# 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/T0381/ # command:# Making conformation for sequence T0381 numbered 1 through 265 Created new target T0381 from T0381.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0381/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/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 # T0381 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 (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 19 :SLARGLAVIRCFDHRNQR 1hw5A 139 :VTGRIAQTLLNLAKQPDA # choosing archetypes in rotamer library T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDG 1hw5A 181 :ETVGRILKMLEDQNLISAHG T0381 71 :SA 1hw5A 202 :TI Number of specific fragments extracted= 4 number of extra gaps= 1 total=4 Number of alignments=1 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 19 :SLARGLAVIRCFDHRNQR 1hw5A 139 :VTGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDGSAF 1hw5A 181 :ETVGRILKMLEDQNLISAHGKTI Number of specific fragments extracted= 3 number of extra gaps= 1 total=7 Number of alignments=2 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 20 :LARGLAVIRCFDHRNQ 1hw5A 140 :TGRIAQTLLNLAKQPD T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDG 1hw5A 181 :ETVGRILKMLEDQNLISAHG Number of specific fragments extracted= 3 number of extra gaps= 1 total=10 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i6xA expands to /projects/compbio/data/pdb/1i6x.pdb.gz 1i6xA:# T0381 read from 1i6xA/merged-good-all-a2m # 1i6xA read from 1i6xA/merged-good-all-a2m # adding 1i6xA to template set # found chain 1i6xA in template set T0381 19 :SLARGLAVIRCFDHRNQ 1i6xA 139 :VTGRIAQTLLNLAKQPD T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=12 Number of alignments=4 # 1i6xA read from 1i6xA/merged-good-all-a2m # found chain 1i6xA in template set T0381 19 :SLARGLAVIRCFDHRNQR 1i6xA 139 :VTGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=14 Number of alignments=5 # 1i6xA read from 1i6xA/merged-good-all-a2m # found chain 1i6xA in template set T0381 20 :LARGLAVIRCFDHRNQR 1i6xA 140 :TGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 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:# T0381 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 (T0381)V127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)P128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)V129 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 15 :D 2cg4A 8 :N T0381 20 :LAR 2cg4A 9 :LDR T0381 25 :AVIRCFDHR 2cg4A 12 :GILEALMGN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2cg4A 21 :ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG T0381 69 :DG 2cg4A 60 :SP T0381 71 :SA 2cg4A 65 :GY T0381 73 :FWL 2cg4A 74 :IIL T0381 88 :SSLSLPEVAQPHLEK 2cg4A 77 :KSAKDYPSALAKLES T0381 107 :VH 2cg4A 92 :LD T0381 120 :DIVYVAR 2cg4A 94 :EVTEAYY T0381 130 :SRIMTVGITI 2cg4A 104 :HYSIFIKVMC T0381 158 :LPDDELDAYLEK 2cg4A 114 :RSIDALQHVLIN Number of specific fragments extracted= 12 number of extra gaps= 1 total=28 Number of alignments=7 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set Warning: unaligning (T0381)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)G118 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 16 :YV 2cg4A 9 :LD T0381 24 :LAVIRCFDHRNQ 2cg4A 11 :RGILEALMGNAR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 2cg4A 23 :TAYAELAKQFGVSPETIHVRVEKMKQAGIITG T0381 69 :DG 2cg4A 60 :SP T0381 72 :AFWLT 2cg4A 65 :GYDVG T0381 87 :LSSLSLPEVAQPHLE 2cg4A 76 :LKSAKDYPSALAKLE T0381 106 :KVHESSSVSI 2cg4A 91 :SLDEVTEAYY T0381 119 :A 2cg4A 104 :H T0381 120 :DIVYVARVP 2cg4A 106 :SIFIKVMCR T0381 159 :PDDELDAYLEK 2cg4A 115 :SIDALQHVLIN Number of specific fragments extracted= 10 number of extra gaps= 1 total=38 Number of alignments=8 # 2cg4A read from 2cg4A/merged-good-all-a2m # found chain 2cg4A in template set Warning: unaligning (T0381)V127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)P128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)V129 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 25 :AVIRCFDH 2cg4A 12 :GILEALMG T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2cg4A 20 :NARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGAR T0381 71 :SAFWLT 2cg4A 64 :LGYDVG T0381 87 :LSSLSLPEVAQPHLEKL 2cg4A 76 :LKSAKDYPSALAKLESL T0381 119 :ADIVYVAR 2cg4A 93 :DEVTEAYY T0381 130 :SRIMTVGITI 2cg4A 104 :HYSIFIKVMC T0381 158 :LPDDELDAYLEK 2cg4A 114 :RSIDALQHVLIN Number of specific fragments extracted= 7 number of extra gaps= 1 total=45 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 # T0381 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 T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0381 69 :DG 2a61A 83 :DP T0381 71 :SAFWLTPRVLELGYSY 2a61A 90 :YFLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHKV 2a61A 106 :IERRENFIEKITSDL T0381 159 :PDDELDAYLEK 2a61A 121 :GKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 7 number of extra gaps= 0 total=52 Number of alignments=10 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0381 69 :DG 2a61A 83 :DP T0381 72 :AFWLTPRVLELGYSY 2a61A 91 :FLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHKV 2a61A 106 :IERRENFIEKITSDL T0381 159 :PDDELDAYLEK 2a61A 121 :GKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 Number of alignments=11 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP T0381 72 :AFWLTPRVLELGYSY 2a61A 91 :FLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHK 2a61A 106 :IERRENFIEKITSD T0381 158 :LPDDELDAYLEK 2a61A 120 :LGKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 6 number of extra gaps= 0 total=65 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 # T0381 read from 1r1tA/merged-good-all-a2m # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0381 4 :TEP 1r1tA 25 :LQA T0381 12 :PSPDYVQSLA 1r1tA 28 :IAPEVAQSLA T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1r1tA 94 :QGRH T0381 73 :FWLT 1r1tA 100 :YQLQ T0381 77 :P 1r1tA 105 :H T0381 91 :SLPEVAQPHLEK 1r1tA 106 :HIVALYQNALDH Number of specific fragments extracted= 8 number of extra gaps= 0 total=73 Number of alignments=13 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0381 4 :TE 1r1tA 25 :LQ T0381 11 :LPSPDYVQSLA 1r1tA 27 :AIAPEVAQSLA T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1r1tA 94 :QGRH T0381 73 :FWLT 1r1tA 100 :YQLQ T0381 94 :EVAQPHLEKLSHKV 1r1tA 105 :HHIVALYQNALDHL Number of specific fragments extracted= 7 number of extra gaps= 0 total=80 Number of alignments=14 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1r1tA 96 :R T0381 72 :AFWLT 1r1tA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEK 1r1tA 104 :DHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=85 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:# T0381 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 T0381 4 :TEP 1smtA 25 :LQA T0381 12 :PSPDYVQSLA 1smtA 28 :IAPEVAQSLA T0381 22 :RGLAVIRCFDH 1smtA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtA 94 :QGRH T0381 73 :FWLT 1smtA 100 :YQLQ T0381 89 :SLSLPEVAQPHLEK 1smtA 104 :DHHIVALYQNALDH Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 Number of alignments=16 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0381 4 :TE 1smtA 25 :LQ T0381 11 :LPSPDYVQSLA 1smtA 27 :AIAPEVAQSLA T0381 22 :RGLAVIRCF 1smtA 47 :NRLRLLSLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtA 56 :ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGS 1smtA 94 :QGR T0381 72 :AFWLT 1smtA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEKL 1smtA 104 :DHHIVALYQNALDHL Number of specific fragments extracted= 7 number of extra gaps= 0 total=99 Number of alignments=17 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0381 22 :RGLAVIRCFD 1smtA 47 :NRLRLLSLLA T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1smtA 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1smtA 95 :G T0381 72 :AFWLT 1smtA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEKL 1smtA 104 :DHHIVALYQNALDHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=104 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:# T0381 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 Warning: unaligning (T0381)E5 because first residue in template chain is (1smtB)A20 T0381 6 :PTEKILP 1smtB 21 :IASELQA T0381 13 :SPDYVQSLA 1smtB 29 :APEVAQSLA T0381 22 :RGLAVIRCFDH 1smtB 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtB 94 :QGRH T0381 73 :FWLT 1smtB 100 :YQLQ T0381 77 :P 1smtB 105 :H T0381 91 :SLPEVAQPHLEK 1smtB 106 :HIVALYQNALDH Number of specific fragments extracted= 8 number of extra gaps= 0 total=112 Number of alignments=19 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set Warning: unaligning (T0381)E5 because first residue in template chain is (1smtB)A20 T0381 6 :PTEKILP 1smtB 21 :IASELQA T0381 13 :SPDYVQSLA 1smtB 29 :APEVAQSLA T0381 22 :RGLAVIRCF 1smtB 47 :NRLRLLSLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtB 56 :ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtB 94 :QGRH T0381 73 :FWLT 1smtB 100 :YQLQ T0381 89 :SLSLPEVAQPHLEK 1smtB 104 :DHHIVALYQNALDH Number of specific fragments extracted= 7 number of extra gaps= 0 total=119 Number of alignments=20 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0381 22 :RGLAVIRCFD 1smtB 47 :NRLRLLSLLA T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1smtB 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1smtB 95 :G T0381 72 :AFWLT 1smtB 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEK 1smtB 104 :DHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=124 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bi0 expands to /projects/compbio/data/pdb/1bi0.pdb.gz 1bi0:Warning: there is no chain 1bi0 will retry with 1bi0A # T0381 read from 1bi0/merged-good-all-a2m # 1bi0 read from 1bi0/merged-good-all-a2m # adding 1bi0 to template set # found chain 1bi0 in template set Warning: unaligning (T0381)L103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)H105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1bi0 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEK 1bi0 96 :KVHDE T0381 106 :K 1bi0 104 :W T0381 155 :LAGLPDDELDAYLEKL 1bi0 105 :EHVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=131 Number of alignments=22 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set Warning: unaligning (T0381)L100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)K102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 1bi0 60 :RSLQMTPTGRTLATAVMR T0381 90 :LSL 1bi0 90 :IGL T0381 93 :PEVAQPH 1bi0 94 :INKVHDE T0381 103 :L 1bi0 104 :W T0381 107 :V 1bi0 105 :E T0381 156 :AGLPDDELDAYLEKL 1bi0 106 :HVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=140 Number of alignments=23 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set Warning: unaligning (T0381)L103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)H105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1bi0 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEK 1bi0 96 :KVHDE T0381 154 :LLAGLPDDELDAYLEKL 1bi0 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=146 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gauA expands to /projects/compbio/data/pdb/2gau.pdb.gz 2gauA:# T0381 read from 2gauA/merged-good-all-a2m # 2gauA read from 2gauA/merged-good-all-a2m # adding 2gauA to template set # found chain 2gauA in template set T0381 20 :LARGLAVIRCFDHR 2gauA 154 :RGRLAETLLILKEN T0381 34 :NQR 2gauA 172 :NDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 4 number of extra gaps= 0 total=150 Number of alignments=25 # 2gauA read from 2gauA/merged-good-all-a2m # found chain 2gauA in template set T0381 18 :QSLARGLAVIRCFDHRNQR 2gauA 156 :RLAETLLILKENFGFENDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=153 Number of alignments=26 # 2gauA read from 2gauA/merged-good-all-a2m # found chain 2gauA in template set T0381 17 :VQSLARGLAVIRCFDHRNQR 2gauA 155 :GRLAETLLILKENFGFENDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=156 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c0wA expands to /projects/compbio/data/pdb/1c0w.pdb.gz 1c0wA:# T0381 read from 1c0wA/merged-good-all-a2m # 1c0wA read from 1c0wA/merged-good-all-a2m # adding 1c0wA to template set # found chain 1c0wA in template set T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1c0wA 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1c0wA 96 :KVHDEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLT 1c0wA 106 :HVMSDEVERRLVKVLKDVSRS T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=161 Number of alignments=28 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 1c0wA 60 :RSLQMTPTGRTLATAVMR T0381 89 :SLSLP 1c0wA 89 :IIGLD T0381 96 :AQPHLEKLSHKVH 1c0wA 94 :INKVHDEACRWEH T0381 157 :GLPDDELDAYLEKL 1c0wA 107 :VMSDEVERRLVKVL T0381 171 :DIQRLT 1c0wA 122 :DVSRSP T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=168 Number of alignments=29 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1c0wA 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1c0wA 96 :KVHDEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLT 1c0wA 106 :HVMSDEVERRLVKVLKDVSRS T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=30 # 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:# T0381 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 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLP 1b1bA 60 :RHLELTEKGRALAIAVMRKHRLA T0381 94 :EVAQPHLEK 1b1bA 95 :EEVHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=179 Number of alignments=31 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1b1bA)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLS 1b1bA 60 :RHLELTEKGRALAIAVMR T0381 89 :SLS 1b1bA 89 :VIG T0381 92 :LPEVAQPHLEK 1b1bA 93 :PWEEVHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=186 Number of alignments=32 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEV 1b1bA 60 :RHLELTEKGRALAIAVMRKHRLAER T0381 96 :AQPHLEK 1b1bA 97 :VHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=192 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j75A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j75A expands to /projects/compbio/data/pdb/1j75.pdb.gz 1j75A:# T0381 read from 1j75A/merged-good-all-a2m # 1j75A read from 1j75A/merged-good-all-a2m # adding 1j75A to template set # found chain 1j75A in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1j75A)G169 T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSS T0381 69 :DGSAFWL 1j75A 162 :EPATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=194 Number of alignments=34 # 1j75A read from 1j75A/merged-good-all-a2m # found chain 1j75A in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1j75A)G169 T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSS T0381 69 :DGSAFWL 1j75A 162 :EPATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=196 Number of alignments=35 # 1j75A read from 1j75A/merged-good-all-a2m # found chain 1j75A in template set T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSSPE T0381 71 :SAFWL 1j75A 164 :ATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=198 Number of alignments=36 # 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:# T0381 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 T0381 22 :RGLAVIRCFDH 1ri7A 28 :IDKKIIKILQN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1ri7A 39 :DGKAPLREISKITGLAESTIHERIRKLRESGVIKK T0381 69 :DG 1ri7A 75 :TA T0381 71 :SAFWL 1ri7A 84 :GYSML T0381 89 :SLSLPEVAQPHLEK 1ri7A 96 :KAGKYSEVASNLAK T0381 107 :V 1ri7A 110 :Y T0381 119 :ADIVYVARVPVSRIMTVGITI 1ri7A 111 :PEIVEVYETTGDYDMVVKIRT T0381 158 :LPDDELDAYLEKLD 1ri7A 132 :KNSEELNNFLDLIG Number of specific fragments extracted= 8 number of extra gaps= 0 total=206 Number of alignments=37 # 1ri7A read from 1ri7A/merged-good-all-a2m # found chain 1ri7A in template set T0381 21 :ARGLAVIRCFDHR 1ri7A 27 :EIDKKIIKILQND T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ri7A 40 :GKAPLREISKITGLAESTIHERIRKLRESGVIKKFT T0381 71 :SAFWL 1ri7A 84 :GYSML T0381 89 :SLSLPEVAQPHLE 1ri7A 96 :KAGKYSEVASNLA T0381 106 :KVHESSSVSIL 1ri7A 109 :KYPEIVEVYET T0381 117 :DGADIVYVARVP 1ri7A 121 :GDYDMVVKIRTK T0381 159 :PDDELDAYLEKL 1ri7A 133 :NSEELNNFLDLI T0381 194 :RA 1ri7A 145 :GS Number of specific fragments extracted= 8 number of extra gaps= 0 total=214 Number of alignments=38 # 1ri7A read from 1ri7A/merged-good-all-a2m # found chain 1ri7A in template set T0381 24 :LAVIRCFDH 1ri7A 30 :KKIIKILQN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ri7A 39 :DGKAPLREISKITGLAESTIHERIRKLRESGVIKKFT T0381 71 :SAFWL 1ri7A 83 :LGYSM T0381 89 :SLSLPEVAQPHLE 1ri7A 96 :KAGKYSEVASNLA T0381 106 :KVHESSSVSIL 1ri7A 109 :KYPEIVEVYET T0381 117 :DGADIVYVARV 1ri7A 121 :GDYDMVVKIRT T0381 158 :LPDDELDAYLEKL 1ri7A 132 :KNSEELNNFLDLI Number of specific fragments extracted= 7 number of extra gaps= 0 total=221 Number of alignments=39 # 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:# T0381 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 (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :F 1i1gA 13 :L T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 14 :EKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :SAFWL 1i1gA 61 :GYSLV T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSS 1i1gA 89 :FVKE T0381 124 :VARVPVSR 1i1gA 93 :LYLSSGDH T0381 134 :TVGITIG 1i1gA 103 :MAVIWAK T0381 159 :PDDELDAYLEK 1i1gA 110 :DGEDLAEIISN Number of specific fragments extracted= 9 number of extra gaps= 3 total=230 Number of alignments=40 # 1i1gA read from 1i1gA/merged-good-all-a2m # found chain 1i1gA in template set Warning: unaligning (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)V107 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)D88 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :FDH 1i1gA 13 :LEK T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 16 :DARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :S 1i1gA 61 :G T0381 73 :FWL 1i1gA 62 :YSL T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSS 1i1gA 89 :FVKE T0381 124 :VARVPVSR 1i1gA 93 :LYLSSGDH T0381 134 :TVGITIG 1i1gA 103 :MAVIWAK T0381 159 :PDDELDAYLEK 1i1gA 110 :DGEDLAEIISN Number of specific fragments extracted= 10 number of extra gaps= 3 total=240 Number of alignments=41 # 1i1gA read from 1i1gA/merged-good-all-a2m # found chain 1i1gA in template set Warning: unaligning (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :FDH 1i1gA 13 :LEK T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 16 :DARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :SAFWL 1i1gA 60 :LGYSL T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSSV 1i1gA 89 :FVKEL T0381 125 :ARVPVSR 1i1gA 94 :YLSSGDH T0381 134 :TVG 1i1gA 103 :MAV T0381 155 :LAGLPDDELDAYLEK 1i1gA 106 :IWAKDGEDLAEIISN Number of specific fragments extracted= 9 number of extra gaps= 3 total=249 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yspA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0381 read from 1yspA/merged-good-all-a2m # 1yspA read from 1yspA/merged-good-all-a2m # found chain 1yspA in training set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDL 1yspA 146 :RFSEERL T0381 243 :SDLIPSLRVTATDIEQDLA 1yspA 153 :QEYVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=253 Number of alignments=43 # 1yspA read from 1yspA/merged-good-all-a2m # found chain 1yspA in training set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDL 1yspA 146 :RFSEERL T0381 243 :SDLIPSLRVTATDIEQDLA 1yspA 153 :QEYVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=257 Number of alignments=44 # 1yspA read from 1yspA/merged-good-all-a2m # found chain 1yspA in training set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDLHS 1yspA 146 :RFSEERLQE T0381 245 :LIPSLRVTATDIEQDLA 1yspA 155 :YVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=261 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qzzA expands to /projects/compbio/data/pdb/1qzz.pdb.gz 1qzzA:# T0381 read from 1qzzA/merged-good-all-a2m # 1qzzA read from 1qzzA/merged-good-all-a2m # adding 1qzzA to template set # found chain 1qzzA in template set Warning: unaligning (T0381)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)G86 T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEG T0381 69 :D 1qzzA 83 :E T0381 71 :SAFWLTP 1qzzA 87 :RPLRPTR T0381 79 :VLELGYSYLSS 1qzzA 115 :AVSHADLAFTG T0381 90 :LSLPE 1qzzA 127 :LDVVR T0381 96 :AQPHL 1qzzA 145 :FWEDL T0381 101 :EKLSHKV 1qzzA 153 :VALADSF T0381 118 :GA 1qzzA 168 :DL T0381 127 :VPVSRIMTVGITIG 1qzzA 178 :YDWSAVRHVLDVGG T0381 146 :YATSMGRVLLAGLPD 1qzzA 192 :GNGGMLAAIALRAPH T0381 161 :DELDAYLEKLDIQ 1qzzA 219 :ERARRRFADAGLA T0381 196 :DGICVLDQELEAGL 1qzzA 232 :DRVTVAEGDFFKPL T0381 227 :VNISTPAARYSLEDL 1qzzA 252 :VLLSFVLLNWSDEDA T0381 246 :IPSLRVTAT 1qzzA 267 :LTILRGCVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=277 Number of alignments=46 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set Warning: unaligning (T0381)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)G86 T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEG T0381 69 :D 1qzzA 83 :E T0381 71 :SAFWLTP 1qzzA 87 :RPLRPTR T0381 79 :VLELGYSYLSS 1qzzA 115 :AVSHADLAFTG T0381 90 :LSLPEV 1qzzA 127 :LDVVRT T0381 96 :AQPHL 1qzzA 145 :FWEDL T0381 101 :EKLSHKV 1qzzA 153 :VALADSF T0381 117 :DGA 1qzzA 167 :EDL T0381 164 :DAYLEKLDIQRL 1qzzA 172 :EAPADAYDWSAV T0381 176 :TERT 1qzzA 204 :APHL T0381 183 :RDELKAAILAVRA 1qzzA 214 :LAGPAERARRRFA T0381 196 :DGICVLDQELEAGL 1qzzA 232 :DRVTVAEGDFFKPL T0381 226 :AVNISTPAARYSLEDL 1qzzA 251 :VVLLSFVLLNWSDEDA T0381 246 :IPSLRVTAT 1qzzA 267 :LTILRGCVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=293 Number of alignments=47 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=296 Number of alignments=48 # 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 # T0381 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 (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLS 2fxaA 103 :YVQLTEEGTEVFWSLLEEFD T0381 92 :LPEVAQPHLEK 2fxaA 128 :VFKGSQPLYHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=300 Number of alignments=49 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLSLPE 2fxaA 103 :YVQLTEEGTEVFWSLLEEFDPTR T0381 95 :VAQPHLEK 2fxaA 131 :GSQPLYHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=304 Number of alignments=50 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLSLPE 2fxaA 103 :YVQLTEEGTEVFWSLLEEFDPTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=307 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dtr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dtr expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtr:Warning: there is no chain 2dtr will retry with 2dtrA # T0381 read from 2dtr/merged-good-all-a2m # 2dtr read from 2dtr/merged-good-all-a2m # adding 2dtr to template set # found chain 2dtr in template set T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEV 2dtr 60 :RSLQMTPTGRTLATAVMRKHRLAER T0381 96 :AQPHLEK 2dtr 97 :VHDEACR T0381 154 :LLAGLPDDELDAYLEKL 2dtr 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=313 Number of alignments=52 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 2dtr 60 :RSLQMTPTGRTLATAVMR T0381 89 :SLSLPEVAQPH 2dtr 94 :INKVHDEACRW T0381 155 :LAGLPDDELDAYLEKL 2dtr 105 :EHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=319 Number of alignments=53 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0381 18 :QS 2dtr 7 :TT T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 2dtr 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 104 :SHKVHE 2dtr 87 :TDIIGL T0381 138 :TIGT 2dtr 93 :DINK T0381 154 :LLAGLPDDELDAYLEKL 2dtr 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=327 Number of alignments=54 # 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 # T0381 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 (T0381)L11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)H162 Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0381)G70 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 T0381 12 :PSPDYVQSL 2b0lA 163 :HHHHMSKAV T0381 21 :ARG 2b0lA 173 :QMA T0381 24 :LAVIRCFD 2b0lA 184 :LEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SAFW 2b0lA 238 :KGTY T0381 75 :LTPRVLELGY 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=336 Number of alignments=55 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0381)G70 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 T0381 21 :ARGLAVIRCFD 2b0lA 181 :YSELEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SA 2b0lA 238 :KG T0381 73 :F 2b0lA 241 :Y T0381 74 :WLTPRVLELGY 2b0lA 244 :VLNNKFLIELE Number of specific fragments extracted= 8 number of extra gaps= 4 total=344 Number of alignments=56 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0381)P6 because first residue in template chain is (2b0lA)H161 Warning: unaligning (T0381)T7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)H162 Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0381)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 T0381 8 :EKILPSPDYVQSLA 2b0lA 163 :HHHHMSKAVVQMAI T0381 22 :RGLAVIRCFD 2b0lA 182 :SELEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SAFW 2b0lA 238 :KGTY T0381 75 :LTPRVLE 2b0lA 245 :LNNKFLI Number of specific fragments extracted= 8 number of extra gaps= 4 total=352 Number of alignments=57 # 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 # T0381 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 # T0381 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 (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVAT 2fbhA 62 :VEGPTLARLLDGLESQGLVRR T0381 69 :DG 2fbhA 86 :AE T0381 71 :SAFWLTPRVLELGYS 2fbhA 92 :KHIVLTPKADVLIAD T0381 92 :LPEVAQPHLEKLSH 2fbhA 107 :IEAIAASVRNDVLT T0381 157 :GLPDDELDAYLEKL 2fbhA 121 :GIDESEQALCQQVL Number of specific fragments extracted= 6 number of extra gaps= 1 total=358 Number of alignments=58 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVAT 2fbhA 62 :VEGPTLARLLDGLESQGLVRR T0381 69 :DG 2fbhA 86 :AE T0381 71 :SAFWLTPRVLELGYSY 2fbhA 92 :KHIVLTPKADVLIADI T0381 93 :PEVAQPHLEKLSH 2fbhA 108 :EAIAASVRNDVLT T0381 157 :GLPDDELDAYLEK 2fbhA 121 :GIDESEQALCQQV T0381 186 :LKAAIL 2fbhA 134 :LLRILA Number of specific fragments extracted= 7 number of extra gaps= 1 total=365 Number of alignments=59 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVATDG 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLA T0381 71 :SA 2fbhA 88 :DR T0381 131 :RIMTVGI 2fbhA 90 :RAKHIVL T0381 176 :TERTITARDELKAAILAVRADG 2fbhA 97 :TPKADVLIADIEAIAASVRNDV T0381 219 :ASG 2fbhA 119 :LTG T0381 236 :YSLEDLHSDLIPSLRVTATD 2fbhA 122 :IDESEQALCQQVLLRILANL Number of specific fragments extracted= 7 number of extra gaps= 1 total=372 Number of alignments=60 # 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 # T0381 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 Warning: unaligning (T0381)S13 because first residue in template chain is (1j5yA)M3 Warning: unaligning (T0381)D202 because last residue in template chain is (1j5yA)E174 T0381 14 :PDYV 1j5yA 4 :KTVR T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 8 :QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 93 :PEVAQPHLEKLSHK 1j5yA 81 :PEEIKEELLCVVRN T0381 118 :GADIVYVARVPVSR 1j5yA 95 :GGRIVDVIVEHPVY T0381 132 :IMTVGITI 1j5yA 110 :EIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTI 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLT T0381 181 :TARDELKAAILAVRADGICVL 1j5yA 153 :PDEETMERIMRELKKKGFLIE Number of specific fragments extracted= 8 number of extra gaps= 0 total=380 Number of alignments=61 # 1j5yA read from 1j5yA/merged-good-all-a2m # found chain 1j5yA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1j5yA)M3 T0381 14 :PDYV 1j5yA 4 :KTVR T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 8 :QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 92 :LPEVAQPHLEKLSHKVHESSSVSILDG 1j5yA 80 :APEEIKEELLCVVRNGGRIVDVIVEHP T0381 129 :VSRIMTVGITI 1j5yA 107 :VYGEIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTIT 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLTL T0381 219 :ASGLTVAAVNIS 1j5yA 142 :SGGVHLHTIEAP T0381 238 :LEDLHSDLIPSLRV 1j5yA 154 :DEETMERIMRELKK Number of specific fragments extracted= 8 number of extra gaps= 0 total=388 Number of alignments=62 # 1j5yA read from 1j5yA/merged-good-all-a2m # found chain 1j5yA in template set Warning: unaligning (T0381)D202 because last residue in template chain is (1j5yA)E174 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 9 :ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 93 :PEVAQPHLEKLSHK 1j5yA 81 :PEEIKEELLCVVRN T0381 118 :GADIVYVARVPVS 1j5yA 95 :GGRIVDVIVEHPV T0381 131 :RIMTVGITI 1j5yA 109 :GEIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTI 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLT T0381 182 :ARDELKAAILAVRADGICVL 1j5yA 154 :DEETMERIMRELKKKGFLIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=395 Number of alignments=63 # 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:# T0381 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 Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 5 :KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKI T0381 243 :SDLIPSLRVTATDIEQDLA 1mkmA 227 :EEYSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=398 Number of alignments=64 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 4 :LKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKI T0381 243 :SDLIPSLRVTATDIEQDLA 1mkmA 227 :EEYSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=401 Number of alignments=65 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 5 :KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDLHS 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEE T0381 245 :LIPSLRVTATDIEQDLA 1mkmA 229 :YSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=404 Number of alignments=66 # 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 # T0381 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 T0381 9 :KILPSPDYVQSL 2ethA 19 :SYLPSNEEISDM T0381 21 :ARGLAVIRCFDHR 2ethA 32 :TTELYAFLYVALF T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVR T0381 69 :DG 2ethA 81 :DP T0381 71 :SAFWLTPRVLELGYSYLSS 2ethA 88 :YRVVLTEKGKEIFGEILSN T0381 97 :QPHLEKLSHK 2ethA 107 :FESLLKSVLE T0381 157 :GLPDDELDAYLEKL 2ethA 117 :KFSEEDFKVVSEGF Number of specific fragments extracted= 7 number of extra gaps= 0 total=411 Number of alignments=67 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set T0381 9 :KILPSPDYVQSL 2ethA 19 :SYLPSNEEISDM T0381 21 :ARGLAVIRCFDHR 2ethA 32 :TTELYAFLYVALF T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVR T0381 69 :DG 2ethA 81 :DP T0381 71 :S 2ethA 86 :R T0381 72 :AFWLTPRVLELGYSYLSS 2ethA 89 :RVVLTEKGKEIFGEILSN T0381 97 :QPHLEKLSHK 2ethA 107 :FESLLKSVLE T0381 157 :GLPDDELDAYLEK 2ethA 117 :KFSEEDFKVVSEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=419 Number of alignments=68 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set T0381 12 :PSPDYVQ 2ethA 22 :PSNEEIS T0381 21 :ARGLAVIRCFDHRN 2ethA 32 :TTELYAFLYVALFG T0381 36 :RRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2ethA 46 :PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREM T0381 130 :SRIMTVGIT 2ethA 85 :RRTYRVVLT T0381 161 :DELDAYLEKL 2ethA 94 :EKGKEIFGEI T0381 180 :ITARDELKAAIL 2ethA 104 :LSNFESLLKSVL T0381 234 :ARYSLEDLHSDLIPSLRVTATDI 2ethA 116 :EKFSEEDFKVVSEGFNRMVEALS Number of specific fragments extracted= 7 number of extra gaps= 0 total=426 Number of alignments=69 # 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:# T0381 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 T0381 8 :EKILPSPDYVQSLARGL 1lj9A 24 :KELSLTRGQYLYLVRVC T0381 32 :HR 1lj9A 41 :EN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lj9A 43 :PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYR T0381 69 :DG 1lj9A 79 :DA T0381 71 :SAFWLTPRVLEL 1lj9A 86 :KRIYATEKGKNV T0381 93 :PEVAQPHLEKLSHK 1lj9A 98 :YPIIVRENQHSNQV T0381 154 :LLAGLPDDELDAYLEKL 1lj9A 112 :ALQGLSEVEISQLADYL T0381 187 :KAAIL 1lj9A 129 :VRMRK Number of specific fragments extracted= 8 number of extra gaps= 0 total=434 Number of alignments=70 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0381 8 :EKILPSPDYVQSLARGLA 1lj9A 24 :KELSLTRGQYLYLVRVCE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYR T0381 69 :DG 1lj9A 79 :DA T0381 71 :SAFWLTPRVLELG 1lj9A 86 :KRIYATEKGKNVY T0381 94 :EVAQPHLEKLSHKVH 1lj9A 99 :PIIVRENQHSNQVAL T0381 156 :AGLPDDELDAYLEK 1lj9A 114 :QGLSEVEISQLADY T0381 183 :R 1lj9A 128 :L T0381 187 :KAAILAVR 1lj9A 129 :VRMRKNVS Number of specific fragments extracted= 8 number of extra gaps= 0 total=442 Number of alignments=71 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0381 9 :KILPSPDYVQSLARGLA 1lj9A 25 :ELSLTRGQYLYLVRVCE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE T0381 128 :PVSRIMTVGIT 1lj9A 81 :SNKKIKRIYAT T0381 161 :DELDAYLE 1lj9A 92 :EKGKNVYP T0381 185 :ELKAAILAVRADG 1lj9A 100 :IIVRENQHSNQVA T0381 219 :ASG 1lj9A 113 :LQG T0381 236 :YSLEDLHSDLIPSLRVTATDIEQDLATV 1lj9A 116 :LSEVEISQLADYLVRMRKNVSEDWEFVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=449 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qgpA expands to /projects/compbio/data/pdb/1qgp.pdb.gz 1qgpA:# T0381 read from 1qgpA/merged-good-all-a2m # 1qgpA read from 1qgpA/merged-good-all-a2m # adding 1qgpA to template set # found chain 1qgpA in template set T0381 12 :PSPDYVQSLAR 1qgpA 131 :QELSIYQDQEQ T0381 25 :AVIRCFDHRNQRR 1qgpA 142 :RILKFLEELGEGK T0381 38 :TLSDVARATDLTRATARRFLLTLVELGYVATDGSAF 1qgpA 157 :TAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTP Number of specific fragments extracted= 3 number of extra gaps= 0 total=452 Number of alignments=73 # 1qgpA read from 1qgpA/merged-good-all-a2m # found chain 1qgpA in template set T0381 13 :SPDYVQ 1qgpA 132 :ELSIYQ T0381 19 :SLARGLAVIRCF 1qgpA 139 :QEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qgpA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qgpA 193 :PLWKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=456 Number of alignments=74 # 1qgpA read from 1qgpA/merged-good-all-a2m # found chain 1qgpA in template set T0381 8 :EKILPSPDYVQ 1qgpA 127 :SSHFQELSIYQ T0381 19 :SLARGLAVIRCFDH 1qgpA 139 :QEQRILKFLEELGE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1qgpA 153 :GKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=459 Number of alignments=75 # 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 # T0381 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 (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 Warning: unaligning (T0381)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)P143 Warning: unaligning (T0381)A145 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)Y146 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A233 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 T0381 21 :ARGLAVIRCFDHR 1bia 5 :TVPLKLIALLANG T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 18 :EFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 77 :P 1bia 70 :K T0381 85 :SYLSSLS 1bia 71 :QILGQLD T0381 92 :LPEVAQPHLE 1bia 86 :VIDSTNQYLL T0381 107 :VHESSSVSIL 1bia 127 :FGANLYLSMF T0381 125 :A 1bia 137 :W T0381 136 :GIT 1bia 138 :RLE T0381 142 :RLP 1bia 144 :AAA T0381 147 :AT 1bia 149 :LS T0381 149 :SMGRVLL 1bia 152 :VIGIVMA T0381 165 :AYLEKLDIQRLT 1bia 159 :EVLRKLGADKVR T0381 211 :S 1bia 171 :V T0381 212 :MAAPIR 1bia 184 :LAGILV T0381 222 :LTVAAVNISTP 1bia 200 :QIVIGAGINMA T0381 236 :YSLEDLHSDLIPSLRVTATDIEQ 1bia 233 :LDRNTLAAMLIRELRAALELFEQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=477 Number of alignments=76 # 1bia read from 1bia/merged-good-all-a2m # found chain 1bia in template set Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 Warning: unaligning (T0381)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)P143 Warning: unaligning (T0381)A145 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)Y146 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A233 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 T0381 21 :ARGLAVIRCFDHR 1bia 5 :TVPLKLIALLANG T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 18 :EFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 83 :GYSYLSSLS 1bia 69 :AKQILGQLD T0381 92 :LPEVAQPHL 1bia 86 :VIDSTNQYL T0381 104 :SHKVHES 1bia 95 :LDRIGEL T0381 111 :SSVSILDG 1bia 106 :ACIAEYQQ T0381 119 :ADIVYVARVPV 1bia 129 :ANLYLSMFWRL T0381 138 :T 1bia 140 :E T0381 142 :RLP 1bia 144 :AAA T0381 147 :AT 1bia 149 :LS T0381 149 :SMGRVLL 1bia 152 :VIGIVMA T0381 165 :AYLEKLDIQRLT 1bia 159 :EVLRKLGADKVR T0381 200 :VLDQELEAGLRSMA 1bia 173 :WPNDLYLQDRKLAG T0381 214 :APIR 1bia 189 :VELT T0381 222 :LTVAAVNISTP 1bia 200 :QIVIGAGINMA T0381 236 :YSLEDLHSDLIPSLRVTATDIEQD 1bia 233 :LDRNTLAAMLIRELRAALELFEQE Number of specific fragments extracted= 18 number of extra gaps= 1 total=495 Number of alignments=77 # 1bia read from 1bia/merged-good-all-a2m # found chain 1bia in template set Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)S125 Warning: unaligning (T0381)I137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)S125 Warning: unaligning (T0381)M150 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)G151 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)D202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)A198 Warning: unaligning (T0381)S220 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 Warning: unaligning (T0381)P232 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)W223 T0381 22 :RGLAVIRCFDH 1bia 6 :VPLKLIALLAN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 17 :GEFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 84 :YSYLSSLS 1bia 70 :KQILGQLD T0381 94 :EVAQPHLE 1bia 88 :DSTNQYLL T0381 105 :HKVHE 1bia 96 :DRIGE T0381 116 :LDGADIVYVARVPV 1bia 101 :LKSGDACIAEYQQA T0381 138 :TIGTRLPAYA 1bia 126 :PFGANLYLSM T0381 148 :TS 1bia 145 :AA T0381 152 :RVLLAGL 1bia 149 :LSLVIGI T0381 162 :ELDAYLEKLDIQRL 1bia 156 :VMAEVLRKLGADKV T0381 198 :ICVL 1bia 189 :VELT T0381 208 :GLRSMAAPIRGA 1bia 199 :AQIVIGAGINMA T0381 233 :AAR 1bia 224 :ITL T0381 236 :YSLEDLHSDLIPSLRVTATDIEQD 1bia 233 :LDRNTLAAMLIRELRAALELFEQE Number of specific fragments extracted= 16 number of extra gaps= 1 total=511 Number of alignments=78 # 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 # T0381 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 T0381 23 :GLAVIRCFDHR 1lnwA 39 :DVHVLKLIDEQ T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lnwA 50 :RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0381 69 :DG 1lnwA 86 :NP T0381 71 :S 1lnwA 91 :R T0381 73 :FWLTPRVLELG 1lnwA 95 :LFLTDEGLAIH T0381 94 :EVAQPHLEKLSHK 1lnwA 106 :QHAEAIMSRVHDE T0381 154 :LLAGLPDDELDAYLEKLD 1lnwA 119 :LFAPLTPVEQATLVHLLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=518 Number of alignments=79 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0381 24 :LAVIRCFDHRNQ 1lnwA 40 :VHVLKLIDEQRG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0381 69 :DG 1lnwA 86 :NP T0381 71 :S 1lnwA 91 :R T0381 72 :AFWLTPRVLELGYS 1lnwA 94 :QLFLTDEGLAIHQH T0381 96 :AQPHLEKLSHKV 1lnwA 108 :AEAIMSRVHDEL T0381 155 :LAGLPDDELDAYLEK 1lnwA 120 :FAPLTPVEQATLVHL T0381 183 :RDELKA 1lnwA 135 :LDQCLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=526 Number of alignments=80 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0381 24 :LAVIRCFDHRNQ 1lnwA 40 :VHVLKLIDEQRG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRER T0381 71 :SA 1lnwA 91 :RS T0381 73 :FWLTPRVLELGYS 1lnwA 95 :LFLTDEGLAIHQH T0381 96 :AQPHLEKLSHKV 1lnwA 108 :AEAIMSRVHDEL T0381 155 :LAGLPDDELDAYLEKL 1lnwA 120 :FAPLTPVEQATLVHLL T0381 191 :L 1lnwA 136 :D Number of specific fragments extracted= 7 number of extra gaps= 0 total=533 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tf1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tf1A expands to /projects/compbio/data/pdb/1tf1.pdb.gz 1tf1A:# T0381 read from 1tf1A/merged-good-all-a2m # 1tf1A read from 1tf1A/merged-good-all-a2m # adding 1tf1A to template set # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 11 :MDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=535 Number of alignments=82 # 1tf1A read from 1tf1A/merged-good-all-a2m # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 12 :DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=537 Number of alignments=83 # 1tf1A read from 1tf1A/merged-good-all-a2m # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 11 :MDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=539 Number of alignments=84 # 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:# T0381 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 T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSY Number of specific fragments extracted= 1 number of extra gaps= 0 total=540 Number of alignments=85 # 1q1hA read from 1q1hA/merged-good-all-a2m # found chain 1q1hA in template set T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSY T0381 71 :SAFWLTP 1q1hA 76 :FIYYWKP Number of specific fragments extracted= 2 number of extra gaps= 0 total=542 Number of alignments=86 # 1q1hA read from 1q1hA/merged-good-all-a2m # found chain 1q1hA in template set T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR Number of specific fragments extracted= 1 number of extra gaps= 0 total=543 Number of alignments=87 # 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:# T0381 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 T0381 21 :ARGLAVIRCFDHR 1jgsA 40 :AAQFKVLCSIRCA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0381 69 :DG 1jgsA 89 :NP T0381 72 :A 1jgsA 94 :R T0381 73 :FWLTPRVLELGYSYL 1jgsA 98 :VKLTTGGAAICEQCH T0381 94 :EVAQPHLEKLS 1jgsA 113 :QLVGQDLHQEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=549 Number of alignments=88 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0381 22 :RGLAVIRCFDHR 1jgsA 41 :AQFKVLCSIRCA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0381 69 :DG 1jgsA 89 :NP T0381 71 :S 1jgsA 94 :R T0381 72 :AFWLTPRVLELGYSY 1jgsA 97 :LVKLTTGGAAICEQC T0381 93 :PEVAQPHLEKLS 1jgsA 112 :HQLVGQDLHQEL T0381 175 :LTERTITARDELKA 1jgsA 124 :TKNLTADEVATLEY Number of specific fragments extracted= 7 number of extra gaps= 0 total=556 Number of alignments=89 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0381 22 :RGLAVIRCFDHRNQ 1jgsA 41 :AQFKVLCSIRCAAC T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1jgsA 55 :ITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP T0381 72 :AFWLTPRVLELGYSY 1jgsA 97 :LVKLTTGGAAICEQC T0381 93 :PEVAQPHLEK 1jgsA 112 :HQLVGQDLHQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=560 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qbjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qbjA expands to /projects/compbio/data/pdb/1qbj.pdb.gz 1qbjA:# T0381 read from 1qbjA/merged-good-all-a2m # 1qbjA read from 1qbjA/merged-good-all-a2m # adding 1qbjA to template set # found chain 1qbjA in template set Warning: unaligning (T0381)P14 because first residue in template chain is (1qbjA)S134 Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 15 :DYVQSLARGLAVIRCF 1qbjA 135 :IYQDQEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=563 Number of alignments=91 # 1qbjA read from 1qbjA/merged-good-all-a2m # found chain 1qbjA in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 15 :DYVQSLARGLAVIRCF 1qbjA 135 :IYQDQEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=566 Number of alignments=92 # 1qbjA read from 1qbjA/merged-good-all-a2m # found chain 1qbjA in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 16 :YVQSLARGLAVIRCFDH 1qbjA 136 :YQDQEQRILKFLEELGE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 153 :GKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=569 Number of alignments=93 # 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 # T0381 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 Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=571 Number of alignments=94 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=573 Number of alignments=95 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=575 Number of alignments=96 # 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:# T0381 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 (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 22 :RGLAVIRCFDH 2cfxA 6 :IDLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVAT 2cfxA 35 :SVTERVRQLESFGIIKQ T0381 69 :D 2cfxA 57 :D T0381 71 :SAFW 2cfxA 62 :GLPV T0381 88 :S 2cfxA 74 :K T0381 94 :EVAQPHLEKLSHKVHESSSVSILDG 2cfxA 75 :NADYERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 10 number of extra gaps= 2 total=585 Number of alignments=97 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 21 :ARGLAVIRCFDH 2cfxA 5 :QIDLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVAT 2cfxA 35 :SVTERVRQLESFGIIKQ T0381 69 :D 2cfxA 57 :D T0381 71 :SA 2cfxA 62 :GL T0381 93 :PEVAQPHLEKLSHKVHESSSVSILDG 2cfxA 74 :KNADYERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 9 number of extra gaps= 2 total=594 Number of alignments=98 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 23 :GLAVIRCFDH 2cfxA 7 :DLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVATD 2cfxA 35 :SVTERVRQLESFGIIKQY T0381 71 :SA 2cfxA 62 :GL T0381 97 :QPHLEKLSHKVHESSSVSILDG 2cfxA 78 :YERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 8 number of extra gaps= 3 total=602 Number of alignments=99 # 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:# T0381 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 Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1ddnA 60 :RSLQMTPTGRTLATAVMRKH T0381 94 :EVAQPHLE 1ddnA 80 :RLAERLLT T0381 105 :HKVHE 1ddnA 88 :DIIGL T0381 149 :SMGRVLLAGLPDDELDAYLEK 1ddnA 99 :DEADRWEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=607 Number of alignments=100 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 16 :YVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 4 :LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1ddnA 60 :RSLQMTPTGRTLATAVMRK T0381 93 :PEVAQPHLE 1ddnA 79 :HRLAERLLT T0381 105 :HKVHE 1ddnA 88 :DIIGL T0381 149 :SMGRVLLAGLPDDELDAYLEK 1ddnA 99 :DEADRWEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=612 Number of alignments=101 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1ddnA 60 :RSLQMTPTGRTLATAVMRK T0381 93 :PEVAQPHLEK 1ddnA 79 :HRLAERLLTD T0381 139 :IGTR 1ddnA 90 :IGLD T0381 154 :LLAGLPDDELDAYLEK 1ddnA 104 :WEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=617 Number of alignments=102 # 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:# T0381 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 T0381 21 :ARGLAVIRCFDH 1r1uA 26 :YNRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0381 69 :DG 1r1uA 74 :QG T0381 71 :SAFWLT 1r1uA 78 :MIYSLD T0381 77 :PRV 1r1uA 85 :IHV T0381 97 :QPHLEKLSHK 1r1uA 88 :ATMLKQAIHH Number of specific fragments extracted= 6 number of extra gaps= 0 total=623 Number of alignments=103 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set Warning: unaligning (T0381)H108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r1uA)H100 T0381 21 :ARGLAVIRCFDH 1r1uA 26 :YNRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0381 69 :DGS 1r1uA 74 :QGQ T0381 72 :AFWLT 1r1uA 79 :IYSLD T0381 94 :EVAQPHLEKLSHKV 1r1uA 85 :IHVATMLKQAIHHA Number of specific fragments extracted= 5 number of extra gaps= 1 total=628 Number of alignments=104 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0381 22 :RGLAVIRCFDH 1r1uA 27 :NRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR T0381 71 :S 1r1uA 75 :G T0381 72 :AFWLT 1r1uA 79 :IYSLD T0381 89 :SLSLPEVAQPHLEK 1r1uA 84 :DIHVATMLKQAIHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=633 Number of alignments=105 # 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:# T0381 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 T0381 20 :LARGLAVIRCFDHR 1ft9A 133 :HDIKQRIAGFFIDH T0381 35 :QR 1ft9A 152 :RQ T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP T0381 77 :PR 1ft9A 207 :VR Number of specific fragments extracted= 5 number of extra gaps= 0 total=638 Number of alignments=106 # 1ft9A read from 1ft9A/merged-good-all-a2m # found chain 1ft9A in template set T0381 20 :LARGLAVIRCFDHR 1ft9A 133 :HDIKQRIAGFFIDH T0381 35 :Q 1ft9A 152 :R T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP Number of specific fragments extracted= 4 number of extra gaps= 0 total=642 Number of alignments=107 # 1ft9A read from 1ft9A/merged-good-all-a2m # found chain 1ft9A in template set T0381 21 :ARGLAVIRCFDH 1ft9A 134 :DIKQRIAGFFID T0381 34 :NQ 1ft9A 151 :GR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP Number of specific fragments extracted= 4 number of extra gaps= 0 total=646 Number of alignments=108 # 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:# T0381 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 (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 16 :YVQSL 1u2wA 35 :ILKAI T0381 21 :ARGLAVIRCFDHR 1u2wA 42 :ENRAKITYALCQD T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 55 :EELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 77 :PRVLELGYSYLSS 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=651 Number of alignments=109 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 17 :VQSL 1u2wA 36 :LKAI T0381 21 :ARGLAVIRCFDHR 1u2wA 42 :ENRAKITYALCQD T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 55 :EELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 93 :PEVAQPHLEKLSHKVHE 1u2wA 101 :DEHIRQIMMIALAHKKE Number of specific fragments extracted= 5 number of extra gaps= 0 total=656 Number of alignments=110 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 15 :DYVQSLA 1u2wA 34 :QILKAIA T0381 22 :RGLAVIRCFDH 1u2wA 43 :NRAKITYALCQ T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 89 :SLSLPEVAQPHLEK 1u2wA 101 :DEHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=661 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1stzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1stzA expands to /projects/compbio/data/pdb/1stz.pdb.gz 1stzA:# T0381 read from 1stzA/merged-good-all-a2m # 1stzA read from 1stzA/merged-good-all-a2m # adding 1stzA to template set # found chain 1stzA in template set Warning: unaligning (T0381)P12 because first residue in template chain is (1stzA)K14 Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 13 :SPDYVQ 1stzA 15 :LNDRQR T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 21 :KVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYLSS 1stzA 75 :AGRIPTDKGLRFYYEEMLK T0381 90 :LS 1stzA 98 :TS T0381 92 :LPEVAQPHLEKLSHKVHESSSV 1stzA 116 :PEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLPA 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLNW T0381 146 :YATSMGRVL 1stzA 196 :RGRTVGEVL T0381 157 :GLPDDELDAYLEKLD 1stzA 244 :TLTLEDIRNLLEEVK T0381 182 :ARDELKAA 1stzA 259 :DQKFLESL T0381 198 :ICVLDQEL 1stzA 272 :TVRIGREI T0381 206 :EAG 1stzA 284 :LEK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDL 1stzA 311 :VTKYDRN T0381 242 :HSDLIPSLRVTATD 1stzA 321 :FEYILNRLSEYFTS Number of specific fragments extracted= 18 number of extra gaps= 2 total=679 Number of alignments=112 # 1stzA read from 1stzA/merged-good-all-a2m # found chain 1stzA in template set Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 14 :PDY 1stzA 16 :NDR T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 19 :QRKVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYL 1stzA 75 :AGRIPTDKGLRFYYEEM T0381 88 :SSLS 1stzA 96 :KETS T0381 92 :LPEVAQPHLEKLSHKVHESSSV 1stzA 116 :PEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLP 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLN T0381 145 :AYATSMGRVL 1stzA 195 :LRGRTVGEVL T0381 157 :GLPDDELDAYLEKLD 1stzA 244 :TLTLEDIRNLLEEVK T0381 182 :ARDELKAA 1stzA 259 :DQKFLESL T0381 198 :ICVLDQELE 1stzA 272 :TVRIGREIG T0381 207 :AG 1stzA 285 :EK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDL 1stzA 311 :VTKYDRN T0381 246 :IPSLRVTATDIEQDL 1stzA 318 :HRVFEYILNRLSEYF Number of specific fragments extracted= 18 number of extra gaps= 2 total=697 Number of alignments=113 # 1stzA read from 1stzA/merged-good-all-a2m # found chain 1stzA in template set Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 18 :RQRKVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYLSS 1stzA 75 :AGRIPTDKGLRFYYEEMLK T0381 90 :LSLPEVAQPHLEKLSHKVHESSSV 1stzA 114 :ADPEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLP 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLN T0381 146 :YATSMGRVL 1stzA 196 :RGRTVGEVL T0381 157 :GLPDDELDAYLEKL 1stzA 244 :TLTLEDIRNLLEEV T0381 181 :TARDELKAA 1stzA 258 :KDQKFLESL T0381 198 :ICVLDQEL 1stzA 272 :TVRIGREI T0381 206 :EAG 1stzA 284 :LEK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDLHSDLIPSLRVTATDIE 1stzA 311 :VTKYDRNHRVFEYILNRLSEYFT Number of specific fragments extracted= 15 number of extra gaps= 2 total=712 Number of alignments=114 # 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 # T0381 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 T0381 21 :ARGL 1lvaA 381 :KILA T0381 28 :RCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lvaA 385 :QIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL T0381 69 :DGSAFWLTPRVLELGYSYLSS 1lvaA 429 :ENDLYAISTERYQAWWQAVTR T0381 90 :LSLPEVAQPHL 1lvaA 475 :SRLPARVYQAL T0381 101 :EKLSHK 1lvaA 487 :EEWSRE T0381 108 :HE 1lvaA 493 :GR T0381 114 :SILDGADI 1lvaA 495 :LQLAANTV T0381 137 :ITIGTRLP 1lvaA 503 :ALAGFTPS T0381 158 :LPDDE 1lvaA 511 :FSETQ T0381 163 :LDAYLEKLDI 1lvaA 522 :LEDKYRVSRW T0381 173 :QRLTERTITARDELKAAILAVRADGICVL 1lvaA 537 :KEVAGSFNLDPSELEELLHYLVREGVLVK T0381 202 :DQE 1lvaA 567 :NDE T0381 234 :ARYSLEDL 1lvaA 570 :FYWHRQAL T0381 243 :SDLIPSLRVTAT 1lvaA 578 :GEAREVIKNLAS T0381 255 :DIEQDLA 1lvaA 597 :EARDALG Number of specific fragments extracted= 15 number of extra gaps= 0 total=727 Number of alignments=115 # 1lvaA read from 1lvaA/merged-good-all-a2m # found chain 1lvaA in template set T0381 21 :ARGLA 1lvaA 381 :KILAQ T0381 29 :CFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lvaA 386 :IIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL T0381 69 :DGSAFWLTPRVLELGYSY 1lvaA 429 :ENDLYAISTERYQAWWQA T0381 96 :AQPHLEKLSHKVHESSSV 1lvaA 447 :VTRALEEFHSRYPLRPGL T0381 114 :SILDGADI 1lvaA 495 :LQLAANTV T0381 137 :ITIGTRLP 1lvaA 503 :ALAGFTPS T0381 158 :LPDDE 1lvaA 511 :FSETQ T0381 163 :LDAYLEKL 1lvaA 519 :LKDLEDKY T0381 171 :DIQRLTERTITARDELKAAILAVRADGICVL 1lvaA 535 :SFKEVAGSFNLDPSELEELLHYLVREGVLVK T0381 219 :ASGL 1lvaA 566 :INDE T0381 234 :ARYSLEDL 1lvaA 570 :FYWHRQAL T0381 243 :SDLIPSLRVTAT 1lvaA 578 :GEAREVIKNLAS T0381 255 :DIEQDLA 1lvaA 597 :EARDALG Number of specific fragments extracted= 13 number of extra gaps= 0 total=740 Number of alignments=116 # 1lvaA read from 1lvaA/merged-good-all-a2m # found chain 1lvaA in template set T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lvaA 382 :ILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLR T0381 71 :SAFWLTPRVLE 1lvaA 431 :DLYAISTERYQ T0381 91 :SLPEVAQPHLEKLSHKVHE 1lvaA 442 :AWWQAVTRALEEFHSRYPL T0381 130 :SRIMT 1lvaA 461 :RPGLA T0381 160 :DDELDAYLEKLD 1lvaA 467 :EELRSRYFSRLP T0381 184 :DELKAA 1lvaA 479 :ARVYQA T0381 190 :ILAVRADGICVLDQE 1lvaA 486 :LEEWSREGRLQLAAN T0381 226 :AVNISTPAARYSLED 1lvaA 501 :TVALAGFTPSFSETQ T0381 246 :IPSLRVTATDIEQDLATV 1lvaA 516 :KKLLKDLEDKYRVSRWQP Number of specific fragments extracted= 9 number of extra gaps= 0 total=749 Number of alignments=117 # 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 # T0381 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 T0381 16 :YVQSLAR 1s3jA 26 :MLESMEK T0381 23 :GLAVIRCFDHR 1s3jA 39 :QLFVLASLKKH T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIAR T0381 70 :G 1s3jA 87 :T T0381 71 :SA 1s3jA 90 :RR T0381 73 :FWLTPRVLELGYSYL 1s3jA 95 :LSLTDEGDIKFEEVL T0381 94 :EVAQPHLEKLSH 1s3jA 110 :AGRKAIMARYLS T0381 157 :GLPDDELDAYLEK 1s3jA 122 :FLTEEEMLQAAHI Number of specific fragments extracted= 8 number of extra gaps= 0 total=757 Number of alignments=118 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set T0381 21 :ARGLAVIRCFDHR 1s3jA 37 :PAQLFVLASLKKH T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIAR T0381 70 :G 1s3jA 87 :T T0381 71 :S 1s3jA 91 :R T0381 73 :FWLTPRVLELGYSY 1s3jA 95 :LSLTDEGDIKFEEV T0381 93 :PEVAQPHLEKLSH 1s3jA 109 :LAGRKAIMARYLS T0381 157 :GLPDDELDAYLEK 1s3jA 122 :FLTEEEMLQAAHI Number of specific fragments extracted= 7 number of extra gaps= 0 total=764 Number of alignments=119 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set T0381 22 :RGLAVIRCFDHRNQ 1s3jA 38 :AQLFVLASLKKHGS T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1s3jA 52 :LKVSEIAERMEVKPSAVTLMADRLEQKNLIARTH T0381 128 :PVSRIMTVGIT 1s3jA 88 :KDRRVIDLSLT T0381 161 :DELDAYLEKL 1s3jA 99 :DEGDIKFEEV T0381 187 :KAAILAVRADG 1s3jA 109 :LAGRKAIMARY T0381 233 :AARYSLEDLHSDLIPSLRVTATDI 1s3jA 120 :LSFLTEEEMLQAAHITAKLAQAAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=770 Number of alignments=120 # 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 # T0381 read from 1on2A/merged-good-all-a2m # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0381 14 :PDYV 1on2A 4 :PSME T0381 21 :ARGLAVIRCFDHR 1on2A 8 :MYIEQIYMLIEEK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 21 :GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVH 1on2A 77 :HELLEQFLRIIG T0381 158 :LPDDELDAYLEKL 1on2A 89 :VDEEKIYNDVEGI T0381 233 :AARYSLEDL 1on2A 102 :EHHLSWNSI T0381 243 :SDLIPSLRVT 1on2A 111 :DRIGDLVQYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=778 Number of alignments=121 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0381 15 :D 1on2A 5 :S T0381 19 :SLARGLAVIRCFDHR 1on2A 6 :MEMYIEQIYMLIEEK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 21 :GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVH 1on2A 77 :HELLEQFLRIIG T0381 158 :LPDDELDAYLEK 1on2A 89 :VDEEKIYNDVEG T0381 232 :PAARYSLEDL 1on2A 101 :IEHHLSWNSI T0381 243 :SDLIPSLRVT 1on2A 111 :DRIGDLVQYF T0381 253 :ATDI 1on2A 127 :KKDL Number of specific fragments extracted= 9 number of extra gaps= 0 total=787 Number of alignments=122 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0381 15 :DYV 1on2A 5 :SME T0381 21 :ARGLAVIRCFDHRN 1on2A 8 :MYIEQIYMLIEEKG T0381 36 :RRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 22 :YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVHE 1on2A 77 :HELLEQFLRIIGV T0381 159 :PDDELDAYLEKL 1on2A 90 :DEEKIYNDVEGI T0381 233 :AARYSLEDLHSDLIPSLR 1on2A 102 :EHHLSWNSIDRIGDLVQY T0381 251 :VTATDIEQD 1on2A 125 :ARKKDLKSI Number of specific fragments extracted= 8 number of extra gaps= 0 total=795 Number of alignments=123 # 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 # T0381 read from 1sfxA/merged-good-all-a2m # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0381 13 :SPDYVQSLARG 1sfxA 1 :MSNPLGELVKA T0381 24 :LAVIRCFDHR 1sfxA 22 :VRIYSLLLER T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1sfxA 32 :GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0381 125 :ARVPVSRIMTVGITI 1sfxA 66 :EIVEKGWVGYIYSAE T0381 159 :PDDELDAYLEKL 1sfxA 81 :KPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=801 Number of alignments=124 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0381 16 :YVQSLAR 1sfxA 8 :LVKALEK T0381 24 :LAVIRCFDHRNQ 1sfxA 22 :VRIYSLLLERGG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0381 126 :RVPVSRIMTVGITI 1sfxA 67 :IVEKGWVGYIYSAE T0381 159 :PDDELDAYLEKL 1sfxA 81 :KPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=807 Number of alignments=125 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0381 11 :LPSPDYVQSLAR 1sfxA 3 :NPLGELVKALEK T0381 23 :GLAVIRCFDHRNQ 1sfxA 21 :DVRIYSLLLERGG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATD 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRRE T0381 126 :RVPVSRIMTVGI 1sfxA 67 :IVEKGWVGYIYS T0381 157 :GLPDDELDAYLEKL 1sfxA 79 :AEKPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=813 Number of alignments=126 # 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 # T0381 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 T0381 12 :PSPDYVQSL 1ulyA 9 :TDPEVIKVM T0381 21 :ARGLAVIRCFD 1ulyA 20 :DTRRKILKLLR T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 86 :YLSSLSLPEVAQPHLEKLSHKV 1ulyA 91 :YLGDEELRYIARSRLKTKIDIF T0381 138 :TIGTR 1ulyA 114 :RLGYQ T0381 158 :LPDDELDAYLEKLDI 1ulyA 119 :FEENELLNIMDRMSQ T0381 181 :TARDELKAAILAVRAD 1ulyA 134 :KEFDATVRISKYIEEK T0381 233 :AARYSLEDLHSDLIPSLRVTAT 1ulyA 153 :LKDFSNEDIIHAIEWLSTAELA Number of specific fragments extracted= 9 number of extra gaps= 0 total=822 Number of alignments=127 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0381 12 :PSPDYVQSL 1ulyA 9 :TDPEVIKVM T0381 21 :ARGLAVIRCF 1ulyA 20 :DTRRKILKLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ulyA 30 :RNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 85 :SYLSSLSLPEVAQPHLEKLSHKVH 1ulyA 90 :LYLGDEELRYIARSRLKTKIDIFK T0381 139 :IGTR 1ulyA 115 :LGYQ T0381 158 :LPDDELDAYLEKL 1ulyA 119 :FEENELLNIMDRM T0381 182 :ARDELKAAILAVRAD 1ulyA 135 :EFDATVRISKYIEEK T0381 232 :PAARYSLEDLHSDLIPSLRVTAT 1ulyA 152 :ALKDFSNEDIIHAIEWLSTAELA Number of specific fragments extracted= 9 number of extra gaps= 0 total=831 Number of alignments=128 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0381 13 :SPDYVQSL 1ulyA 10 :DPEVIKVM T0381 21 :ARGLAVIRCFD 1ulyA 20 :DTRRKILKLLR T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 87 :LSSLSLPEVAQPHLEKLSHKVH 1ulyA 92 :LGDEELRYIARSRLKTKIDIFK T0381 139 :IGT 1ulyA 115 :LGY T0381 157 :GLPDDELDAYLEKL 1ulyA 118 :QFEENELLNIMDRM T0381 179 :TITARDELKAAILAVRADG 1ulyA 132 :SQKEFDATVRISKYIEEKE T0381 203 :QE 1ulyA 151 :DA T0381 233 :AARYSLEDLHSDLIPSLRVTA 1ulyA 153 :LKDFSNEDIIHAIEWLSTAEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=841 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dbbA expands to /projects/compbio/data/pdb/2dbb.pdb.gz 2dbbA:# T0381 read from 2dbbA/merged-good-all-a2m # 2dbbA read from 2dbbA/merged-good-all-a2m # adding 2dbbA to template set # found chain 2dbbA in template set Warning: unaligning (T0381)P12 because first residue in template chain is (2dbbA)K6 T0381 13 :SPDYV 2dbbA 7 :LDRVD T0381 24 :LAVIRCFDHR 2dbbA 12 :MQLVKILSEN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2dbbA 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRK T0381 69 :DG 2dbbA 60 :PD T0381 71 :SAFW 2dbbA 66 :GYMY T0381 91 :SLPEVAQPHLEKLSH 2dbbA 77 :KVPSDADKVISEISD T0381 107 :VHESSSVSILDG 2dbbA 92 :IEYVKSVEKGVG T0381 119 :ADIVYVARVPV 2dbbA 105 :YNIIVRLLLPK T0381 159 :PDDELDAYLEK 2dbbA 116 :DIKDAENLISE T0381 193 :VRAD 2dbbA 127 :FLQR Number of specific fragments extracted= 10 number of extra gaps= 0 total=851 Number of alignments=130 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set T0381 21 :ARGLAVIRCFDHRNQ 2dbbA 9 :RVDMQLVKILSENSR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 2dbbA 24 :LTYRELADILNTTRQRIARRIDKLKKLGIIRK T0381 71 :SAFWL 2dbbA 66 :GYMYA T0381 91 :SLPEVAQPHLEKLSH 2dbbA 77 :KVPSDADKVISEISD T0381 107 :VHESSSVSILDGA 2dbbA 92 :IEYVKSVEKGVGR T0381 120 :DIVYVARVPV 2dbbA 106 :NIIVRLLLPK T0381 182 :ARDELKAAILAVRAD 2dbbA 116 :DIKDAENLISEFLQR Number of specific fragments extracted= 7 number of extra gaps= 0 total=858 Number of alignments=131 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set T0381 24 :LAVIRCFDH 2dbbA 12 :MQLVKILSE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFT T0381 72 :AFWL 2dbbA 66 :GYMY T0381 91 :SLPEV 2dbbA 77 :KVPSD T0381 100 :LEKLSHKVH 2dbbA 82 :ADKVISEIS T0381 109 :ESSSVSILDG 2dbbA 94 :YVKSVEKGVG T0381 119 :ADIVYVARVPV 2dbbA 105 :YNIIVRLLLPK T0381 159 :PDDELDAYLEKL 2dbbA 116 :DIKDAENLISEF T0381 172 :IQR 2dbbA 128 :LQR Number of specific fragments extracted= 9 number of extra gaps= 0 total=867 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ysqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0381 read from 1ysqA/merged-good-all-a2m # 1ysqA read from 1ysqA/merged-good-all-a2m # found chain 1ysqA in training set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSR 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTT T0381 132 :IMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 49 :MLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTP 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLS T0381 238 :LEDL 1ysqA 152 :TSRL T0381 242 :HSDLIPSLRVTATDIEQDLAT 1ysqA 160 :EKNLLKPLRETAQAISNELGF Number of specific fragments extracted= 6 number of extra gaps= 1 total=873 Number of alignments=133 # 1ysqA read from 1ysqA/merged-good-all-a2m # found chain 1ysqA in training set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRI 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTG T0381 133 :MTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 50 :LRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTPAARY 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLSTSRL T0381 237 :SL 1ysqA 159 :GE T0381 243 :SDLIPSLRVTATDIEQDLAT 1ysqA 161 :KNLLKPLRETAQAISNELGF Number of specific fragments extracted= 6 number of extra gaps= 1 total=879 Number of alignments=134 # 1ysqA read from 1ysqA/merged-good-all-a2m # found chain 1ysqA in training set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVS 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPT T0381 131 :RIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 48 :GMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTPAARY 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLSTSRL T0381 237 :SLEDLHSDLIPSLRVTATDIEQ 1ysqA 159 :GEKNLLKPLRETAQAISNELGF Number of specific fragments extracted= 5 number of extra gaps= 1 total=884 Number of alignments=135 # 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 # T0381 read from 1hw1A/merged-good-all-a2m # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRN 1hw1A 15 :YIIESIWNNR T0381 35 :QR 1hw1A 28 :GT T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 73 :FW 1hw1A 69 :TK T0381 75 :LTPRVLEL 1hw1A 78 :SGLNILET T0381 84 :YSYLSSLSLPEVAQPHLEKLSHKV 1hw1A 86 :LARLDHESVPQLIDNLLSVRTNIS T0381 145 :AYATSM 1hw1A 112 :FIRTAF T0381 159 :PDDELDAYLEKLD 1hw1A 120 :HPDKAQEVLATAN T0381 178 :RTITARDELKAAILAVRAD 1hw1A 133 :EVADHADAFAELDYNIFRG T0381 237 :SLEDL 1hw1A 158 :NPIYG T0381 243 :SDLIPSLRVTATDIEQDL 1hw1A 183 :PEARSLALGFYHKLSALC T0381 261 :A 1hw1A 203 :G Number of specific fragments extracted= 13 number of extra gaps= 0 total=897 Number of alignments=136 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRN 1hw1A 15 :YIIESIWNNR T0381 35 :Q 1hw1A 28 :G T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 75 :LTPRVLEL 1hw1A 78 :SGLNILET T0381 84 :YSYLSSLSLPEVAQPHLEKLSHKV 1hw1A 86 :LARLDHESVPQLIDNLLSVRTNIS T0381 145 :AYATSM 1hw1A 112 :FIRTAF T0381 159 :PDDELDAYLEKLD 1hw1A 120 :HPDKAQEVLATAN T0381 178 :RTITARDELKAAILAVRAD 1hw1A 133 :EVADHADAFAELDYNIFRG T0381 237 :SLEDLH 1hw1A 158 :NPIYGL T0381 243 :SDLIPSLRVTATDIEQDL 1hw1A 183 :PEARSLALGFYHKLSALC T0381 261 :A 1hw1A 203 :G Number of specific fragments extracted= 12 number of extra gaps= 0 total=909 Number of alignments=137 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRNQR 1hw1A 15 :YIIESIWNNRFP T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 75 :LTPRVLELG 1hw1A 78 :SGLNILETL T0381 85 :SYLSSLSLPEVAQPHLEKLSHKV 1hw1A 87 :ARLDHESVPQLIDNLLSVRTNIS T0381 147 :AT 1hw1A 114 :RT T0381 155 :LAGLPDDELDAYLEKL 1hw1A 116 :AFRQHPDKAQEVLATA T0381 177 :ERTITARDELKAAILAVRAD 1hw1A 132 :NEVADHADAFAELDYNIFRG T0381 239 :EDLHSDLIPSLRVTATDIEQ 1hw1A 183 :PEARSLALGFYHKLSALCSE Number of specific fragments extracted= 9 number of extra gaps= 0 total=918 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fnaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fnaA expands to /projects/compbio/data/pdb/2fna.pdb.gz 2fnaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 996, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fnaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1457, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 2fnaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 2fnaA/merged-good-all-a2m # 2fnaA read from 2fnaA/merged-good-all-a2m # adding 2fnaA to template set # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFD 2fnaA 289 :KRYLNIMRTLS T0381 35 :QRRTLSDVARAT 2fnaA 300 :KCGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=921 Number of alignments=139 # 2fnaA read from 2fnaA/merged-good-all-a2m # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFD 2fnaA 289 :KRYLNIMRTLS T0381 35 :QRRTLSDVARAT 2fnaA 300 :KCGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=924 Number of alignments=140 # 2fnaA read from 2fnaA/merged-good-all-a2m # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFDH 2fnaA 289 :KRYLNIMRTLSK T0381 36 :RRTLSDVARAT 2fnaA 301 :CGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=927 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0381 read from 1r7jA/merged-good-all-a2m # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0381 13 :SPD 1r7jA 4 :KSK T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHK 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=930 Number of alignments=142 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHK 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINSV Number of specific fragments extracted= 2 number of extra gaps= 0 total=932 Number of alignments=143 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSH 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINS Number of specific fragments extracted= 2 number of extra gaps= 0 total=934 Number of alignments=144 # 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:# T0381 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 T0381 16 :YVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1004 :LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1f5tA 1060 :RSLQMTPTGRTLATAVMRKH T0381 98 :PHLEKLSHKV 1f5tA 1080 :RLAERLLTDI T0381 108 :H 1f5tA 1091 :G T0381 127 :VPVSR 1f5tA 1092 :LDINK T0381 150 :MGRVLLAGLPDDELDAYLEKL 1f5tA 1100 :EADRWEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=940 Number of alignments=145 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set Warning: unaligning (T0381)P14 because first residue in template chain is (1f5tA)K1002 T0381 15 :DYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1003 :DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1f5tA 1060 :RSLQMTPTGRTLATAVMRK T0381 97 :QPHLEKLSHKV 1f5tA 1079 :HRLAERLLTDI T0381 108 :HE 1f5tA 1091 :GL T0381 138 :TIGT 1f5tA 1093 :DINK T0381 147 :ATSMGRVLLAGLPDDELDAYLEKL 1f5tA 1097 :VHDEADRWEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=946 Number of alignments=146 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0381 15 :DYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1003 :DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1f5tA 1060 :RSLQMTPTGRTLATAVMRKH T0381 94 :EVAQPHLE 1f5tA 1080 :RLAERLLT T0381 106 :KV 1f5tA 1088 :DI T0381 139 :IGTR 1f5tA 1090 :IGLD T0381 154 :LLAGLPDDELDAYLEKL 1f5tA 1104 :WEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=952 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1td5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1td5A expands to /projects/compbio/data/pdb/1td5.pdb.gz 1td5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1td5A/merged-good-all-a2m # 1td5A read from 1td5A/merged-good-all-a2m # adding 1td5A to template set # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 5 :RNLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRV T0381 243 :SDLIPSLRVTATDIEQDLAT 1td5A 159 :TEFGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=955 Number of alignments=148 # 1td5A read from 1td5A/merged-good-all-a2m # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 6 :NLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRV T0381 243 :SDLIPSLRVTATDIEQDLAT 1td5A 159 :TEFGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=958 Number of alignments=149 # 1td5A read from 1td5A/merged-good-all-a2m # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 5 :RNLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDLHS 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTE T0381 245 :LIPSLRVTATDIEQDLAT 1td5A 161 :FGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=961 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fx7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fx7A expands to /projects/compbio/data/pdb/1fx7.pdb.gz 1fx7A:Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1fx7A # T0381 read from 1fx7A/merged-good-all-a2m # 1fx7A read from 1fx7A/merged-good-all-a2m # adding 1fx7A to template set # found chain 1fx7A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1fx7A)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1fx7A 60 :RHLELTEKGRALAIAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1fx7A 96 :EVHAEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLTERTIT 1fx7A 106 :HVMSEDVERRLVKVLNNPTTSPFGNP Number of specific fragments extracted= 4 number of extra gaps= 0 total=965 Number of alignments=151 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1fx7A)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLS 1fx7A 60 :RHLELTEKGRALAIAVMR T0381 89 :SLSLPEV 1fx7A 91 :GLPWEEV T0381 100 :LEKLSHKVH 1fx7A 98 :HAEACRWEH T0381 157 :GLPDDELDAYLEKLDIQRLTERTIT 1fx7A 107 :VMSEDVERRLVKVLNNPTTSPFGNP T0381 187 :KAAILAVRADGI 1fx7A 178 :IDLITRLKDAGV T0381 206 :EAGLRSM 1fx7A 190 :VPNARVT T0381 216 :I 1fx7A 197 :V T0381 217 :RGASGLTVA 1fx7A 199 :TTPGGGVTI Number of specific fragments extracted= 9 number of extra gaps= 0 total=974 Number of alignments=152 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1fx7A 60 :RHLELTEKGRALAIAVMRKHRLAERLL T0381 98 :PHLEKLSHKVH 1fx7A 96 :EVHAEACRWEH T0381 157 :GLPDDELDAYLEKLDIQRLTERTIT 1fx7A 107 :VMSEDVERRLVKVLNNPTTSPFGNP Number of specific fragments extracted= 4 number of extra gaps= 0 total=978 Number of alignments=153 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0381//projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0381/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0381)A43.CB, (T0381)A53.CB) [> 2.8330 = 4.7217 < 6.1382] w=1.0000 to align # Constraint # added constraint: constraint((T0381)V42.CB, (T0381)A53.CB) [> 3.1410 = 5.2350 < 6.8055] w=1.0000 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)A53.CB) [> 3.2080 = 5.3467 < 6.9507] w=1.0000 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)R54.CB) [> 3.5813 = 5.9689 < 7.7596] w=0.9825 to align # Constraint # added constraint: constraint((T0381)L57.CB, (T0381)V66.CB) [> 3.9009 = 6.5015 < 8.4519] w=0.9796 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)V42.CB) [> 3.6389 = 6.0649 < 7.8844] w=0.9521 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)L57.CB) [> 4.0127 = 6.6878 < 8.6941] w=0.9482 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)R50.CB) [> 3.5814 = 5.9690 < 7.7597] w=0.9441 to align # Constraint # added constraint: constraint((T0381)S40.CB, (T0381)R50.CB) [> 3.8680 = 6.4467 < 8.3807] w=0.9195 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)T46.CB) [> 3.8831 = 6.4719 < 8.4134] w=0.8378 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)A45.CB) [> 3.6150 = 6.0250 < 7.8325] w=0.7939 to align # Constraint # added constraint: constraint((T0381)R37.CB, (T0381)F73.CB) [> 3.4100 = 5.6833 < 7.3884] w=0.7823 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)F56.CB) [> 3.7594 = 6.2657 < 8.1455] w=0.7754 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)L75.CB) [> 3.5552 = 5.9253 < 7.7028] w=0.7717 to align # Constraint # added constraint: constraint((T0381)L57.CB, (T0381)F73.CB) [> 3.8008 = 6.3347 < 8.2351] w=0.7512 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)L75.CB) [> 4.1299 = 6.8832 < 8.9481] w=0.7478 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L60.CB) [> 4.2087 = 7.0145 < 9.1188] w=0.7471 to align # Constraint # added constraint: constraint((T0381)I27.CB, (T0381)V66.CB) [> 4.4152 = 7.3586 < 9.5662] w=0.7324 to align # Constraint # added constraint: constraint((T0381)T38.CB, (T0381)F73.CB) [> 4.3271 = 7.2119 < 9.3754] w=0.7303 to align # Constraint # added constraint: constraint((T0381)T38.CB, (T0381)A72.CB) [> 3.4084 = 5.6806 < 7.3848] w=0.7233 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)F73.CB) [> 4.2217 = 7.0362 < 9.1471] w=0.7188 to align # Constraint # added constraint: constraint((T0381)V42.CB, (T0381)L57.CB) [> 4.4209 = 7.3682 < 9.5787] w=0.7174 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)V42.CB) [> 3.6794 = 6.1323 < 7.9719] w=0.7006 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)L60.CB) [> 4.1241 = 6.8736 < 8.9357] w=0.6941 to align # Constraint # added constraint: constraint((T0381)A43.CB, (T0381)T52.CB) [> 4.4582 = 7.4303 < 9.6594] w=0.6917 to align # Constraint # added constraint: constraint((T0381)A25.CB, (T0381)T46.CB) [> 3.5116 = 5.8527 < 7.6085] w=0.6744 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)T76.CB) [> 3.5093 = 5.8489 < 7.6035] w=0.6725 to align # Constraint # added constraint: constraint((T0381)I27.CB, (T0381)L60.CB) [> 4.2303 = 7.0505 < 9.1657] w=0.6719 to align # Constraint # added constraint: constraint((T0381)A67.CB, (T0381)T76.CB) [> 3.4109 = 5.6849 < 7.3904] w=0.6602 to align # Constraint # added constraint: constraint((T0381)G64.CA, (T0381)T76.CB) [> 3.2309 = 5.3848 < 7.0002] w=0.6600 to align # Constraint # added constraint: constraint((T0381)R37.CB, (T0381)A72.CB) [> 3.7032 = 6.1720 < 8.0237] w=0.6502 to align # Constraint # added constraint: constraint((T0381)I27.CB, (T0381)L75.CB) [> 3.8414 = 6.4024 < 8.3231] w=0.6491 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)L57.CB) [> 4.1937 = 6.9894 < 9.0863] w=0.6483 to align # Constraint # added constraint: constraint((T0381)R22.CB, (T0381)T46.CB) [> 3.6682 = 6.1137 < 7.9478] w=0.6446 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)T76.CB) [> 3.7072 = 6.1787 < 8.0323] w=0.6384 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V66.CB) [> 3.9667 = 6.6112 < 8.5946] w=0.6350 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)F56.CB) [> 3.4002 = 5.6670 < 7.3671] w=0.6300 to align # Constraint # added constraint: constraint((T0381)V26.CB, (T0381)A53.CB) [> 4.2714 = 7.1190 < 9.2547] w=0.5982 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V42.CB) [> 4.4312 = 7.3853 < 9.6009] w=0.5915 to align # Constraint # added constraint: constraint((T0381)R36.CB, (T0381)A72.CB) [> 2.8210 = 4.7016 < 6.1121] w=0.5731 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)L75.CB) [> 3.2443 = 5.4071 < 7.0293] w=0.5542 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)W74.CB) [> 3.8541 = 6.4235 < 8.3506] w=0.5482 to align # Constraint # added constraint: constraint((T0381)R22.CB, (T0381)F56.CB) [> 3.6175 = 6.0292 < 7.8380] w=0.5070 to align # Constraint # added constraint: constraint((T0381)R36.CB, (T0381)W74.CB) [> 2.8329 = 4.7215 < 6.1380] w=0.4967 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)T46.CB) [> 4.0290 = 6.7150 < 8.7295] w=0.4862 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)V79.CB) [> 2.3720 = 3.9533 < 5.1393] w=0.4801 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)R78.CB) [> 3.4715 = 5.7857 < 7.5215] w=0.4413 to align # Constraint # added constraint: constraint((T0381)G64.CA, (T0381)R78.CB) [> 3.5031 = 5.8385 < 7.5900] w=0.4340 to align # Constraint # added constraint: constraint((T0381)D31.CB, (T0381)L75.CB) [> 3.6732 = 6.1221 < 7.9587] w=0.4323 to align # Constraint # added constraint: constraint((T0381)G64.CA, (T0381)V79.CB) [> 4.1490 = 6.9151 < 8.9896] w=0.4104 to align # Constraint # added constraint: constraint((T0381)R22.CB, (T0381)L48.CB) [> 4.0519 = 6.7531 < 8.7790] w=0.3946 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)V79.CB) [> 3.2316 = 5.3859 < 7.0017] w=0.3922 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)L82.CB) [> 3.8867 = 6.4778 < 8.4211] w=0.3848 to align # Constraint # added constraint: constraint((T0381)L60.CB, (T0381)V79.CB) [> 4.3524 = 7.2541 < 9.4303] w=0.3684 to align # Constraint # added constraint: constraint((T0381)I27.CB, (T0381)V79.CB) [> 4.0830 = 6.8049 < 8.8464] w=0.3585 to align # Constraint # added constraint: constraint((T0381)R37.CB, (T0381)W74.CB) [> 4.4648 = 7.4414 < 9.6738] w=0.3573 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)L60.CB) [> 4.0092 = 6.6820 < 8.6866] w=0.3333 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)Y86.CB) [> 3.6775 = 6.1291 < 7.9678] w=0.3216 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)F56.CB) [> 3.6133 = 6.0221 < 7.8287] w=0.3210 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)G83.CA) [> 3.2827 = 5.4712 < 7.1126] w=0.3203 to align # Constraint # added constraint: constraint((T0381)R28.CB, (T0381)G83.CA) [> 3.7164 = 6.1940 < 8.0522] w=0.3106 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)T46.CB) [> 3.8200 = 6.3667 < 8.2767] w=0.2773 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)Y65.CB) [> 3.9681 = 6.6135 < 8.5976] w=0.2593 to align # Constraint # added constraint: constraint((T0381)L167.CB, (T0381)R183.CB) [> 3.5448 = 5.9079 < 7.6803] w=0.2564 to align # Constraint # added constraint: constraint((T0381)L167.CB, (T0381)L186.CB) [> 4.1426 = 6.9043 < 8.9756] w=0.2560 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)F56.CB) [> 3.9685 = 6.6142 < 8.5984] w=0.2242 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)Y123.CB) [> 3.7220 = 6.2034 < 8.0644] w=0.2184 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L75.CB) [> 4.0426 = 6.7376 < 8.7589] w=0.2086 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L82.CB) [> 3.5980 = 5.9967 < 7.7957] w=0.2051 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)L60.CB) [> 4.4225 = 7.3708 < 9.5820] w=0.2047 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)D41.CB) [> 4.0838 = 6.8063 < 8.8482] w=0.2029 to align # Constraint # added constraint: constraint((T0381)L24.CB, (T0381)V66.CB) [> 4.6299 = 7.7166 < 10.0315] w=0.2015 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)L63.CB) [> 4.4164 = 7.3607 < 9.5689] w=0.2003 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)Y123.CB) [> 3.4605 = 5.7675 < 7.4977] w=0.2001 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)Y123.CB) [> 3.9344 = 6.5573 < 8.5245] w=0.2001 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V113.CB) [> 3.6571 = 6.0952 < 7.9238] w=0.2000 to align # Constraint # added constraint: constraint((T0381)R28.CB, (T0381)L75.CB) [> 4.2755 = 7.1258 < 9.2635] w=0.1941 to align # Constraint # added constraint: constraint((T0381)L103.CB, (T0381)S248.CB) [> 3.6890 = 6.1484 < 7.9929] w=0.1928 to align # Constraint # added constraint: constraint((T0381)R22.CB, (T0381)T52.CB) [> 4.1838 = 6.9729 < 9.0648] w=0.1923 to align # Constraint # added constraint: constraint((T0381)I172.CB, (T0381)R183.CB) [> 4.2030 = 7.0050 < 9.1065] w=0.1920 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)T59.CB) [> 4.3679 = 7.2798 < 9.4638] w=0.1855 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)N228.CB) [> 4.1079 = 6.8465 < 8.9004] w=0.1791 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A225.CB) [> 2.7187 = 4.5311 < 5.8904] w=0.1790 to align # Constraint # added constraint: constraint((T0381)D31.CB, (T0381)L80.CB) [> 4.1362 = 6.8937 < 8.9619] w=0.1771 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)R126.CB) [> 4.0581 = 6.7636 < 8.7927] w=0.1768 to align # Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A226.CB) [> 3.4175 = 5.6958 < 7.4046] w=0.1759 to align # Constraint # added constraint: constraint((T0381)A213.CB, (T0381)N228.CB) [> 2.5174 = 4.1957 < 5.4543] w=0.1759 to align # Constraint # added constraint: constraint((T0381)A213.CB, (T0381)V227.CB) [> 3.9423 = 6.5705 < 8.5416] w=0.1759 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)I229.CB) [> 3.0026 = 5.0043 < 6.5056] w=0.1759 to align # Constraint # added constraint: constraint((T0381)A96.CB, (T0381)V113.CB) [> 3.4258 = 5.7096 < 7.4225] w=0.1759 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)I229.CB) [> 3.3417 = 5.5694 < 7.2403] w=0.1742 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V227.CB) [> 4.1996 = 6.9994 < 9.0992] w=0.1742 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)A225.CB) [> 3.6605 = 6.1009 < 7.9311] w=0.1742 to align # Constraint # added constraint: constraint((T0381)V227.CB, (T0381)T252.CB) [> 3.5709 = 5.9515 < 7.7369] w=0.1741 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V124.CB) [> 3.4828 = 5.8047 < 7.5462] w=0.1719 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A125.CB) [> 4.2762 = 7.1271 < 9.2652] w=0.1715 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I229.CB) [> 4.3007 = 7.1678 < 9.3181] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)S230.CB) [> 3.0564 = 5.0940 < 6.6223] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)I229.CB) [> 3.4271 = 5.7119 < 7.4255] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V227.CB) [> 4.3987 = 7.3313 < 9.5306] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)N228.CB) [> 2.7516 = 4.5859 < 5.9617] w=0.1710 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)A226.CB) [> 4.5220 = 7.5367 < 9.7976] w=0.1710 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V227.CB) [> 3.4459 = 5.7432 < 7.4661] w=0.1710 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)M212.CB) [> 3.7247 = 6.2079 < 8.0702] w=0.1710 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)A213.CB) [> 3.9309 = 6.5515 < 8.5169] w=0.1710 to align # Constraint # added constraint: constraint((T0381)C199.CB, (T0381)A213.CB) [> 3.2411 = 5.4019 < 7.0224] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S211.CB, (T0381)I229.CB) [> 3.9993 = 6.6654 < 8.6651] w=0.1710 to align # Constraint # added constraint: constraint((T0381)S211.CB, (T0381)S230.CB) [> 2.8215 = 4.7026 < 6.1134] w=0.1710 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)N228.CB) [> 3.9474 = 6.5791 < 8.5528] w=0.1710 to align # Constraint # added constraint: constraint((T0381)A213.CB, (T0381)I229.CB) [> 4.5333 = 7.5555 < 9.8222] w=0.1710 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A226.CB) [> 3.9969 = 6.6615 < 8.6600] w=0.1710 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)V227.CB) [> 3.4765 = 5.7941 < 7.5324] w=0.1710 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)V227.CB) [> 3.7489 = 6.2482 < 8.1226] w=0.1710 to align # Constraint # added constraint: constraint((T0381)L103.CB, (T0381)L249.CB) [> 4.0633 = 6.7722 < 8.8039] w=0.1703 to align # Constraint # added constraint: constraint((T0381)A21.CB, (T0381)G83.CA) [> 4.2553 = 7.0921 < 9.2198] w=0.1696 to align # Constraint # added constraint: constraint((T0381)A21.CB, (T0381)L82.CB) [> 4.0882 = 6.8136 < 8.8577] w=0.1691 to align # Constraint # added constraint: constraint((T0381)L163.CB, (T0381)L186.CB) [> 3.8933 = 6.4889 < 8.4355] w=0.1672 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S111.CB) [> 2.8183 = 4.6971 < 6.1062] w=0.1661 to align # Constraint # added constraint: constraint((T0381)L103.CB, (T0381)I229.CB) [> 3.9936 = 6.6560 < 8.6528] w=0.1661 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V124.CB) [> 4.0620 = 6.7700 < 8.8010] w=0.1661 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)V124.CB) [> 3.0079 = 5.0132 < 6.5171] w=0.1661 to align # Constraint # added constraint: constraint((T0381)C199.CB, (T0381)M212.CB) [> 4.2073 = 7.0121 < 9.1157] w=0.1661 to align # Constraint # added constraint: constraint((T0381)S211.CB, (T0381)N228.CB) [> 3.2207 = 5.3678 < 6.9782] w=0.1661 to align # Constraint # added constraint: constraint((T0381)A213.CB, (T0381)A226.CB) [> 3.0060 = 5.0099 < 6.5129] w=0.1661 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A253.CB) [> 3.0915 = 5.1525 < 6.6982] w=0.1661 to align # Constraint # added constraint: constraint((T0381)V227.CB, (T0381)L249.CB) [> 3.6377 = 6.0628 < 7.8817] w=0.1661 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)R126.CB) [> 4.0891 = 6.8151 < 8.8597] w=0.1647 to align # Constraint # added constraint: constraint((T0381)L155.CB, (T0381)Y166.CB) [> 4.1968 = 6.9946 < 9.0930] w=0.1638 to align # Constraint # added constraint: constraint((T0381)A25.CB, (T0381)G83.CA) [> 3.3775 = 5.6293 < 7.3180] w=0.1623 to align # Constraint # added constraint: constraint((T0381)A25.CB, (T0381)Y86.CB) [> 2.8139 = 4.6899 < 6.0969] w=0.1623 to align # Constraint # added constraint: constraint((T0381)A25.CB, (T0381)L87.CB) [> 3.5054 = 5.8423 < 7.5950] w=0.1623 to align # Constraint # added constraint: constraint((T0381)R28.CB, (T0381)L80.CB) [> 4.6504 = 7.7507 < 10.0759] w=0.1623 to align # Constraint # added constraint: constraint((T0381)R28.CB, (T0381)Y84.CB) [> 4.2431 = 7.0718 < 9.1934] w=0.1623 to align # Constraint # added constraint: constraint((T0381)S88.CB, (T0381)L163.CB) [> 4.0572 = 6.7621 < 8.7907] w=0.1623 to align # Constraint # added constraint: constraint((T0381)I229.CB, (T0381)L245.CB) [> 3.3905 = 5.6508 < 7.3461] w=0.1621 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)L245.CB) [> 3.7442 = 6.2403 < 8.1124] w=0.1621 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)V224.CB) [> 4.3130 = 7.1883 < 9.3447] w=0.1609 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A226.CB) [> 3.0838 = 5.1398 < 6.6817] w=0.1609 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A225.CB) [> 3.8746 = 6.4576 < 8.3949] w=0.1609 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)I256.CB) [> 3.1327 = 5.2212 < 6.7876] w=0.1600 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)L249.CB) [> 2.8449 = 4.7414 < 6.1639] w=0.1600 to align # Constraint # added constraint: constraint((T0381)H99.CB, (T0381)T252.CB) [> 2.8965 = 4.8274 < 6.2757] w=0.1600 to align # Constraint # added constraint: constraint((T0381)V227.CB, (T0381)A253.CB) [> 3.1800 = 5.2999 < 6.8899] w=0.1598 to align # Constraint # added constraint: constraint((T0381)I229.CB, (T0381)L249.CB) [> 3.6759 = 6.1265 < 7.9645] w=0.1598 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)A145.CB) [> 3.6224 = 6.0373 < 7.8485] w=0.1588 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L241.CB) [> 3.9479 = 6.5799 < 8.5539] w=0.1579 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I137.CB) [> 3.3982 = 5.6637 < 7.3629] w=0.1578 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T46.CB) [> 4.2928 = 7.1547 < 9.3011] w=0.1565 to align # Constraint # added constraint: constraint((T0381)S104.CB, (T0381)V127.CB) [> 2.7310 = 4.5517 < 5.9172] w=0.1558 to align # Constraint # added constraint: constraint((T0381)L163.CB, (T0381)I190.CB) [> 4.2349 = 7.0581 < 9.1755] w=0.1553 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V227.CB) [> 4.2529 = 7.0881 < 9.2146] w=0.1553 to align # Constraint # added constraint: constraint((T0381)H99.CB, (T0381)D255.CB) [> 3.4091 = 5.6819 < 7.3864] w=0.1539 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L245.CB) [> 3.1313 = 5.2189 < 6.7846] w=0.1539 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)A226.CB) [> 3.7420 = 6.2367 < 8.1077] w=0.1527 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)S230.CB) [> 4.2695 = 7.1158 < 9.2505] w=0.1527 to align # Constraint # added constraint: constraint((T0381)T176.CB, (T0381)E204.CB) [> 3.5899 = 5.9831 < 7.7781] w=0.1527 to align # Constraint # added constraint: constraint((T0381)L175.CB, (T0381)L205.CB) [> 3.3842 = 5.6404 < 7.3326] w=0.1527 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)L143.CB) [> 4.1765 = 6.9608 < 9.0490] w=0.1527 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)A225.CB) [> 3.2372 = 5.3954 < 7.0140] w=0.1527 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)A125.CB) [> 3.8976 = 6.4960 < 8.4447] w=0.1527 to align # Constraint # added constraint: constraint((T0381)R217.CB, (T0381)E257.CB) [> 2.7623 = 4.6039 < 5.9851] w=0.1518 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)L249.CB) [> 3.4308 = 5.7180 < 7.4334] w=0.1506 to align # Constraint # added constraint: constraint((T0381)L103.CB, (T0381)V227.CB) [> 4.2758 = 7.1263 < 9.2642] w=0.1496 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)R142.CB) [> 2.8430 = 4.7383 < 6.1598] w=0.1478 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)L143.CB) [> 3.9937 = 6.6562 < 8.6531] w=0.1478 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)A145.CB) [> 3.9593 = 6.5989 < 8.5786] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)R142.CB) [> 4.1523 = 6.9206 < 8.9967] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)L143.CB) [> 2.5169 = 4.1948 < 5.4532] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)P144.CB) [> 4.5001 = 7.5002 < 9.7503] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)T148.CB) [> 3.6095 = 6.0158 < 7.8205] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)G151.CA) [> 2.8119 = 4.6865 < 6.0925] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)L154.CB) [> 3.8357 = 6.3928 < 8.3106] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T141.CB) [> 4.3169 = 7.1948 < 9.3532] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)R142.CB) [> 3.4860 = 5.8100 < 7.5530] w=0.1478 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)T141.CB) [> 2.6733 = 4.4555 < 5.7921] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L154.CB) [> 3.8200 = 6.3667 < 8.2767] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L155.CB) [> 3.4245 = 5.7075 < 7.4197] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A145.CB, (T0381)Y166.CB) [> 3.9128 = 6.5214 < 8.4778] w=0.1478 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)I180.CB) [> 3.7548 = 6.2581 < 8.1355] w=0.1478 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L186.CB) [> 3.4688 = 5.7813 < 7.5157] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L175.CB) [> 3.3692 = 5.6154 < 7.3000] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)T179.CB) [> 3.0925 = 5.1542 < 6.7005] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)I180.CB) [> 4.2980 = 7.1633 < 9.3122] w=0.1478 to align # Constraint # added constraint: constraint((T0381)P93.CB, (T0381)A125.CB) [> 3.2276 = 5.3793 < 6.9931] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V127.CB) [> 2.8966 = 4.8277 < 6.2761] w=0.1478 to align # Constraint # added constraint: constraint((T0381)E101.CB, (T0381)V127.CB) [> 3.4098 = 5.6830 < 7.3879] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S104.CB, (T0381)V129.CB) [> 3.8980 = 6.4967 < 8.4457] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)P128.CB) [> 3.0357 = 5.0594 < 6.5773] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V129.CB) [> 3.1472 = 5.2454 < 6.8190] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V127.CB) [> 2.8358 = 4.7263 < 6.1441] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)R126.CB) [> 3.0517 = 5.0862 < 6.6120] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)M150.CB) [> 4.1357 = 6.8929 < 8.9607] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)R126.CB) [> 4.3069 = 7.1782 < 9.3316] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)M150.CB) [> 2.4584 = 4.0973 < 5.3264] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)G151.CA) [> 4.1651 = 6.9419 < 9.0244] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)N228.CB) [> 4.0182 = 6.6971 < 8.7062] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)L154.CB) [> 3.0037 = 5.0062 < 6.5081] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A119.CB, (T0381)A145.CB) [> 3.6784 = 6.1307 < 7.9699] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A119.CB, (T0381)K169.CB) [> 3.6614 = 6.1024 < 7.9331] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A119.CB, (T0381)L170.CB) [> 3.3839 = 5.6399 < 7.3318] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A226.CB) [> 3.4502 = 5.7504 < 7.4755] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L155.CB, (T0381)I190.CB) [> 3.3835 = 5.6392 < 7.3309] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A156.CB, (T0381)I190.CB) [> 2.6903 = 4.4838 < 5.8289] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A156.CB, (T0381)L191.CB) [> 4.6067 = 7.6778 < 9.9812] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A156.CB, (T0381)R194.CB) [> 2.7792 = 4.6320 < 6.0216] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G157.CA, (T0381)P215.CB) [> 4.3164 = 7.1939 < 9.3521] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G157.CA, (T0381)T223.CB) [> 3.6576 = 6.0960 < 7.9248] w=0.1478 to align # Constraint # added constraint: constraint((T0381)T176.CB, (T0381)A207.CB) [> 3.3777 = 5.6296 < 7.3184] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R178.CB, (T0381)D202.CB) [> 3.7772 = 6.2954 < 8.1840] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I180.CB, (T0381)A189.CB) [> 3.5814 = 5.9690 < 7.7597] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I180.CB, (T0381)E204.CB) [> 3.9602 = 6.6004 < 8.5805] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G197.CA, (T0381)A214.CB) [> 3.9262 = 6.5437 < 8.5069] w=0.1478 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)I246.CB) [> 3.0076 = 5.0128 < 6.5166] w=0.1478 to align # Constraint # added constraint: constraint((T0381)C199.CB, (T0381)A214.CB) [> 4.5582 = 7.5970 < 9.8761] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)S230.CB) [> 3.8290 = 6.3816 < 8.2961] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G218.CA, (T0381)E257.CB) [> 3.6991 = 6.1652 < 8.0147] w=0.1478 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L205.CB) [> 2.9527 = 4.9211 < 6.3975] w=0.1478 to align # Constraint # added constraint: constraint((T0381)T148.CB, (T0381)L205.CB) [> 3.4265 = 5.7109 < 7.4241] w=0.1478 to align # Constraint # added constraint: constraint((T0381)T148.CB, (T0381)A213.CB) [> 4.5646 = 7.6077 < 9.8900] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)C199.CB) [> 2.7195 = 4.5324 < 5.8922] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)S211.CB) [> 2.3686 = 3.9477 < 5.1320] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)M212.CB) [> 3.5055 = 5.8426 < 7.5953] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)A213.CB) [> 2.1430 = 3.5717 < 4.6432] w=0.1478 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)N228.CB) [> 3.2516 = 5.4193 < 7.0451] w=0.1478 to align # Constraint # added constraint: constraint((T0381)M150.CB, (T0381)A213.CB) [> 2.6810 = 4.4683 < 5.8088] w=0.1478 to align # Constraint # added constraint: constraint((T0381)M150.CB, (T0381)A226.CB) [> 2.4189 = 4.0315 < 5.2410] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G151.CA, (T0381)A213.CB) [> 4.3159 = 7.1932 < 9.3512] w=0.1478 to align # Constraint # added constraint: constraint((T0381)G151.CA, (T0381)A226.CB) [> 3.9557 = 6.5928 < 8.5707] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)T223.CB) [> 3.6967 = 6.1611 < 8.0094] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A226.CB) [> 2.6971 = 4.4952 < 5.8437] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)P215.CB) [> 2.9077 = 4.8462 < 6.3000] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A214.CB) [> 3.6300 = 6.0501 < 7.8651] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)A213.CB) [> 2.7258 = 4.5431 < 5.9060] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)C199.CB) [> 2.7217 = 4.5361 < 5.8970] w=0.1478 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)V193.CB) [> 3.7998 = 6.3331 < 8.2330] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)A213.CB) [> 4.3195 = 7.1991 < 9.3588] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)C199.CB) [> 2.4824 = 4.1374 < 5.3786] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)V193.CB) [> 3.3817 = 5.6362 < 7.3271] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)I190.CB) [> 3.9126 = 6.5210 < 8.4773] w=0.1478 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)A189.CB) [> 3.9486 = 6.5810 < 8.5553] w=0.1478 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)T59.CB) [> 4.4473 = 7.4122 < 9.6359] w=0.1476 to align # Constraint # added constraint: constraint((T0381)V95.CB, (T0381)D259.CB) [> 2.9683 = 4.9472 < 6.4314] w=0.1457 to align # Constraint # added constraint: constraint((T0381)A96.CB, (T0381)I256.CB) [> 3.1644 = 5.2741 < 6.8563] w=0.1457 to align # Constraint # added constraint: constraint((T0381)H99.CB, (T0381)I256.CB) [> 3.2003 = 5.3338 < 6.9340] w=0.1457 to align # Constraint # added constraint: constraint((T0381)K102.CB, (T0381)T252.CB) [> 3.9687 = 6.6145 < 8.5989] w=0.1457 to align # Constraint # added constraint: constraint((T0381)L103.CB, (T0381)T252.CB) [> 2.9344 = 4.8906 < 6.3578] w=0.1457 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)I246.CB) [> 3.4466 = 5.7443 < 7.4676] w=0.1457 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)R250.CB) [> 3.1347 = 5.2245 < 6.7918] w=0.1457 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A253.CB) [> 2.5754 = 4.2923 < 5.5799] w=0.1457 to align # Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A253.CB) [> 3.9481 = 6.5802 < 8.5543] w=0.1457 to align # Constraint # added constraint: constraint((T0381)I216.CB, (T0381)L260.CB) [> 4.2463 = 7.0773 < 9.2004] w=0.1457 to align # Constraint # added constraint: constraint((T0381)V227.CB, (T0381)I256.CB) [> 4.0866 = 6.8110 < 8.8544] w=0.1457 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)V79.CB) [> 4.5483 = 7.5805 < 9.8546] w=0.1431 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)S211.CB) [> 4.1782 = 6.9637 < 9.0528] w=0.1414 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)S230.CB) [> 4.0969 = 6.8281 < 8.8766] w=0.1414 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)R250.CB) [> 3.9115 = 6.5192 < 8.4749] w=0.1396 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)T138.CB) [> 4.2737 = 7.1229 < 9.2597] w=0.1395 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)I137.CB) [> 3.8969 = 6.4948 < 8.4432] w=0.1389 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)I246.CB) [> 4.1998 = 6.9996 < 9.0995] w=0.1353 to align # Constraint # added constraint: constraint((T0381)G208.CA, (T0381)A233.CB) [> 2.6587 = 4.4312 < 5.7605] w=0.1332 to align # Constraint # added constraint: constraint((T0381)V95.CB, (T0381)I256.CB) [> 3.5674 = 5.9456 < 7.7293] w=0.1293 to align # Constraint # added constraint: constraint((T0381)F30.CB, (T0381)A45.CB) [> 4.4945 = 7.4909 < 9.7381] w=0.1291 to align # Constraint # added constraint: constraint((T0381)E109.CB, (T0381)T231.CB) [> 2.5491 = 4.2485 < 5.5231] w=0.1281 to align # Constraint # added constraint: constraint((T0381)A125.CB, (T0381)I139.CB) [> 3.8825 = 6.4708 < 8.4121] w=0.1281 to align # Constraint # added constraint: constraint((T0381)R126.CB, (T0381)I139.CB) [> 3.4981 = 5.8302 < 7.5793] w=0.1281 to align # Constraint # added constraint: constraint((T0381)T148.CB, (T0381)L201.CB) [> 3.3649 = 5.6081 < 7.2905] w=0.1281 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)V200.CB) [> 3.6698 = 6.1163 < 7.9511] w=0.1281 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)I198.CB) [> 3.9938 = 6.6564 < 8.6533] w=0.1281 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)P215.CB) [> 4.2240 = 7.0399 < 9.1519] w=0.1281 to align # Constraint # added constraint: constraint((T0381)L175.CB, (T0381)E206.CB) [> 4.1221 = 6.8703 < 8.9313] w=0.1281 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)R210.CB) [> 4.3408 = 7.2347 < 9.4051] w=0.1281 to align # Constraint # added constraint: constraint((T0381)L201.CB, (T0381)R210.CB) [> 3.9114 = 6.5191 < 8.4748] w=0.1281 to align # Constraint # added constraint: constraint((T0381)L201.CB, (T0381)S211.CB) [> 2.7011 = 4.5018 < 5.8524] w=0.1281 to align # Constraint # added constraint: constraint((T0381)V61.CB, (T0381)F73.CB) [> 4.4365 = 7.3942 < 9.6125] w=0.1239 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I139.CB) [> 3.0463 = 5.0772 < 6.6003] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)G140.CA) [> 3.1462 = 5.2436 < 6.8167] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)R142.CB) [> 4.6810 = 7.8016 < 10.1420] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V124.CB, (T0381)I139.CB) [> 3.7505 = 6.2509 < 8.1262] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V124.CB, (T0381)G140.CA) [> 4.1422 = 6.9036 < 8.9747] w=0.1232 to align # Constraint # added constraint: constraint((T0381)R126.CB, (T0381)I137.CB) [> 4.0206 = 6.7010 < 8.7113] w=0.1232 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)P232.CB) [> 3.5875 = 5.9792 < 7.7730] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)L209.CB) [> 4.2174 = 7.0290 < 9.1376] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)S230.CB) [> 2.9919 = 4.9865 < 6.4824] w=0.1232 to align # Constraint # added constraint: constraint((T0381)P144.CB, (T0381)L205.CB) [> 4.1421 = 6.9035 < 8.9745] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)G140.CA) [> 3.3225 = 5.5374 < 7.1987] w=0.1232 to align # Constraint # added constraint: constraint((T0381)I121.CB, (T0381)A226.CB) [> 4.3309 = 7.2181 < 9.3836] w=0.1232 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)P144.CB) [> 4.1281 = 6.8802 < 8.9443] w=0.1232 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A213.CB) [> 4.5202 = 7.5336 < 9.7937] w=0.1232 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)L143.CB) [> 3.9155 = 6.5258 < 8.4835] w=0.1232 to align # Constraint # added constraint: constraint((T0381)S104.CB, (T0381)P128.CB) [> 4.5237 = 7.5394 < 9.8013] w=0.1232 to align # Constraint # added constraint: constraint((T0381)H99.CB, (T0381)V227.CB) [> 4.5003 = 7.5005 < 9.7506] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Q97.CB, (T0381)A125.CB) [> 3.9415 = 6.5691 < 8.5398] w=0.1232 to align # Constraint # added constraint: constraint((T0381)A96.CB, (T0381)A125.CB) [> 3.7575 = 6.2625 < 8.1412] w=0.1232 to align # Constraint # added constraint: constraint((T0381)L92.CB, (T0381)V224.CB) [> 4.0645 = 6.7741 < 8.8064] w=0.1232 to align # Constraint # added constraint: constraint((T0381)N228.CB, (T0381)L249.CB) [> 4.4288 = 7.3814 < 9.5958] w=0.1232 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)P232.CB) [> 4.4549 = 7.4248 < 9.6523] w=0.1232 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)T231.CB) [> 3.8036 = 6.3394 < 8.2412] w=0.1232 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)P232.CB) [> 4.1511 = 6.9184 < 8.9939] w=0.1232 to align # Constraint # added constraint: constraint((T0381)G208.CA, (T0381)P232.CB) [> 3.7220 = 6.2034 < 8.0644] w=0.1232 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)M212.CB) [> 3.4057 = 5.6761 < 7.3789] w=0.1232 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)L249.CB) [> 3.6363 = 6.0604 < 7.8785] w=0.1232 to align # Constraint # added constraint: constraint((T0381)G157.CA, (T0381)I190.CB) [> 4.6511 = 7.7519 < 10.0775] w=0.1232 to align # Constraint # added constraint: constraint((T0381)R152.CB, (T0381)L201.CB) [> 4.1840 = 6.9734 < 9.0654] w=0.1232 to align # Constraint # added constraint: constraint((T0381)G151.CA, (T0381)C199.CB) [> 4.3801 = 7.3003 < 9.4903] w=0.1232 to align # Constraint # added constraint: constraint((T0381)M150.CB, (T0381)S211.CB) [> 4.3661 = 7.2768 < 9.4599] w=0.1232 to align # Constraint # added constraint: constraint((T0381)S149.CB, (T0381)L201.CB) [> 2.6203 = 4.3671 < 5.6773] w=0.1232 to align # Constraint # added constraint: constraint((T0381)T148.CB, (T0381)S211.CB) [> 3.8242 = 6.3736 < 8.2857] w=0.1232 to align # Constraint # added constraint: constraint((T0381)T148.CB, (T0381)E204.CB) [> 4.3958 = 7.3263 < 9.5242] w=0.1232 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)L201.CB) [> 4.1526 = 6.9210 < 8.9972] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)T179.CB) [> 4.6213 = 7.7021 < 10.0128] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L170.CB) [> 3.8904 = 6.4840 < 8.4292] w=0.1232 to align # Constraint # added constraint: constraint((T0381)A145.CB, (T0381)L170.CB) [> 4.0791 = 6.7986 < 8.8382] w=0.1232 to align # Constraint # added constraint: constraint((T0381)Q203.CB, (T0381)A233.CB) [> 3.8576 = 6.4294 < 8.3582] w=0.1232 to align # Constraint # added constraint: constraint((T0381)P215.CB, (T0381)A225.CB) [> 4.4822 = 7.4703 < 9.7114] w=0.1217 to align # Constraint # added constraint: constraint((T0381)I27.CB, (T0381)A96.CB) [> 3.7849 = 6.3082 < 8.2007] w=0.1188 to align # Constraint # added constraint: constraint((T0381)V42.CB, (T0381)F56.CB) [> 4.5949 = 7.6582 < 9.9557] w=0.1152 to align # Constraint # added constraint: constraint((T0381)S85.CB, (T0381)D160.CB) [> 4.6487 = 7.7478 < 10.0722] w=0.1150 to align # Constraint # added constraint: constraint((T0381)A225.CB, (T0381)I256.CB) [> 4.5741 = 7.6235 < 9.9106] w=0.1150 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)A233.CB) [> 3.0791 = 5.1318 < 6.6714] w=0.1150 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)A233.CB) [> 4.1314 = 6.8856 < 8.9513] w=0.1150 to align # Constraint # added constraint: constraint((T0381)V95.CB, (T0381)L260.CB) [> 3.8656 = 6.4427 < 8.3755] w=0.1150 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)L87.CB) [> 4.5631 = 7.6051 < 9.8866] w=0.1140 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)L241.CB) [> 3.7812 = 6.3021 < 8.1927] w=0.1136 to align # Constraint # added constraint: constraint((T0381)L63.CB, (T0381)R78.CB) [> 4.3535 = 7.2559 < 9.4326] w=0.1083 to align # Constraint # added constraint: constraint((T0381)Q18.CB, (T0381)A156.CB) [> 2.5753 = 4.2921 < 5.5798] w=0.1081 to align # Constraint # added constraint: constraint((T0381)Y86.CB, (T0381)L155.CB) [> 3.2044 = 5.3407 < 6.9429] w=0.1078 to align # Constraint # added constraint: constraint((T0381)V95.CB, (T0381)Y166.CB) [> 3.8472 = 6.4120 < 8.3355] w=0.1067 to align # Constraint # added constraint: constraint((T0381)A96.CB, (T0381)V227.CB) [> 4.3431 = 7.2386 < 9.4101] w=0.1061 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)L48.CB) [> 3.9833 = 6.6389 < 8.6305] w=0.1052 to align # Constraint # added constraint: constraint((T0381)V224.CB, (T0381)L260.CB) [> 4.2529 = 7.0882 < 9.2147] w=0.1046 to align # Constraint # added constraint: constraint((T0381)R217.CB, (T0381)L260.CB) [> 4.3489 = 7.2481 < 9.4226] w=0.1046 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A145.CB) [> 4.3930 = 7.3216 < 9.5181] w=0.1046 to align # Constraint # added constraint: constraint((T0381)L92.CB, (T0381)I115.CB) [> 4.5487 = 7.5812 < 9.8555] w=0.1034 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)R126.CB) [> 4.4782 = 7.4636 < 9.7027] w=0.1034 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)T231.CB) [> 3.8389 = 6.3982 < 8.3177] w=0.1034 to align # Constraint # added constraint: constraint((T0381)L143.CB, (T0381)L205.CB) [> 4.1276 = 6.8794 < 8.9432] w=0.0985 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)L143.CB) [> 4.3563 = 7.2605 < 9.4387] w=0.0985 to align # Constraint # added constraint: constraint((T0381)D117.CB, (T0381)R142.CB) [> 4.3731 = 7.2884 < 9.4750] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)G151.CA) [> 4.5824 = 7.6373 < 9.9284] w=0.0985 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)L154.CB) [> 4.1557 = 6.9261 < 9.0039] w=0.0985 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)T231.CB) [> 4.7035 = 7.8392 < 10.1910] w=0.0985 to align # Constraint # added constraint: constraint((T0381)Q97.CB, (T0381)V127.CB) [> 4.5829 = 7.6382 < 9.9296] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L92.CB, (T0381)I216.CB) [> 4.2698 = 7.1164 < 9.2514] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L92.CB, (T0381)V124.CB) [> 4.4234 = 7.3723 < 9.5839] w=0.0985 to align # Constraint # added constraint: constraint((T0381)G197.CA, (T0381)I246.CB) [> 4.5482 = 7.5804 < 9.8545] w=0.0985 to align # Constraint # added constraint: constraint((T0381)G197.CA, (T0381)P215.CB) [> 4.1554 = 6.9257 < 9.0035] w=0.0985 to align # Constraint # added constraint: constraint((T0381)A189.CB, (T0381)C199.CB) [> 4.5978 = 7.6629 < 9.9618] w=0.0985 to align # Constraint # added constraint: constraint((T0381)D164.CB, (T0381)R183.CB) [> 4.2713 = 7.1189 < 9.2546] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L158.CB, (T0381)T223.CB) [> 4.2194 = 7.0324 < 9.1421] w=0.0985 to align # Constraint # added constraint: constraint((T0381)A156.CB, (T0381)P215.CB) [> 4.2727 = 7.1211 < 9.2575] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L155.CB, (T0381)L186.CB) [> 4.6937 = 7.8228 < 10.1697] w=0.0985 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A225.CB) [> 4.5051 = 7.5085 < 9.7611] w=0.0985 to align # Constraint # added constraint: constraint((T0381)V153.CB, (T0381)G197.CA) [> 4.6053 = 7.6755 < 9.9782] w=0.0985 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)L155.CB) [> 4.1809 = 6.9681 < 9.0585] w=0.0985 to align # Constraint # added constraint: constraint((T0381)P144.CB, (T0381)L175.CB) [> 4.2198 = 7.0330 < 9.1429] w=0.0985 to align # Constraint # added constraint: constraint((T0381)Y236.CB, (T0381)L245.CB) [> 4.2488 = 7.0813 < 9.2057] w=0.0972 to align # Constraint # added constraint: constraint((T0381)A219.CB, (T0381)L260.CB) [> 3.8250 = 6.3750 < 8.2875] w=0.0964 to align # Constraint # added constraint: constraint((T0381)S85.CB, (T0381)V95.CB) [> 3.8606 = 6.4343 < 8.3646] w=0.0961 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)L158.CB) [> 4.0206 = 6.7011 < 8.7114] w=0.0955 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I137.CB) [> 4.3041 = 7.1736 < 9.3256] w=0.0946 to align # Constraint # added constraint: constraint((T0381)L75.CB, (T0381)P93.CB) [> 3.4064 = 5.6773 < 7.3804] w=0.0944 to align # Constraint # added constraint: constraint((T0381)L167.CB, (T0381)K187.CB) [> 3.6028 = 6.0047 < 7.8061] w=0.0940 to align # Constraint # added constraint: constraint((T0381)Y84.CB, (T0381)T181.CB) [> 2.9001 = 4.8335 < 6.2836] w=0.0933 to align # Constraint # added constraint: constraint((T0381)Y84.CB, (T0381)A182.CB) [> 2.4899 = 4.1498 < 5.3948] w=0.0933 to align # Constraint # added constraint: constraint((T0381)S85.CB, (T0381)E185.CB) [> 4.4452 = 7.4087 < 9.6313] w=0.0933 to align # Constraint # added constraint: constraint((T0381)L87.CB, (T0381)T181.CB) [> 3.1886 = 5.3144 < 6.9087] w=0.0933 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)G136.CA) [> 3.8763 = 6.4605 < 8.3987] w=0.0927 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)S230.CB) [> 4.6212 = 7.7020 < 10.0127] w=0.0922 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)Y236.CB) [> 2.6158 = 4.3596 < 5.6675] w=0.0903 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T59.CB) [> 3.3680 = 5.6133 < 7.2972] w=0.0902 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V124.CB) [> 3.4443 = 5.7405 < 7.4627] w=0.0895 to align # Constraint # added constraint: constraint((T0381)I229.CB, (T0381)S248.CB) [> 4.4858 = 7.4763 < 9.7192] w=0.0880 to align # Constraint # added constraint: constraint((T0381)L75.CB, (T0381)L92.CB) [> 2.9752 = 4.9587 < 6.4463] w=0.0867 to align # Constraint # added constraint: constraint((T0381)L92.CB, (T0381)L167.CB) [> 4.4424 = 7.4039 < 9.6251] w=0.0858 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)S230.CB) [> 4.5015 = 7.5025 < 9.7533] w=0.0837 to align # Constraint # added constraint: constraint((T0381)I172.CB, (T0381)L186.CB) [> 3.9842 = 6.6403 < 8.6324] w=0.0814 to align # Constraint # added constraint: constraint((T0381)H108.CB, (T0381)S130.CB) [> 4.1553 = 6.9254 < 9.0030] w=0.0814 to align # Constraint # added constraint: constraint((T0381)I137.CB, (T0381)S230.CB) [> 4.5668 = 7.6113 < 9.8947] w=0.0809 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S112.CB) [> 4.4254 = 7.3756 < 9.5883] w=0.0800 to align # Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)F56.CB) [> 4.0698 = 6.7830 < 8.8179] w=0.0792 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)I229.CB) [> 4.6166 = 7.6943 < 10.0026] w=0.0788 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)T223.CB) [> 4.1924 = 6.9873 < 9.0835] w=0.0788 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)V224.CB) [> 3.5248 = 5.8747 < 7.6371] w=0.0788 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A225.CB) [> 4.0849 = 6.8082 < 8.8507] w=0.0788 to align # Constraint # added constraint: constraint((T0381)V124.CB, (T0381)A225.CB) [> 4.2762 = 7.1270 < 9.2651] w=0.0788 to align # Constraint # added constraint: constraint((T0381)A96.CB, (T0381)L170.CB) [> 4.1440 = 6.9067 < 8.9787] w=0.0784 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)L154.CB) [> 3.6460 = 6.0767 < 7.8998] w=0.0774 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)A53.CB) [> 4.7056 = 7.8426 < 10.1953] w=0.0753 to align # Constraint # added constraint: constraint((T0381)E109.CB, (T0381)R235.CB) [> 4.3752 = 7.2921 < 9.4797] w=0.0739 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)T134.CB) [> 3.5541 = 5.9236 < 7.7006] w=0.0739 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)L154.CB) [> 4.5178 = 7.5297 < 9.7887] w=0.0739 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)A226.CB) [> 4.7255 = 7.8758 < 10.2385] w=0.0739 to align # Constraint # added constraint: constraint((T0381)V129.CB, (T0381)T231.CB) [> 4.2245 = 7.0409 < 9.1531] w=0.0739 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)T231.CB) [> 3.7426 = 6.2376 < 8.1089] w=0.0739 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)P232.CB) [> 4.4308 = 7.3847 < 9.6001] w=0.0739 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)T252.CB) [> 4.4996 = 7.4993 < 9.7491] w=0.0739 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)T231.CB) [> 4.4057 = 7.3428 < 9.5456] w=0.0739 to align # Constraint # added constraint: constraint((T0381)L201.CB, (T0381)M212.CB) [> 4.5925 = 7.6542 < 9.9504] w=0.0739 to align # Constraint # added constraint: constraint((T0381)C199.CB, (T0381)S211.CB) [> 4.3206 = 7.2009 < 9.3612] w=0.0724 to align # Constraint # added constraint: constraint((T0381)L58.CB, (T0381)T68.CB) [> 4.4596 = 7.4327 < 9.6625] w=0.0719 to align # Constraint # added constraint: constraint((T0381)L90.CB, (T0381)L155.CB) [> 2.3609 = 3.9349 < 5.1154] w=0.0696 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L75.CB) [> 4.5119 = 7.5198 < 9.7758] w=0.0685 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)A213.CB) [> 4.5862 = 7.6437 < 9.9368] w=0.0675 to align # Constraint # added constraint: constraint((T0381)G208.CA, (T0381)A234.CB) [> 4.4030 = 7.3384 < 9.5399] w=0.0657 to align # Constraint # added constraint: constraint((T0381)I190.CB, (T0381)C199.CB) [> 4.2227 = 7.0378 < 9.1491] w=0.0636 to align # Constraint # added constraint: constraint((T0381)T76.CB, (T0381)S89.CB) [> 2.7911 = 4.6519 < 6.0475] w=0.0627 to align # Constraint # added constraint: constraint((T0381)I139.CB, (T0381)Y166.CB) [> 3.6888 = 6.1480 < 7.9924] w=0.0604 to align # Constraint # added constraint: constraint((T0381)I139.CB, (T0381)L163.CB) [> 2.8855 = 4.8092 < 6.2520] w=0.0604 to align # Constraint # added constraint: constraint((T0381)I139.CB, (T0381)E162.CB) [> 2.4570 = 4.0949 < 5.3234] w=0.0604 to align # Constraint # added constraint: constraint((T0381)I139.CB, (T0381)P159.CB) [> 3.6811 = 6.1352 < 7.9758] w=0.0604 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V124.CB) [> 4.1016 = 6.8360 < 8.8868] w=0.0600 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)T52.CB) [> 3.8229 = 6.3716 < 8.2830] w=0.0597 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)L241.CB) [> 3.7923 = 6.3205 < 8.2166] w=0.0575 to align # Constraint # added constraint: constraint((T0381)R131.CB, (T0381)R235.CB) [> 4.5565 = 7.5942 < 9.8724] w=0.0575 to align # Constraint # added constraint: constraint((T0381)R131.CB, (T0381)T231.CB) [> 4.4011 = 7.3351 < 9.5356] w=0.0575 to align # Constraint # added constraint: constraint((T0381)S19.CB, (T0381)A53.CB) [> 4.3385 = 7.2309 < 9.4001] w=0.0569 to align # Constraint # added constraint: constraint((T0381)T38.CB, (T0381)T134.CB) [> 4.1102 = 6.8503 < 8.9054] w=0.0551 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)G136.CA) [> 3.3639 = 5.6065 < 7.2885] w=0.0551 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)I137.CB) [> 3.8451 = 6.4085 < 8.3311] w=0.0551 to align # Constraint # added constraint: constraint((T0381)A67.CB, (T0381)G136.CA) [> 3.6823 = 6.1372 < 7.9784] w=0.0551 to align # Constraint # added constraint: constraint((T0381)T68.CB, (T0381)T134.CB) [> 3.4458 = 5.7431 < 7.4660] w=0.0551 to align # Constraint # added constraint: constraint((T0381)T68.CB, (T0381)G136.CA) [> 3.8185 = 6.3642 < 8.2734] w=0.0551 to align # Constraint # added constraint: constraint((T0381)V124.CB, (T0381)V135.CB) [> 3.6809 = 6.1348 < 7.9752] w=0.0544 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)N228.CB) [> 4.5742 = 7.6236 < 9.9107] w=0.0542 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V227.CB) [> 4.6347 = 7.7246 < 10.0419] w=0.0542 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)H242.CB) [> 3.8384 = 6.3973 < 8.3164] w=0.0532 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V122.CB) [> 4.5367 = 7.5611 < 9.8294] w=0.0523 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)V124.CB) [> 2.6621 = 4.4369 < 5.7680] w=0.0523 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)L209.CB) [> 4.0911 = 6.8184 < 8.8640] w=0.0493 to align # Constraint # added constraint: constraint((T0381)R126.CB, (T0381)G136.CA) [> 4.4369 = 7.3948 < 9.6133] w=0.0493 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)I139.CB) [> 4.1600 = 6.9334 < 9.0134] w=0.0493 to align # Constraint # added constraint: constraint((T0381)G118.CA, (T0381)A145.CB) [> 4.6307 = 7.7179 < 10.0332] w=0.0493 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)A226.CB) [> 4.4036 = 7.3393 < 9.5411] w=0.0493 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)S211.CB) [> 4.5960 = 7.6601 < 9.9581] w=0.0493 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)M133.CB) [> 3.9315 = 6.5525 < 8.5183] w=0.0493 to align # Constraint # added constraint: constraint((T0381)S211.CB, (T0381)T231.CB) [> 4.6492 = 7.7487 < 10.0733] w=0.0493 to align # Constraint # added constraint: constraint((T0381)D202.CB, (T0381)L238.CB) [> 3.6686 = 6.1143 < 7.9485] w=0.0493 to align # Constraint # added constraint: constraint((T0381)A156.CB, (T0381)T223.CB) [> 4.5898 = 7.6497 < 9.9446] w=0.0493 to align # Constraint # added constraint: constraint((T0381)Y146.CB, (T0381)T181.CB) [> 4.4683 = 7.4472 < 9.6814] w=0.0493 to align # Constraint # added constraint: constraint((T0381)G136.CA, (T0381)S230.CB) [> 4.7544 = 7.9240 < 10.3013] w=0.0493 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)S211.CB) [> 4.7584 = 7.9307 < 10.3099] w=0.0493 to align # Constraint # added constraint: constraint((T0381)T134.CB, (T0381)P232.CB) [> 4.1134 = 6.8557 < 8.9124] w=0.0493 to align # Constraint # added constraint: constraint((T0381)T134.CB, (T0381)T231.CB) [> 3.4623 = 5.7706 < 7.5018] w=0.0493 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)T231.CB) [> 3.2908 = 5.4847 < 7.1302] w=0.0493 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)S230.CB) [> 4.0164 = 6.6940 < 8.7022] w=0.0493 to align # Constraint # added constraint: constraint((T0381)V124.CB, (T0381)T134.CB) [> 3.7175 = 6.1959 < 8.0547] w=0.0488 to align # Constraint # added constraint: constraint((T0381)P215.CB, (T0381)V227.CB) [> 4.3808 = 7.3014 < 9.4918] w=0.0478 to align # Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)G64.CA) [> 4.2666 = 7.1109 < 9.2442] w=0.0475 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)Y123.CB) [> 3.4859 = 5.8098 < 7.5528] w=0.0474 to align # Constraint # added constraint: constraint((T0381)A67.CB, (T0381)P77.CB) [> 3.6694 = 6.1156 < 7.9503] w=0.0472 to align # Constraint # added constraint: constraint((T0381)G64.CA, (T0381)P77.CB) [> 3.9244 = 6.5408 < 8.5030] w=0.0472 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)D244.CB) [> 4.0361 = 6.7269 < 8.7449] w=0.0471 to align # Constraint # added constraint: constraint((T0381)S91.CB, (T0381)R174.CB) [> 4.6501 = 7.7502 < 10.0752] w=0.0466 to align # Constraint # added constraint: constraint((T0381)L57.CB, (T0381)A72.CB) [> 4.2076 = 7.0127 < 9.1165] w=0.0459 to align # Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A253.CB) [> 4.0283 = 6.7138 < 8.7280] w=0.0450 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S110.CB) [> 3.2683 = 5.4472 < 7.0813] w=0.0440 to align # Constraint # added constraint: constraint((T0381)A43.CB, (T0381)R54.CB) [> 4.7319 = 7.8865 < 10.2524] w=0.0435 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A125.CB) [> 4.1370 = 6.8950 < 8.9635] w=0.0429 to align # Constraint # added constraint: constraint((T0381)G23.CA, (T0381)L82.CB) [> 4.4182 = 7.3637 < 9.5728] w=0.0429 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)G136.CA) [> 3.2204 = 5.3673 < 6.9775] w=0.0419 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V135.CB) [> 3.5630 = 5.9384 < 7.7199] w=0.0419 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)I137.CB) [> 4.1362 = 6.8937 < 8.9618] w=0.0419 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)G136.CA) [> 3.5205 = 5.8674 < 7.6276] w=0.0419 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)T138.CB) [> 4.2125 = 7.0208 < 9.1270] w=0.0419 to align # Constraint # added constraint: constraint((T0381)L75.CB, (T0381)L90.CB) [> 4.7304 = 7.8840 < 10.2492] w=0.0412 to align # Constraint # added constraint: constraint((T0381)T231.CB, (T0381)L245.CB) [> 4.5697 = 7.6162 < 9.9010] w=0.0411 to align # Constraint # added constraint: constraint((T0381)D120.CB, (T0381)I137.CB) [> 3.8135 = 6.3558 < 8.2625] w=0.0406 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)Y123.CB) [> 4.5309 = 7.5515 < 9.8170] w=0.0402 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)T138.CB) [> 3.6833 = 6.1389 < 7.9805] w=0.0389 to align # Constraint # added constraint: constraint((T0381)L90.CB, (T0381)K106.CB) [> 4.5023 = 7.5039 < 9.7550] w=0.0387 to align # Constraint # added constraint: constraint((T0381)Y65.CB, (T0381)G83.CA) [> 4.6814 = 7.8023 < 10.1430] w=0.0368 to align # Constraint # added constraint: constraint((T0381)V17.CB, (T0381)R55.CB) [> 3.7895 = 6.3158 < 8.2105] w=0.0334 to align # Constraint # added constraint: constraint((T0381)V17.CB, (T0381)T52.CB) [> 4.2945 = 7.1575 < 9.3048] w=0.0334 to align # Constraint # added constraint: constraint((T0381)R210.CB, (T0381)L238.CB) [> 3.0416 = 5.0693 < 6.5901] w=0.0328 to align # Constraint # added constraint: constraint((T0381)I132.CB, (T0381)T231.CB) [> 4.0290 = 6.7149 < 8.7294] w=0.0328 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)I132.CB) [> 2.8189 = 4.6981 < 6.1075] w=0.0328 to align # Constraint # added constraint: constraint((T0381)E109.CB, (T0381)I132.CB) [> 3.2696 = 5.4493 < 7.0841] w=0.0328 to align # Constraint # added constraint: constraint((T0381)H108.CB, (T0381)I132.CB) [> 3.6356 = 6.0593 < 7.8770] w=0.0328 to align # Constraint # added constraint: constraint((T0381)V17.CB, (T0381)L82.CB) [> 4.5530 = 7.5883 < 9.8648] w=0.0327 to align # Constraint # added constraint: constraint((T0381)V17.CB, (T0381)Y86.CB) [> 3.6001 = 6.0002 < 7.8002] w=0.0327 to align # Constraint # added constraint: constraint((T0381)L63.CB, (T0381)V79.CB) [> 4.3315 = 7.2191 < 9.3849] w=0.0322 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)I137.CB) [> 4.3254 = 7.2090 < 9.3717] w=0.0321 to align # Constraint # added constraint: constraint((T0381)D196.CB, (T0381)A233.CB) [> 4.1141 = 6.8569 < 8.9139] w=0.0320 to align # Constraint # added constraint: constraint((T0381)W74.CB, (T0381)V127.CB) [> 3.4161 = 5.6936 < 7.4016] w=0.0319 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)V135.CB) [> 3.2265 = 5.3775 < 6.9907] w=0.0310 to align # Constraint # added constraint: constraint((T0381)D69.CB, (T0381)M133.CB) [> 3.9621 = 6.6034 < 8.5844] w=0.0310 to align # Constraint # added constraint: constraint((T0381)V66.CB, (T0381)P77.CB) [> 3.6985 = 6.1642 < 8.0134] w=0.0308 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)A213.CB) [> 4.4794 = 7.4657 < 9.7054] w=0.0295 to align # Constraint # added constraint: constraint((T0381)M150.CB, (T0381)P215.CB) [> 4.4091 = 7.3485 < 9.5531] w=0.0295 to align # Constraint # added constraint: constraint((T0381)L20.CB, (T0381)V79.CB) [> 3.8910 = 6.4850 < 8.4305] w=0.0293 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)I137.CB) [> 3.8455 = 6.4092 < 8.3319] w=0.0282 to align # Constraint # added constraint: constraint((T0381)A189.CB, (T0381)L245.CB) [> 3.5257 = 5.8761 < 7.6389] w=0.0280 to align # Constraint # added constraint: constraint((T0381)G64.CA, (T0381)T138.CB) [> 3.1062 = 5.1770 < 6.7301] w=0.0277 to align # Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)L48.CB) [> 3.6827 = 6.1377 < 7.9791] w=0.0272 to align # Constraint # added constraint: constraint((T0381)L63.CB, (T0381)L82.CB) [> 4.7345 = 7.8908 < 10.2580] w=0.0250 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A213.CB) [> 4.7857 = 7.9762 < 10.3691] w=0.0246 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)I216.CB) [> 4.7804 = 7.9673 < 10.3574] w=0.0246 to align # Constraint # added constraint: constraint((T0381)V129.CB, (T0381)S230.CB) [> 4.0891 = 6.8152 < 8.8598] w=0.0246 to align # Constraint # added constraint: constraint((T0381)R131.CB, (T0381)P232.CB) [> 4.7407 = 7.9012 < 10.2716] w=0.0246 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)A234.CB) [> 4.7418 = 7.9030 < 10.2739] w=0.0246 to align # Constraint # added constraint: constraint((T0381)V61.CB, (T0381)T76.CB) [> 4.4419 = 7.4032 < 9.6242] w=0.0246 to align # Constraint # added constraint: constraint((T0381)S89.CB, (T0381)I115.CB) [> 3.8861 = 6.4768 < 8.4199] w=0.0246 to align # Constraint # added constraint: constraint((T0381)D196.CB, (T0381)R250.CB) [> 4.4336 = 7.3894 < 9.6062] w=0.0246 to align # Constraint # added constraint: constraint((T0381)I198.CB, (T0381)P215.CB) [> 4.6353 = 7.7254 < 10.0431] w=0.0246 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)S248.CB) [> 4.7957 = 7.9928 < 10.3907] w=0.0246 to align # Constraint # added constraint: constraint((T0381)L158.CB, (T0381)L222.CB) [> 4.7664 = 7.9440 < 10.3272] w=0.0246 to align # Constraint # added constraint: constraint((T0381)G157.CA, (T0381)L222.CB) [> 4.7859 = 7.9764 < 10.3694] w=0.0246 to align # Constraint # added constraint: constraint((T0381)L155.CB, (T0381)T223.CB) [> 4.6867 = 7.8111 < 10.1545] w=0.0246 to align # Constraint # added constraint: constraint((T0381)L155.CB, (T0381)V193.CB) [> 4.6282 = 7.7137 < 10.0278] w=0.0246 to align # Constraint # added constraint: constraint((T0381)C29.CB, (T0381)F73.CB) [> 4.5791 = 7.6318 < 9.9213] w=0.0246 to align # Constraint # added constraint: constraint((T0381)M133.CB, (T0381)R178.CB) [> 4.0585 = 6.7641 < 8.7934] w=0.0245 to align # Constraint # added constraint: constraint((T0381)Y166.CB, (T0381)K187.CB) [> 3.7743 = 6.2905 < 8.1777] w=0.0245 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T138.CB) [> 3.5193 = 5.8655 < 7.6252] w=0.0236 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)V122.CB) [> 4.5083 = 7.5139 < 9.7681] w=0.0233 to align # Constraint # added constraint: constraint((T0381)P215.CB, (T0381)V224.CB) [> 4.1575 = 6.9291 < 9.0078] w=0.0232 to align # Constraint # added constraint: constraint((T0381)A219.CB, (T0381)L241.CB) [> 4.0803 = 6.8006 < 8.8408] w=0.0230 to align # Constraint # added constraint: constraint((T0381)L39.CB, (T0381)W74.CB) [> 4.4507 = 7.4178 < 9.6432] w=0.0226 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)T138.CB) [> 3.4463 = 5.7438 < 7.4669] w=0.0207 to align # Constraint # added constraint: constraint((T0381)L80.CB, (T0381)L238.CB) [> 4.5951 = 7.6585 < 9.9561] w=0.0183 to align # Constraint # added constraint: constraint((T0381)L80.CB, (T0381)D202.CB) [> 4.6227 = 7.7046 < 10.0160] w=0.0183 to align # Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L201.CB) [> 3.3438 = 5.5731 < 7.2450] w=0.0183 to align # Constraint # added constraint: constraint((T0381)V129.CB, (T0381)V224.CB) [> 4.7480 = 7.9133 < 10.2873] w=0.0183 to align # Constraint # added constraint: constraint((T0381)G118.CA, (T0381)G140.CA) [> 4.5625 = 7.6042 < 9.8855] w=0.0183 to align # Constraint # added constraint: constraint((T0381)A119.CB, (T0381)G140.CA) [> 3.9230 = 6.5384 < 8.4999] w=0.0183 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)T134.CB) [> 3.9569 = 6.5948 < 8.5733] w=0.0183 to align # Constraint # added constraint: constraint((T0381)V122.CB, (T0381)V135.CB) [> 4.4495 = 7.4158 < 9.6405] w=0.0183 to align # Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)T52.CB) [> 3.7845 = 6.3075 < 8.1997] w=0.0171 to align # Constraint # added constraint: constraint((T0381)I132.CB, (T0381)P232.CB) [> 4.0729 = 6.7882 < 8.8247] w=0.0164 to align # Constraint # added constraint: constraint((T0381)A207.CB, (T0381)A233.CB) [> 4.5228 = 7.5381 < 9.7995] w=0.0164 to align # Constraint # added constraint: constraint((T0381)Y16.CB, (T0381)L82.CB) [> 3.2680 = 5.4466 < 7.0806] w=0.0163 to align # Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L92.CB) [> 4.3745 = 7.2908 < 9.4780] w=0.0156 to align # Constraint # added constraint: constraint((T0381)R194.CB, (T0381)A219.CB) [> 3.6309 = 6.0514 < 7.8669] w=0.0154 to align # Constraint # added constraint: constraint((T0381)D196.CB, (T0381)A219.CB) [> 4.5108 = 7.5180 < 9.7734] w=0.0154 to align # Constraint # added constraint: constraint((T0381)G197.CA, (T0381)S220.CB) [> 3.5095 = 5.8491 < 7.6039] w=0.0154 to align # Constraint # added constraint: constraint((T0381)S220.CB, (T0381)Y236.CB) [> 4.3149 = 7.1915 < 9.3489] w=0.0154 to align # Constraint # added constraint: constraint((T0381)G221.CA, (T0381)Y236.CB) [> 2.8825 = 4.8041 < 6.2454] w=0.0154 to align # Constraint # added constraint: constraint((T0381)G221.CA, (T0381)S237.CB) [> 4.3801 = 7.3002 < 9.4903] w=0.0154 to align # Constraint # added constraint: constraint((T0381)A125.CB, (T0381)V135.CB) [> 4.1542 = 6.9237 < 9.0009] w=0.0153 to align # Constraint # added constraint: constraint((T0381)L143.CB, (T0381)A192.CB) [> 4.4950 = 7.4916 < 9.7391] w=0.0151 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)G140.CA) [> 4.0650 = 6.7750 < 8.8074] w=0.0150 to align # Constraint # added constraint: constraint((T0381)E81.CB, (T0381)P93.CB) [> 3.9079 = 6.5131 < 8.4670] w=0.0148 to align # Constraint # added constraint: constraint((T0381)Y86.CB, (T0381)H242.CB) [> 3.1578 = 5.2631 < 6.8420] w=0.0147 to align # Constraint # added constraint: constraint((T0381)L80.CB, (T0381)K106.CB) [> 4.5232 = 7.5387 < 9.8003] w=0.0141 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)T254.CB) [> 4.1615 = 6.9358 < 9.0166] w=0.0141 to align # Constraint # added constraint: constraint((T0381)L209.CB, (T0381)V251.CB) [> 3.4097 = 5.6828 < 7.3876] w=0.0141 to align # Constraint # added constraint: constraint((T0381)E206.CB, (T0381)S248.CB) [> 4.2277 = 7.0462 < 9.1600] w=0.0141 to align # Constraint # added constraint: constraint((T0381)V17.CB, (T0381)R78.CB) [> 2.8291 = 4.7151 < 6.1297] w=0.0136 to align # Constraint # added constraint: constraint((T0381)L116.CB, (T0381)L222.CB) [> 4.3976 = 7.3293 < 9.5281] w=0.0131 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)V224.CB) [> 2.9629 = 4.9381 < 6.4196] w=0.0131 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A226.CB) [> 3.4698 = 5.7829 < 7.5178] w=0.0131 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)N228.CB) [> 4.0915 = 6.8192 < 8.8650] w=0.0131 to align # Constraint # added constraint: constraint((T0381)W74.CB, (T0381)G140.CA) [> 3.2897 = 5.4829 < 7.1277] w=0.0125 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S114.CB) [> 4.1551 = 6.9252 < 9.0027] w=0.0124 to align # Constraint # added constraint: constraint((T0381)A219.CB, (T0381)A253.CB) [> 3.7346 = 6.2243 < 8.0916] w=0.0122 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)Y123.CB) [> 3.7040 = 6.1734 < 8.0254] w=0.0121 to align # Constraint # added constraint: constraint((T0381)L80.CB, (T0381)V95.CB) [> 4.4722 = 7.4536 < 9.6897] w=0.0102 to align # Constraint # added constraint: constraint((T0381)A147.CB, (T0381)T223.CB) [> 4.1966 = 6.9943 < 9.0926] w=0.0098 to align # Constraint # added constraint: constraint((T0381)P144.CB, (T0381)T223.CB) [> 4.7850 = 7.9750 < 10.3674] w=0.0098 to align # Constraint # added constraint: constraint((T0381)P144.CB, (T0381)I216.CB) [> 4.5164 = 7.5274 < 9.7856] w=0.0098 to align # Constraint # added constraint: constraint((T0381)P144.CB, (T0381)A214.CB) [> 3.9196 = 6.5327 < 8.4926] w=0.0098 to align # Constraint # added constraint: constraint((T0381)A125.CB, (T0381)A225.CB) [> 3.4622 = 5.7703 < 7.5014] w=0.0098 to align # Constraint # added constraint: constraint((T0381)A125.CB, (T0381)V224.CB) [> 4.5692 = 7.6153 < 9.8999] w=0.0098 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)V224.CB) [> 2.9134 = 4.8557 < 6.3124] w=0.0098 to align # Constraint # added constraint: constraint((T0381)L154.CB, (T0381)I229.CB) [> 4.6977 = 7.8295 < 10.1784] w=0.0098 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)A225.CB) [> 3.2208 = 5.3680 < 6.9784] w=0.0082 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)A226.CB) [> 4.3771 = 7.2952 < 9.4837] w=0.0082 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V227.CB) [> 3.5391 = 5.8985 < 7.6680] w=0.0082 to align # Constraint # added constraint: constraint((T0381)S111.CB, (T0381)A225.CB) [> 4.4161 = 7.3602 < 9.5682] w=0.0082 to align # Constraint # added constraint: constraint((T0381)S112.CB, (T0381)A225.CB) [> 4.0586 = 6.7643 < 8.7936] w=0.0082 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)T223.CB) [> 3.3899 = 5.6498 < 7.3447] w=0.0082 to align # Constraint # added constraint: constraint((T0381)D117.CB, (T0381)I132.CB) [> 3.4278 = 5.7130 < 7.4269] w=0.0082 to align # Constraint # added constraint: constraint((T0381)D117.CB, (T0381)M133.CB) [> 2.9217 = 4.8695 < 6.3303] w=0.0082 to align # Constraint # added constraint: constraint((T0381)V113.CB, (T0381)V224.CB) [> 4.2267 = 7.0445 < 9.1579] w=0.0082 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)T223.CB) [> 4.0192 = 6.6986 < 8.7082] w=0.0082 to align # Constraint # added constraint: constraint((T0381)I115.CB, (T0381)L222.CB) [> 4.2661 = 7.1102 < 9.2432] w=0.0082 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)A225.CB) [> 4.3777 = 7.2961 < 9.4850] w=0.0080 to align # Constraint # added constraint: constraint((T0381)S211.CB, (T0381)A225.CB) [> 3.1954 = 5.3257 < 6.9234] w=0.0080 to align # Constraint # added constraint: constraint((T0381)S110.CB, (T0381)V193.CB) [> 4.2711 = 7.1185 < 9.2540] w=0.0080 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)I229.CB) [> 2.8471 = 4.7452 < 6.1688] w=0.0075 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)N228.CB) [> 4.0341 = 6.7235 < 8.7406] w=0.0075 to align # Constraint # added constraint: constraint((T0381)G83.CA, (T0381)L100.CB) [> 4.7955 = 7.9926 < 10.3903] w=0.0075 to align # Constraint # added constraint: constraint((T0381)I172.CB, (T0381)L222.CB) [> 3.3689 = 5.6148 < 7.2992] w=0.0075 to align # Constraint # added constraint: constraint((T0381)L222.CB, (T0381)A234.CB) [> 2.9445 = 4.9075 < 6.3797] w=0.0075 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)I229.CB) [> 4.3302 = 7.2170 < 9.3820] w=0.0075 to align # Constraint # added constraint: constraint((T0381)V200.CB, (T0381)N228.CB) [> 2.5442 = 4.2403 < 5.5123] w=0.0075 to align # Constraint # added constraint: constraint((T0381)I132.CB, (T0381)N228.CB) [> 2.4431 = 4.0719 < 5.2934] w=0.0075 to align # Constraint # added constraint: constraint((T0381)R78.CB, (T0381)H99.CB) [> 3.7444 = 6.2406 < 8.1128] w=0.0074 to align # Constraint # added constraint: constraint((T0381)R54.CB, (T0381)M133.CB) [> 4.7753 = 7.9589 < 10.3466] w=0.0074 to align # Constraint # added constraint: constraint((T0381)V135.CB, (T0381)N228.CB) [> 3.3044 = 5.5073 < 7.1595] w=0.0070 to align # Constraint # added constraint: constraint((T0381)I10.CB, (T0381)P77.CB) [> 4.6699 = 7.7832 < 10.1182] w=0.0068 to align # Constraint # added constraint: constraint((T0381)I10.CB, (T0381)R78.CB) [> 3.5246 = 5.8743 < 7.6365] w=0.0068 to align # Constraint # added constraint: constraint((T0381)S114.CB, (T0381)A145.CB) [> 3.1576 = 5.2626 < 6.8414] w=0.0061 to align # Constraint # added constraint: constraint((T0381)V107.CB, (T0381)V224.CB) [> 4.6097 = 7.6828 < 9.9876] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)A145.CB) [> 3.2750 = 5.4584 < 7.0959] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)A226.CB) [> 4.2394 = 7.0658 < 9.1855] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V227.CB) [> 2.9941 = 4.9901 < 6.4872] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)N228.CB) [> 4.5711 = 7.6185 < 9.9041] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)I229.CB) [> 4.6661 = 7.7768 < 10.1099] w=0.0049 to align # Constraint # added constraint: constraint((T0381)P77.CB, (T0381)Y86.CB) [> 4.4186 = 7.3643 < 9.5735] w=0.0049 to align # Constraint # added constraint: constraint((T0381)P77.CB, (T0381)L87.CB) [> 3.9039 = 6.5065 < 8.4584] w=0.0049 to align # Constraint # added constraint: constraint((T0381)L100.CB, (T0381)S211.CB) [> 2.9151 = 4.8585 < 6.3160] w=0.0049 to align # Constraint # added constraint: constraint((T0381)M212.CB, (T0381)V227.CB) [> 3.6734 = 6.1224 < 7.9591] w=0.0049 to align # Constraint # added constraint: constraint((T0381)A213.CB, (T0381)S230.CB) [> 3.8001 = 6.3334 < 8.2335] w=0.0049 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)V224.CB) [> 4.6717 = 7.7861 < 10.1220] w=0.0049 to align # Constraint # added constraint: constraint((T0381)A214.CB, (T0381)A225.CB) [> 3.5867 = 5.9778 < 7.7712] w=0.0049 to align # Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A226.CB) [> 4.5773 = 7.6289 < 9.9175] w=0.0049 to align # Constraint # added constraint: constraint((T0381)R217.CB, (T0381)A234.CB) [> 2.4339 = 4.0564 < 5.2733] w=0.0049 to align # Constraint # added constraint: constraint((T0381)G218.CA, (T0381)A234.CB) [> 2.8951 = 4.8252 < 6.2727] w=0.0049 to align # Constraint # added constraint: constraint((T0381)R174.CB, (T0381)A207.CB) [> 3.9987 = 6.6644 < 8.6638] w=0.0049 to align # Constraint # added constraint: constraint((T0381)V127.CB, (T0381)V224.CB) [> 4.6946 = 7.8243 < 10.1715] w=0.0049 to align # Constraint # added constraint: constraint((T0381)A145.CB, (T0381)A213.CB) [> 4.3291 = 7.2152 < 9.3798] w=0.0049 to align # Constraint # added constraint: constraint((T0381)T141.CB, (T0381)G218.CA) [> 3.8612 = 6.4353 < 8.3659] w=0.0049 to align # Constraint # added constraint: constraint((T0381)R142.CB, (T0381)P215.CB) [> 3.1686 = 5.2810 < 6.8653] w=0.0049 to align # Constraint # added constraint: constraint((T0381)R142.CB, (T0381)G218.CA) [> 3.7497 = 6.2496 < 8.1245] w=0.0049 to align # Constraint # added constraint: constraint((T0381)Y123.CB, (T0381)V193.CB) [> 4.7733 = 7.9555 < 10.3422] w=0.0040 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0381/ # command:# reading script from file servers-clean.under Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-6.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-6.pdb.gz.gz for input Trying chimera-4-6.pdb.gz Error: Couldn't open file chimera-4-6.pdb.gz or chimera-4-6.pdb.gz.gz for input Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-8.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/chimera-4-8.pdb.gz.gz for input Trying chimera-4-8.pdb.gz Error: Couldn't open file chimera-4-8.pdb.gz or chimera-4-8.pdb.gz.gz for input Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.pdb.gz.gz for input Trying tr380.gromacs0.pdb.gz Error: Couldn't open file tr380.gromacs0.pdb.gz or tr380.gromacs0.pdb.gz.gz for input Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.repack-nonPC.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.gromacs0.repack-nonPC.pdb.gz.gz for input Trying tr380.gromacs0.repack-nonPC.pdb.gz Error: Couldn't open file tr380.gromacs0.repack-nonPC.pdb.gz or tr380.gromacs0.repack-nonPC.pdb.gz.gz for input Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.pdb.gz.gz for input Trying tr380.pdb.gz Error: Couldn't open file tr380.pdb.gz or tr380.pdb.gz.gz for input Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.repack-nonPC.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/tr380.repack-nonPC.pdb.gz.gz for input Trying tr380.repack-nonPC.pdb.gz Error: Couldn't open file tr380.repack-nonPC.pdb.gz or tr380.repack-nonPC.pdb.gz.gz for input # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/ Error: can't open file chimera-4-6.pdb.gz in ReadConformPDB Error: can't open file chimera-4-8.pdb.gz in ReadConformPDB Error: can't open file tr380.gromacs0.pdb.gz in ReadConformPDB Error: can't open file tr380.gromacs0.repack-nonPC.pdb.gz in ReadConformPDB Error: can't open file tr380.pdb.gz in ReadConformPDB Error: can't open file tr380.repack-nonPC.pdb.gz in ReadConformPDB # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS4.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS4.pdb.gz.gz for input Trying servers/3D-JIGSAW_TS4.pdb.gz Error: Couldn't open file servers/3D-JIGSAW_TS4.pdb.gz or servers/3D-JIGSAW_TS4.pdb.gz.gz for input Error: can't open file servers/3D-JIGSAW_TS4.pdb.gz in ReadConformPDB # naming current conformation 3D-JIGSAW_TS4 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/3D-JIGSAW_TS5.pdb.gz.gz for input Trying servers/3D-JIGSAW_TS5.pdb.gz Error: Couldn't open file servers/3D-JIGSAW_TS5.pdb.gz or servers/3D-JIGSAW_TS5.pdb.gz.gz for input Error: can't open file servers/3D-JIGSAW_TS5.pdb.gz in ReadConformPDB # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 224 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 228 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 256 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 231 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 Skipped atom 50, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 52, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 54, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 418, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 420, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 422, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 259 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 261 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 Faking rotamer for incomplete or colinear backbone at (T0381)K102 Faking rotamer for incomplete or colinear backbone at (T0381)K102 # Found a chain break before 257 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/Frankenstein_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/Frankenstein_TS5.pdb.gz.gz for input Trying servers/Frankenstein_TS5.pdb.gz Error: Couldn't open file servers/Frankenstein_TS5.pdb.gz or servers/Frankenstein_TS5.pdb.gz.gz for input Error: can't open file servers/Frankenstein_TS5.pdb.gz in ReadConformPDB # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 263 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 264 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 263 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 242 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 176 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 262 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 176 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS3.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS3.pdb.gz.gz for input Trying servers/ROKKY_TS3.pdb.gz Error: Couldn't open file servers/ROKKY_TS3.pdb.gz or servers/ROKKY_TS3.pdb.gz.gz for input Error: can't open file servers/ROKKY_TS3.pdb.gz in ReadConformPDB # naming current conformation ROKKY_TS3 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS4.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS4.pdb.gz.gz for input Trying servers/ROKKY_TS4.pdb.gz Error: Couldn't open file servers/ROKKY_TS4.pdb.gz or servers/ROKKY_TS4.pdb.gz.gz for input Error: can't open file servers/ROKKY_TS4.pdb.gz in ReadConformPDB # naming current conformation ROKKY_TS4 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS5.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/ROKKY_TS5.pdb.gz.gz for input Trying servers/ROKKY_TS5.pdb.gz Error: Couldn't open file servers/ROKKY_TS5.pdb.gz or servers/ROKKY_TS5.pdb.gz.gz for input Error: can't open file servers/ROKKY_TS5.pdb.gz in ReadConformPDB # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 307, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 538, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 540, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 542, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 544, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 554, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 556, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 560, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 562, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 564, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 566, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 568, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 570, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 572, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 574, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 576, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 578, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 586, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 588, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 657, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 231 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 262 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 260 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 262 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 180 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0381)L11.O and (T0381)P12.N only 0.000 apart, marking (T0381)P12.N as missing # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0381)K9.O and (T0381)I10.N only 0.000 apart, marking (T0381)I10.N as missing WARNING: atoms too close: (T0381)Q35.O and (T0381)R36.N only 0.000 apart, marking (T0381)R36.N as missing WARNING: atoms too close: (T0381)V129.O and (T0381)S130.N only 0.000 apart, marking (T0381)S130.N as missing # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0381)T254.O and (T0381)D255.N only 0.000 apart, marking (T0381)D255.N as missing # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0381)V153.O and (T0381)L154.N only 0.000 apart, marking (T0381)L154.N as missing # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0381)E206.O and (T0381)A207.N only 0.000 apart, marking (T0381)A207.N as missing # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 13 < previous residue 263 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 13 < previous residue 263 in servers/nFOLD_TS4.pdb.gz # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 54 < previous residue 263 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation panther2_TS1 Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/panther3_TS1.pdb.gz or /projects/compbio/experiments/protein-predict/casp7/T0381/decoys/servers/panther3_TS1.pdb.gz.gz for input Trying servers/panther3_TS1.pdb.gz Error: Couldn't open file servers/panther3_TS1.pdb.gz or servers/panther3_TS1.pdb.gz.gz for input Error: can't open file servers/panther3_TS1.pdb.gz in ReadConformPDB # naming current conformation panther3_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0381 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.3363 model score -0.3404 model score -0.2958 model score -0.3232 model score -0.3252 model score -0.3268 model score -0.3268 model score -0.3285 model score -0.3283 model score -0.3264 model score -0.3283 model score -0.3283 model score 0.6154 model score -0.4096 model score -0.3730 model score -0.3655 model score -0.2920 model score -0.3154 model score 1.4138 model score 1.3968 model score 1.7226 model score 1.4850 model score 1.5821 model score -0.4194 model score -0.3716 model score -0.3740 model score -0.3783 model score -0.3817 model score -0.3782 model score -0.3553 model score -0.3657 model score -0.3616 model score -0.3643 model score -0.3739 model score -0.3612 model score -0.3197 model score -0.3506 model score 0.4120 model score 0.3771 model score 0.4671 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3761 model score -0.3726 model score -0.3715 model score -0.3809 model score -0.3690 model score -0.3923 model score -0.3739 model score -0.3553 model score -0.3778 model score -0.3690 model score -0.3655 model score -0.4096 model score -0.3889 model score -0.2920 model score -0.3154 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2773 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2773 model score 1.2770 model score 2.3556 model score 2.0063 model score 2.2365 model score 2.2594 model score 2.2470 model score -0.3745 model score 0.6304 model score 0.6660 model score 0.6971 model score 0.6919 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3737 model score -0.3394 model score -0.3723 model score -0.2821 model score -0.2745 model score -0.3842 model score -0.3918 model score 1.4993 model score 1.7796 model score -0.3671 model score -0.3844 model score -0.3884 model score -0.3767 model score -0.3892 model score -0.3744 model score -0.4251 model score -0.4181 model score -0.3870 model score -0.3027 model score 0.3976 model score 0.6798 model score 1.6733 model score -0.3580 model score -0.3178 model score 0.4373 model score 0.4135 model score 0.4775 model score 1.2770 model score -0.3954 model score -0.3899 model score 1.4436 model score 1.4454 model score 1.4655 model score -0.3899 model score -0.2971 model score 1.4461 model score 1.4454 model score 1.4694 model score -0.3765 model score -0.4613 model score -0.3814 model score -0.4577 model score -0.4478 model score -0.3580 model score -0.3781 model score -0.3593 model score -0.3733 model score -0.3365 model score -0.3718 model score -0.3170 model score -0.3820 model score -0.3891 model score 0.3859 model score -0.3927 model score -0.3687 model score -0.3888 model score -0.3617 model score -0.4016 model score -0.3888 model score -0.3814 model score -0.3936 model score -0.3936 model score -0.3936 model score -0.3936 model score -0.3936 model score -0.3935 model score -0.3928 model score -0.3941 model score -0.3917 model score -0.3842 model score -0.3858 model score -0.3752 model score -0.2710 model score -0.3714 model score -0.3846 model score -0.3607 model score -0.3839 model score -0.3749 model score -0.3839 model score -0.3330 model score -0.3815 model score -0.3897 model score 1.4925 model score 1.4475 model score 1.4673 model score -0.3928 model score -0.3939 model score -0.3939 model score -0.3935 model score -0.3941 model score -0.3647 model score -0.3852 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2770 model score -0.3498 model score -0.3731 model score -0.2012 model score 0.5029 model score 0.3819 model score -0.3786 model score -0.3773 model score 1.2825 model score 1.3619 model score 1.3529 model score -0.3773 model score -0.3911 model score 1.2105 model score 1.3347 model score 1.3529 model score -0.3786 model score -0.3730 model score 1.2593 model score 1.3314 model score 1.3529 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2770 model score 1.2771 model score -0.3592 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2770 model score 1.2771 model score -0.4114 model score -0.4190 model score -0.3791 model score -0.4093 model score -0.4236 model score -0.3860 model score -0.3732 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.4489 model score 0.3993 model score 0.4485 model score 0.4134 model score 0.4046 model score 1.9210 model score 1.8864 model score 2.3709 model score 2.4194 model score 2.2384 model score -0.3920 model score -0.4003 model score 0.3455 model score 0.4908 model score 0.2938 model score -0.3421 model score 0.3613 model score 0.3613 model score -0.3362 model score -0.3362 model score -0.3929 model score 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USE_EVALUE, weight: 0.6874 eval: 0.0406 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7629 eval: 0.0308 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7629 eval: 0.0308 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7629 eval: 0.0308 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.8574 eval: 0.0185 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.8574 eval: 0.0185 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.8574 eval: 0.0185 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9000 eval: 0.0130 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9000 eval: 0.0130 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9000 eval: 0.0130 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9964 eval: 0.0005 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9964 eval: 0.0005 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9964 eval: 0.0005 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USE_EVALUE, weight: 0.9181 eval: 0.0106 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9038 eval: 0.0125 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9038 eval: 0.0125 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9038 eval: 0.0125 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9806 eval: 0.0025 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9806 eval: 0.0025 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9806 eval: 0.0025 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4868 eval: 0.0667 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4868 eval: 0.0667 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4868 eval: 0.0667 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4127 eval: 0.0763 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4127 eval: 0.0763 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.4127 eval: 0.0763 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7110 eval: 0.0375 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7110 eval: 0.0375 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.7110 eval: 0.0375 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9989 eval: 0.0001 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9712 eval: 0.0037 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9712 eval: 0.0037 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9712 eval: 0.0037 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9763 eval: 0.0031 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9763 eval: 0.0031 min: 0.0000 max: 0.1169 USE_EVALUE, weight: 0.9763 eval: 0.0031 min: 0.0000 max: 0.1169 Number of contacts in models: 258 Number of contacts in alignments: 153 NUMB_ALIGNS: 153 Adding 9119 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -436.8015, CN propb: -436.8015 weights: 0.3371 constraints: 744 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 744 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 744 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 8375 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 8375 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 9119 # command: