISD 1r1tA 98 :VYYQLQDHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=78 Number of alignments=13 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0337 8 :DRVDMQLVKILSE 1r1tA 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FTII 1r1tA 91 :YRKQ T0337 65 :LGY 1r1tA 95 :GRH T0337 73 :LIKSKVPSDADKVISEISD 1r1tA 99 :YYQLQDHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=83 Number of alignments=14 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0337 7 :LDRVDMQLVKILSE 1r1tA 44 :ADPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 75 :KSKVPS 1r1tA 91 :YRKQGR T0337 97 :SV 1r1tA 97 :HV T0337 110 :RLLL 1r1tA 99 :YYQL T0337 116 :DIKDAENLISEFLQR 1r1tA 103 :QDHHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=89 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtA expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtA:# T0337 read from 1smtA/merged-good-all-a2m # 1smtA read from 1smtA/merged-good-all-a2m # adding 1smtA to template set # found chain 1smtA in template set T0337 8 :DRVDMQLVKILSE 1smtA 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FTI 1smtA 91 :YRK T0337 73 :LIKSKVPSDADKVISEISD 1smtA 99 :YYQLQDHHIVALYQNALDH Number of specific fragments extracted= 4 number of extra gaps= 0 total=93 Number of alignments=16 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0337 8 :DRVDMQLVKILSE 1smtA 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FTII 1smtA 91 :YRKQ T0337 73 :LIKSKVPSDADKVISEISD 1smtA 99 :YYQLQDHHIVALYQNALDH Number of specific fragments extracted= 4 number of extra gaps= 0 total=97 Number of alignments=17 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0337 7 :LDRVDMQLVKILSE 1smtA 44 :ADPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 75 :KSKVPS 1smtA 91 :YRKQGR T0337 98 :V 1smtA 98 :V T0337 110 :RLLL 1smtA 99 :YYQL T0337 116 :DIKDAENLISEFLQR 1smtA 103 :QDHHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=103 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtB expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtB:# T0337 read from 1smtB/merged-good-all-a2m # 1smtB read from 1smtB/merged-good-all-a2m # adding 1smtB to template set # found chain 1smtB in template set T0337 8 :DRVDMQLVKILSE 1smtB 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FT 1smtB 91 :YR T0337 66 :GY 1smtB 95 :GR T0337 73 :LIKSKVPSDADKVISEISDIE 1smtB 99 :YYQLQDHHIVALYQNALDHLQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=108 Number of alignments=19 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0337 8 :DRVDMQLVKILSE 1smtB 45 :DPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 56 :FT 1smtB 91 :YR T0337 66 :GY 1smtB 96 :RH T0337 73 :LIKSKVPSDADKVISEISDI 1smtB 99 :YYQLQDHHIVALYQNALDHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=113 Number of alignments=20 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0337 7 :LDRVDMQLVKILSE 1smtB 44 :ADPNRLRLLSLLAR T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVS T0337 75 :KSKVPS 1smtB 91 :YRKQGR T0337 97 :SV 1smtB 97 :HV T0337 110 :RLLL 1smtB 99 :YYQL T0337 116 :DIKDAENLISEFLQR 1smtB 103 :QDHHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=119 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b1bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b1bA expands to /projects/compbio/data/pdb/1b1b.pdb.gz 1b1bA:# T0337 read from 1b1bA/merged-good-all-a2m # 1b1bA read from 1b1bA/merged-good-all-a2m # adding 1b1bA to template set # found chain 1b1bA in template set T0337 13 :QLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1b1bA 14 :TIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLR T0337 76 :S 1b1bA 56 :V T0337 78 :VPSD 1b1bA 57 :AGDR T0337 82 :ADKVISEIS 1b1bA 65 :TEKGRALAI Number of specific fragments extracted= 4 number of extra gaps= 0 total=123 Number of alignments=22 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0337 8 :DRVDM 1b1bA 6 :DTTEM T0337 13 :QLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1b1bA 14 :TIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLR T0337 76 :SKVPSD 1b1bA 56 :VAGDRH T0337 111 :LLLP 1b1bA 62 :LELT T0337 118 :KDAENLISEFLQ 1b1bA 66 :EKGRALAIAVMR Number of specific fragments extracted= 5 number of extra gaps= 0 total=128 Number of alignments=23 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0337 19 :SENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1b1bA 20 :EEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRV T0337 61 :D 1b1bA 57 :A T0337 63 :D 1b1bA 58 :G T0337 66 :GYMYAI 1b1bA 59 :DRHLEL T0337 82 :ADKVISEIS 1b1bA 65 :TEKGRALAI Number of specific fragments extracted= 5 number of extra gaps= 0 total=133 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sd4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sd4A expands to /projects/compbio/data/pdb/1sd4.pdb.gz 1sd4A: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 # T0337 read from 1sd4A/merged-good-all-a2m # 1sd4A read from 1sd4A/merged-good-all-a2m # adding 1sd4A to template set # found chain 1sd4A in template set Warning: unaligning (T0337)M4 because first residue in template chain is (1sd4A)Q5 T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADIL 1sd4A 6 :VEISMAEWDVMNIIWDKKSVSANEIVVEI T0337 34 :NTTRQRIARRIDKLKKLGIIRK 1sd4A 39 :EVSDKTIRTLITRLYKKEIIKR T0337 66 :GY 1sd4A 65 :NI T0337 73 :LIKSK 1sd4A 68 :FYSSN T0337 78 :VPSDADK 1sd4A 74 :KEDDIKM T0337 88 :EISD 1sd4A 81 :KTAK T0337 92 :I 1sd4A 91 :Y T0337 114 :PKDIKDAENLISE 1sd4A 92 :GGDMKSLVLNFAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=141 Number of alignments=25 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set Warning: unaligning (T0337)M4 because first residue in template chain is (1sd4A)Q5 T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADIL 1sd4A 6 :VEISMAEWDVMNIIWDKKSVSANEIVVEI T0337 34 :NTTRQRIARRIDKLKKLGIIRK 1sd4A 39 :EVSDKTIRTLITRLYKKEIIKR T0337 66 :GY 1sd4A 65 :NI T0337 73 :LIKSK 1sd4A 68 :FYSSN T0337 78 :VPSDA 1sd4A 74 :KEDDI T0337 86 :ISEISD 1sd4A 79 :KMKTAK T0337 93 :EYVKSVEKGVGR 1sd4A 96 :KSLVLNFAKNEE T0337 115 :KDIKDAENLI 1sd4A 108 :LNNKEIEELR T0337 126 :EFLQR 1sd4A 118 :DILND Number of specific fragments extracted= 9 number of extra gaps= 0 total=150 Number of alignments=26 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set Warning: unaligning (T0337)M4 because first residue in template chain is (1sd4A)Q5 T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADIL 1sd4A 6 :VEISMAEWDVMNIIWDKKSVSANEIVVEI T0337 34 :NTTRQRIARRIDKLKKLGIIRKFT 1sd4A 39 :EVSDKTIRTLITRLYKKEIIKRYK T0337 66 :GYM 1sd4A 65 :NIY T0337 72 :VLIKSKVPSDADKVISE 1sd4A 68 :FYSSNIKEDDIKMKTAK T0337 90 :SDIE 1sd4A 89 :KLYG T0337 115 :KDIKDAENLISE 1sd4A 93 :GDMKSLVLNFAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=156 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z91A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z91A expands to /projects/compbio/data/pdb/1z91.pdb.gz 1z91A:# T0337 read from 1z91A/merged-good-all-a2m # 1z91A read from 1z91A/merged-good-all-a2m # adding 1z91A to template set # found chain 1z91A in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKL 1z91A 35 :KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSV T0337 73 :LIKS 1z91A 97 :LISL T0337 82 :ADKVISE 1z91A 101 :TEDGALL T0337 89 :ISDIEYVKSVEKG 1z91A 111 :AVDIPGTILGLSK T0337 115 :KDIKDAENL 1z91A 124 :QSGEDLKQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=161 Number of alignments=28 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1z91A 36 :LNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITR T0337 59 :I 1z91A 90 :E T0337 77 :KVPSD 1z91A 91 :EDERS T0337 82 :ADKVISE 1z91A 101 :TEDGALL T0337 89 :ISDIEYVKSVEKG 1z91A 111 :AVDIPGTILGLSK T0337 115 :KDIKDAENLISEFLQ 1z91A 124 :QSGEDLKQLKSALYT Number of specific fragments extracted= 6 number of extra gaps= 0 total=167 Number of alignments=29 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKL 1z91A 35 :KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSV T0337 74 :IKSKV 1z91A 97 :LISLT T0337 79 :PSDADKVISE 1z91A 112 :VDIPGTILGL T0337 115 :KDIKDAENLISEFLQ 1z91A 123 :KQSGEDLKQLKSALY Number of specific fragments extracted= 4 number of extra gaps= 0 total=171 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ri7A expands to /projects/compbio/data/pdb/1ri7.pdb.gz 1ri7A:# T0337 read from 1ri7A/merged-good-all-a2m # 1ri7A read from 1ri7A/merged-good-all-a2m # adding 1ri7A to template set # found chain 1ri7A in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1ri7A)L25 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGY 1ri7A 26 :DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGY T0337 68 :MYAIVLIKS 1ri7A 87 :MLAFILVKV T0337 78 :VPSDADKVISEISDIEYVKSVEKGVGRYNIIVRLLL 1ri7A 96 :KAGKYSEVASNLAKYPEIVEVYETTGDYDMVVKIRT T0337 115 :KDIKDAENLI 1ri7A 132 :KNSEELNNFL T0337 126 :EFLQRIKNAENVEVILISEVRKFEII 1ri7A 142 :DLIGSIPGVEGTHTMIVLKTHKETTE Number of specific fragments extracted= 5 number of extra gaps= 0 total=176 Number of alignments=31 # 1ri7A read from 1ri7A/merged-good-all-a2m # found chain 1ri7A in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1ri7A)L25 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGY 1ri7A 26 :DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGY T0337 68 :MYAIVLIKS 1ri7A 87 :MLAFILVKV T0337 78 :VPSDADKVISEISDIEYVKSVEKGVGRYNIIVRLLL 1ri7A 96 :KAGKYSEVASNLAKYPEIVEVYETTGDYDMVVKIRT T0337 115 :KDIKDAENLI 1ri7A 132 :KNSEELNNFL T0337 126 :EFLQRIKNAENVEVILISEVRKFEI 1ri7A 142 :DLIGSIPGVEGTHTMIVLKTHKETT Number of specific fragments extracted= 5 number of extra gaps= 0 total=181 Number of alignments=32 # 1ri7A read from 1ri7A/merged-good-all-a2m # found chain 1ri7A in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1ri7A)L25 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGYMYAIVLIKSKVPSDADKVISEISDIEYVKSVEKGVGRYNIIVRLLL 1ri7A 26 :DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGYSMLAFILVKVKAGKYSEVASNLAKYPEIVEVYETTGDYDMVVKIRT T0337 115 :KDIKDAEN 1ri7A 132 :KNSEELNN T0337 124 :ISEFLQRIKNAENVEVILISEVRK 1ri7A 140 :FLDLIGSIPGVEGTHTMIVLKTHK Number of specific fragments extracted= 3 number of extra gaps= 0 total=184 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i1gA expands to /projects/compbio/data/pdb/1i1g.pdb.gz 1i1gA:# T0337 read from 1i1gA/merged-good-all-a2m # 1i1gA read from 1i1gA/merged-good-all-a2m # adding 1i1gA to template set # found chain 1i1gA in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1i1gA)I2 Warning: unaligning (T0337)D8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1gA)E4 Warning: unaligning (T0337)R9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1gA)E4 Warning: unaligning (T0337)K16 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0337)I17 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0337)I59 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I55 Warning: unaligning (T0337)P60 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I55 Warning: unaligning (T0337)I92 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)D88 Warning: unaligning (T0337)E93 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0337)N106 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0337)I107 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0337 10 :VDMQLV 1i1gA 5 :RDKIIL T0337 18 :LSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 1i1gA 13 :LEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYTI T0337 61 :DIDKLGY 1i1gA 56 :NPKKLGY T0337 68 :MYAIVLIKS 1i1gA 64 :LVTITGVDT T0337 78 :VPSDADKVISEISD 1i1gA 73 :KPEKLFEVAEKLKE T0337 94 :YVKSVEKGVGRY 1i1gA 89 :FVKELYLSSGDH T0337 108 :IVRLLL 1i1gA 103 :MAVIWA T0337 115 :KDIKDAENLISEFLQRIKNAENVEVILI 1i1gA 109 :KDGEDLAEIISNKIGKIEGVTKVCPAII Number of specific fragments extracted= 8 number of extra gaps= 4 total=192 Number of alignments=34 # 1i1gA read from 1i1gA/merged-good-all-a2m # found chain 1i1gA in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1i1gA)I2 Warning: unaligning (T0337)D8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1gA)E4 Warning: unaligning (T0337)R9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1gA)E4 Warning: unaligning (T0337)K16 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0337)I17 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0337)I59 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I55 Warning: unaligning (T0337)P60 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I55 Warning: unaligning (T0337)I92 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)D88 Warning: unaligning (T0337)E93 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0337)N106 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0337)I107 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0337 10 :VDMQLV 1i1gA 5 :RDKIIL T0337 18 :LSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 1i1gA 13 :LEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYTI T0337 61 :DIDKLGY 1i1gA 56 :NPKKLGY T0337 68 :MYAIVLIKS 1i1gA 64 :LVTITGVDT T0337 78 :VPSDADKVISEISD 1i1gA 73 :KPEKLFEVAEKLKE T0337 94 :YVKSVEKGVGRY 1i1gA 89 :FVKELYLSSGDH T0337 108 :IVRLLL 1i1gA 103 :MAVIWA T0337 115 :KDIKDAENLISEFLQRIKNAENVEVILI 1i1gA 109 :KDGEDLAEIISNKIGKIEGVTKVCPAII Number of specific fragments extracted= 8 number of extra gaps= 4 total=200 Number of alignments=35 # 1i1gA read from 1i1gA/merged-good-all-a2m # found chain 1i1gA in template set Warning: unaligning (T0337)L7 because first residue in template chain is (1i1gA)I2 Warning: unaligning (T0337)D8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i1gA)E4 Warning: unaligning (T0337)R9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i1gA)E4 Warning: unaligning (T0337)K16 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0337)I17 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0337)I59 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I55 Warning: unaligning (T0337)P60 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I55 Warning: unaligning (T0337)I92 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)D88 Warning: unaligning (T0337)E93 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0337)N106 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0337)I107 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0337 10 :VDMQLV 1i1gA 5 :RDKIIL T0337 18 :LSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 1i1gA 13 :LEKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYTI T0337 61 :DIDKLGYMYAIVLIKSKVPSDADKVISEISD 1i1gA 56 :NPKKLGYSLVTITGVDTKPEKLFEVAEKLKE T0337 94 :YVKSVEKGVGRY 1i1gA 89 :FVKELYLSSGDH T0337 108 :IVRLLL 1i1gA 103 :MAVIWA T0337 115 :KDIKDAENLISEFLQRIKNAENVEVIL 1i1gA 109 :KDGEDLAEIISNKIGKIEGVTKVCPAI Number of specific fragments extracted= 6 number of extra gaps= 4 total=206 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g6nA expands to /projects/compbio/data/pdb/1g6n.pdb.gz 1g6nA:# T0337 read from 1g6nA/merged-good-all-a2m # 1g6nA read from 1g6nA/merged-good-all-a2m # adding 1g6nA to template set # found chain 1g6nA in template set T0337 8 :DRVDMQLVKILSENSRL 1g6nA 140 :TGRIAQTLLNLAKQPDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1g6nA 168 :TRQEIGQIVGCSRETVGRILKMLEDQNLIS Number of specific fragments extracted= 2 number of extra gaps= 0 total=208 Number of alignments=37 # 1g6nA read from 1g6nA/merged-good-all-a2m # found chain 1g6nA in template set T0337 8 :DRVDMQLVKILSENSRL 1g6nA 140 :TGRIAQTLLNLAKQPDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1g6nA 168 :TRQEIGQIVGCSRETVGRILKMLEDQNLIS Number of specific fragments extracted= 2 number of extra gaps= 0 total=210 Number of alignments=38 # 1g6nA read from 1g6nA/merged-good-all-a2m # found chain 1g6nA in template set T0337 15 :VKILSENSRL 1g6nA 147 :LLNLAKQPDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1g6nA 168 :TRQEIGQIVGCSRETVGRILKMLEDQNLIS T0337 55 :KFTIIP 1g6nA 200 :GKTIVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=213 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fxaA expands to /projects/compbio/data/pdb/2fxa.pdb.gz 2fxaA: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 Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2fxaA 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 Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2fxaA 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 Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2fxaA 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 # T0337 read from 2fxaA/merged-good-all-a2m # 2fxaA read from 2fxaA/merged-good-all-a2m # adding 2fxaA to template set # found chain 2fxaA in template set Warning: unaligning (T0337)I59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0337)G66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 2fxaA 41 :PYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLR T0337 56 :FTI 2fxaA 92 :FSK T0337 73 :LIKS 2fxaA 103 :YVQL T0337 82 :ADKVISEISDI 2fxaA 107 :TEEGTEVFWSL Number of specific fragments extracted= 4 number of extra gaps= 0 total=217 Number of alignments=40 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0337)I59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0337)G66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 2fxaA 41 :PYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLR T0337 56 :FTI 2fxaA 92 :FSK T0337 73 :LIKS 2fxaA 103 :YVQL T0337 82 :ADKVISEISDI 2fxaA 107 :TEEGTEVFWSL Number of specific fragments extracted= 4 number of extra gaps= 0 total=221 Number of alignments=41 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0337)I59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0337)G66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0337 3 :CMRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 2fxaA 40 :KPYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEERGYLR T0337 56 :FTI 2fxaA 92 :FSK T0337 67 :Y 2fxaA 103 :Y T0337 73 :LIK 2fxaA 104 :VQL T0337 82 :ADKVISEISDI 2fxaA 107 :TEEGTEVFWSL T0337 128 :L 2fxaA 118 :L Number of specific fragments extracted= 6 number of extra gaps= 0 total=227 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0337 read from 2b0lA/merged-good-all-a2m # 2b0lA read from 2b0lA/merged-good-all-a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0337)E20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0337)N21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0337)R42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0337)R43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0337)I53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0337)R54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0337)T57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0337)D91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0337 6 :KLDRVDMQLVKILS 2b0lA 178 :SLSYSELEAIEHIF T0337 22 :SRL 2b0lA 194 :LDG T0337 25 :TYRELADILNTTRQRIA 2b0lA 202 :VASKIADRVGITRSVIV T0337 44 :IDKLKKLGI 2b0lA 221 :LRKLESAGV T0337 72 :VLIKS 2b0lA 240 :TYIKV T0337 81 :DADKVISEIS 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 6 number of extra gaps= 5 total=233 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0337)E20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0337)N21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0337)R42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0337)R43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0337)I53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0337)R54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0337)T57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0337)I58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0337)I59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0337)D91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0337 6 :KLDRVDMQLVKILS 2b0lA 178 :SLSYSELEAIEHIF T0337 22 :SRL 2b0lA 194 :LDG T0337 25 :TYRELADILNTTRQRIA 2b0lA 202 :VASKIADRVGITRSVIV T0337 44 :IDKLKKLGI 2b0lA 221 :LRKLESAGV T0337 56 :F 2b0lA 232 :S T0337 72 :VLIKS 2b0lA 240 :TYIKV T0337 81 :DADKVISEIS 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 7 number of extra gaps= 5 total=240 Number of alignments=43 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0337)E20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0337)N21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0337)R42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0337)R43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0337)I53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0337)R54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0337)K75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0337)S76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0337)K77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0337)G103 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0337)R104 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0337)E126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0337 5 :RKLDRVDMQLVKILS 2b0lA 177 :SSLSYSELEAIEHIF T0337 22 :SRL 2b0lA 194 :LDG T0337 25 :TYRELADILNTTRQRIA 2b0lA 202 :VASKIADRVGITRSVIV T0337 44 :IDKLKKLGI 2b0lA 221 :LRKLESAGV T0337 74 :I 2b0lA 232 :S T0337 105 :YNIIVRLLL 2b0lA 238 :KGTYIKVLN T0337 118 :KDAENLIS 2b0lA 247 :NKFLIELE Number of specific fragments extracted= 7 number of extra gaps= 5 total=247 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xnpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA # T0337 read from 1xnpA/merged-good-all-a2m # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0337 read from 2fbhA/merged-good-all-a2m # 2fbhA read from 2fbhA/merged-good-all-a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0337)L33 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0337)N34 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0337 12 :MQLVKILSENSRL 2fbhA 38 :WLVLLHLARHRDS T0337 25 :TYRELADI 2fbhA 52 :TQRELAQS T0337 35 :TTRQRIARRIDKLKKLGIIRKF 2fbhA 62 :VEGPTLARLLDGLESQGLVRRL T0337 59 :IPDIDK 2fbhA 84 :AVAEDR T0337 73 :LIKS 2fbhA 93 :HIVL T0337 78 :VP 2fbhA 97 :TP T0337 80 :SDADKVISEISDIEYVK 2fbhA 102 :VLIADIEAIAASVRNDV T0337 101 :GVG 2fbhA 119 :LTG T0337 115 :KDIKDAENLISE 2fbhA 122 :IDESEQALCQQV Number of specific fragments extracted= 9 number of extra gaps= 1 total=256 Number of alignments=45 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0337)L33 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0337)N34 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0337 12 :MQLVKILSENSRL 2fbhA 38 :WLVLLHLARHRDS T0337 25 :TYRELADI 2fbhA 52 :TQRELAQS T0337 35 :TTRQRIARRIDKLKKLGIIRK 2fbhA 62 :VEGPTLARLLDGLESQGLVRR T0337 57 :T 2fbhA 83 :L T0337 59 :IPDIDK 2fbhA 84 :AVAEDR T0337 73 :LIKSKVP 2fbhA 93 :HIVLTPK T0337 80 :SDADKVISEISDIEYV 2fbhA 102 :VLIADIEAIAASVRND T0337 100 :KGVG 2fbhA 118 :VLTG T0337 115 :KDIKDAENLI 2fbhA 122 :IDESEQALCQ T0337 126 :EFLQR 2fbhA 132 :QVLLR Number of specific fragments extracted= 10 number of extra gaps= 1 total=266 Number of alignments=46 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0337)L33 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0337)N34 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0337 14 :LVKILSENSRL 2fbhA 40 :VLLHLARHRDS T0337 25 :TYRELADI 2fbhA 52 :TQRELAQS T0337 35 :TTRQRIARRIDKLKKLGIIRKF 2fbhA 62 :VEGPTLARLLDGLESQGLVRRL T0337 59 :IPDIDKLGYMY 2fbhA 84 :AVAEDRRAKHI T0337 76 :SKV 2fbhA 95 :VLT T0337 79 :PSDADKVISEISDIEY 2fbhA 101 :DVLIADIEAIAASVRN T0337 102 :V 2fbhA 120 :T T0337 115 :KDIKDAENLISEFLQR 2fbhA 121 :GIDESEQALCQQVLLR Number of specific fragments extracted= 8 number of extra gaps= 1 total=274 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j5yA expands to /projects/compbio/data/pdb/1j5y.pdb.gz 1j5yA: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 # T0337 read from 1j5yA/merged-good-all-a2m # 1j5yA read from 1j5yA/merged-good-all-a2m # adding 1j5yA to template set # found chain 1j5yA in template set T0337 9 :RVDMQLVKILSENSRL 1j5yA 9 :ERLKSIVRILERSKEP T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGI 1j5yA 26 :SGAQLAEELSVSRQVIVQDIAYLRSLGY T0337 53 :I 1j5yA 55 :I T0337 54 :RKFTIIPDI 1j5yA 58 :TPRGYVLAG T0337 66 :GY 1j5yA 67 :GK T0337 68 :MYAIVLIKS 1j5yA 71 :VSRLVAVKH T0337 78 :VPSDADKVI 1j5yA 80 :APEEIKEEL T0337 96 :KSVEKGVGR 1j5yA 89 :LCVVRNGGR T0337 105 :YN 1j5yA 99 :VD T0337 109 :VRLLLP 1j5yA 101 :VIVEHP T0337 116 :DIKDAENLI 1j5yA 119 :SEEEVLKFV T0337 126 :EFLQRIK 1j5yA 128 :NLMEMAK T0337 133 :NAENVEVILISEV 1j5yA 140 :TLSGGVHLHTIEA Number of specific fragments extracted= 13 number of extra gaps= 0 total=287 Number of alignments=48 # 1j5yA read from 1j5yA/merged-good-all-a2m # found chain 1j5yA in template set T0337 9 :RVDMQLVKILSENSRL 1j5yA 9 :ERLKSIVRILERSKEP T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGI 1j5yA 26 :SGAQLAEELSVSRQVIVQDIAYLRSLGY T0337 54 :R 1j5yA 58 :T T0337 57 :TIIPDIDK 1j5yA 61 :GYVLAGGK T0337 68 :MYAIVLIKS 1j5yA 71 :VSRLVAVKH T0337 78 :VPSDADKV 1j5yA 80 :APEEIKEE T0337 95 :VKSVEKGVGRY 1j5yA 88 :LLCVVRNGGRI T0337 106 :NIIV 1j5yA 100 :DVIV T0337 116 :DIKDAENLI 1j5yA 119 :SEEEVLKFV T0337 126 :EFLQRIK 1j5yA 128 :NLMEMAK T0337 133 :NAENVEVILISEV 1j5yA 140 :TLSGGVHLHTIEA Number of specific fragments extracted= 11 number of extra gaps= 0 total=298 Number of alignments=49 # 1j5yA read from 1j5yA/merged-good-all-a2m # found chain 1j5yA in template set T0337 9 :RVDMQLVKILSENSRL 1j5yA 9 :ERLKSIVRILERSKEP T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGI 1j5yA 26 :SGAQLAEELSVSRQVIVQDIAYLRSLGY T0337 54 :RKFTIIPDIDKL 1j5yA 73 :RLVAVKHAPEEI T0337 66 :GYMYA 1j5yA 95 :GGRIV T0337 72 :VLIKSKV 1j5yA 100 :DVIVEHP T0337 79 :PSDADKVISEISDIEY 1j5yA 120 :EEEVLKFVNLMEMAKT T0337 100 :KGVGRYNIIVRLLL 1j5yA 139 :LTLSGGVHLHTIEA T0337 116 :DIKDAENLISEFLQRIK 1j5yA 153 :PDEETMERIMRELKKKG Number of specific fragments extracted= 8 number of extra gaps= 0 total=306 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0337 read from 1mkmA/merged-good-all-a2m # 1mkmA read from 1mkmA/merged-good-all-a2m # adding 1mkmA to template set # found chain 1mkmA in template set T0337 9 :RVDMQLVKILSENSRL 1mkmA 5 :KKAFEILDFIVKNPGD T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRK 1mkmA 22 :SVSEIAEKFNMSVSNAYKYMVVLEEKGFVLR T0337 66 :GY 1mkmA 55 :DK T0337 75 :KSKVPSDADKVISEISD 1mkmA 57 :RYVPGYKLIEYGSFVLR T0337 115 :KDIKDAENLISEFLQRI 1mkmA 76 :NIRDIAHDHLVDIMKRT T0337 136 :NVEVILISE 1mkmA 93 :GETVHLILK Number of specific fragments extracted= 6 number of extra gaps= 0 total=312 Number of alignments=51 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0337 9 :RVDMQLVKILSENSRL 1mkmA 5 :KKAFEILDFIVKNPGD T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRK 1mkmA 22 :SVSEIAEKFNMSVSNAYKYMVVLEEKGFVLR T0337 75 :KSKVPSDADK 1mkmA 57 :RYVPGYKLIE T0337 85 :VISEIS 1mkmA 77 :IRDIAH T0337 93 :EYVKSVEKGVGRY 1mkmA 83 :DHLVDIMKRTGET T0337 108 :IVRLLLP 1mkmA 96 :VHLILKD Number of specific fragments extracted= 6 number of extra gaps= 0 total=318 Number of alignments=52 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0337 9 :RVDMQLVKILSENSRL 1mkmA 5 :KKAFEILDFIVKNPGD T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKF 1mkmA 22 :SVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0337 57 :TIIPDID 1mkmA 57 :RYVPGYK T0337 64 :KLGYMYAIVL 1mkmA 91 :RTGETVHLIL T0337 76 :SKV 1mkmA 101 :KDG T0337 81 :DADKVISEISDI 1mkmA 167 :NPRVLKRELEKI T0337 96 :KSVEKGV 1mkmA 194 :IMCVGVP T0337 103 :GRYNIIVRLLL 1mkmA 206 :GYPVAGVSISG T0337 115 :KDIKDAENLISEFLQR 1mkmA 224 :EKIEEYSDVLKEKAEE Number of specific fragments extracted= 9 number of extra gaps= 0 total=327 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ethA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ethA expands to /projects/compbio/data/pdb/2eth.pdb.gz 2ethA: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 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 Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2ethA # T0337 read from 2ethA/merged-good-all-a2m # 2ethA read from 2ethA/merged-good-all-a2m # adding 2ethA to template set # found chain 2ethA in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGII 2ethA 28 :SDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLV T0337 57 :TIIPDIDKLGY 2ethA 77 :VREMDPVDRRT T0337 73 :LIKS 2ethA 89 :RVVL T0337 79 :PSDADKVISEISDI 2ethA 93 :TEKGKEIFGEILSN Number of specific fragments extracted= 4 number of extra gaps= 0 total=331 Number of alignments=54 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGI 2ethA 28 :SDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGL T0337 56 :FTIIPDIDKLGY 2ethA 76 :VVREMDPVDRRT T0337 73 :LIKS 2ethA 89 :RVVL T0337 79 :PSDADKVISEISDIEYVKSVEKGVG 2ethA 93 :TEKGKEIFGEILSNFESLLKSVLEK T0337 114 :P 2ethA 118 :F T0337 116 :DIKDAENLISE 2ethA 119 :SEEDFKVVSEG Number of specific fragments extracted= 6 number of extra gaps= 0 total=337 Number of alignments=55 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 2ethA 29 :DMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVV T0337 58 :IIPDIDKLGYMYAIV 2ethA 78 :REMDPVDRRTYRVVL T0337 79 :PSDADKVISEISD 2ethA 93 :TEKGKEIFGEILS T0337 116 :DIKDAENLIS 2ethA 106 :NFESLLKSVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=341 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0337 read from 1lj9A/merged-good-all-a2m # 1lj9A read from 1lj9A/merged-good-all-a2m # adding 1lj9A to template set # found chain 1lj9A in template set T0337 13 :QLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1lj9A 34 :LYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIY T0337 58 :IIPDIDKLGY 1lj9A 76 :RQEDASNKKI T0337 73 :LIKS 1lj9A 87 :RIYA T0337 78 :VP 1lj9A 91 :TE T0337 80 :SDADKVISEISDIEYVKSV 1lj9A 96 :NVYPIIVRENQHSNQVALQ T0337 103 :G 1lj9A 115 :G T0337 115 :KDIKDAENLISE 1lj9A 116 :LSEVEISQLADY T0337 128 :LQ 1lj9A 128 :LV Number of specific fragments extracted= 8 number of extra gaps= 0 total=349 Number of alignments=57 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0337 13 :QLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGII 1lj9A 34 :LYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFI T0337 57 :TIIPDIDKLGY 1lj9A 75 :YRQEDASNKKI T0337 73 :LIKS 1lj9A 87 :RIYA T0337 78 :VP 1lj9A 91 :TE T0337 80 :SDADKVISEISDIEYVK 1lj9A 96 :NVYPIIVRENQHSNQVA T0337 101 :GVG 1lj9A 113 :LQG T0337 115 :KDIKDAENLI 1lj9A 116 :LSEVEISQLA T0337 126 :EFLQR 1lj9A 126 :DYLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=357 Number of alignments=58 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1lj9A 25 :ELSLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIY T0337 58 :IIPDIDKLGYM 1lj9A 76 :RQEDASNKKIK T0337 74 :IKSKV 1lj9A 87 :RIYAT T0337 79 :PSDADKVISEISDIEYVKS 1lj9A 95 :KNVYPIIVRENQHSNQVAL T0337 102 :VG 1lj9A 114 :QG T0337 115 :KDIKDAENLISEFLQ 1lj9A 116 :LSEVEISQLADYLVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=363 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fseA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fseA expands to /projects/compbio/data/pdb/1fse.pdb.gz 1fseA:Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 286, because occupancy 1.000 <= existing 1.000 in 1fseA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1fseA # T0337 read from 1fseA/merged-good-all-a2m # 1fseA read from 1fseA/merged-good-all-a2m # adding 1fseA to template set # found chain 1fseA in template set Warning: unaligning (T0337)C3 because first residue in template chain is (1fseA)S8 T0337 4 :MRKLDRVDMQLVKILSEN 1fseA 9 :KPLLTKREREVFELLVQD T0337 24 :LTYRELADILNTTRQRIARRIDKLKKL 1fseA 27 :KTTKEIASELFISEKTVRNHISNAMQK T0337 65 :LGY 1fseA 54 :LGV T0337 80 :SDADKVISEISDIEYV 1fseA 57 :KGRSQAVVELLRMGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=367 Number of alignments=60 # 1fseA read from 1fseA/merged-good-all-a2m # found chain 1fseA in template set Warning: unaligning (T0337)C3 because first residue in template chain is (1fseA)S8 T0337 4 :MRKLDRVDMQLVKILSEN 1fseA 9 :KPLLTKREREVFELLVQD T0337 24 :LTYRELADILNTTRQRIARRIDKLKKL 1fseA 27 :KTTKEIASELFISEKTVRNHISNAMQK T0337 65 :LGY 1fseA 54 :LGV T0337 80 :SDADKVISEISDIEYV 1fseA 57 :KGRSQAVVELLRMGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=371 Number of alignments=61 # 1fseA read from 1fseA/merged-good-all-a2m # found chain 1fseA in template set T0337 5 :RKLDRVDMQLVKILSEN 1fseA 10 :PLLTKREREVFELLVQD T0337 24 :LTYRELADILNTTRQRIARRIDKLKK 1fseA 27 :KTTKEIASELFISEKTVRNHISNAMQ T0337 64 :KLGY 1fseA 53 :KLGV T0337 80 :SDADKVISEISDIEYV 1fseA 57 :KGRSQAVVELLRMGEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=375 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1okrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1okrA expands to /projects/compbio/data/pdb/1okr.pdb.gz 1okrA:# T0337 read from 1okrA/merged-good-all-a2m # 1okrA read from 1okrA/merged-good-all-a2m # adding 1okrA to template set # found chain 1okrA in template set Warning: unaligning (T0337)C3 because first residue in template chain is (1okrA)K4 Warning: unaligning (T0337)M4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)Y6 Warning: unaligning (T0337)R5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADIL 1okrA 7 :EISSAEWEVMNIIWMKKYASANNIIEEI T0337 34 :NTTRQRIARRIDKLKKLGII 1okrA 39 :DWSPKTIRTLITRLYKKGFI T0337 54 :RKFTIIPDI 1okrA 67 :FQYYSLVEE T0337 83 :DKVISEISD 1okrA 76 :SDIKYKTSK T0337 95 :VKSVE 1okrA 87 :INKVY T0337 114 :PKDIKDAENLISE 1okrA 92 :KGGFNSLVLNFVE Number of specific fragments extracted= 6 number of extra gaps= 0 total=381 Number of alignments=63 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0337)C3 because first residue in template chain is (1okrA)K4 Warning: unaligning (T0337)M4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)Y6 Warning: unaligning (T0337)R5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADIL 1okrA 7 :EISSAEWEVMNIIWMKKYASANNIIEEI T0337 34 :NTTRQRIARRIDKLKKLGII 1okrA 39 :DWSPKTIRTLITRLYKKGFI T0337 54 :RKFTIIPDIDKL 1okrA 67 :FQYYSLVEESDI T0337 78 :VPSDADKVISEISD 1okrA 91 :YKGGFNSLVLNFVE T0337 115 :KDIKDAENLI 1okrA 108 :LSQDEIEELR T0337 126 :E 1okrA 118 :N Number of specific fragments extracted= 6 number of extra gaps= 0 total=387 Number of alignments=64 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0337)C3 because first residue in template chain is (1okrA)K4 Warning: unaligning (T0337)M4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)Y6 Warning: unaligning (T0337)R5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 Warning: unaligning (T0337)I62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0337)D63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADIL 1okrA 7 :EISSAEWEVMNIIWMKKYASANNIIEEI T0337 34 :NTTRQRIARRIDKLKKLGIIRK 1okrA 39 :DWSPKTIRTLITRLYKKGFIDR T0337 59 :IPD 1okrA 61 :KKD T0337 70 :AIVLIKSKV 1okrA 66 :IFQYYSLVE T0337 79 :P 1okrA 92 :K T0337 115 :KDIKDAENLISE 1okrA 93 :GGFNSLVLNFVE Number of specific fragments extracted= 6 number of extra gaps= 1 total=393 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2csbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2csbA expands to /projects/compbio/data/pdb/2csb.pdb.gz 2csbA: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 Skipped atom 2044, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2046, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2048, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2050, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2052, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2054, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2056, because occupancy 0.400 <= existing 0.600 in 2csbA 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 Skipped atom 2751, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2753, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2755, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2757, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2759, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2761, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2763, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2810, because occupancy 0.500 <= existing 0.500 in 2csbA 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 Skipped atom 3905, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3907, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3909, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3911, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4115, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4117, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4119, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4121, because occupancy 0.400 <= existing 0.600 in 2csbA # T0337 read from 2csbA/merged-good-all-a2m # 2csbA read from 2csbA/merged-good-all-a2m # adding 2csbA to template set # found chain 2csbA in template set Warning: unaligning (T0337)K46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 Warning: unaligning (T0337)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2csbA)R250 T0337 7 :LDRVDMQLVKILSENSRLTYRELADILNTT 2csbA 181 :IDEKEERILEILRENPWTPHDEIARRLGLS T0337 37 :RQRIARRID 2csbA 240 :ERTAKRHVK T0337 48 :KK 2csbA 251 :DR T0337 81 :DADKVISEISDI 2csbA 253 :LLEELYEHLEEL T0337 128 :LQR 2csbA 265 :SER Number of specific fragments extracted= 5 number of extra gaps= 1 total=398 Number of alignments=66 # 2csbA read from 2csbA/merged-good-all-a2m # found chain 2csbA in template set Warning: unaligning (T0337)K46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 Warning: unaligning (T0337)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2csbA)R250 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTT 2csbA 180 :PIDEKEERILEILRENPWTPHDEIARRLGLS T0337 37 :RQRIARRID 2csbA 240 :ERTAKRHVK T0337 48 :KK 2csbA 251 :DR T0337 81 :DADKVISEISDI 2csbA 253 :LLEELYEHLEEL T0337 98 :VEKGVGR 2csbA 265 :SERYLRH T0337 114 :PKDIKDAENLISEFLQRI 2csbA 272 :PLTRRWIVEHKRDIMRRY Number of specific fragments extracted= 6 number of extra gaps= 1 total=404 Number of alignments=67 # 2csbA read from 2csbA/merged-good-all-a2m # found chain 2csbA in template set Warning: unaligning (T0337)E88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 Warning: unaligning (T0337)I89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2csbA)R250 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIA 2csbA 180 :PIDEKEERILEILRENPWTPHDEIARRLGLSVSEVE T0337 75 :KSKVPSDADKVIS 2csbA 236 :IEYDERTAKRHVK T0337 90 :SDI 2csbA 251 :DRL T0337 117 :IKDAENLISEFLQR 2csbA 254 :LEELYEHLEELSER Number of specific fragments extracted= 4 number of extra gaps= 1 total=408 Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bia/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bia expands to /projects/compbio/data/pdb/1bia.pdb.gz 1bia:Warning: there is no chain 1bia will retry with 1biaA # T0337 read from 1bia/merged-good-all-a2m # 1bia read from 1bia/merged-good-all-a2m # adding 1bia to template set # found chain 1bia in template set Warning: unaligning (T0337)S80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)S125 Warning: unaligning (T0337)K100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)S125 Warning: unaligning (T0337)D116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 T0337 1 :MDC 1bia 1 :MKD T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGI 1bia 4 :NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0337 53 :IRKFTIIPD 1bia 76 :LDGGSVAVL T0337 62 :IDKLGYMYAIVLIKS 1bia 98 :IGELKSGDACIAEYQ T0337 78 :VP 1bia 113 :QA T0337 101 :GVGRYNIIVRLLLPK 1bia 126 :PFGANLYLSMFWRLE T0337 120 :AE 1bia 149 :LS T0337 123 :LISEFLQRI 1bia 156 :VMAEVLRKL T0337 133 :NAENVEVILISEVRKFEI 1bia 165 :GADKVRVKWPNDLYLQDR Number of specific fragments extracted= 9 number of extra gaps= 0 total=417 Number of alignments=69 # 1bia read from 1bia/merged-good-all-a2m # found chain 1bia in template set Warning: unaligning (T0337)S80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)S125 Warning: unaligning (T0337)K100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)S125 Warning: unaligning (T0337)D116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGI 1bia 2 :KDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0337 53 :IRKFTIIP 1bia 76 :LDGGSVAV T0337 62 :IDKLGYMYAIVLIKS 1bia 98 :IGELKSGDACIAEYQ T0337 78 :VP 1bia 113 :QA T0337 101 :GVGRYNIIVRLLLPK 1bia 126 :PFGANLYLSMFWRLE T0337 120 :AE 1bia 149 :LS T0337 123 :LISEFLQRI 1bia 156 :VMAEVLRKL T0337 133 :NAENVEVI 1bia 165 :GADKVRVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=425 Number of alignments=70 # 1bia read from 1bia/merged-good-all-a2m # found chain 1bia in template set T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGI 1bia 4 :NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0337 57 :TIIPDIDK 1bia 49 :DVFTVPGK T0337 74 :IKSKV 1bia 57 :GYSLP T0337 81 :DADKVIS 1bia 68 :NAKQILG T0337 101 :GVGRYNIIVRLLL 1bia 75 :QLDGGSVAVLPVI T0337 115 :KDI 1bia 88 :DST T0337 121 :ENLIS 1bia 91 :NQYLL T0337 129 :QRIKNAENVEVILI 1bia 96 :DRIGELKSGDACIA Number of specific fragments extracted= 8 number of extra gaps= 0 total=433 Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lnwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lnwA expands to /projects/compbio/data/pdb/1lnw.pdb.gz 1lnwA: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 # T0337 read from 1lnwA/merged-good-all-a2m # 1lnwA read from 1lnwA/merged-good-all-a2m # adding 1lnwA to template set # found chain 1lnwA in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1lnwA 33 :LDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0337 73 :LIKS 1lnwA 94 :QLFL T0337 78 :VP 1lnwA 98 :TD T0337 80 :SDADKVISEISDIEYVKS 1lnwA 103 :AIHQHAEAIMSRVHDELF T0337 100 :K 1lnwA 121 :A T0337 114 :PKDIKDAENLIS 1lnwA 122 :PLTPVEQATLVH Number of specific fragments extracted= 6 number of extra gaps= 0 total=439 Number of alignments=72 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1lnwA 32 :RLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0337 76 :SKVPSD 1lnwA 85 :RNPSDQ T0337 82 :ADKVISEISDIEYVKSVEK 1lnwA 98 :TDEGLAIHQHAEAIMSRVH T0337 101 :GVG 1lnwA 120 :FAP T0337 115 :KDIKDAENLIS 1lnwA 123 :LTPVEQATLVH Number of specific fragments extracted= 5 number of extra gaps= 0 total=444 Number of alignments=73 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFT 1lnwA 32 :RLDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRER T0337 60 :PDIDKLGY 1lnwA 86 :NPSDQRSF T0337 74 :IKSKV 1lnwA 94 :QLFLT T0337 81 :DADKVISEISDIEYVKS 1lnwA 104 :IHQHAEAIMSRVHDELF T0337 114 :PKDIKDAENLISE 1lnwA 122 :PLTPVEQATLVHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=449 Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q1hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q1hA expands to /projects/compbio/data/pdb/1q1h.pdb.gz 1q1hA:# T0337 read from 1q1hA/merged-good-all-a2m # 1q1hA read from 1q1hA/merged-good-all-a2m # adding 1q1hA to template set # found chain 1q1hA in template set T0337 12 :MQLVKILSENSRL 1q1hA 21 :IDVLRILLDKGTE T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1q1hA 35 :TDEEIANQLNIKVNDVRKKLNLLEEQGFVS Number of specific fragments extracted= 2 number of extra gaps= 0 total=451 Number of alignments=75 # 1q1hA read from 1q1hA/merged-good-all-a2m # found chain 1q1hA in template set T0337 12 :MQLVKILSENSRL 1q1hA 21 :IDVLRILLDKGTE T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1q1hA 35 :TDEEIANQLNIKVNDVRKKLNLLEEQGFVS Number of specific fragments extracted= 2 number of extra gaps= 0 total=453 Number of alignments=76 # 1q1hA read from 1q1hA/merged-good-all-a2m # found chain 1q1hA in template set T0337 12 :MQLVKILSENSRL 1q1hA 21 :IDVLRILLDKGTE T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1q1hA 35 :TDEEIANQLNIKVNDVRKKLNLLEEQGFVS T0337 56 :FT 1q1hA 65 :YR Number of specific fragments extracted= 3 number of extra gaps= 0 total=456 Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0337 read from 1jgsA/merged-good-all-a2m # 1jgsA read from 1jgsA/merged-good-all-a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0337 4 :MRKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1jgsA 35 :PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0337 59 :IPDIDKLGYM 1jgsA 87 :LPNPNDKRGV T0337 73 :LIKS 1jgsA 97 :LVKL T0337 78 :VP 1jgsA 101 :TT T0337 80 :SDADKVISEISDI 1jgsA 106 :AICEQCHQLVGQD T0337 128 :L 1jgsA 119 :L Number of specific fragments extracted= 6 number of extra gaps= 0 total=462 Number of alignments=78 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1jgsA 36 :LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0337 59 :IPDIDKLGY 1jgsA 87 :LPNPNDKRG T0337 73 :LIKS 1jgsA 97 :LVKL T0337 82 :ADKVISEISDI 1jgsA 101 :TTGGAAICEQC T0337 121 :ENLISEFLQR 1jgsA 112 :HQLVGQDLHQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=467 Number of alignments=79 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1jgsA 36 :LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0337 59 :IPDIDKLGYM 1jgsA 87 :LPNPNDKRGV T0337 70 :A 1jgsA 97 :L T0337 75 :KSKV 1jgsA 98 :VKLT T0337 83 :DKVISEISD 1jgsA 102 :TGGAAICEQ T0337 120 :AENLISEFLQR 1jgsA 111 :CHQLVGQDLHQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=473 Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0337 read from 1ub9A/merged-good-all-a2m # 1ub9A read from 1ub9A/merged-good-all-a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPD 1ub9A 15 :NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIAD T0337 73 :LIKS 1ub9A 73 :VVEI T0337 82 :ADKVISEISDI 1ub9A 77 :TDFGMEEAKRF Number of specific fragments extracted= 3 number of extra gaps= 0 total=476 Number of alignments=81 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1ub9A 15 :NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKT T0337 57 :T 1ub9A 63 :Y T0337 75 :KSKVPSD 1ub9A 64 :KVIADRP T0337 110 :RLLLP 1ub9A 73 :VVEIT T0337 118 :KDAENLISEFLQRI 1ub9A 78 :DFGMEEAKRFLSSL Number of specific fragments extracted= 5 number of extra gaps= 0 total=481 Number of alignments=82 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPD 1ub9A 15 :NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIAD T0337 66 :GYMY 1ub9A 69 :RPRT T0337 72 :VLIK 1ub9A 73 :VVEI T0337 82 :ADKVISEISDI 1ub9A 77 :TDFGMEEAKRF T0337 121 :ENLISEFLQ 1ub9A 88 :LSSLKAVID Number of specific fragments extracted= 5 number of extra gaps= 0 total=486 Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA: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 # T0337 read from 2g7uA/merged-good-all-a2m # 2g7uA read from 2g7uA/merged-good-all-a2m # adding 2g7uA to template set # found chain 2g7uA in template set T0337 16 :KILSENSRL 2g7uA 16 :FAVLLAFDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRK 2g7uA 30 :TLAELATEAGLSRPAVRRILLTLQKLGYVAG T0337 66 :GY 2g7uA 62 :GG T0337 73 :LIKS 2g7uA 64 :RWSL T0337 78 :VPSD 2g7uA 68 :TPRV T0337 82 :ADKVISEIS 2g7uA 81 :SHALIEAAM T0337 93 :EYVKSVEKGVGRYNIIVRLL 2g7uA 90 :PRLLEVAEKTQESASLGVLD T0337 136 :NVEVILISEVR 2g7uA 110 :GADVVYAARVP Number of specific fragments extracted= 8 number of extra gaps= 0 total=494 Number of alignments=84 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0337 16 :KILSENSRL 2g7uA 16 :FAVLLAFDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRK 2g7uA 30 :TLAELATEAGLSRPAVRRILLTLQKLGYVAG T0337 57 :TIIPDIDKL 2g7uA 64 :RWSLTPRVL T0337 78 :VPSDADKVISEIS 2g7uA 77 :HYSESHALIEAAM T0337 93 :EYVKSVEKGVGRYNII 2g7uA 90 :PRLLEVAEKTQESASL T0337 111 :LLLP 2g7uA 106 :GVLD T0337 136 :NVEVILISEVRK 2g7uA 110 :GADVVYAARVPV Number of specific fragments extracted= 7 number of extra gaps= 0 total=501 Number of alignments=85 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0337 16 :KILSENSRL 2g7uA 16 :FAVLLAFDA T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRK 2g7uA 30 :TLAELATEAGLSRPAVRRILLTLQKLGYVAG T0337 57 :T 2g7uA 64 :R T0337 75 :KSKVPS 2g7uA 65 :WSLTPR T0337 81 :DADKVISEIS 2g7uA 80 :ESHALIEAAM T0337 93 :EYVKSVEKGVGRYNIIVRLLL 2g7uA 90 :PRLLEVAEKTQESASLGVLDG Number of specific fragments extracted= 6 number of extra gaps= 0 total=507 Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cfxA expands to /projects/compbio/data/pdb/2cfx.pdb.gz 2cfxA:# T0337 read from 2cfxA/merged-good-all-a2m # 2cfxA read from 2cfxA/merged-good-all-a2m # adding 2cfxA to template set # found chain 2cfxA in template set Warning: unaligning (T0337)R5 because first residue in template chain is (2cfxA)M1 Warning: unaligning (T0337)R37 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0337)Q38 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0337)T57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0337)I58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 Warning: unaligning (T0337)L111 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0337)L112 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 Warning: unaligning (T0337)E135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)Q127 Warning: unaligning (T0337)N136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)Q127 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTT 2cfxA 2 :KLDQIDLNIIEELKKDSRLSMRELGRKIKLS T0337 39 :RIARRIDKLKKLGIIRKF 2cfxA 35 :SVTERVRQLESFGIIKQY T0337 59 :IPDIDKLGY 2cfxA 55 :EVDQKKLGL T0337 68 :MYAIVLIKS 2cfxA 65 :VSCIVEATV T0337 78 :VPSDADKVISEISDIEYVKSVEKGVGRYNIIVR 2cfxA 74 :KNADYERFKSYIQTLPNIEFCYRIAGAACYMLK T0337 113 :L 2cfxA 109 :A T0337 115 :KDIKDAENLISE 2cfxA 110 :ESLEAVEDFINK T0337 131 :IKNA 2cfxA 122 :TSPY T0337 137 :VEVILISEVR 2cfxA 128 :TVTHVIFSEI Number of specific fragments extracted= 9 number of extra gaps= 4 total=516 Number of alignments=87 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0337)R5 because first residue in template chain is (2cfxA)M1 Warning: unaligning (T0337)R37 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0337)Q38 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0337)T57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0337)I58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 Warning: unaligning (T0337)L111 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0337)L112 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 Warning: unaligning (T0337)E135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)Q127 Warning: unaligning (T0337)N136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)Q127 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTT 2cfxA 2 :KLDQIDLNIIEELKKDSRLSMRELGRKIKLS T0337 39 :RIARRIDKLKKLGIIRKF 2cfxA 35 :SVTERVRQLESFGIIKQY T0337 59 :IPDIDKLGY 2cfxA 55 :EVDQKKLGL T0337 68 :MYAIVLIKS 2cfxA 65 :VSCIVEATV T0337 78 :VPSDADKVISEISDIEYVKSVEKGVGRYNIIVR 2cfxA 74 :KNADYERFKSYIQTLPNIEFCYRIAGAACYMLK T0337 113 :L 2cfxA 109 :A T0337 115 :KDIKDAENLI 2cfxA 110 :ESLEAVEDFI T0337 129 :QRIKNA 2cfxA 120 :NKTSPY T0337 137 :VEVILISEVRKF 2cfxA 128 :TVTHVIFSEIDT Number of specific fragments extracted= 9 number of extra gaps= 4 total=525 Number of alignments=88 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0337)R37 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0337)Q38 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0337)T57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0337)I58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 Warning: unaligning (T0337)L111 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0337)L112 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 Warning: unaligning (T0337)E135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)Q127 Warning: unaligning (T0337)N136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)Q127 T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTT 2cfxA 2 :KLDQIDLNIIEELKKDSRLSMRELGRKIKLS T0337 39 :RIARRIDKLKKLGIIRKF 2cfxA 35 :SVTERVRQLESFGIIKQY T0337 59 :IPDIDKLGYMYAIVLIKSKVPSDADKVISEISDIEYVKSVEKGVGRYNIIVR 2cfxA 55 :EVDQKKLGLPVSCIVEATVKNADYERFKSYIQTLPNIEFCYRIAGAACYMLK T0337 113 :L 2cfxA 109 :A T0337 115 :KDIKDAENLI 2cfxA 110 :ESLEAVEDFI T0337 129 :QRIKNA 2cfxA 120 :NKTSPY T0337 137 :VEVILISEVRK 2cfxA 128 :TVTHVIFSEID Number of specific fragments extracted= 7 number of extra gaps= 4 total=532 Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ddnA expands to /projects/compbio/data/pdb/1ddn.pdb.gz 1ddnA:# T0337 read from 1ddnA/merged-good-all-a2m # 1ddnA read from 1ddnA/merged-good-all-a2m # adding 1ddnA to template set # found chain 1ddnA in template set T0337 14 :LVKILSENSRL 1ddnA 14 :TIYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1ddnA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 76 :S 1ddnA 56 :V T0337 78 :VPSD 1ddnA 57 :ASDR T0337 82 :ADKVISEIS 1ddnA 72 :ATAVMRKHR T0337 95 :VKSVEKGVG 1ddnA 83 :ERLLTDIIG T0337 115 :KDIKDAENLISEFL 1ddnA 92 :LDINKVHDEADRWE Number of specific fragments extracted= 7 number of extra gaps= 0 total=539 Number of alignments=90 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set T0337 8 :DRVDMQL 1ddnA 6 :DTTEMYL T0337 15 :VKILSENSRL 1ddnA 15 :IYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1ddnA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 76 :S 1ddnA 56 :V T0337 78 :VPSD 1ddnA 57 :ASDR T0337 82 :ADKVISEIS 1ddnA 72 :ATAVMRKHR T0337 94 :YVKSVEKGVG 1ddnA 82 :AERLLTDIIG T0337 115 :KDIKDAENLISEFL 1ddnA 92 :LDINKVHDEADRWE Number of specific fragments extracted= 8 number of extra gaps= 0 total=547 Number of alignments=91 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set T0337 15 :VKILSENSRL 1ddnA 15 :IYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1ddnA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 60 :PDI 1ddnA 56 :VAS T0337 66 :GYMYA 1ddnA 59 :DRSLQ T0337 77 :KV 1ddnA 64 :MT T0337 79 :PSDADKVISEIS 1ddnA 69 :RTLATAVMRKHR T0337 99 :EK 1ddnA 86 :LT T0337 102 :V 1ddnA 88 :D T0337 114 :PKDIKDAENLISEFLQRI 1ddnA 91 :GLDINKVHDEADRWEHVM Number of specific fragments extracted= 9 number of extra gaps= 0 total=556 Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r1uA expands to /projects/compbio/data/pdb/1r1u.pdb.gz 1r1uA:# T0337 read from 1r1uA/merged-good-all-a2m # 1r1uA read from 1r1uA/merged-good-all-a2m # adding 1r1uA to template set # found chain 1r1uA in template set T0337 8 :DRVDMQLVKILSE 1r1uA 25 :DYNRIRIMELLSV T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0337 66 :GY 1r1uA 75 :GQ T0337 73 :LIKSKVPSDADKVISEISD 1r1uA 79 :IYSLDDIHVATMLKQAIHH Number of specific fragments extracted= 4 number of extra gaps= 0 total=560 Number of alignments=93 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0337 8 :DRVDMQLVKILSE 1r1uA 25 :DYNRIRIMELLSV T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0337 73 :LIKSKVPSDADKVISEISD 1r1uA 79 :IYSLDDIHVATMLKQAIHH Number of specific fragments extracted= 3 number of extra gaps= 0 total=563 Number of alignments=94 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0337 8 :DRVDMQLVKILSE 1r1uA 25 :DYNRIRIMELLSV T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0337 76 :SKVPS 1r1uA 72 :KRQGQ T0337 110 :RLLL 1r1uA 79 :IYSL T0337 116 :DIKDAENLISEFLQR 1r1uA 83 :DDIHVATMLKQAIHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=568 Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ft9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ft9A expands to /projects/compbio/data/pdb/1ft9.pdb.gz 1ft9A:# T0337 read from 1ft9A/merged-good-all-a2m # 1ft9A read from 1ft9A/merged-good-all-a2m # adding 1ft9A to template set # found chain 1ft9A in template set T0337 8 :DRVDMQLVKILSENSRL 1ft9A 133 :HDIKQRIAGFFIDHANT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1ft9A 165 :TVEEIANLIGSSRQTTSTALNSLIKEGYIS T0337 76 :SKVPSD 1ft9A 195 :RQGRGH T0337 111 :LLL 1ft9A 201 :YTI T0337 115 :KDIKDAEN 1ft9A 204 :PNLVRLKA Number of specific fragments extracted= 5 number of extra gaps= 0 total=573 Number of alignments=96 # 1ft9A read from 1ft9A/merged-good-all-a2m # found chain 1ft9A in template set T0337 9 :RVDMQLVKILSENSRL 1ft9A 134 :DIKQRIAGFFIDHANT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1ft9A 165 :TVEEIANLIGSSRQTTSTALNSLIKEGYIS T0337 76 :SKVPSD 1ft9A 195 :RQGRGH T0337 111 :LLLP 1ft9A 201 :YTIP T0337 116 :DIKDAEN 1ft9A 205 :NLVRLKA Number of specific fragments extracted= 5 number of extra gaps= 0 total=578 Number of alignments=97 # 1ft9A read from 1ft9A/merged-good-all-a2m # found chain 1ft9A in template set T0337 8 :DRVDMQLVKILSENSRL 1ft9A 133 :HDIKQRIAGFFIDHANT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKF 1ft9A 165 :TVEEIANLIGSSRQTTSTALNSLIKEGYISRQ T0337 79 :PS 1ft9A 197 :GR T0337 111 :LLL 1ft9A 201 :YTI T0337 115 :KDIKDAEN 1ft9A 204 :PNLVRLKA Number of specific fragments extracted= 5 number of extra gaps= 0 total=583 Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u2wA expands to /projects/compbio/data/pdb/1u2w.pdb.gz 1u2wA:# T0337 read from 1u2wA/merged-good-all-a2m # 1u2wA read from 1u2wA/merged-good-all-a2m # adding 1u2wA to template set # found chain 1u2wA in template set Warning: unaligning (T0337)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1u2wA 41 :DENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVN T0337 60 :P 1u2wA 88 :F T0337 73 :LIKSKVPSDADKVISEISD 1u2wA 96 :LYSLGDEHIRQIMMIALAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=586 Number of alignments=99 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0337)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1u2wA 41 :DENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVN T0337 60 :P 1u2wA 88 :F T0337 73 :LIKSKVPSDADKVISEIS 1u2wA 96 :LYSLGDEHIRQIMMIALA Number of specific fragments extracted= 3 number of extra gaps= 0 total=589 Number of alignments=100 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0337)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0337)G66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1u2wA 41 :DENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVN T0337 56 :F 1u2wA 88 :F T0337 67 :Y 1u2wA 95 :A T0337 110 :RLLL 1u2wA 96 :LYSL T0337 116 :DIKDAENLISEFLQR 1u2wA 100 :GDEHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=594 Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lvaA expands to /projects/compbio/data/pdb/1lva.pdb.gz 1lvaA: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 # T0337 read from 1lvaA/merged-good-all-a2m # 1lvaA read from 1lvaA/merged-good-all-a2m # adding 1lvaA to template set # found chain 1lvaA in template set T0337 12 :MQLVKILSENSRL 1lvaA 381 :KILAQIIQEHREG T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 1lvaA 395 :DWQEAATRASLSLEETRKLLQSMAAAGQVTLLRV T0337 65 :LGYMYAI 1lvaA 429 :ENDLYAI T0337 78 :VPSDADKVISEISDI 1lvaA 436 :STERYQAWWQAVTRA T0337 93 :EYVKSVEKGVG 1lvaA 452 :EEFHSRYPLRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=599 Number of alignments=102 # 1lvaA read from 1lvaA/merged-good-all-a2m # found chain 1lvaA in template set T0337 12 :MQLVKILSENSRL 1lvaA 381 :KILAQIIQEHREG T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 1lvaA 395 :DWQEAATRASLSLEETRKLLQSMAAAGQVTLLRV T0337 65 :LGYMYAI 1lvaA 429 :ENDLYAI T0337 78 :VPSDADKVISEISDI 1lvaA 436 :STERYQAWWQAVTRA T0337 93 :EYVKSVEKGVGR 1lvaA 452 :EEFHSRYPLRPG T0337 107 :I 1lvaA 464 :L T0337 116 :DIKDAEN 1lvaA 465 :AREELRS Number of specific fragments extracted= 7 number of extra gaps= 0 total=606 Number of alignments=103 # 1lvaA read from 1lvaA/merged-good-all-a2m # found chain 1lvaA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=606 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s3jA expands to /projects/compbio/data/pdb/1s3j.pdb.gz 1s3jA: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 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 Skipped atom 993, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.350 <= existing 0.530 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.400 <= existing 0.600 in 1s3jA # T0337 read from 1s3jA/merged-good-all-a2m # 1s3jA read from 1s3jA/merged-good-all-a2m # adding 1s3jA to template set # found chain 1s3jA in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDK 1s3jA 34 :GVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRV T0337 72 :VLIKS 1s3jA 93 :IDLSL T0337 78 :VPSD 1s3jA 98 :TDEG T0337 82 :ADKVISEISDIE 1s3jA 105 :FEEVLAGRKAIM T0337 97 :SVEKGV 1s3jA 117 :ARYLSF T0337 115 :KDIKDAENL 1s3jA 123 :LTEEEMLQA Number of specific fragments extracted= 6 number of extra gaps= 0 total=612 Number of alignments=104 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDK 1s3jA 34 :GVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRV T0337 73 :LIKS 1s3jA 94 :DLSL T0337 78 :VPS 1s3jA 98 :TDE T0337 82 :ADKVISEISDI 1s3jA 105 :FEEVLAGRKAI T0337 96 :KSVEKGV 1s3jA 116 :MARYLSF T0337 115 :KDIKDAENLI 1s3jA 123 :LTEEEMLQAA Number of specific fragments extracted= 6 number of extra gaps= 0 total=618 Number of alignments=105 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKL 1s3jA 34 :GVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVI T0337 74 :IKSKVPS 1s3jA 94 :DLSLTDE T0337 81 :DADKVISEISDIEYVK 1s3jA 104 :KFEEVLAGRKAIMARY T0337 100 :KGV 1s3jA 120 :LSF T0337 115 :KDIKDAENLI 1s3jA 123 :LTEEEMLQAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=623 Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1je8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1je8A expands to /projects/compbio/data/pdb/1je8.pdb.gz 1je8A: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 # T0337 read from 1je8A/merged-good-all-a2m # 1je8A read from 1je8A/merged-good-all-a2m # adding 1je8A to template set # found chain 1je8A in template set T0337 3 :CMRKLDRVDMQLVKILSE 1je8A 152 :DVNQLTPRERDILKLIAQ T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKL 1je8A 170 :GLPNKMIARRLDITESTVKVHVKHMLKK T0337 65 :LGY 1je8A 198 :MKL T0337 80 :SDADKVISEISD 1je8A 201 :KSRVEAAVWVHQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=627 Number of alignments=107 # 1je8A read from 1je8A/merged-good-all-a2m # found chain 1je8A in template set T0337 3 :CMRKLDRVDMQLVKILSE 1je8A 152 :DVNQLTPRERDILKLIAQ T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKL 1je8A 170 :GLPNKMIARRLDITESTVKVHVKHMLKK T0337 65 :LGY 1je8A 198 :MKL T0337 80 :SDADKVISEISD 1je8A 201 :KSRVEAAVWVHQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=631 Number of alignments=108 # 1je8A read from 1je8A/merged-good-all-a2m # found chain 1je8A in template set Warning: unaligning (T0337)D2 because first residue in template chain is (1je8A)R151 T0337 3 :CMRKLDRVDMQLVKILSE 1je8A 152 :DVNQLTPRERDILKLIAQ T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKL 1je8A 170 :GLPNKMIARRLDITESTVKVHVKHMLKK T0337 65 :LGY 1je8A 198 :MKL T0337 80 :SDADKVISEISD 1je8A 201 :KSRVEAAVWVHQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=635 Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1y0uA/merged-good-all-a2m # 1y0uA read from 1y0uA/merged-good-all-a2m # found chain 1y0uA in training set T0337 8 :DRVDMQLVKILSE 1y0uA 28 :NPVRRKILRMLDK T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1y0uA 41 :GRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIER Number of specific fragments extracted= 2 number of extra gaps= 0 total=637 Number of alignments=110 # 1y0uA read from 1y0uA/merged-good-all-a2m # found chain 1y0uA in training set T0337 8 :DRVDMQLVKILSE 1y0uA 28 :NPVRRKILRMLDK T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1y0uA 41 :GRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIER Number of specific fragments extracted= 2 number of extra gaps= 0 total=639 Number of alignments=111 # 1y0uA read from 1y0uA/merged-good-all-a2m # found chain 1y0uA in training set T0337 7 :LDRVDMQLVKILSE 1y0uA 27 :TNPVRRKILRMLDK T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1y0uA 41 :GRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIER Number of specific fragments extracted= 2 number of extra gaps= 0 total=641 Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1on2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1on2A/merged-good-all-a2m # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0337 10 :VDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1on2A 9 :YIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY T0337 66 :GY 1on2A 56 :KY T0337 73 :LIKS 1on2A 59 :GLVL T0337 78 :VP 1on2A 63 :TS T0337 80 :SDADKVISE 1on2A 68 :KIGKRLVYR T0337 92 :IEYVKSVEKGVG 1on2A 77 :HELLEQFLRIIG T0337 114 :PKDIKDAEN 1on2A 104 :HLSWNSIDR T0337 124 :ISEFLQR 1on2A 113 :IGDLVQY Number of specific fragments extracted= 8 number of extra gaps= 0 total=649 Number of alignments=113 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0337 10 :VDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1on2A 9 :YIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY T0337 73 :LIKS 1on2A 59 :GLVL T0337 78 :V 1on2A 63 :T T0337 83 :DKVISEISD 1on2A 64 :SKGKKIGKR T0337 92 :IEYVKSVEKGVG 1on2A 77 :HELLEQFLRIIG T0337 115 :KDIKDAENLI 1on2A 105 :LSWNSIDRIG T0337 126 :EFLQRIKN 1on2A 115 :DLVQYFEE Number of specific fragments extracted= 7 number of extra gaps= 0 total=656 Number of alignments=114 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0337 13 :QLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1on2A 12 :QIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY T0337 62 :IDKLGYMYA 1on2A 55 :EKYRGLVLT T0337 83 :DKVISEISDI 1on2A 64 :SKGKKIGKRL T0337 118 :KDAENLISEFLQ 1on2A 74 :VYRHELLEQFLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=660 Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1sfxA/merged-good-all-a2m # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1sfxA 15 :LSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0337 78 :VPSD 1sfxA 69 :EKGW T0337 110 :RLLL 1sfxA 76 :IYSA T0337 115 :KDIKDAENLISEFLQ 1sfxA 80 :EKPEKVLKEFKSSIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=664 Number of alignments=116 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0337 6 :KLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 1sfxA 16 :SFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0337 76 :S 1sfxA 68 :V T0337 78 :VPSD 1sfxA 69 :EKGW T0337 110 :RLLLP 1sfxA 76 :IYSAE T0337 116 :DIKDAENLISEFLQR 1sfxA 81 :KPEKVLKEFKSSILG Number of specific fragments extracted= 5 number of extra gaps= 0 total=669 Number of alignments=117 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0337 5 :RKLDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKF 1sfxA 15 :LSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE T0337 59 :IPDIDKLGYMYA 1sfxA 67 :IVEKGWVGYIYS T0337 76 :SKVPSDADKVIS 1sfxA 79 :AEKPEKVLKEFK T0337 119 :DAENLISEFLQ 1sfxA 91 :SSILGEIERIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=673 Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ulyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ulyA expands to /projects/compbio/data/pdb/1uly.pdb.gz 1ulyA: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 # T0337 read from 1ulyA/merged-good-all-a2m # 1ulyA read from 1ulyA/merged-good-all-a2m # adding 1ulyA to template set # found chain 1ulyA in template set T0337 7 :LDRVDMQLVKILS 1ulyA 18 :LEDTRRKILKLLR T0337 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPD 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMK T0337 65 :LGYMYAIVLIKS 1ulyA 72 :GNLVEKYYGRTA T0337 77 :KVPSDADKVISEIS 1ulyA 93 :GDEELRYIARSRLK T0337 91 :DIEYVK 1ulyA 108 :KIDIFK T0337 100 :KGVGR 1ulyA 114 :RLGYQ T0337 115 :KDIKDAENLISEFLQ 1ulyA 119 :FEENELLNIMDRMSQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=680 Number of alignments=119 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0337 7 :LDRVDMQLVKILSE 1ulyA 18 :LEDTRRKILKLLRN T0337 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPD 1ulyA 32 :KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMK T0337 65 :LGYMYAIVLIKS 1ulyA 72 :GNLVEKYYGRTA T0337 79 :PSD 1ulyA 92 :LGD T0337 83 :DKVISEISD 1ulyA 95 :EELRYIARS T0337 92 :IEYVKSVEKGVG 1ulyA 105 :LKTKIDIFKRLG T0337 114 :P 1ulyA 119 :F T0337 116 :DIKDAENLISEF 1ulyA 120 :EENELLNIMDRM T0337 128 :LQRIKNAEN 1ulyA 147 :EEKEDALKD Number of specific fragments extracted= 9 number of extra gaps= 0 total=689 Number of alignments=120 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0337 7 :LDRVDMQLVKILS 1ulyA 18 :LEDTRRKILKLLR T0337 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGYMYA 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYG T0337 71 :IVLIKSKV 1ulyA 86 :FYINLYLG T0337 79 :PS 1ulyA 95 :EE T0337 81 :DADKVISEISDIEY 1ulyA 104 :RLKTKIDIFKRLGY T0337 114 :PKDIKDAENLISEFL 1ulyA 118 :QFEENELLNIMDRMS Number of specific fragments extracted= 6 number of extra gaps= 0 total=695 Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p4xA expands to /projects/compbio/data/pdb/1p4x.pdb.gz 1p4xA:# T0337 read from 1p4xA/merged-good-all-a2m # 1p4xA read from 1p4xA/merged-good-all-a2m # adding 1p4xA to template set # found chain 1p4xA in template set T0337 6 :KLDRVDMQLVKILSENSRL 1p4xA 155 :TLSFVEFTILAIITSQNKN T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDK 1p4xA 176 :LLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERK T0337 72 :VLIKS 1p4xA 216 :ILIHM T0337 78 :VPSDADKVISEISDI 1p4xA 221 :DDAQQDHAEQLLAQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=699 Number of alignments=122 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0337 6 :KLDRVDMQLVKILSENSRL 1p4xA 155 :TLSFVEFTILAIITSQNKN T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGII 1p4xA 176 :LLKDLIETIHHKYPQTVRALNNLKKQGYL T0337 57 :TIIPDIDKLGY 1p4xA 205 :IKERSTEDERK T0337 73 :LIKS 1p4xA 217 :LIHM T0337 78 :VPSDADKVISEISDI 1p4xA 221 :DDAQQDHAEQLLAQV Number of specific fragments extracted= 5 number of extra gaps= 0 total=704 Number of alignments=123 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0337 7 :LDRVDMQLVKILSENSRL 1p4xA 156 :LSFVEFTILAIITSQNKN T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIRKFT 1p4xA 176 :LLKDLIETIHHKYPQTVRALNNLKKQGYLIKER T0337 61 :DIDKLGYM 1p4xA 209 :STEDERKI T0337 74 :IKSKVPSDADKVISEISDI 1p4xA 217 :LIHMDDAQQDHAEQLLAQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=708 Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xd7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xd7A expands to /projects/compbio/data/pdb/1xd7.pdb.gz 1xd7A:# T0337 read from 1xd7A/merged-good-all-a2m # 1xd7A read from 1xd7A/merged-good-all-a2m # adding 1xd7A to template set # found chain 1xd7A in template set Warning: unaligning (T0337)D91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xd7A)N94 Warning: unaligning (T0337)G103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xd7A)N94 T0337 9 :RVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1xd7A 9 :AVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILT T0337 75 :KS 1xd7A 63 :SL T0337 77 :KVPSD 1xd7A 66 :KDPAD T0337 82 :ADKVISEIS 1xd7A 73 :LLEVYRAVQ T0337 104 :R 1xd7A 95 :P T0337 115 :KDIKDAEN 1xd7A 96 :KCPVGKKI Number of specific fragments extracted= 6 number of extra gaps= 0 total=714 Number of alignments=125 # 1xd7A read from 1xd7A/merged-good-all-a2m # found chain 1xd7A in template set Warning: unaligning (T0337)D91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xd7A)N94 Warning: unaligning (T0337)G103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xd7A)N94 T0337 9 :RVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1xd7A 9 :AVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILT T0337 55 :KFTIIPDIDKL 1xd7A 61 :GASLKKDPADI T0337 82 :ADKVISEIS 1xd7A 73 :LLEVYRAVQ T0337 104 :R 1xd7A 95 :P T0337 115 :KDIKD 1xd7A 96 :KCPVG T0337 120 :AENLISEFLQR 1xd7A 103 :IQNALDETFES Number of specific fragments extracted= 6 number of extra gaps= 0 total=720 Number of alignments=126 # 1xd7A read from 1xd7A/merged-good-all-a2m # found chain 1xd7A in template set Warning: unaligning (T0337)D91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xd7A)N94 Warning: unaligning (T0337)G103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xd7A)N94 T0337 9 :RVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIR 1xd7A 9 :AVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILT T0337 60 :PDIDKLGYM 1xd7A 55 :SRAGVPGAS T0337 75 :KSKVPS 1xd7A 64 :LKKDPA T0337 81 :DADKVISEIS 1xd7A 72 :SLLEVYRAVQ T0337 104 :RYN 1xd7A 95 :PKC T0337 115 :KDIKDAENLISEF 1xd7A 98 :PVGKKIQNALDET Number of specific fragments extracted= 6 number of extra gaps= 0 total=726 Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0337 read from 1hw1A/merged-good-all-a2m # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0337 10 :VDMQLVKILSEN 1hw1A 12 :AEEYIIESIWNN T0337 22 :SRL 1hw1A 28 :GTI T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1hw1A 33 :AERELSELIGVTRTTLREVLQRLARDGWLT T0337 55 :KFTII 1hw1A 68 :PTKVN T0337 60 :PDIDKL 1hw1A 78 :SGLNIL T0337 78 :VPSD 1hw1A 90 :DHES T0337 82 :ADKVISEISDI 1hw1A 98 :IDNLLSVRTNI T0337 93 :EYVKSVEKGVGRY 1hw1A 122 :DKAQEVLATANEV T0337 114 :PKDIKDAENLISEFLQ 1hw1A 135 :ADHADAFAELDYNIFR Number of specific fragments extracted= 9 number of extra gaps= 0 total=735 Number of alignments=128 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0337 11 :DMQLVKILSEN 1hw1A 13 :EEYIIESIWNN T0337 23 :RL 1hw1A 24 :RF T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1hw1A 33 :AERELSELIGVTRTTLREVLQRLARDGWLT T0337 55 :KFTII 1hw1A 68 :PTKVN T0337 60 :PDIDKL 1hw1A 78 :SGLNIL T0337 78 :VPSD 1hw1A 90 :DHES T0337 82 :ADKVISEISDI 1hw1A 98 :IDNLLSVRTNI T0337 93 :EYVKSVEKGVGRY 1hw1A 122 :DKAQEVLATANEV T0337 114 :PKDIKDAENLISEFLQRI 1hw1A 135 :ADHADAFAELDYNIFRGL Number of specific fragments extracted= 9 number of extra gaps= 0 total=744 Number of alignments=129 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0337 11 :DMQLVKILSENSRL 1hw1A 13 :EEYIIESIWNNRFP T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1hw1A 33 :AERELSELIGVTRTTLREVLQRLARDGWLT T0337 60 :PDI 1hw1A 63 :IQH T0337 66 :GYMYA 1hw1A 66 :GKPTK T0337 77 :KV 1hw1A 71 :VN T0337 79 :PSDADKVISEISDI 1hw1A 95 :PQLIDNLLSVRTNI T0337 93 :EYVKSVEKGVGRY 1hw1A 122 :DKAQEVLATANEV T0337 114 :PKDIKDAENLISEFLQ 1hw1A 135 :ADHADAFAELDYNIFR Number of specific fragments extracted= 8 number of extra gaps= 0 total=752 Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5tA expands to /projects/compbio/data/pdb/1f5t.pdb.gz 1f5tA:# T0337 read from 1f5tA/merged-good-all-a2m # 1f5tA read from 1f5tA/merged-good-all-a2m # adding 1f5tA to template set # found chain 1f5tA in template set T0337 14 :LVKILSENSRL 1f5tA 1014 :TIYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1f5tA 1026 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 76 :S 1f5tA 1056 :V T0337 78 :VPSD 1f5tA 1057 :ASDR T0337 82 :ADKVISEIS 1f5tA 1072 :ATAVMRKHR Number of specific fragments extracted= 5 number of extra gaps= 0 total=757 Number of alignments=131 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0337 15 :VKILSENSRL 1f5tA 1015 :IYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1f5tA 1026 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 76 :S 1f5tA 1056 :V T0337 78 :VPSD 1f5tA 1057 :ASDR T0337 114 :P 1f5tA 1065 :T T0337 118 :KDAENLISEFLQRI 1f5tA 1066 :PTGRTLATAVMRKH Number of specific fragments extracted= 6 number of extra gaps= 0 total=763 Number of alignments=132 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0337 15 :VKILSENSRL 1f5tA 1015 :IYELEEEGVT T0337 25 :TYRELADILNTTRQRIARRIDKLKKLGIIR 1f5tA 1026 :LRARIAERLEQSGPTVSQTVARMERDGLVV T0337 77 :KVPSD 1f5tA 1056 :VASDR T0337 111 :LLLPKDIKDAENLISEFLQ 1f5tA 1062 :LQMTPTGRTLATAVMRKHR Number of specific fragments extracted= 4 number of extra gaps= 0 total=767 Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0337 read from 2fbiA/merged-good-all-a2m # 2fbiA read from 2fbiA/merged-good-all-a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0337)G66 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0337)Y67 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTI 2fbiA 33 :TEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKA T0337 62 :I 2fbiA 84 :P T0337 68 :MYA 2fbiA 88 :RRV T0337 73 :LIKS 2fbiA 91 :YVNL T0337 82 :ADKVISEISDIE 2fbiA 95 :TEKGQQCFVSMS T0337 115 :KDIKDAENLISE 2fbiA 107 :GDMEKNYQRIQE Number of specific fragments extracted= 6 number of extra gaps= 2 total=773 Number of alignments=134 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0337)D63 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0337)K64 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK 2fbiA 33 :TEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRR T0337 59 :IPDI 2fbiA 81 :WKAP T0337 65 :LGY 2fbiA 87 :QRR T0337 73 :LIKS 2fbiA 91 :YVNL T0337 82 :ADKVISEISDIEYVKSVEK 2fbiA 95 :TEKGQQCFVSMSGDMEKNY T0337 116 :DIKDAENLI 2fbiA 121 :GEEKLAQLL T0337 126 :EFLQRI 2fbiA 130 :ELLNEL Number of specific fragments extracted= 7 number of extra gaps= 2 total=780 Number of alignments=135 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0337)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0337)L7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0337)D63 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0337)K64 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0337 8 :DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFT 2fbiA 33 :TEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERDGIVRRWK T0337 61 :DI 2fbiA 83 :AP T0337 65 :LGYM 2fbiA 87 :QRRV T0337 74 :IKSKV 2fbiA 91 :YVNLT T0337 83 :DKVISEISDIE 2fbiA 96 :EKGQQCFVSMS T0337 115 :KDIKDAENLISEF 2fbiA 107 :GDMEKNYQRIQER Number of specific fragments extracted= 6 number of extra gaps= 2 total=786 Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zljA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zljA expands to /projects/compbio/data/pdb/1zlj.pdb.gz 1zljA: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 # T0337 read from 1zljA/merged-good-all-a2m # 1zljA read from 1zljA/merged-good-all-a2m # adding 1zljA to template set # found chain 1zljA in template set Warning: unaligning (T0337)D2 because first residue in template chain is (1zljA)D145 T0337 3 :CMRKLDRVDMQLVKILSE 1zljA 146 :PLSGLTDQERTLLGLLSE T0337 23 :RLTYRELADILNTTRQRIARRIDKLKK 1zljA 164 :GLTNKQIADRMFLAEKTVKNYVSRLLA T0337 64 :KLGY 1zljA 191 :KLGM T0337 80 :SDADKVISEISD 1zljA 195 :ERRTQAAVFATE Number of specific fragments extracted= 4 number of extra gaps= 0 total=790 Number of alignments=137 # 1zljA read from 1zljA/merged-good-all-a2m # found chain 1zljA in template set Warning: unaligning (T0337)D2 because first residue in template chain is (1zljA)D145 T0337 3 :CMRKLDRVDMQLVKILSE 1zljA 146 :PLSGLTDQERTLLGLLSE T0337 23 :RLTYRELADILNTTRQRIARRIDKLKKL 1zljA 164 :GLTNKQIADRMFLAEKTVKNYVSRLLAK T0337 65 :LGY 1zljA 192 :LGM T0337 80 :SDADKVISEISDI 1zljA 195 :ERRTQAAVFATEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=794 Number of alignments=138 # 1zljA read from 1zljA/merged-good-all-a2m # found chain 1zljA in template set Warning: unaligning (T0337)D2 because first residue in template chain is (1zljA)D145 T0337 3 :CMRKLDRVDMQLVKILSE 1zljA 146 :PLSGLTDQERTLLGLLSE T0337 23 :RLTYRELADILNTTRQRIARRIDKLKK 1zljA 164 :GLTNKQIADRMFLAEKTVKNYVSRLLA T0337 64 :KLGY 1zljA 191 :KLGM T0337 80 :SDADKVISEISDI 1zljA 195 :ERRTQAAVFATEL Number of specific fragments extracted= 4 number of extra gaps= 0 total=798 Number of alignments=139 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0337//projects/compbio/experiments/protein-predict/casp7/T0337/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0337//projects/compbio/experiments/protein-predict/casp7/T0337/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0337/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0337/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((T0337)A30.CB, (T0337)I40.CB) [> 2.8582 = 4.7636 < 6.1926] w=1.0000 to align # Constraint # added constraint: constraint((T0337)L29.CB, (T0337)I40.CB) [> 3.2086 = 5.3477 < 6.9520] w=1.0000 to align # Constraint # added constraint: constraint((T0337)Y26.CB, (T0337)I40.CB) [> 3.2917 = 5.4862 < 7.1321] w=1.0000 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)L29.CB) [> 3.7600 = 6.2667 < 8.1467] w=0.9655 to align # Constraint # added constraint: constraint((T0337)Y26.CB, (T0337)I44.CB) [> 4.0394 = 6.7323 < 8.7520] w=0.9302 to align # Constraint # added constraint: constraint((T0337)Y26.CB, (T0337)A41.CB) [> 3.5939 = 5.9898 < 7.7867] w=0.9301 to align # Constraint # added constraint: constraint((T0337)I17.CB, (T0337)L29.CB) [> 3.6155 = 6.0258 < 7.8335] w=0.8893 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)L47.CB) [> 4.1478 = 6.9131 < 8.9870] w=0.8857 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)L33.CB) [> 4.0984 = 6.8306 < 8.8798] w=0.8845 to align # Constraint # added constraint: constraint((T0337)I17.CB, (T0337)I32.CB) [> 3.7003 = 6.1672 < 8.0174] w=0.8808 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)L47.CB) [> 4.0605 = 6.7674 < 8.7977] w=0.8634 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)R43.CB) [> 3.3726 = 5.6210 < 7.3072] w=0.8627 to align # Constraint # added constraint: constraint((T0337)I44.CB, (T0337)I53.CB) [> 3.9068 = 6.5114 < 8.4648] w=0.8601 to align # Constraint # added constraint: constraint((T0337)D11.CB, (T0337)L47.CB) [> 3.6412 = 6.0686 < 7.8892] w=0.8264 to align # Constraint # added constraint: constraint((T0337)R27.CB, (T0337)R37.CB) [> 3.7192 = 6.1987 < 8.0584] w=0.8165 to align # Constraint # added constraint: constraint((T0337)Y26.CB, (T0337)R37.CB) [> 3.4330 = 5.7217 < 7.4383] w=0.8165 to align # Constraint # added constraint: constraint((T0337)D11.CB, (T0337)R43.CB) [> 3.4134 = 5.6891 < 7.3958] w=0.8108 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)I40.CB) [> 4.1795 = 6.9658 < 9.0556] w=0.7927 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I52.CB) [> 3.9830 = 6.6384 < 8.6299] w=0.7927 to align # Constraint # added constraint: constraint((T0337)V10.CB, (T0337)R43.CB) [> 3.5763 = 5.9605 < 7.7486] w=0.7917 to align # Constraint # added constraint: constraint((T0337)D11.CB, (T0337)K46.CB) [> 4.1301 = 6.8835 < 8.9485] w=0.7308 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I53.CB) [> 4.0808 = 6.8014 < 8.8418] w=0.7229 to align # Constraint # added constraint: constraint((T0337)I17.CB, (T0337)L33.CB) [> 4.0289 = 6.7149 < 8.7293] w=0.6918 to align # Constraint # added constraint: constraint((T0337)V10.CB, (T0337)L33.CB) [> 4.0037 = 6.6729 < 8.6747] w=0.6655 to align # Constraint # added constraint: constraint((T0337)A30.CB, (T0337)R39.CB) [> 4.3884 = 7.3141 < 9.5083] w=0.6580 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)L29.CB) [> 4.3814 = 7.3023 < 9.4930] w=0.6004 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I53.CB) [> 4.4303 = 7.3837 < 9.5989] w=0.5842 to align # Constraint # added constraint: constraint((T0337)V10.CB, (T0337)T35.CB) [> 4.0121 = 6.6868 < 8.6928] w=0.5615 to align # Constraint # added constraint: constraint((T0337)L29.CB, (T0337)I44.CB) [> 4.3892 = 7.3153 < 9.5099] w=0.5407 to align # Constraint # added constraint: constraint((T0337)D11.CB, (T0337)I52.CB) [> 4.5660 = 7.6100 < 9.8929] w=0.4338 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)V85.CB) [> 3.8625 = 6.4375 < 8.3688] w=0.4308 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)S76.CB) [> 3.7567 = 6.2611 < 8.1395] w=0.4222 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)K75.CB) [> 3.9381 = 6.5636 < 8.5326] w=0.4119 to align # Constraint # added constraint: constraint((T0337)R54.CB, (T0337)K75.CB) [> 3.5096 = 5.8493 < 7.6040] w=0.3730 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)K75.CB) [> 3.7884 = 6.3140 < 8.2082] w=0.3675 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)S76.CB) [> 3.3331 = 5.5551 < 7.2217] w=0.3607 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I86.CB) [> 3.7162 = 6.1937 < 8.0518] w=0.3451 to align # Constraint # added constraint: constraint((T0337)R54.CB, (T0337)S76.CB) [> 4.0149 = 6.6915 < 8.6989] w=0.3420 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)S76.CB) [> 4.2671 = 7.1118 < 9.2453] w=0.3209 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I74.CB) [> 3.6463 = 6.0771 < 7.9003] w=0.3209 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)I74.CB) [> 4.2249 = 7.0415 < 9.1539] w=0.3140 to align # Constraint # added constraint: constraint((T0337)Y26.CB, (T0337)I74.CB) [> 4.0933 = 6.8222 < 8.8688] w=0.3140 to align # Constraint # added constraint: constraint((T0337)R23.CB, (T0337)I74.CB) [> 3.7213 = 6.2022 < 8.0629] w=0.3133 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)I74.CB) [> 3.4457 = 5.7429 < 7.4657] w=0.3131 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)L73.CB) [> 3.5974 = 5.9957 < 7.7944] w=0.3053 to align # Constraint # added constraint: constraint((T0337)I44.CB, (T0337)I74.CB) [> 3.7706 = 6.2844 < 8.1697] w=0.2907 to align # Constraint # added constraint: constraint((T0337)R54.CB, (T0337)I74.CB) [> 4.3067 = 7.1778 < 9.3311] w=0.2819 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)S76.CB) [> 3.6657 = 6.1095 < 7.9423] w=0.2751 to align # Constraint # added constraint: constraint((T0337)K16.CB, (T0337)I89.CB) [> 4.2383 = 7.0639 < 9.1831] w=0.2722 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)Y67.CB) [> 3.7324 = 6.2207 < 8.0869] w=0.2551 to align # Constraint # added constraint: constraint((T0337)I44.CB, (T0337)K55.CB) [> 4.0882 = 6.8136 < 8.8577] w=0.2543 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)S76.CB) [> 4.0496 = 6.7494 < 8.7742] w=0.2520 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)A82.CB) [> 3.4711 = 5.7852 < 7.5207] w=0.2518 to align # Constraint # added constraint: constraint((T0337)I17.CB, (T0337)E28.CB) [> 4.3415 = 7.2358 < 9.4066] w=0.2407 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)V85.CB) [> 3.0723 = 5.1206 < 6.6567] w=0.2364 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)I74.CB) [> 3.6954 = 6.1590 < 8.0068] w=0.2323 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I89.CB) [> 3.3082 = 5.5137 < 7.1679] w=0.2230 to align # Constraint # added constraint: constraint((T0337)L47.CB, (T0337)V85.CB) [> 4.1953 = 6.9921 < 9.0897] w=0.2210 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)K77.CB) [> 3.9111 = 6.5185 < 8.4741] w=0.2205 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)K77.CB) [> 3.7336 = 6.2226 < 8.0894] w=0.2093 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I44.CB) [> 4.3957 = 7.3261 < 9.5239] w=0.2025 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)V85.CB) [> 3.1828 = 5.3046 < 6.8960] w=0.1943 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I89.CB) [> 3.2847 = 5.4745 < 7.1169] w=0.1866 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)L73.CB) [> 3.9047 = 6.5078 < 8.4601] w=0.1857 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)A82.CB) [> 3.3949 = 5.6582 < 7.3556] w=0.1822 to align # Constraint # added constraint: constraint((T0337)R54.CB, (T0337)K77.CB) [> 3.4495 = 5.7491 < 7.4738] w=0.1800 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)V78.CB) [> 3.8102 = 6.3503 < 8.2554] w=0.1798 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)K75.CB) [> 4.1307 = 6.8846 < 8.9500] w=0.1788 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)K84.CB) [> 3.9302 = 6.5502 < 8.5153] w=0.1741 to align # Constraint # added constraint: constraint((T0337)M12.CB, (T0337)V85.CB) [> 3.8772 = 6.4619 < 8.4005] w=0.1719 to align # Constraint # added constraint: constraint((T0337)Q13.CB, (T0337)T35.CB) [> 4.5022 = 7.5036 < 9.7547] w=0.1650 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)V78.CB) [> 3.5582 = 5.9303 < 7.7094] w=0.1643 to align # Constraint # added constraint: constraint((T0337)N21.CB, (T0337)I32.CB) [> 4.2647 = 7.1078 < 9.2401] w=0.1636 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)A82.CB) [> 3.2949 = 5.4914 < 7.1389] w=0.1617 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)V85.CB) [> 4.1179 = 6.8631 < 8.9220] w=0.1554 to align # Constraint # added constraint: constraint((T0337)S22.CB, (T0337)K75.CB) [> 3.8758 = 6.4596 < 8.3975] w=0.1548 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)E88.CB) [> 3.7980 = 6.3300 < 8.2290] w=0.1510 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)V85.CB) [> 3.5971 = 5.9952 < 7.7938] w=0.1507 to align # Constraint # added constraint: constraint((T0337)L7.CB, (T0337)I52.CB) [> 4.3834 = 7.3056 < 9.4973] w=0.1451 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)L73.CB) [> 3.5534 = 5.9224 < 7.6991] w=0.1430 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)V85.CB) [> 3.5057 = 5.8428 < 7.5956] w=0.1428 to align # Constraint # added constraint: constraint((T0337)V10.CB, (T0337)I40.CB) [> 4.4820 = 7.4700 < 9.7111] w=0.1421 to align # Constraint # added constraint: constraint((T0337)S22.CB, (T0337)S76.CB) [> 3.8961 = 6.4935 < 8.4415] w=0.1402 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)A82.CB) [> 3.8010 = 6.3350 < 8.2355] w=0.1354 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)I74.CB) [> 3.4419 = 5.7365 < 7.4575] w=0.1352 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)I108.CB) [> 4.0938 = 6.8231 < 8.8700] w=0.1324 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)I108.CB) [> 3.7984 = 6.3306 < 8.2298] w=0.1324 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)I108.CB) [> 4.0708 = 6.7847 < 8.8201] w=0.1324 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)E88.CB) [> 4.3045 = 7.1741 < 9.3263] w=0.1320 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)L128.CB) [> 3.9413 = 6.5689 < 8.5396] w=0.1268 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)V109.CB) [> 3.6017 = 6.0029 < 7.8037] w=0.1246 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)R110.CB) [> 4.0309 = 6.7182 < 8.7337] w=0.1246 to align # Constraint # added constraint: constraint((T0337)Y67.CB, (T0337)L113.CB) [> 3.6944 = 6.1572 < 8.0044] w=0.1246 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)I140.CB) [> 4.2703 = 7.1172 < 9.2523] w=0.1168 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)V109.CB) [> 3.7817 = 6.3028 < 8.1937] w=0.1168 to align # Constraint # added constraint: constraint((T0337)Y67.CB, (T0337)L112.CB) [> 2.8927 = 4.8212 < 6.2676] w=0.1168 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)A82.CB) [> 4.0304 = 6.7174 < 8.7326] w=0.1167 to align # Constraint # added constraint: constraint((T0337)L7.CB, (T0337)L50.CB) [> 4.2375 = 7.0625 < 9.1812] w=0.1166 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)M68.CB) [> 3.8573 = 6.4288 < 8.3575] w=0.1151 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)M68.CB) [> 3.7754 = 6.2923 < 8.1800] w=0.1143 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)K75.CB) [> 4.2145 = 7.0241 < 9.1314] w=0.1120 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)Y105.CB) [> 3.6478 = 6.0797 < 7.9037] w=0.1091 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)Y105.CB) [> 3.3376 = 5.5627 < 7.2315] w=0.1091 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)I108.CB) [> 3.0291 = 5.0485 < 6.5630] w=0.1091 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)L113.CB) [> 4.2870 = 7.1450 < 9.2885] w=0.1091 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)L113.CB) [> 3.7779 = 6.2965 < 8.1855] w=0.1091 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)R110.CB) [> 3.9276 = 6.5461 < 8.5099] w=0.1090 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)I140.CB) [> 3.0469 = 5.0782 < 6.6017] w=0.1090 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)I140.CB) [> 3.8959 = 6.4932 < 8.4411] w=0.1090 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)E138.CB) [> 3.1810 = 5.3017 < 6.8923] w=0.1090 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)V139.CB) [> 4.1625 = 6.9375 < 9.0187] w=0.1090 to align # Constraint # added constraint: constraint((T0337)V78.CB, (T0337)N133.CB) [> 3.6933 = 6.1556 < 8.0022] w=0.1090 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)I107.CB) [> 3.2898 = 5.4829 < 7.1278] w=0.1090 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)L111.CB) [> 3.7386 = 6.2310 < 8.1003] w=0.1090 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)L73.CB) [> 4.2467 = 7.0778 < 9.2011] w=0.1089 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)L73.CB) [> 3.8199 = 6.3665 < 8.2764] w=0.1088 to align # Constraint # added constraint: constraint((T0337)S97.CB, (T0337)R110.CB) [> 2.8368 = 4.7280 < 6.1464] w=0.1069 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I86.CB) [> 4.1811 = 6.9686 < 9.0591] w=0.1065 to align # Constraint # added constraint: constraint((T0337)A120.CB, (T0337)L141.CB) [> 4.4466 = 7.4111 < 9.6344] w=0.1013 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)R110.CB) [> 4.2846 = 7.1410 < 9.2834] w=0.1013 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)V98.CB) [> 3.4448 = 5.7413 < 7.4636] w=0.1013 to align # Constraint # added constraint: constraint((T0337)Y105.CB, (T0337)E138.CB) [> 4.1063 = 6.8439 < 8.8971] w=0.1013 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)V109.CB) [> 3.9828 = 6.6380 < 8.6294] w=0.1013 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)L113.CB) [> 3.3152 = 5.5253 < 7.1828] w=0.1013 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)I86.CB) [> 3.4589 = 5.7648 < 7.4943] w=0.1012 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)I142.CB) [> 3.9240 = 6.5399 < 8.5019] w=0.1012 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)I142.CB) [> 3.5879 = 5.9799 < 7.7739] w=0.1012 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)I107.CB) [> 3.9654 = 6.6090 < 8.5917] w=0.1012 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)L111.CB) [> 4.0674 = 6.7791 < 8.8128] w=0.1012 to align # Constraint # added constraint: constraint((T0337)D11.CB, (T0337)L50.CB) [> 4.5700 = 7.6167 < 9.9017] w=0.1011 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)L73.CB) [> 3.4542 = 5.7570 < 7.4841] w=0.1010 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)T35.CB) [> 4.3678 = 7.2796 < 9.4635] w=0.1007 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)L113.CB) [> 4.3171 = 7.1952 < 9.3537] w=0.0944 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)V139.CB) [> 3.4560 = 5.7599 < 7.4879] w=0.0936 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)V139.CB) [> 3.9479 = 6.5798 < 8.5538] w=0.0936 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)L141.CB) [> 3.3463 = 5.5772 < 7.2503] w=0.0936 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)L141.CB) [> 4.1837 = 6.9728 < 9.0646] w=0.0936 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)D116.CB) [> 3.8084 = 6.3473 < 8.2515] w=0.0936 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)K115.CB) [> 3.9773 = 6.6288 < 8.6174] w=0.0936 to align # Constraint # added constraint: constraint((T0337)Y67.CB, (T0337)K115.CB) [> 3.4739 = 5.7898 < 7.5267] w=0.0936 to align # Constraint # added constraint: constraint((T0337)G66.CA, (T0337)K115.CB) [> 3.3573 = 5.5955 < 7.2741] w=0.0936 to align # Constraint # added constraint: constraint((T0337)S22.CB, (T0337)F56.CB) [> 2.8972 = 4.8286 < 6.2772] w=0.0936 to align # Constraint # added constraint: constraint((T0337)A120.CB, (T0337)V139.CB) [> 4.1536 = 6.9228 < 8.9996] w=0.0936 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)V109.CB) [> 3.0498 = 5.0830 < 6.6079] w=0.0936 to align # Constraint # added constraint: constraint((T0337)S97.CB, (T0337)V109.CB) [> 4.0874 = 6.8123 < 8.8561] w=0.0936 to align # Constraint # added constraint: constraint((T0337)K96.CB, (T0337)R110.CB) [> 2.9299 = 4.8832 < 6.3482] w=0.0936 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)V109.CB) [> 3.3451 = 5.5751 < 7.2476] w=0.0936 to align # Constraint # added constraint: constraint((T0337)Y94.CB, (T0337)L113.CB) [> 3.8692 = 6.4487 < 8.3833] w=0.0936 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)V109.CB) [> 3.9225 = 6.5375 < 8.4987] w=0.0936 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)A134.CB) [> 3.4034 = 5.6723 < 7.3740] w=0.0936 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)V137.CB) [> 3.7307 = 6.2178 < 8.0832] w=0.0936 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)V137.CB) [> 3.8985 = 6.4975 < 8.4467] w=0.0936 to align # Constraint # added constraint: constraint((T0337)I124.CB, (T0337)V139.CB) [> 3.8128 = 6.3546 < 8.2610] w=0.0935 to align # Constraint # added constraint: constraint((T0337)L113.CB, (T0337)L123.CB) [> 3.8734 = 6.4556 < 8.3923] w=0.0935 to align # Constraint # added constraint: constraint((T0337)L128.CB, (T0337)V137.CB) [> 3.5957 = 5.9928 < 7.7907] w=0.0935 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)I107.CB) [> 3.9830 = 6.6383 < 8.6298] w=0.0935 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)I108.CB) [> 3.9075 = 6.5125 < 8.4662] w=0.0935 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)R110.CB) [> 4.1006 = 6.8344 < 8.8847] w=0.0935 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)V137.CB) [> 3.8933 = 6.4888 < 8.4354] w=0.0934 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)L141.CB) [> 4.0087 = 6.6812 < 8.6856] w=0.0934 to align # Constraint # added constraint: constraint((T0337)I92.CB, (T0337)L123.CB) [> 4.2949 = 7.1582 < 9.3057] w=0.0934 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)L112.CB) [> 4.0217 = 6.7028 < 8.7137] w=0.0934 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)I58.CB) [> 4.2831 = 7.1385 < 9.2800] w=0.0933 to align # Constraint # added constraint: constraint((T0337)L65.CB, (T0337)V85.CB) [> 3.7425 = 6.2375 < 8.1088] w=0.0932 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)I74.CB) [> 4.2210 = 7.0349 < 9.1454] w=0.0932 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)Y69.CB) [> 3.6217 = 6.0362 < 7.8471] w=0.0919 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)F56.CB) [> 4.1581 = 6.9302 < 9.0092] w=0.0917 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)L111.CB) [> 3.2875 = 5.4792 < 7.1230] w=0.0866 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)L112.CB) [> 4.1586 = 6.9311 < 9.0104] w=0.0866 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)L113.CB) [> 3.7887 = 6.3144 < 8.2087] w=0.0866 to align # Constraint # added constraint: constraint((T0337)I124.CB, (T0337)V137.CB) [> 3.3177 = 5.5295 < 7.1883] w=0.0858 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)A134.CB) [> 3.9729 = 6.6214 < 8.6079] w=0.0858 to align # Constraint # added constraint: constraint((T0337)I117.CB, (T0337)L141.CB) [> 4.5951 = 7.6585 < 9.9560] w=0.0857 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)D61.CB) [> 4.3687 = 7.2812 < 9.4656] w=0.0857 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)P79.CB) [> 3.4927 = 5.8211 < 7.5675] w=0.0856 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)I107.CB) [> 3.8824 = 6.4706 < 8.4118] w=0.0856 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)I142.CB) [> 2.9697 = 4.9496 < 6.4344] w=0.0856 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)V109.CB) [> 3.7734 = 6.2889 < 8.1756] w=0.0856 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)L112.CB) [> 3.6453 = 6.0754 < 7.8980] w=0.0856 to align # Constraint # added constraint: constraint((T0337)D61.CB, (T0337)L73.CB) [> 3.7295 = 6.2158 < 8.0805] w=0.0856 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)K75.CB) [> 4.2045 = 7.0074 < 9.1097] w=0.0856 to align # Constraint # added constraint: constraint((T0337)A30.CB, (T0337)A41.CB) [> 4.5625 = 7.6042 < 9.8855] w=0.0851 to align # Constraint # added constraint: constraint((T0337)L7.CB, (T0337)V85.CB) [> 3.7879 = 6.3131 < 8.2071] w=0.0848 to align # Constraint # added constraint: constraint((T0337)S22.CB, (T0337)T57.CB) [> 4.3399 = 7.2332 < 9.4032] w=0.0840 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I58.CB) [> 3.6621 = 6.1034 < 7.9345] w=0.0836 to align # Constraint # added constraint: constraint((T0337)V102.CB, (T0337)K115.CB) [> 3.7809 = 6.3015 < 8.1919] w=0.0795 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)I108.CB) [> 4.2499 = 7.0831 < 9.2080] w=0.0779 to align # Constraint # added constraint: constraint((T0337)K96.CB, (T0337)L112.CB) [> 3.4286 = 5.7143 < 7.4286] w=0.0779 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)I107.CB) [> 4.1788 = 6.9646 < 9.0540] w=0.0779 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)K75.CB) [> 3.8920 = 6.4866 < 8.4326] w=0.0779 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)R110.CB) [> 4.2344 = 7.0573 < 9.1746] w=0.0778 to align # Constraint # added constraint: constraint((T0337)L111.CB, (T0337)V139.CB) [> 3.9188 = 6.5313 < 8.4907] w=0.0778 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)V85.CB) [> 4.1128 = 6.8546 < 8.9110] w=0.0778 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)E138.CB) [> 3.7363 = 6.2271 < 8.0953] w=0.0778 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)K64.CB) [> 3.7950 = 6.3249 < 8.2224] w=0.0778 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)Y67.CB) [> 3.0961 = 5.1602 < 6.7083] w=0.0778 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)L65.CB) [> 3.5979 = 5.9965 < 7.7954] w=0.0777 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)M68.CB) [> 3.7536 = 6.2560 < 8.1328] w=0.0777 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)L111.CB) [> 3.9523 = 6.5872 < 8.5633] w=0.0777 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)A70.CB) [> 4.1666 = 6.9444 < 9.0277] w=0.0770 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)A70.CB) [> 3.6528 = 6.0879 < 7.9143] w=0.0762 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)A70.CB) [> 3.5232 = 5.8720 < 7.6336] w=0.0755 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)R110.CB) [> 4.0943 = 6.8239 < 8.8710] w=0.0755 to align # Constraint # added constraint: constraint((T0337)E88.CB, (T0337)I131.CB) [> 3.4465 = 5.7442 < 7.4674] w=0.0709 to align # Constraint # added constraint: constraint((T0337)Y94.CB, (T0337)L123.CB) [> 3.5597 = 5.9329 < 7.7127] w=0.0709 to align # Constraint # added constraint: constraint((T0337)I62.CB, (T0337)L112.CB) [> 3.3493 = 5.5822 < 7.2569] w=0.0702 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)A134.CB) [> 3.9885 = 6.6475 < 8.6418] w=0.0702 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)E135.CB) [> 3.4247 = 5.7078 < 7.4201] w=0.0702 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)N133.CB) [> 2.8421 = 4.7369 < 6.1579] w=0.0702 to align # Constraint # added constraint: constraint((T0337)Y94.CB, (T0337)L111.CB) [> 3.1015 = 5.1692 < 6.7199] w=0.0702 to align # Constraint # added constraint: constraint((T0337)Y94.CB, (T0337)L112.CB) [> 3.4382 = 5.7303 < 7.4494] w=0.0702 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)L111.CB) [> 3.3565 = 5.5942 < 7.2725] w=0.0702 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)I107.CB) [> 3.6705 = 6.1175 < 7.9527] w=0.0702 to align # Constraint # added constraint: constraint((T0337)L33.CB, (T0337)R43.CB) [> 4.5975 = 7.6625 < 9.9612] w=0.0701 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)M68.CB) [> 3.9902 = 6.6503 < 8.6454] w=0.0701 to align # Constraint # added constraint: constraint((T0337)G101.CA, (T0337)K115.CB) [> 3.0403 = 5.0672 < 6.5873] w=0.0701 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)Y69.CB) [> 3.7895 = 6.3158 < 8.2105] w=0.0701 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)E138.CB) [> 4.2393 = 7.0655 < 9.1852] w=0.0700 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)I58.CB) [> 4.0181 = 6.6969 < 8.7060] w=0.0700 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)V85.CB) [> 3.5463 = 5.9105 < 7.6837] w=0.0700 to align # Constraint # added constraint: constraint((T0337)Y67.CB, (T0337)V85.CB) [> 3.0940 = 5.1567 < 6.7037] w=0.0700 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)Y67.CB) [> 4.0461 = 6.7435 < 8.7665] w=0.0699 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)E121.CB) [> 3.5139 = 5.8565 < 7.6135] w=0.0699 to align # Constraint # added constraint: constraint((T0337)G103.CA, (T0337)K115.CB) [> 3.1369 = 5.2282 < 6.7967] w=0.0639 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)L111.CB) [> 4.4310 = 7.3850 < 9.6004] w=0.0633 to align # Constraint # added constraint: constraint((T0337)K100.CB, (T0337)K115.CB) [> 3.3928 = 5.6547 < 7.3511] w=0.0630 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)L111.CB) [> 3.7405 = 6.2341 < 8.1044] w=0.0624 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)I117.CB) [> 3.7061 = 6.1768 < 8.0299] w=0.0624 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)D119.CB) [> 4.2684 = 7.1140 < 9.2481] w=0.0624 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)L141.CB) [> 3.8983 = 6.4971 < 8.4462] w=0.0624 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)V139.CB) [> 3.0823 = 5.1371 < 6.6782] w=0.0624 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)I140.CB) [> 3.7553 = 6.2589 < 8.1365] w=0.0624 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)I124.CB) [> 4.4960 = 7.4934 < 9.7414] w=0.0624 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)V137.CB) [> 3.4221 = 5.7034 < 7.4145] w=0.0624 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)E138.CB) [> 4.1271 = 6.8785 < 8.9420] w=0.0624 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)Y105.CB) [> 2.3010 = 3.8350 < 4.9854] w=0.0624 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)N106.CB) [> 3.5884 = 5.9807 < 7.7749] w=0.0623 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)S90.CB) [> 3.8665 = 6.4442 < 8.3775] w=0.0623 to align # Constraint # added constraint: constraint((T0337)G101.CA, (T0337)A120.CB) [> 4.4214 = 7.3691 < 9.5798] w=0.0623 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)L111.CB) [> 4.0625 = 6.7709 < 8.8021] w=0.0623 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)V85.CB) [> 3.8878 = 6.4797 < 8.4237] w=0.0623 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)M68.CB) [> 3.6492 = 6.0820 < 7.9066] w=0.0623 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)I107.CB) [> 4.2482 = 7.0803 < 9.2044] w=0.0623 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)I74.CB) [> 3.3224 = 5.5373 < 7.1985] w=0.0622 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)V72.CB) [> 3.8808 = 6.4680 < 8.4085] w=0.0622 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)M68.CB) [> 3.7120 = 6.1866 < 8.0426] w=0.0621 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)G66.CA) [> 4.0364 = 6.7273 < 8.7455] w=0.0621 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)V72.CB) [> 3.8035 = 6.3391 < 8.2408] w=0.0613 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I124.CB) [> 3.4260 = 5.7099 < 7.4229] w=0.0610 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)Y69.CB) [> 3.8215 = 6.3692 < 8.2800] w=0.0599 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)L112.CB) [> 3.6548 = 6.0913 < 7.9187] w=0.0599 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)R110.CB) [> 3.3864 = 5.6441 < 7.3373] w=0.0599 to align # Constraint # added constraint: constraint((T0337)K100.CB, (T0337)A120.CB) [> 3.9597 = 6.5995 < 8.5794] w=0.0552 to align # Constraint # added constraint: constraint((T0337)V109.CB, (T0337)L128.CB) [> 4.2949 = 7.1581 < 9.3055] w=0.0546 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)Y105.CB) [> 3.8552 = 6.4253 < 8.3529] w=0.0545 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)L112.CB) [> 3.7324 = 6.2206 < 8.0868] w=0.0545 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)I89.CB) [> 3.9845 = 6.6408 < 8.6331] w=0.0545 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)A70.CB) [> 4.1480 = 6.9134 < 8.9874] w=0.0545 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)Y69.CB) [> 3.6449 = 6.0748 < 7.8972] w=0.0545 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)I108.CB) [> 4.2804 = 7.1341 < 9.2743] w=0.0544 to align # Constraint # added constraint: constraint((T0337)I92.CB, (T0337)I117.CB) [> 3.6669 = 6.1116 < 7.9451] w=0.0544 to align # Constraint # added constraint: constraint((T0337)I92.CB, (T0337)A120.CB) [> 3.3715 = 5.6192 < 7.3049] w=0.0544 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)I71.CB) [> 3.3724 = 5.6207 < 7.3069] w=0.0536 to align # Constraint # added constraint: constraint((T0337)S22.CB, (T0337)I74.CB) [> 4.1726 = 6.9544 < 9.0407] w=0.0536 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)K75.CB) [> 4.2396 = 7.0659 < 9.1857] w=0.0536 to align # Constraint # added constraint: constraint((T0337)K55.CB, (T0337)V72.CB) [> 3.6894 = 6.1490 < 7.9936] w=0.0535 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)Y69.CB) [> 3.2675 = 5.4459 < 7.0797] w=0.0529 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I124.CB) [> 3.3577 = 5.5961 < 7.2749] w=0.0521 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)R110.CB) [> 3.5513 = 5.9189 < 7.6946] w=0.0520 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)S76.CB) [> 3.9583 = 6.5972 < 8.5764] w=0.0469 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)I131.CB) [> 3.2503 = 5.4171 < 7.0423] w=0.0468 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)I131.CB) [> 4.2824 = 7.1374 < 9.2786] w=0.0468 to align # Constraint # added constraint: constraint((T0337)Y105.CB, (T0337)N136.CB) [> 4.4062 = 7.3437 < 9.5468] w=0.0468 to align # Constraint # added constraint: constraint((T0337)L111.CB, (T0337)L128.CB) [> 4.6867 = 7.8112 < 10.1545] w=0.0468 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)R104.CB) [> 4.1198 = 6.8663 < 8.9261] w=0.0468 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)A134.CB) [> 3.4821 = 5.8036 < 7.5446] w=0.0468 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)N106.CB) [> 4.4711 = 7.4518 < 9.6874] w=0.0468 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)I107.CB) [> 4.4778 = 7.4630 < 9.7019] w=0.0468 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)V109.CB) [> 4.3956 = 7.3260 < 9.5239] w=0.0468 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)D83.CB) [> 4.2270 = 7.0450 < 9.1585] w=0.0467 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I89.CB) [> 4.1571 = 6.9284 < 9.0070] w=0.0467 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)K75.CB) [> 4.1157 = 6.8595 < 8.9173] w=0.0467 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)Y69.CB) [> 3.7710 = 6.2850 < 8.1705] w=0.0467 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)A70.CB) [> 3.2369 = 5.3948 < 7.0132] w=0.0467 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)A70.CB) [> 3.4326 = 5.7210 < 7.4373] w=0.0467 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)R110.CB) [> 4.3852 = 7.3086 < 9.5012] w=0.0467 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)V109.CB) [> 4.1242 = 6.8737 < 8.9359] w=0.0467 to align # Constraint # added constraint: constraint((T0337)R110.CB, (T0337)I142.CB) [> 4.2275 = 7.0458 < 9.1596] w=0.0467 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)Y69.CB) [> 3.7027 = 6.1712 < 8.0225] w=0.0467 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)V109.CB) [> 4.2433 = 7.0722 < 9.1938] w=0.0467 to align # Constraint # added constraint: constraint((T0337)L50.CB, (T0337)L65.CB) [> 3.0635 = 5.1058 < 6.6375] w=0.0466 to align # Constraint # added constraint: constraint((T0337)K64.CB, (T0337)L73.CB) [> 4.1139 = 6.8564 < 8.9134] w=0.0466 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)V139.CB) [> 4.1936 = 6.9893 < 9.0862] w=0.0466 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)I140.CB) [> 4.4018 = 7.3363 < 9.5372] w=0.0466 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)V145.CB) [> 4.3767 = 7.2946 < 9.4829] w=0.0466 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)L111.CB) [> 4.2221 = 7.0369 < 9.1479] w=0.0466 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)I74.CB) [> 4.3918 = 7.3197 < 9.5156] w=0.0459 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)L73.CB) [> 3.5717 = 5.9529 < 7.7387] w=0.0458 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)L73.CB) [> 3.5893 = 5.9821 < 7.7767] w=0.0458 to align # Constraint # added constraint: constraint((T0337)L7.CB, (T0337)I89.CB) [> 4.2989 = 7.1649 < 9.3144] w=0.0456 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)I71.CB) [> 4.0409 = 6.7348 < 8.7552] w=0.0443 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)S125.CB) [> 4.2792 = 7.1320 < 9.2716] w=0.0443 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)F127.CB) [> 3.6376 = 6.0627 < 7.8815] w=0.0403 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)K75.CB) [> 4.2671 = 7.1119 < 9.2454] w=0.0390 to align # Constraint # added constraint: constraint((T0337)L7.CB, (T0337)D81.CB) [> 4.2081 = 7.0135 < 9.1175] w=0.0390 to align # Constraint # added constraint: constraint((T0337)F56.CB, (T0337)S76.CB) [> 3.8375 = 6.3959 < 8.3147] w=0.0390 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)A70.CB) [> 4.2376 = 7.0627 < 9.1815] w=0.0389 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)R104.CB) [> 4.4259 = 7.3765 < 9.5895] w=0.0389 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)I89.CB) [> 4.2328 = 7.0546 < 9.1711] w=0.0389 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I92.CB) [> 4.3783 = 7.2972 < 9.4864] w=0.0389 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)I71.CB) [> 4.2599 = 7.0998 < 9.2297] w=0.0389 to align # Constraint # added constraint: constraint((T0337)I108.CB, (T0337)L141.CB) [> 4.3861 = 7.3102 < 9.5032] w=0.0388 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)L141.CB) [> 4.0393 = 6.7322 < 8.7518] w=0.0388 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)I142.CB) [> 4.3695 = 7.2825 < 9.4672] w=0.0388 to align # Constraint # added constraint: constraint((T0337)T57.CB, (T0337)S76.CB) [> 4.3155 = 7.1926 < 9.3504] w=0.0388 to align # Constraint # added constraint: constraint((T0337)V109.CB, (T0337)L141.CB) [> 3.5294 = 5.8824 < 7.6471] w=0.0388 to align # Constraint # added constraint: constraint((T0337)V109.CB, (T0337)I140.CB) [> 4.2871 = 7.1452 < 9.2888] w=0.0388 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)I74.CB) [> 4.3169 = 7.1948 < 9.3533] w=0.0388 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)L65.CB) [> 4.6435 = 7.7392 < 10.0609] w=0.0381 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)K75.CB) [> 3.6396 = 6.0660 < 7.8859] w=0.0380 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)K75.CB) [> 4.1494 = 6.9157 < 8.9904] w=0.0380 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I62.CB) [> 2.8715 = 4.7859 < 6.2216] w=0.0371 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)R110.CB) [> 3.8942 = 6.4903 < 8.4374] w=0.0365 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)P60.CB) [> 3.5971 = 5.9952 < 7.7937] w=0.0360 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)P60.CB) [> 4.1605 = 6.9342 < 9.0144] w=0.0342 to align # Constraint # added constraint: constraint((T0337)R54.CB, (T0337)P114.CB) [> 3.5040 = 5.8400 < 7.5920] w=0.0340 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)P114.CB) [> 3.9091 = 6.5152 < 8.4697] w=0.0340 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)P114.CB) [> 3.7250 = 6.2083 < 8.0708] w=0.0340 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)I124.CB) [> 4.3890 = 7.3151 < 9.5096] w=0.0327 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)Y69.CB) [> 4.2118 = 7.0197 < 9.1256] w=0.0319 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)P60.CB) [> 3.5878 = 5.9797 < 7.7736] w=0.0319 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)I142.CB) [> 4.6741 = 7.7901 < 10.1272] w=0.0312 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)K115.CB) [> 4.2382 = 7.0637 < 9.1828] w=0.0312 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)V72.CB) [> 3.4068 = 5.6780 < 7.3814] w=0.0312 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)V72.CB) [> 3.5738 = 5.9562 < 7.7431] w=0.0312 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)Y69.CB) [> 3.8823 = 6.4704 < 8.4115] w=0.0312 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)I74.CB) [> 3.4859 = 5.8098 < 7.5527] w=0.0312 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)I89.CB) [> 4.6086 = 7.6810 < 9.9853] w=0.0312 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)L65.CB) [> 3.6417 = 6.0695 < 7.8903] w=0.0312 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)I89.CB) [> 4.2440 = 7.0734 < 9.1954] w=0.0311 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)I108.CB) [> 3.6675 = 6.1125 < 7.9462] w=0.0311 to align # Constraint # added constraint: constraint((T0337)L73.CB, (T0337)L111.CB) [> 3.6549 = 6.0916 < 7.9190] w=0.0311 to align # Constraint # added constraint: constraint((T0337)I58.CB, (T0337)V72.CB) [> 3.8523 = 6.4205 < 8.3467] w=0.0311 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)I107.CB) [> 3.7105 = 6.1842 < 8.0394] w=0.0311 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I71.CB) [> 4.3796 = 7.2993 < 9.4891] w=0.0311 to align # Constraint # added constraint: constraint((T0337)I107.CB, (T0337)L141.CB) [> 3.3663 = 5.6104 < 7.2935] w=0.0311 to align # Constraint # added constraint: constraint((T0337)M68.CB, (T0337)R110.CB) [> 3.4285 = 5.7142 < 7.4285] w=0.0311 to align # Constraint # added constraint: constraint((T0337)L111.CB, (T0337)I140.CB) [> 4.3514 = 7.2524 < 9.4281] w=0.0311 to align # Constraint # added constraint: constraint((T0337)I108.CB, (T0337)I142.CB) [> 3.6525 = 6.0875 < 7.9138] w=0.0311 to align # Constraint # added constraint: constraint((T0337)Y105.CB, (T0337)E144.CB) [> 3.6927 = 6.1544 < 8.0007] w=0.0311 to align # Constraint # added constraint: constraint((T0337)R110.CB, (T0337)I140.CB) [> 3.2922 = 5.4870 < 7.1331] w=0.0311 to align # Constraint # added constraint: constraint((T0337)D61.CB, (T0337)I74.CB) [> 3.9010 = 6.5016 < 8.4521] w=0.0311 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)T57.CB) [> 3.9949 = 6.6581 < 8.6556] w=0.0311 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)G103.CA) [> 3.6311 = 6.0518 < 7.8673] w=0.0311 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)V145.CB) [> 4.4315 = 7.3858 < 9.6016] w=0.0310 to align # Constraint # added constraint: constraint((T0337)V95.CB, (T0337)K115.CB) [> 4.4763 = 7.4605 < 9.6987] w=0.0303 to align # Constraint # added constraint: constraint((T0337)V98.CB, (T0337)L111.CB) [> 4.1235 = 6.8724 < 8.9341] w=0.0287 to align # Constraint # added constraint: constraint((T0337)D61.CB, (T0337)A70.CB) [> 3.3374 = 5.5623 < 7.2310] w=0.0287 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)P60.CB) [> 3.0524 = 5.0873 < 6.6136] w=0.0282 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)K115.CB) [> 3.6673 = 6.1121 < 7.9458] w=0.0248 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)F127.CB) [> 3.8954 = 6.4923 < 8.4400] w=0.0240 to align # Constraint # added constraint: constraint((T0337)R104.CB, (T0337)E138.CB) [> 4.5739 = 7.6231 < 9.9101] w=0.0234 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)I59.CB) [> 4.7658 = 7.9430 < 10.3259] w=0.0234 to align # Constraint # added constraint: constraint((T0337)M4.CB, (T0337)V15.CB) [> 4.7108 = 7.8513 < 10.2066] w=0.0234 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)L33.CB) [> 3.1574 = 5.2622 < 6.8409] w=0.0234 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I52.CB) [> 4.0457 = 6.7428 < 8.7656] w=0.0234 to align # Constraint # added constraint: constraint((T0337)N21.CB, (T0337)L33.CB) [> 2.9319 = 4.8866 < 6.3526] w=0.0234 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)I108.CB) [> 4.1278 = 6.8797 < 8.9436] w=0.0234 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)I108.CB) [> 2.5381 = 4.2302 < 5.4992] w=0.0234 to align # Constraint # added constraint: constraint((T0337)K96.CB, (T0337)N106.CB) [> 4.3718 = 7.2863 < 9.4721] w=0.0234 to align # Constraint # added constraint: constraint((T0337)S97.CB, (T0337)N106.CB) [> 4.7361 = 7.8935 < 10.2615] w=0.0234 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)S76.CB) [> 4.3761 = 7.2935 < 9.4815] w=0.0234 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)R110.CB) [> 4.5797 = 7.6328 < 9.9226] w=0.0234 to align # Constraint # added constraint: constraint((T0337)I59.CB, (T0337)S76.CB) [> 3.9375 = 6.5625 < 8.5312] w=0.0234 to align # Constraint # added constraint: constraint((T0337)N106.CB, (T0337)E144.CB) [> 3.8829 = 6.4715 < 8.4130] w=0.0233 to align # Constraint # added constraint: constraint((T0337)N106.CB, (T0337)V145.CB) [> 2.7970 = 4.6617 < 6.0602] w=0.0233 to align # Constraint # added constraint: constraint((T0337)I107.CB, (T0337)I142.CB) [> 4.7270 = 7.8784 < 10.2419] w=0.0233 to align # Constraint # added constraint: constraint((T0337)I107.CB, (T0337)S143.CB) [> 3.7684 = 6.2807 < 8.1649] w=0.0233 to align # Constraint # added constraint: constraint((T0337)I108.CB, (T0337)S143.CB) [> 3.2677 = 5.4462 < 7.0800] w=0.0233 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)Y69.CB) [> 4.6242 = 7.7070 < 10.0191] w=0.0233 to align # Constraint # added constraint: constraint((T0337)L111.CB, (T0337)L141.CB) [> 3.5062 = 5.8436 < 7.5967] w=0.0233 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)L111.CB) [> 4.7392 = 7.8986 < 10.2682] w=0.0233 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)V102.CB) [> 2.5443 = 4.2406 < 5.5127] w=0.0233 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)R110.CB) [> 4.4623 = 7.4371 < 9.6683] w=0.0233 to align # Constraint # added constraint: constraint((T0337)R110.CB, (T0337)V139.CB) [> 4.1299 = 6.8832 < 8.9482] w=0.0233 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)P114.CB) [> 3.8066 = 6.3443 < 8.2475] w=0.0233 to align # Constraint # added constraint: constraint((T0337)R110.CB, (T0337)L141.CB) [> 4.5567 = 7.5945 < 9.8728] w=0.0233 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)G103.CA) [> 3.0353 = 5.0588 < 6.5765] w=0.0233 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)V102.CB) [> 3.8640 = 6.4400 < 8.3719] w=0.0233 to align # Constraint # added constraint: constraint((T0337)Y105.CB, (T0337)S143.CB) [> 4.0423 = 6.7372 < 8.7583] w=0.0232 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)L141.CB) [> 3.8053 = 6.3422 < 8.2449] w=0.0232 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)I52.CB) [> 3.8149 = 6.3582 < 8.2657] w=0.0232 to align # Constraint # added constraint: constraint((T0337)G101.CA, (T0337)L123.CB) [> 4.2595 = 7.0992 < 9.2290] w=0.0232 to align # Constraint # added constraint: constraint((T0337)G101.CA, (T0337)F127.CB) [> 4.4886 = 7.4809 < 9.7252] w=0.0232 to align # Constraint # added constraint: constraint((T0337)V102.CB, (T0337)F127.CB) [> 4.0989 = 6.8315 < 8.8809] w=0.0232 to align # Constraint # added constraint: constraint((T0337)T25.CB, (T0337)I71.CB) [> 3.5608 = 5.9346 < 7.7150] w=0.0225 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)V72.CB) [> 3.3978 = 5.6630 < 7.3618] w=0.0225 to align # Constraint # added constraint: constraint((T0337)P60.CB, (T0337)I71.CB) [> 4.1763 = 6.9605 < 9.0487] w=0.0225 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I62.CB) [> 4.6399 = 7.7332 < 10.0531] w=0.0216 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)I71.CB) [> 4.5106 = 7.5177 < 9.7730] w=0.0210 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)V98.CB) [> 4.4235 = 7.3726 < 9.5843] w=0.0210 to align # Constraint # added constraint: constraint((T0337)K75.CB, (T0337)L111.CB) [> 2.9959 = 4.9931 < 6.4911] w=0.0210 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)K75.CB) [> 4.3979 = 7.3298 < 9.5287] w=0.0210 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)K115.CB) [> 3.7794 = 6.2990 < 8.1887] w=0.0197 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)K115.CB) [> 4.0816 = 6.8027 < 8.8435] w=0.0197 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)L111.CB) [> 3.3789 = 5.6315 < 7.3210] w=0.0173 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)I131.CB) [> 4.3501 = 7.2501 < 9.4252] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)I74.CB) [> 4.3577 = 7.2629 < 9.4417] w=0.0156 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)V72.CB) [> 4.4526 = 7.4210 < 9.6473] w=0.0156 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)I74.CB) [> 3.9419 = 6.5699 < 8.5408] w=0.0156 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I74.CB) [> 3.8285 = 6.3808 < 8.2951] w=0.0156 to align # Constraint # added constraint: constraint((T0337)D8.CB, (T0337)R39.CB) [> 4.6954 = 7.8257 < 10.1734] w=0.0156 to align # Constraint # added constraint: constraint((T0337)S19.CB, (T0337)V72.CB) [> 3.4494 = 5.7490 < 7.4737] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)V72.CB) [> 4.3993 = 7.3322 < 9.5319] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I53.CB, (T0337)M68.CB) [> 3.8779 = 6.4631 < 8.4020] w=0.0156 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)M68.CB) [> 4.1620 = 6.9366 < 9.0176] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)K115.CB) [> 4.0686 = 6.7810 < 8.8153] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)S143.CB) [> 2.8739 = 4.7898 < 6.2267] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I108.CB, (T0337)E144.CB) [> 4.3369 = 7.2281 < 9.3965] w=0.0156 to align # Constraint # added constraint: constraint((T0337)Y105.CB, (T0337)R146.CB) [> 2.6108 = 4.3513 < 5.6567] w=0.0156 to align # Constraint # added constraint: constraint((T0337)E99.CB, (T0337)R146.CB) [> 4.5459 = 7.5766 < 9.8496] w=0.0156 to align # Constraint # added constraint: constraint((T0337)L14.CB, (T0337)S76.CB) [> 3.9891 = 6.6484 < 8.6430] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)D63.CB) [> 3.1864 = 5.3107 < 6.9039] w=0.0156 to align # Constraint # added constraint: constraint((T0337)G103.CA, (T0337)P114.CB) [> 3.6599 = 6.0999 < 7.9298] w=0.0156 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)V102.CB) [> 4.5284 = 7.5473 < 9.8115] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)G101.CA) [> 4.3320 = 7.2200 < 9.3860] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)V102.CB) [> 3.0610 = 5.1016 < 6.6321] w=0.0156 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)I108.CB) [> 3.9621 = 6.6035 < 8.5845] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)V102.CB) [> 3.8064 = 6.3441 < 8.2473] w=0.0156 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)G103.CA) [> 2.5082 = 4.1803 < 5.4344] w=0.0156 to align # Constraint # added constraint: constraint((T0337)V137.CB, (T0337)K147.CB) [> 4.0057 = 6.6761 < 8.6789] w=0.0155 to align # Constraint # added constraint: constraint((T0337)N136.CB, (T0337)K147.CB) [> 3.6774 = 6.1290 < 7.9677] w=0.0155 to align # Constraint # added constraint: constraint((T0337)A41.CB, (T0337)M68.CB) [> 3.9642 = 6.6070 < 8.5891] w=0.0155 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)V109.CB) [> 3.2724 = 5.4540 < 7.0902] w=0.0155 to align # Constraint # added constraint: constraint((T0337)S76.CB, (T0337)I108.CB) [> 4.4274 = 7.3790 < 9.5927] w=0.0155 to align # Constraint # added constraint: constraint((T0337)I74.CB, (T0337)L111.CB) [> 3.3714 = 5.6190 < 7.3047] w=0.0155 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)V109.CB) [> 3.6581 = 6.0969 < 7.9260] w=0.0155 to align # Constraint # added constraint: constraint((T0337)L111.CB, (T0337)A134.CB) [> 3.4026 = 5.6710 < 7.3723] w=0.0155 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)S143.CB) [> 4.3126 = 7.1877 < 9.3440] w=0.0155 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)S143.CB) [> 3.2801 = 5.4669 < 7.1069] w=0.0155 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)S143.CB) [> 4.7126 = 7.8544 < 10.2107] w=0.0155 to align # Constraint # added constraint: constraint((T0337)V72.CB, (T0337)S143.CB) [> 3.1502 = 5.2503 < 6.8254] w=0.0155 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)M68.CB) [> 3.6936 = 6.1560 < 8.0028] w=0.0155 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)L73.CB) [> 4.2954 = 7.1591 < 9.3068] w=0.0146 to align # Constraint # added constraint: constraint((T0337)A70.CB, (T0337)V85.CB) [> 3.5172 = 5.8620 < 7.6206] w=0.0132 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)Y69.CB) [> 3.8832 = 6.4721 < 8.4137] w=0.0086 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)I71.CB) [> 4.2619 = 7.1031 < 9.2341] w=0.0078 to align # Constraint # added constraint: constraint((T0337)K48.CB, (T0337)A70.CB) [> 4.7338 = 7.8897 < 10.2566] w=0.0078 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)V72.CB) [> 3.7548 = 6.2579 < 8.1353] w=0.0078 to align # Constraint # added constraint: constraint((T0337)L18.CB, (T0337)V109.CB) [> 4.4662 = 7.4437 < 9.6769] w=0.0078 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)L111.CB) [> 4.3410 = 7.2349 < 9.4054] w=0.0078 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)Y69.CB) [> 4.2466 = 7.0777 < 9.2010] w=0.0078 to align # Constraint # added constraint: constraint((T0337)I52.CB, (T0337)A70.CB) [> 3.7259 = 6.2098 < 8.0727] w=0.0078 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)V85.CB) [> 2.0302 = 3.3837 < 4.3988] w=0.0078 to align # Constraint # added constraint: constraint((T0337)Y69.CB, (T0337)I89.CB) [> 3.5029 = 5.8383 < 7.5897] w=0.0078 to align # Constraint # added constraint: constraint((T0337)I89.CB, (T0337)R110.CB) [> 3.5851 = 5.9751 < 7.7676] w=0.0078 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)L141.CB) [> 4.1860 = 6.9767 < 9.0697] w=0.0078 to align # Constraint # added constraint: constraint((T0337)V85.CB, (T0337)V109.CB) [> 3.5477 = 5.9129 < 7.6868] w=0.0078 to align # Constraint # added constraint: constraint((T0337)D8.CB, (T0337)L111.CB) [> 4.6900 = 7.8166 < 10.1616] w=0.0078 to align # Constraint # added constraint: constraint((T0337)V109.CB, (T0337)S143.CB) [> 3.4149 = 5.6915 < 7.3990] w=0.0078 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)I89.CB) [> 3.4289 = 5.7149 < 7.4293] w=0.0054 to align # Constraint # added constraint: constraint((T0337)I71.CB, (T0337)V85.CB) [> 2.1816 = 3.6360 < 4.7268] w=0.0054 to align # Constraint # added constraint: constraint((T0337)V15.CB, (T0337)L111.CB) [> 3.1701 = 5.2835 < 6.8686] w=0.0035 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0337/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0337/decoys/ # command:Using radius: 8.0000 Using models AND alignments for constraints USE_EVALUE, weight: 0.9944 eval: 0.0066 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9944 eval: 0.0066 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9944 eval: 0.0066 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9956 eval: 0.0053 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9956 eval: 0.0053 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9956 eval: 0.0053 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9996 eval: 0.0005 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9996 eval: 0.0005 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9996 eval: 0.0005 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9785 eval: 0.0255 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9785 eval: 0.0255 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9785 eval: 0.0255 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7098 eval: 0.3444 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7098 eval: 0.3444 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7098 eval: 0.3444 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6964 eval: 0.3603 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6964 eval: 0.3603 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6964 eval: 0.3603 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9913 eval: 0.0103 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9913 eval: 0.0103 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9913 eval: 0.0103 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6357 eval: 0.4324 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6357 eval: 0.4324 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.6357 eval: 0.4324 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9958 eval: 0.0049 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9958 eval: 0.0049 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9958 eval: 0.0049 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9996 eval: 0.0005 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9996 eval: 0.0005 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9914 eval: 0.0102 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9914 eval: 0.0102 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9914 eval: 0.0102 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0020 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0020 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0020 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0014 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0014 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0014 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9926 eval: 0.0088 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9926 eval: 0.0088 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9926 eval: 0.0088 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.8869 eval: 0.1343 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.8869 eval: 0.1343 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.8869 eval: 0.1343 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0021 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0021 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9983 eval: 0.0021 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9980 eval: 0.0024 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9980 eval: 0.0024 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9980 eval: 0.0024 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9729 eval: 0.0322 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9729 eval: 0.0322 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9729 eval: 0.0322 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9985 eval: 0.0018 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9985 eval: 0.0018 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9985 eval: 0.0018 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0002 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9991 eval: 0.0011 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9991 eval: 0.0011 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9991 eval: 0.0011 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.1000 eval: 1.0683 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.1000 eval: 1.0683 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.1000 eval: 1.0683 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9899 eval: 0.0120 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9899 eval: 0.0120 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9899 eval: 0.0120 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7621 eval: 0.2824 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7621 eval: 0.2824 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.7621 eval: 0.2824 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9998 eval: 0.0003 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9962 eval: 0.0045 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9962 eval: 0.0045 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9992 eval: 0.0009 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9992 eval: 0.0009 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9992 eval: 0.0009 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0004 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0004 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9997 eval: 0.0004 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9889 eval: 0.0132 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9889 eval: 0.0132 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9889 eval: 0.0132 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0013 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0013 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9989 eval: 0.0013 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9861 eval: 0.0165 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9861 eval: 0.0165 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9861 eval: 0.0165 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9994 eval: 0.0007 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9994 eval: 0.0007 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9994 eval: 0.0007 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9912 eval: 0.0105 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9912 eval: 0.0105 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9912 eval: 0.0105 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.4484 eval: 0.6548 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.4484 eval: 0.6548 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.4484 eval: 0.6548 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 USE_EVALUE, weight: 0.9990 eval: 0.0012 min: 0.0000 max: 1.0683 Number of contacts in models: 0 Number of contacts in alignments: 139 NUMB_ALIGNS: 139 Adding 1629 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: -263.9966, CN propb: -263.9966 weights: 0.1246 constraints: 463 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 463 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 463 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 1166 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 1166 # 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 1629 # command: