parameters: 0.6 1.3 0.5 200 50 # 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:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 139 Done printing distance constraints # command: