# 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/T0342/ # command:# Making conformation for sequence T0342 numbered 1 through 188 Created new target T0342 from T0342.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0342/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0342//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0342/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0342//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0342/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0342/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0342/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bzlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bzlA expands to /projects/compbio/data/pdb/2bzl.pdb.gz 2bzlA:Skipped atom 1123, because occupancy 0.3 <= existing 0.700 in 2bzlA Skipped atom 1127, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1129, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1131, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1133, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1135, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1137, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1139, because occupancy 0.300 <= existing 0.700 in 2bzlA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2119, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2121, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2123, because occupancy 0.500 <= existing 0.500 in 2bzlA Skipped atom 2125, because occupancy 0.500 <= existing 0.500 in 2bzlA # T0342 read from 2bzlA/merged-good-all-a2m # 2bzlA read from 2bzlA/merged-good-all-a2m # adding 2bzlA to template set # found chain 2bzlA in template set T0342 2 :ANSGCKDVTGPDEESFLY 2bzlA 946 :EENRVELIPTKENNTGYI # choosing archetypes in rotamer library T0342 38 :AAFFCVARLQDFKLDF 2bzlA 964 :NASHIKVVVGGAEWHY T0342 68 :IATIFQS 2bzlA 980 :IATQGPL T0342 100 :V 2bzlA 1048 :S T0342 103 :GMYVVIEVKVATQ 2bzlA 1049 :VCYATTGLKVKHL T0342 116 :EGKEITCRSYLMTN 2bzlA 1063 :SGQERTVWHLQYTD T0342 130 :YESAPPS 2bzlA 1078 :PDHGCPE T0342 137 :PQYKKIICMGAKE 2bzlA 1090 :LSYLEEIQSVRRH T0342 163 :IE 2bzlA 1103 :TN T0342 165 :PNDYTG 2bzlA 1107 :LEGTKN Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 Number of alignments=1 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set T0342 3 :NSGCKDVTGPDE 2bzlA 946 :EENRVELIPTKE T0342 33 :LRNPSAAFFCVARLQDFKLDF 2bzlA 959 :NTGYINASHIKVVVGGAEWHY T0342 68 :IATIFQSPG 2bzlA 980 :IATQGPLPH T0342 99 :GVK 2bzlA 1047 :DSV T0342 104 :MYVVIEVKVAT 2bzlA 1050 :CYATTGLKVKH T0342 115 :QEGKEITCRSYLMTN 2bzlA 1062 :LSGQERTVWHLQYTD T0342 130 :YESAPP 2bzlA 1078 :PDHGCP T0342 136 :SPQYKKIIC 2bzlA 1086 :VQGFLSYLE T0342 155 :EYQEKLKAIEPN 2bzlA 1095 :EIQSVRRHTNSM T0342 167 :DYTGKV 2bzlA 1109 :GTKNRH Number of specific fragments extracted= 10 number of extra gaps= 0 total=20 Number of alignments=2 # 2bzlA read from 2bzlA/merged-good-all-a2m # found chain 2bzlA in template set T0342 42 :CVARLQDFKLDFG 2bzlA 1031 :SSATYGKFKVTTK T0342 60 :TSQTWHGGIAT 2bzlA 1044 :FRTDSVCYATT T0342 81 :G 2bzlA 1055 :G T0342 108 :IEVKVATQEGKEITCRSYLMTNYESAPPSP 2bzlA 1056 :LKVKHLLSGQERTVWHLQYTDWPDHGCPED T0342 138 :QYKKIICMGAKEN 2bzlA 1091 :SYLEEIQSVRRHT T0342 164 :EPNDYTG 2bzlA 1106 :MLEGTKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=26 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hw7A expands to /projects/compbio/data/pdb/1hw7.pdb.gz 1hw7A:Skipped atom 702, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 704, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 706, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 708, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 710, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 712, because occupancy 0.480 <= existing 0.520 in 1hw7A # T0342 read from 1hw7A/merged-good-all-a2m # 1hw7A read from 1hw7A/merged-good-all-a2m # adding 1hw7A to template set # found chain 1hw7A in template set Warning: unaligning (T0342)K85 because of BadResidue code BAD_PEPTIDE at template residue (1hw7A)E99 T0342 38 :AAFFCVARLQD 1hw7A 63 :FDGDITVQLQG T0342 57 :Q 1hw7A 74 :D T0342 62 :QTWHGGIATI 1hw7A 75 :GPMNLAVING T0342 74 :SPGDEVWGVVW 1hw7A 85 :NNNQQMRGVAR T0342 86 :MNKSN 1hw7A 100 :IPENA T0342 91 :LNSL 1hw7A 106 :LKTL T0342 98 :EG 1hw7A 110 :VG T0342 103 :GMY 1hw7A 112 :NGY T0342 108 :IEVKVATQEG 1hw7A 115 :VVITITPSEG T0342 118 :KEI 1hw7A 166 :KPA T0342 122 :CRSYLMTNYESAPPSPQ 1hw7A 169 :AGGMLLQVMPAQNAQQD T0342 153 :PLEYQEKL 1hw7A 186 :DFDHLATL T0342 161 :KAIEPNDYTGKVSEEIEDIIKKGE 1hw7A 195 :ETIKTEELLTLPANEVLWRLYHEE T0342 187 :TL 1hw7A 221 :TV Number of specific fragments extracted= 14 number of extra gaps= 1 total=40 Number of alignments=4 # 1hw7A read from 1hw7A/merged-good-all-a2m # found chain 1hw7A in template set T0342 31 :IHLRNPSAAFFCVARLQD 1hw7A 56 :LLTATLKFDGDITVQLQG T0342 61 :SQTWHGGIATI 1hw7A 74 :DGPMNLAVING T0342 74 :SPGDE 1hw7A 85 :NNNQQ T0342 79 :VWGVVWKMN 1hw7A 113 :GYVVITITP T0342 88 :KSNLNSLDEQEGVK 1hw7A 140 :ACLEDYFMRSEQLP T0342 105 :YVVI 1hw7A 154 :TRLF T0342 110 :VKVATQEGKEI 1hw7A 158 :IRTGDVDGKPA T0342 122 :CRSYLMTNYESAPPSPQ 1hw7A 169 :AGGMLLQVMPAQNAQQD T0342 153 :PLEYQEKL 1hw7A 186 :DFDHLATL T0342 161 :KAIEPNDYTGKVSEEIEDIIKKGETQTL 1hw7A 195 :ETIKTEELLTLPANEVLWRLYHEEEVTV Number of specific fragments extracted= 10 number of extra gaps= 0 total=50 Number of alignments=5 # 1hw7A read from 1hw7A/merged-good-all-a2m # found chain 1hw7A in template set T0342 29 :ERIHLRNPSAAFFCVARLQD 1hw7A 54 :TSLLTATLKFDGDITVQLQG T0342 49 :FKLDFGNSQ 1hw7A 80 :AVINGNNNQ T0342 65 :HGGIATIFQSPGDEVWGVV 1hw7A 113 :GYVVITITPSEGERYQGVV T0342 86 :MN 1hw7A 133 :LE T0342 88 :KSNLNSLDEQEGVKS 1hw7A 140 :ACLEDYFMRSEQLPT T0342 106 :VV 1hw7A 155 :RL T0342 109 :EVKVATQEGKEITCRSYLMTNYESAPPSPQYKKI 1hw7A 157 :FIRTGDVDGKPAAGGMLLQVMPAQNAQQDDFDHL T0342 157 :QEKLKAIEPNDYTGKVSEEIEDIIKKGETQTL 1hw7A 191 :ATLTETIKTEELLTLPANEVLWRLYHEEEVTV Number of specific fragments extracted= 8 number of extra gaps= 0 total=58 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g0qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g0qA expands to /projects/compbio/data/pdb/2g0q.pdb.gz 2g0qA:# T0342 read from 2g0qA/merged-good-all-a2m # 2g0qA read from 2g0qA/merged-good-all-a2m # adding 2g0qA to template set # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFG 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQRFRL T0342 61 :SQ 2g0qA 56 :KG T0342 66 :GGIATIFQSPGDEVWG 2g0qA 58 :RLYPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQEG 2g0qA 75 :VLMGVTSDELENLDAVEG T0342 103 :GMYVVIEVKVATQE 2g0qA 93 :NEYERVTVGIVRED T0342 117 :GKEITCRSYLMTNYESAPPS 2g0qA 108 :SEKMAVKTYMWINKADPDMF T0342 155 :EYQEKLKAI 2g0qA 131 :NFEEWKRLH T0342 169 :TGKVSEEIEDIIKKGETQ 2g0qA 140 :KKKFIETFKKIMECKKKP Number of specific fragments extracted= 8 number of extra gaps= 0 total=66 Number of alignments=7 # 2g0qA read from 2g0qA/merged-good-all-a2m # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKL 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQR T0342 61 :SQTWHGGIATIFQSPGDEVWG 2g0qA 53 :FRLKGRLYPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQE 2g0qA 75 :VLMGVTSDELENLDAVE T0342 102 :SGMYVVIEVKVATQE 2g0qA 92 :GNEYERVTVGIVRED T0342 117 :GKEITCRSYLMTN 2g0qA 108 :SEKMAVKTYMWIN T0342 130 :YESAPPS 2g0qA 123 :DPDMFGE T0342 155 :EYQEKLK 2g0qA 131 :NFEEWKR T0342 178 :DIIKKG 2g0qA 138 :LHKKKF Number of specific fragments extracted= 8 number of extra gaps= 0 total=74 Number of alignments=8 # 2g0qA read from 2g0qA/merged-good-all-a2m # found chain 2g0qA in template set Warning: unaligning (T0342)V9 because first residue in template chain is (2g0qA)C10 Warning: unaligning (T0342)Q186 because last residue in template chain is (2g0qA)Q158 T0342 10 :TGPDEESFLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKL 2g0qA 11 :SSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQR T0342 53 :FGNSQGK 2g0qA 53 :FRLKGRL T0342 68 :IATIFQSPGDEVWG 2g0qA 60 :YPCIVPSEKGEVHG T0342 82 :VVWKMNKSNLNSLDEQEG 2g0qA 75 :VLMGVTSDELENLDAVEG T0342 103 :GMYVVIEVKV 2g0qA 93 :NEYERVTVGI T0342 113 :ATQEGKEITCRSYLM 2g0qA 104 :REDNSEKMAVKTYMW T0342 128 :TNYESAPPS 2g0qA 121 :KADPDMFGE T0342 155 :EYQEKLKAIEP 2g0qA 131 :NFEEWKRLHKK T0342 170 :GKVSEEIEDIIKKGET 2g0qA 142 :KFIETFKKIMECKKKP Number of specific fragments extracted= 9 number of extra gaps= 0 total=83 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eejA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eejA expands to /projects/compbio/data/pdb/1eej.pdb.gz 1eejA:# T0342 read from 1eejA/merged-good-all-a2m # 1eejA read from 1eejA/merged-good-all-a2m # adding 1eejA to template set # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDF 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVL T0342 64 :WHGGIATI 1eejA 32 :TNSGVLYI T0342 73 :QS 1eejA 40 :TD T0342 75 :PGD 1eejA 84 :PQE T0342 120 :ITCRSYLMTN 1eejA 116 :ITVRYLAFPR T0342 130 :YESA 1eejA 127 :GLDS T0342 138 :QYKKIICMGAKENGLPLEYQEKLKAIEPNDYTGK 1eejA 131 :DAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCD T0342 172 :VSEEIEDIIK 1eejA 166 :DIADHYALGV Number of specific fragments extracted= 8 number of extra gaps= 0 total=91 Number of alignments=10 # 1eejA read from 1eejA/merged-good-all-a2m # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDFG 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVLT T0342 65 :HGGIATI 1eejA 33 :NSGVLYI T0342 74 :SPGDE 1eejA 40 :TDDGK T0342 79 :VWGVVWKM 1eejA 116 :ITVRYLAF T0342 88 :KSNLNSLDEQE 1eejA 130 :SDAEKEMKAIW T0342 99 :GVKSGM 1eejA 178 :GVSGTP T0342 111 :KVATQEGKEIT 1eejA 184 :AVVLSNGTLVP T0342 132 :SAPPSPQYKKIICMGAKE 1eejA 195 :GYQPPKEMKEFLDEHQKM Number of specific fragments extracted= 8 number of extra gaps= 0 total=99 Number of alignments=11 # 1eejA read from 1eejA/merged-good-all-a2m # found chain 1eejA in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDF 1eejA 6 :QQTLAKMGIKSSDIQPAPVAGMKTVL T0342 64 :WHGGIATIF 1eejA 32 :TNSGVLYIT T0342 74 :SPGDEV 1eejA 41 :DDGKHI T0342 80 :WGVVWKMN 1eejA 48 :QGPMYDVS T0342 90 :NLNSLDEQEGVKSGMY 1eejA 63 :TNKMLLKQLNALEKEM T0342 110 :VKVATQEGKEI 1eejA 79 :IVYKAPQEKHV T0342 155 :EYQEKLKAIEPN 1eejA 131 :DAEKEMKAIWCA T0342 170 :GKVSEEIEDIIKKGE 1eejA 143 :KDKNKAFDDVMAGKS Number of specific fragments extracted= 8 number of extra gaps= 0 total=107 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mdbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mdbA expands to /projects/compbio/data/pdb/1mdb.pdb.gz 1mdbA:# T0342 read from 1mdbA/merged-good-all-a2m # 1mdbA read from 1mdbA/merged-good-all-a2m # adding 1mdbA to template set # found chain 1mdbA in template set Warning: unaligning (T0342)G183 because last residue in template chain is (1mdbA)G536 T0342 6 :CKDVTGPDEESFLYFAYG 1mdbA 368 :DHDRDVKPGETGHLLTRG T0342 24 :SNLLTERIHL 1mdbA 392 :YYKAEEHNAA T0342 34 :RNPSAAFFCVARL 1mdbA 403 :FTEDGFYRTGDIV T0342 50 :KL 1mdbA 416 :RL T0342 57 :QGKTSQTWHGG 1mdbA 418 :TRDGYIVVEGR T0342 72 :FQSPGDEVW 1mdbA 433 :INRGGEKVA T0342 95 :DEQE 1mdbA 443 :EEVE T0342 99 :GVK 1mdbA 451 :AHP T0342 103 :GMYVVIEVKVATQEGK 1mdbA 454 :AVHDAAMVSMPDQFLG T0342 120 :ITCRSYLMT 1mdbA 470 :ERSCVFIIP T0342 130 :YESAPPSPQYKKIICM 1mdbA 479 :RDEAPKAAELKAFLRE T0342 161 :KAIEPNDYTG 1mdbA 495 :RGLAAYKIPD T0342 171 :KVSEEIEDIIKK 1mdbA 524 :ALREAISEKLLA Number of specific fragments extracted= 13 number of extra gaps= 0 total=120 Number of alignments=13 # 1mdbA read from 1mdbA/merged-good-all-a2m # found chain 1mdbA in template set Warning: unaligning (T0342)G183 because last residue in template chain is (1mdbA)G536 T0342 7 :KDVTGPDEESFLYFAYGSN 1mdbA 369 :HDRDVKPGETGHLLTRGPY T0342 26 :LLTERIH 1mdbA 394 :KAEEHNA T0342 33 :LRNPSAAFFCVARL 1mdbA 402 :SFTEDGFYRTGDIV T0342 50 :KL 1mdbA 416 :RL T0342 61 :SQTWHGGIATI 1mdbA 418 :TRDGYIVVEGR T0342 72 :FQSPGDEV 1mdbA 433 :INRGGEKV T0342 94 :LDEQE 1mdbA 442 :AEEVE T0342 99 :GV 1mdbA 451 :AH T0342 102 :SGMYVVIEVKVATQEGKE 1mdbA 453 :PAVHDAAMVSMPDQFLGE T0342 121 :TCRSYLMT 1mdbA 471 :RSCVFIIP T0342 130 :YESAPPSPQYKKIICM 1mdbA 479 :RDEAPKAAELKAFLRE T0342 161 :KAIEPNDYTG 1mdbA 495 :RGLAAYKIPD T0342 171 :KVSEEIEDIIKK 1mdbA 524 :ALREAISEKLLA Number of specific fragments extracted= 13 number of extra gaps= 0 total=133 Number of alignments=14 # 1mdbA read from 1mdbA/merged-good-all-a2m # found chain 1mdbA in template set T0342 6 :CKDVTGPDEESFLYFAYGSNLL 1mdbA 368 :DHDRDVKPGETGHLLTRGPYTI T0342 28 :TERIHLRN 1mdbA 396 :EEHNAASF T0342 36 :PSAAFFCVARL 1mdbA 405 :EDGFYRTGDIV T0342 52 :DF 1mdbA 416 :RL T0342 56 :S 1mdbA 418 :T T0342 65 :HGGIATIF 1mdbA 419 :RDGYIVVE T0342 73 :QSPGDEV 1mdbA 434 :NRGGEKV T0342 91 :LNSLDEQEGV 1mdbA 443 :EEVENHLLAH T0342 102 :SGMYVVIEVKVATQEGKEITCRSYLM 1mdbA 453 :PAVHDAAMVSMPDQFLGERSCVFIIP T0342 131 :ESAPPSPQ 1mdbA 479 :RDEAPKAA T0342 142 :IICMGAKENGLPL 1mdbA 487 :ELKAFLRERGLAA Number of specific fragments extracted= 11 number of extra gaps= 0 total=144 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jroB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jroB expands to /projects/compbio/data/pdb/1jro.pdb.gz 1jroB:# T0342 read from 1jroB/merged-good-all-a2m # 1jroB read from 1jroB/merged-good-all-a2m # adding 1jroB to template set # found chain 1jroB in template set T0342 30 :RIHLRNPSAAFFCVARLQDFKLDF 1jroB 588 :AAYMARISLSATGFYATPKLSWDR T0342 59 :KTSQTWHGGIATI 1jroB 612 :LRGQGRPFLYFAY T0342 81 :GVVW 1jroB 625 :GAAI T0342 108 :IEVKVATQEG 1jroB 629 :TEVVIDRLTG T0342 118 :KEITCRSYLMT 1jroB 641 :RILRTDILHDA T0342 132 :SAPPSPQ 1jroB 652 :GASLNPA T0342 139 :YKKIICMGA 1jroB 664 :IEGAYVQGA Number of specific fragments extracted= 7 number of extra gaps= 0 total=151 Number of alignments=16 # 1jroB read from 1jroB/merged-good-all-a2m # found chain 1jroB in template set T0342 30 :RIHLRNPSAAFFCVARLQDF 1jroB 588 :AAYMARISLSATGFYATPKL T0342 52 :DFGNSQGKTSQTWHGGIATI 1jroB 608 :SWDRLRGQGRPFLYFAYGAA T0342 78 :EVWGVV 1jroB 628 :ITEVVI T0342 101 :KSGMYVVI 1jroB 636 :LTGENRIL T0342 121 :TCRSYLMT 1jroB 644 :RTDILHDA T0342 132 :SAPPSPQ 1jroB 652 :GASLNPA T0342 139 :YKKIICMGA 1jroB 664 :IEGAYVQGA Number of specific fragments extracted= 7 number of extra gaps= 0 total=158 Number of alignments=17 # 1jroB read from 1jroB/merged-good-all-a2m # found chain 1jroB in template set T0342 142 :IICMGAKENGLP 1jroB 584 :EIVAAAYMARIS Number of specific fragments extracted= 1 number of extra gaps= 0 total=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wduA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wduA expands to /projects/compbio/data/pdb/1wdu.pdb.gz 1wduA:# T0342 read from 1wduA/merged-good-all-a2m # 1wduA read from 1wduA/merged-good-all-a2m # adding 1wduA to template set # found chain 1wduA in template set Warning: unaligning (T0342)E15 because first residue in template chain is (1wduA)P21 Warning: unaligning (T0342)F53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wduA)K66 Warning: unaligning (T0342)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wduA)K66 T0342 16 :SFLYFAYGSNLLTERIHLRN 1wduA 22 :PYRVLQANLQRKKLATAELA T0342 37 :SA 1wduA 48 :KA T0342 42 :CVARLQDF 1wduA 50 :AIALIQEP T0342 52 :D 1wduA 58 :Y T0342 60 :TSQTW 1wduA 67 :GFRGV T0342 67 :GIATIFQSPGDEVWGVVWKMN 1wduA 72 :RVFQSTAQGDGTVKAAIAVFD T0342 100 :VK 1wduA 100 :YP T0342 103 :GM 1wduA 102 :QL T0342 107 :VIEVKVATQ 1wduA 108 :IVVVGIRTR T0342 117 :GKEITCRSYLMT 1wduA 117 :AWEITLVSYYFE T0342 132 :SAPPSPQYKKIICMGAKENG 1wduA 129 :PDKPIESYLEQIKRVERKMG T0342 162 :AIEPNDYTGKVSEEIEDIIKKG 1wduA 163 :TWWGSKEDDARGDQLMGTLGEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=171 Number of alignments=18 # 1wduA read from 1wduA/merged-good-all-a2m # found chain 1wduA in template set Warning: unaligning (T0342)E15 because first residue in template chain is (1wduA)P21 Warning: unaligning (T0342)F53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wduA)K66 Warning: unaligning (T0342)K59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wduA)K66 T0342 16 :SFLYFAYGSNLLTERIH 1wduA 22 :PYRVLQANLQRKKLATA T0342 40 :FFCVARLQDFK 1wduA 48 :KAAIALIQEPY T0342 60 :TSQT 1wduA 67 :GFRG T0342 66 :GGIATIFQSPGDEVWGVVWKM 1wduA 71 :VRVFQSTAQGDGTVKAAIAVF T0342 88 :KSN 1wduA 101 :PQL T0342 102 :SGM 1wduA 105 :TNN T0342 107 :VIEVKVATQE 1wduA 108 :IVVVGIRTRA T0342 118 :KEITCRSYLMT 1wduA 118 :WEITLVSYYFE T0342 132 :SAPPSPQYKKIICMGAKENGL 1wduA 129 :PDKPIESYLEQIKRVERKMGP T0342 167 :DYTGKVSEEIEDIIKKGE 1wduA 168 :KEDDARGDQLMGTLGELG Number of specific fragments extracted= 10 number of extra gaps= 0 total=181 Number of alignments=19 # 1wduA read from 1wduA/merged-good-all-a2m # found chain 1wduA in template set Warning: unaligning (T0342)E15 because first residue in template chain is (1wduA)P21 Warning: unaligning (T0342)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wduA)K66 T0342 16 :SFLYFAYGSNLLTER 1wduA 22 :PYRVLQANLQRKKLA T0342 31 :IHLRN 1wduA 40 :LAIEA T0342 51 :LDFGNSQ 1wduA 52 :ALIQEPY T0342 65 :HGGIATIFQSPGDEVWGVVWKMN 1wduA 70 :GVRVFQSTAQGDGTVKAAIAVFD T0342 100 :VKSG 1wduA 100 :YPQL T0342 104 :MYVVIEVKVATQE 1wduA 105 :TNNIVVVGIRTRA T0342 118 :KEITCRSYL 1wduA 118 :WEITLVSYY T0342 130 :YESAPPSPQYKKIICMGAKEN 1wduA 127 :FEPDKPIESYLEQIKRVERKM Number of specific fragments extracted= 8 number of extra gaps= 0 total=189 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ab5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ab5A expands to /projects/compbio/data/pdb/2ab5.pdb.gz 2ab5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 2ab5A/merged-good-all-a2m # 2ab5A read from 2ab5A/merged-good-all-a2m # adding 2ab5A to template set # found chain 2ab5A in template set T0342 69 :ATIFQSPG 2ab5A 278 :ITISKKGK T0342 78 :EVWGVVW 2ab5A 286 :YLLYELG T0342 85 :KMN 2ab5A 294 :EMH T0342 88 :KSNLNSLDEQE 2ab5A 300 :IQLLYKIKNIL T0342 103 :GMYVVIEVKVATQEGKEITCRSYLMTN 2ab5A 311 :GIGKVTIKKLKMKDGTIKEMCKFNVRN T0342 137 :PQYKKIICMGAKE 2ab5A 339 :NHLKNIIIPIFNK T0342 163 :IEPNDYTGKVSEEIEDIIKKGE 2ab5A 352 :YPMLTNKHYDYLYFKDNLLKDI Number of specific fragments extracted= 7 number of extra gaps= 0 total=196 Number of alignments=21 # 2ab5A read from 2ab5A/merged-good-all-a2m # found chain 2ab5A in template set T0342 68 :IATIFQSPG 2ab5A 277 :WITISKKGK T0342 78 :EVWGVV 2ab5A 286 :YLLYEL T0342 84 :WKMNKSN 2ab5A 293 :IEMHIRD T0342 91 :LNSLDEQEGV 2ab5A 303 :LYKIKNILGI T0342 105 :YVVIEVKVATQEGKEITCRSYLMTN 2ab5A 313 :GKVTIKKLKMKDGTIKEMCKFNVRN T0342 137 :PQYKKIICMGAKENGL 2ab5A 339 :NHLKNIIIPIFNKYPM T0342 153 :PLEYQEK 2ab5A 359 :HYDYLYF T0342 160 :L 2ab5A 369 :L T0342 161 :KAIEPNDYT 2ab5A 371 :KDIKYYNDL Number of specific fragments extracted= 9 number of extra gaps= 0 total=205 Number of alignments=22 # 2ab5A read from 2ab5A/merged-good-all-a2m # found chain 2ab5A in template set T0342 67 :GIATIFQSPGDEVWGVVWKMN 2ab5A 276 :GWITISKKGKYLLYELGIEMH T0342 88 :KSNLNSLDEQEG 2ab5A 300 :IQLLYKIKNILG T0342 104 :MYVVIEVKVATQEGKEITCRSYLMTN 2ab5A 312 :IGKVTIKKLKMKDGTIKEMCKFNVRN T0342 136 :SPQYKKIICMGAKEN 2ab5A 338 :KNHLKNIIIPIFNKY T0342 154 :LEYQEKLKA 2ab5A 363 :LYFKDNLLK T0342 163 :IEPNDYTGKVSEEIEDIIK 2ab5A 379 :LSYYLRPIKPFNTTEDILN Number of specific fragments extracted= 6 number of extra gaps= 0 total=211 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f7fA expands to /projects/compbio/data/pdb/2f7f.pdb.gz 2f7fA:Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 2019, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3037, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3041, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3043, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3045, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3047, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3049, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3051, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3053, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3055, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3057, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3059, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3306, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3310, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3312, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3314, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3316, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3318, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3587, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3591, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3593, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3595, because occupancy 0.500 <= existing 0.500 in 2f7fA Skipped atom 3597, because occupancy 0.500 <= existing 0.500 in 2f7fA # T0342 read from 2f7fA/merged-good-all-a2m # 2f7fA read from 2f7fA/merged-good-all-a2m # adding 2f7fA to template set # found chain 2f7fA in template set Warning: unaligning (T0342)A38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)E94 Warning: unaligning (T0342)A39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)E94 Warning: unaligning (T0342)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)A102 Warning: unaligning (T0342)Q97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)Y323 Warning: unaligning (T0342)E98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)Y323 T0342 28 :TERIHLRNPS 2f7fA 83 :PEDFLTYLAN T0342 40 :FFCVAR 2f7fA 95 :FKCTVR T0342 47 :QDFKLDF 2f7fA 103 :LEGDLVF T0342 62 :QT 2f7fA 110 :NN T0342 66 :GGIATIFQS 2f7fA 112 :EPLIQIEGP T0342 75 :PGDEVW 2f7fA 306 :QKSKID T0342 83 :VWKMN 2f7fA 312 :VWGVG T0342 92 :NSLDE 2f7fA 317 :TKLIT T0342 99 :GVKSGMYVVIEVKVATQEG 2f7fA 324 :DQPALGAVFKLVSIEGEDG T0342 118 :KEIT 2f7fA 406 :KYVR T0342 130 :YESAPPSPQYKKIICMGAKE 2f7fA 427 :VYELPTLDEIKQYAKENLDS T0342 152 :LPLEYQ 2f7fA 447 :LHEEYK T0342 164 :EPNDYTG 2f7fA 453 :RDLNPQK T0342 171 :KVSEEIEDIIKKG 2f7fA 467 :DCWNHKMNLLEKV Number of specific fragments extracted= 14 number of extra gaps= 3 total=225 Number of alignments=24 # 2f7fA read from 2f7fA/merged-good-all-a2m # found chain 2f7fA in template set Warning: unaligning (T0342)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)Y323 Warning: unaligning (T0342)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)Y323 Warning: unaligning (T0342)G54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)S351 Warning: unaligning (T0342)N55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)N353 Warning: unaligning (T0342)S56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)N353 Warning: unaligning (T0342)K85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)L383 Warning: unaligning (T0342)M86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)L383 T0342 19 :YFAYGSNLL 2f7fA 312 :VWGVGTKLI T0342 30 :R 2f7fA 321 :T T0342 33 :LRNPSAA 2f7fA 325 :QPALGAV T0342 41 :FCVARLQD 2f7fA 332 :FKLVSIEG T0342 49 :FKLDF 2f7fA 344 :MKDTI T0342 57 :QGKTSQTWHGGIATIFQSPGDEVWGVVW 2f7fA 354 :AEKVTTPGKKQVWRITRKSDKKSEGDYV T0342 103 :GM 2f7fA 385 :NE T0342 109 :EVKVAT 2f7fA 393 :EIYMFH T0342 115 :QE 2f7fA 400 :VH T0342 118 :KEIT 2f7fA 406 :KYVR T0342 127 :MTN 2f7fA 413 :ARP T0342 130 :YESAPPSPQYKKIICMGAKE 2f7fA 427 :VYELPTLDEIKQYAKENLDS T0342 152 :LPLEYQ 2f7fA 447 :LHEEYK T0342 164 :EPNDYTG 2f7fA 453 :RDLNPQK T0342 171 :KVSEEIEDIIKKGET 2f7fA 467 :DCWNHKMNLLEKVRK Number of specific fragments extracted= 15 number of extra gaps= 3 total=240 Number of alignments=25 # 2f7fA read from 2f7fA/merged-good-all-a2m # found chain 2f7fA in template set Warning: unaligning (T0342)K85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f7fA)L383 Warning: unaligning (T0342)M86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f7fA)L383 Warning: unaligning (T0342)T185 because last residue in template chain is (2f7fA)H485 T0342 51 :LDFGNSQGKTSQTW 2f7fA 335 :VSIEGEDGQMKDTI T0342 65 :HGGIATIFQSPGDEVWGVVW 2f7fA 362 :KKQVWRITRKSDKKSEGDYV T0342 98 :EGVKSGMYVVIEVKVATQEGKEIT 2f7fA 384 :WNEDPRQEEEIYMFHPVHTFINKY T0342 122 :CRSYLM 2f7fA 411 :FEARPV T0342 128 :TNYESAPPSPQYKKIICMGAKEN 2f7fA 425 :KRVYELPTLDEIKQYAKENLDSL T0342 151 :GLP 2f7fA 459 :KYP T0342 154 :LEYQEKLKA 2f7fA 466 :TDCWNHKMN T0342 175 :EIEDIIKKGE 2f7fA 475 :LLEKVRKDVK Number of specific fragments extracted= 8 number of extra gaps= 1 total=248 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f71A expands to /projects/compbio/data/pdb/2f71.pdb.gz 2f71A:Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 166, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 170, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 172, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 174, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 176, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 178, because occupancy 0.450 <= existing 0.450 in 2f71A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 1977, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1981, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 1983, because occupancy 0.200 <= existing 0.800 in 2f71A Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2352, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2473, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2477, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2479, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2481, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2493, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 2f71A Skipped atom 2503, because occupancy 0.500 <= existing 0.500 in 2f71A # T0342 read from 2f71A/merged-good-all-a2m # 2f71A read from 2f71A/merged-good-all-a2m # adding 2f71A to template set # found chain 2f71A in template set T0342 29 :ERIHLRN 2f71A 38 :PKNKNRN T0342 36 :PSAAFFCVARLQDFKLDF 2f71A 64 :NDYINASLIKMEEAQRSY T0342 68 :IATIFQS 2f71A 82 :ILTQGPL T0342 75 :PGDEVWGVVW 2f71A 136 :EDTNLKLTLI T0342 101 :KSGMYVVIEVKVATQE 2f71A 149 :IKSYYTVRQLELENLT T0342 117 :GKEITCRSYLMTN 2f71A 166 :QETREILHFHYTT T0342 130 :YESAPPSPQ 2f71A 181 :DFGVPESPA T0342 139 :YKKIICMGAK 2f71A 191 :FLNFLFKVRE T0342 150 :NG 2f71A 201 :SG Number of specific fragments extracted= 9 number of extra gaps= 0 total=257 Number of alignments=27 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set Warning: unaligning (T0342)H32 because of BadResidue code BAD_PEPTIDE in next template residue (2f71A)Q61 Warning: unaligning (T0342)L33 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)Q61 Warning: unaligning (T0342)R34 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)E62 Warning: unaligning (T0342)N35 because of BadResidue code BAD_PEPTIDE at template residue (2f71A)D63 T0342 36 :PSAAFFCVARLQDFKLDF 2f71A 64 :NDYINASLIKMEEAQRSY T0342 68 :IATIFQSPG 2f71A 82 :ILTQGPLPN T0342 102 :SGMYVVIEVKVATQE 2f71A 150 :KSYYTVRQLELENLT T0342 117 :GKEITCRSYLMTN 2f71A 166 :QETREILHFHYTT T0342 130 :YESAPPSPQ 2f71A 181 :DFGVPESPA T0342 139 :YKKIICMGAKEN 2f71A 191 :FLNFLFKVRESG Number of specific fragments extracted= 6 number of extra gaps= 1 total=263 Number of alignments=28 # 2f71A read from 2f71A/merged-good-all-a2m # found chain 2f71A in template set T0342 4 :SGCKDVTGPDEESF 2f71A 119 :LKCAQYWPQKEEKE T0342 44 :ARLQDFKLDFGNSQ 2f71A 133 :MIFEDTNLKLTLIS T0342 71 :IFQ 2f71A 147 :EDI T0342 102 :SGMYVVIEVKVA 2f71A 150 :KSYYTVRQLELE T0342 114 :TQEGKEITCRSYLMTNYES 2f71A 163 :LTTQETREILHFHYTTWPD T0342 133 :APPSP 2f71A 183 :GVPES T0342 138 :QYKKIICMG 2f71A 190 :SFLNFLFKV T0342 148 :KE 2f71A 199 :RE Number of specific fragments extracted= 8 number of extra gaps= 0 total=271 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g4wR/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g4wR expands to /projects/compbio/data/pdb/1g4w.pdb.gz 1g4wR:# T0342 read from 1g4wR/merged-good-all-a2m # 1g4wR read from 1g4wR/merged-good-all-a2m # adding 1g4wR to template set # found chain 1g4wR in template set T0342 35 :NPS 1g4wR 325 :LSD T0342 38 :AAFFCVARL 1g4wR 330 :PVPVNTLTF T0342 62 :QTWHGGIATIFQS 1g4wR 339 :DGKPVALAGSYPK T0342 75 :PG 1g4wR 397 :GE T0342 79 :VWGVVWKM 1g4wR 399 :VHTNSQKV T0342 88 :KSN 1g4wR 407 :SSA T0342 101 :KSGMYVVIEVKVAT 1g4wR 411 :QGEAIDQYNMQLSC T0342 116 :EGKEITCRSYLMTN 1g4wR 425 :GEKRYTIPVLHVKN T0342 130 :YESAPPSPQYKKIICMGAKENGLP 1g4wR 441 :DHQPLPSTDQLEYLADRVKNSNQN T0342 164 :EPNDYTG 1g4wR 465 :GAPGRSS Number of specific fragments extracted= 10 number of extra gaps= 0 total=281 Number of alignments=30 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set T0342 60 :TSQTWHGGIATI 1g4wR 325 :LSDGMPVPVNTL T0342 73 :QSPGDE 1g4wR 337 :TFDGKP T0342 79 :VWGVVWKM 1g4wR 399 :VHTNSQKV T0342 88 :KSN 1g4wR 407 :SSA T0342 102 :SGMYVVIEVKVAT 1g4wR 412 :GEAIDQYNMQLSC T0342 116 :EGKEITCRSYLMTN 1g4wR 425 :GEKRYTIPVLHVKN T0342 130 :YESAPPSPQYKKIICMGAKENGLP 1g4wR 441 :DHQPLPSTDQLEYLADRVKNSNQN Number of specific fragments extracted= 7 number of extra gaps= 0 total=288 Number of alignments=31 # 1g4wR read from 1g4wR/merged-good-all-a2m # found chain 1g4wR in template set T0342 28 :TERIHLRNPSAAFFCVARLQDFKLDFGNSQGK 1g4wR 378 :EDQMQAKQLPPYFRGSYTFGEVHTNSQKVSSA T0342 100 :VKSGMYVVIEVKVATQEGKEIT 1g4wR 410 :SQGEAIDQYNMQLSCGEKRYTI T0342 122 :CRSYLMTNYESAPPSPQYKKIICMGAKEN 1g4wR 433 :VLHVKNWPDHQPLPSTDQLEYLADRVKNS Number of specific fragments extracted= 3 number of extra gaps= 0 total=291 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wu7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wu7A expands to /projects/compbio/data/pdb/1wu7.pdb.gz 1wu7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 1wu7A/merged-good-all-a2m # 1wu7A read from 1wu7A/merged-good-all-a2m # adding 1wu7A to template set # found chain 1wu7A in template set T0342 30 :RIHLRNPSAAFFCVAR 1wu7A 88 :RMVTSRKDLQRPLRWY T0342 46 :LQDFKL 1wu7A 105 :FPKVWR T0342 54 :GNSQGKTSQTWHGGI 1wu7A 111 :YEEPQAGRYREHYQF T0342 69 :ATIFQS 1wu7A 127 :ADIFGS T0342 76 :GDEVWGVVWKM 1wu7A 302 :GESVPAVGFGM T0342 88 :KSNLNSLDEQEGVKSGM 1wu7A 314 :DAVISLLLKRENVQIPR T0342 116 :EGK 1wu7A 331 :EKK T0342 123 :RSYLMTN 1wu7A 334 :SVYICRV T0342 133 :APPSPQYKK 1wu7A 341 :GKINSSIMN T0342 155 :EYQEKLKAIE 1wu7A 350 :EYSRKLRERG T0342 165 :PNDYTGKVSEEIEDIIKKG 1wu7A 363 :TVEIMERGLSAQLKYASAI Number of specific fragments extracted= 11 number of extra gaps= 0 total=302 Number of alignments=33 # 1wu7A read from 1wu7A/merged-good-all-a2m # found chain 1wu7A in template set T0342 46 :LQDFKLDFGN 1wu7A 254 :VKNVRYDFSI T0342 58 :GKTSQTWHGGIATIFQSPGDE 1wu7A 264 :VRGLSYYTGIVFEAYDRSGQF T0342 79 :VWGVVWKMNKSNLNSLDEQEGVK 1wu7A 305 :VPAVGFGMGDAVISLLLKRENVQ T0342 114 :TQEGKE 1wu7A 328 :IPREKK T0342 123 :RSYLMTN 1wu7A 334 :SVYICRV T0342 133 :A 1wu7A 341 :G T0342 151 :GLPLEYQEKL 1wu7A 342 :KINSSIMNEY T0342 161 :KAIEPNDYT 1wu7A 353 :RKLRERGMN T0342 170 :GKVSEEIEDIIKKGE 1wu7A 368 :ERGLSAQLKYASAIG Number of specific fragments extracted= 9 number of extra gaps= 0 total=311 Number of alignments=34 # 1wu7A read from 1wu7A/merged-good-all-a2m # found chain 1wu7A in template set T0342 11 :GPDEESFL 1wu7A 70 :DKGGREVT T0342 26 :LLTERIHLRN 1wu7A 82 :ATPSTVRMVT T0342 36 :PSAAFFCVARLQDFKLDFGNSQGKTSQTW 1wu7A 94 :KDLQRPLRWYSFPKVWRYEEPQAGRYREH T0342 65 :HGGIATIFQSPGDE 1wu7A 271 :TGIVFEAYDRSGQF T0342 79 :VWGVVWKMNKSNLNSLDEQEGVKSG 1wu7A 305 :VPAVGFGMGDAVISLLLKRENVQIP T0342 117 :GKEITCRSYLMTNY 1wu7A 330 :REKKSVYICRVGKI T0342 136 :SPQYKK 1wu7A 344 :NSSIMN T0342 155 :EYQEKLKAIEPN 1wu7A 350 :EYSRKLRERGMN T0342 167 :DYTGKVSEEIEDIIKKG 1wu7A 366 :IMERGLSAQLKYASAIG Number of specific fragments extracted= 9 number of extra gaps= 0 total=320 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vkbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vkbA expands to /projects/compbio/data/pdb/1vkb.pdb.gz 1vkbA:Skipped atom 175, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 177, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 181, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 233, because occupancy 0.200 <= existing 0.800 in 1vkbA Skipped atom 235, because occupancy 0.200 <= existing 0.800 in 1vkbA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 323, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 325, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1vkbA Skipped atom 686, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 688, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 690, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 692, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 711, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 713, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 719, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 721, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 723, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 725, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 1072, because occupancy 0.350 <= existing 0.650 in 1vkbA Skipped atom 1074, because occupancy 0.350 <= existing 0.650 in 1vkbA # T0342 read from 1vkbA/merged-good-all-a2m # 1vkbA read from 1vkbA/merged-good-all-a2m # adding 1vkbA to template set # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNLLTERIHLRN 1vkbA 0 :HMAHIFVYGTLKRGQPNHKVM T0342 36 :PSAAFFCVARLQD 1vkbA 26 :GLAAFRGRGCTVE T0342 49 :FKLDF 1vkbA 40 :FPLVI T0342 59 :KTSQTW 1vkbA 45 :AGEHNI T0342 69 :ATIFQSPG 1vkbA 51 :PWLLYLPG T0342 77 :DEVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 61 :HCVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQE 1vkbA 86 :SMYQRTALQVQVLE T0342 118 :KEITCRSYLMTN 1vkbA 108 :DSVQCFVYTTAT T0342 130 :YESAPPS 1vkbA 124 :WLFLPYH T0342 164 :EPNDYTG 1vkbA 131 :ESYDSEG Number of specific fragments extracted= 10 number of extra gaps= 0 total=330 Number of alignments=36 # 1vkbA read from 1vkbA/merged-good-all-a2m # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNLLTERIH 1vkbA 0 :HMAHIFVYGTLKRGQPNH T0342 33 :LR 1vkbA 23 :HS T0342 38 :AAFFCVARLQD 1vkbA 28 :AAFRGRGCTVE T0342 49 :FKLDFGNSQG 1vkbA 40 :FPLVIAGEHN T0342 68 :IATIFQSPG 1vkbA 50 :IPWLLYLPG T0342 77 :DEVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 61 :HCVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQE 1vkbA 86 :SMYQRTALQVQVLE T0342 118 :KEITCRSYLMTN 1vkbA 108 :DSVQCFVYTTAT T0342 130 :YES 1vkbA 129 :YHE Number of specific fragments extracted= 9 number of extra gaps= 0 total=339 Number of alignments=37 # 1vkbA read from 1vkbA/merged-good-all-a2m # found chain 1vkbA in template set Warning: unaligning (T0342)E14 because first residue in template chain is (1vkbA)H-1 T0342 15 :ESFLYFAYGSNL 1vkbA 0 :HMAHIFVYGTLK T0342 27 :LTERIH 1vkbA 16 :NHKVML T0342 33 :LRNPSAAFFCVARLQD 1vkbA 23 :HSHGLAAFRGRGCTVE T0342 49 :FKLDFGN 1vkbA 40 :FPLVIAG T0342 65 :HGGIATIFQSPGD 1vkbA 47 :EHNIPWLLYLPGK T0342 78 :EVWGVVWKMNKSNLNSLDEQEGVK 1vkbA 62 :CVTGEIYEVDEQMLRFLDDFEDCP T0342 103 :GMYVVIEVKVATQ 1vkbA 86 :SMYQRTALQVQVL T0342 117 :GKEITCRSYLMTNYESA 1vkbA 107 :GDSVQCFVYTTATYAPE Number of specific fragments extracted= 8 number of extra gaps= 0 total=347 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bv5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bv5A expands to /projects/compbio/data/pdb/2bv5.pdb.gz 2bv5A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 603, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 604, because occupancy 0.350 <= existing 0.650 in 2bv5A Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 2bv5A Bad short name: OCD for alphabet: pdb_atoms Bad short name: OCD for alphabet: pdb_atoms Skipped atom 1796, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1797, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1798, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 1799, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2140, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2141, because occupancy 0.500 <= existing 0.500 in 2bv5A Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 2bv5A # T0342 read from 2bv5A/merged-good-all-a2m # 2bv5A read from 2bv5A/merged-good-all-a2m # adding 2bv5A to template set # found chain 2bv5A in template set T0342 4 :SGCKDVTGPDEE 2bv5A 281 :FEIPMNFVDPKE T0342 26 :LLTERIHLRN 2bv5A 293 :YDIPGLVRKN T0342 36 :PSAAFF 2bv5A 305 :KTILPN T0342 47 :QDFKLDFGNSQ 2bv5A 311 :PHSRVCLTSPD T0342 59 :KTSQTWHGGIATIFQS 2bv5A 322 :PDDPLSSYINANYIRG T0342 75 :PG 2bv5A 396 :DG T0342 79 :VWGVVWKM 2bv5A 398 :VEITVQKV T0342 100 :VKSGMYVVIEVKVAT 2bv5A 406 :IHTEDYRLRLISLKS T0342 116 :EGKEITCRSYLMTNYESAPPS 2bv5A 421 :GTEERGLKHYWFTSWPDQKTP T0342 137 :PQYKKIIC 2bv5A 445 :PPLLHLVR T0342 175 :EIEDIIKKGETQTL 2bv5A 453 :EVEEAAQQEGPHCA Number of specific fragments extracted= 11 number of extra gaps= 0 total=358 Number of alignments=39 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set T0342 5 :GCKDVTGPDEE 2bv5A 282 :EIPMNFVDPKE T0342 26 :LLTERIHLRNPSAAFF 2bv5A 295 :IPGLVRKNRYKTILPN T0342 48 :DFKLDFGN 2bv5A 312 :HSRVCLTS T0342 57 :QGKTSQTWHGGIATIFQSPGDE 2bv5A 320 :PDPDDPLSSYINANYIRGYGGE T0342 79 :VWGVVWKM 2bv5A 398 :VEITVQKV T0342 102 :SGMYVVIEVKVAT 2bv5A 408 :TEDYRLRLISLKS T0342 116 :EGKEITCRSYLMTNYESAPP 2bv5A 421 :GTEERGLKHYWFTSWPDQKT T0342 136 :SPQYKKIIC 2bv5A 444 :APPLLHLVR T0342 175 :EIEDIIKKGETQTL 2bv5A 453 :EVEEAAQQEGPHCA Number of specific fragments extracted= 9 number of extra gaps= 0 total=367 Number of alignments=40 # 2bv5A read from 2bv5A/merged-good-all-a2m # found chain 2bv5A in template set Warning: unaligning (T0342)L18 because of BadResidue code BAD_PEPTIDE in next template residue (2bv5A)I346 Warning: unaligning (T0342)Y19 because of BadResidue code BAD_PEPTIDE at template residue (2bv5A)I346 T0342 11 :GPDEESF 2bv5A 338 :YGGEEKV T0342 20 :FAYGSN 2bv5A 347 :ATQGPI T0342 26 :LLTERIHLRN 2bv5A 354 :STVADFWRMV T0342 36 :PSAAFFCVARLQDFKLDFG 2bv5A 385 :TEYWPEEQVAYDGVEITVQ T0342 70 :TIFQS 2bv5A 404 :KVIHT T0342 103 :GMYVVIEVKVATQEGKEITCRSYLMTNYESAPPSP 2bv5A 409 :EDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDR T0342 138 :QYKKIICMGAKENG 2bv5A 449 :HLVREVEEAAQQEG Number of specific fragments extracted= 7 number of extra gaps= 1 total=374 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ln1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ln1A expands to /projects/compbio/data/pdb/1ln1.pdb.gz 1ln1A:# T0342 read from 1ln1A/merged-good-all-a2m # 1ln1A read from 1ln1A/merged-good-all-a2m # adding 1ln1A to template set # found chain 1ln1A in template set Warning: unaligning (T0342)G183 because last residue in template chain is (1ln1A)Y210 T0342 26 :LLTERIHLRNPSAAFFCVARLQDFKLDF 1ln1A 73 :MDSDYRKQWDQYVKELYEQECNGETVVY T0342 55 :NSQ 1ln1A 104 :KYP T0342 61 :SQTWHGGIATI 1ln1A 107 :FPMSNRDYVYL T0342 72 :FQSPGDEVWGVVWKM 1ln1A 123 :LDMEGRKIHVILARS T0342 87 :N 1ln1A 139 :S T0342 88 :KSN 1ln1A 141 :PQL T0342 99 :GVKSG 1ln1A 144 :GERSG T0342 105 :YVVIEVK 1ln1A 155 :YKQSLAI T0342 113 :ATQEGKEITCRSYLMT 1ln1A 162 :ESDGKKGSKVFMYYFD T0342 130 :YESAPPSPQYKKI 1ln1A 178 :NPGGQIPSWLINW T0342 147 :AKENGLP 1ln1A 191 :AAKNGVP T0342 171 :KVSEEIEDIIKK 1ln1A 198 :NFLKDMARACQN Number of specific fragments extracted= 12 number of extra gaps= 0 total=386 Number of alignments=42 # 1ln1A read from 1ln1A/merged-good-all-a2m # found chain 1ln1A in template set Warning: unaligning (T0342)G183 because last residue in template chain is (1ln1A)Y210 T0342 26 :LLTERIHLRNPSAAFFCVARLQDFKLDF 1ln1A 73 :MDSDYRKQWDQYVKELYEQECNGETVVY T0342 55 :NSQGKTS 1ln1A 104 :KYPFPMS T0342 65 :HGGIATI 1ln1A 111 :NRDYVYL T0342 72 :FQSPGDEVWGVVWKM 1ln1A 123 :LDMEGRKIHVILARS T0342 87 :N 1ln1A 139 :S T0342 88 :KSN 1ln1A 141 :PQL T0342 99 :GVKSG 1ln1A 144 :GERSG T0342 104 :MYVVIEVKVAT 1ln1A 154 :QYKQSLAIESD T0342 116 :EGKEITCRSYLM 1ln1A 165 :GKKGSKVFMYYF T0342 130 :YESAPPSPQYKKIIC 1ln1A 178 :NPGGQIPSWLINWAA T0342 149 :ENGL 1ln1A 193 :KNGV T0342 170 :GKVSEEIEDIIKK 1ln1A 197 :PNFLKDMARACQN Number of specific fragments extracted= 12 number of extra gaps= 0 total=398 Number of alignments=43 # 1ln1A read from 1ln1A/merged-good-all-a2m # found chain 1ln1A in template set T0342 29 :ERIHLRN 1ln1A 11 :EQFWEAC T0342 36 :PSAAFFCVARLQDFKLDFGNSQGKTSQTW 1ln1A 26 :AGADWQLLVETSGISIYRLLDKKTGLYEY T0342 104 :MYVVIEVKVATQEGKEIT 1ln1A 115 :VYLRQRRDLDMEGRKIHV T0342 122 :CRSYLMTN 1ln1A 172 :FMYYFDNP T0342 132 :SAP 1ln1A 180 :GGQ T0342 152 :LPLEYQEKLK 1ln1A 183 :IPSWLINWAA T0342 169 :TGKVSEEIED 1ln1A 193 :KNGVPNFLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=405 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zba3/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0342/1zba3/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0342/1zba3/merged-good-all-a2m.gz for input Trying 1zba3/merged-good-all-a2m Error: Couldn't open file 1zba3/merged-good-all-a2m or 1zba3/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fh7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fh7A expands to /projects/compbio/data/pdb/2fh7.pdb.gz 2fh7A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1794, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1796, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1798, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1800, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1802, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1804, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1806, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1808, because occupancy 0.300 <= existing 0.700 in 2fh7A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3718, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3720, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3722, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3724, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3726, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3728, because occupancy 0.500 <= existing 0.500 in 2fh7A Skipped atom 3730, because occupancy 0.500 <= existing 0.500 in 2fh7A # T0342 read from 2fh7A/merged-good-all-a2m # 2fh7A read from 2fh7A/merged-good-all-a2m # adding 2fh7A to template set # found chain 2fh7A in template set Warning: unaligning (T0342)A162 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)I163 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)E164 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 38 :AAFFCVARLQDFKL 2fh7A 1444 :SDYINANYVDGYRR T0342 62 :QT 2fh7A 1458 :QN T0342 67 :GIATIFQS 2fh7A 1460 :AYIATQGP T0342 76 :GDEVWG 2fh7A 1797 :ERSARY T0342 82 :VVWKMN 2fh7A 1806 :VVDPMA T0342 100 :VKSGMYVVIEVKVATQ 2fh7A 1813 :YNMPQYILREFKVTDA T0342 116 :EGKEITCRSYLMTN 2fh7A 1830 :DGQSRTVRQFQFTD T0342 130 :YESAP 2fh7A 1846 :EQGVP T0342 135 :PSPQYKKIICM 2fh7A 1852 :SGEGFIDFIGQ T0342 156 :YQEKLK 2fh7A 1863 :VHKTKE T0342 165 :P 2fh7A 1872 :Q Number of specific fragments extracted= 11 number of extra gaps= 1 total=416 Number of alignments=45 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0342)E149 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)N150 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)G151 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 34 :RNPSAAFF 2fh7A 1505 :WPNRGTET T0342 42 :CVARLQDFKL 2fh7A 1516 :IQVTLLDTIE T0342 61 :SQTWHGGIATIFQSPGDE 2fh7A 1526 :LATFCVRTFSLHKNGSSE T0342 88 :KSNLNSLDEQE 2fh7A 1758 :AETTEDFWRML T0342 99 :GVK 2fh7A 1814 :NMP T0342 104 :MYVVIEVKVAT 2fh7A 1817 :QYILREFKVTD T0342 115 :QEGKEITCRSYLMTN 2fh7A 1829 :RDGQSRTVRQFQFTD T0342 130 :YESAPP 2fh7A 1845 :PEQGVP T0342 136 :S 2fh7A 1853 :G T0342 137 :PQYKKIICMGAK 2fh7A 1857 :IDFIGQVHKTKE T0342 152 :LP 2fh7A 1872 :QD Number of specific fragments extracted= 11 number of extra gaps= 1 total=427 Number of alignments=46 # 2fh7A read from 2fh7A/merged-good-all-a2m # found chain 2fh7A in template set Warning: unaligning (T0342)C42 because of BadResidue code BAD_PEPTIDE in next template residue (2fh7A)K1781 Warning: unaligning (T0342)V43 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)K1781 Warning: unaligning (T0342)E149 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2fh7A)F1870 Warning: unaligning (T0342)N150 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2fh7A)F1870 Warning: unaligning (T0342)G151 because of BadResidue code BAD_PEPTIDE at template residue (2fh7A)G1871 T0342 9 :VTGPDEESFLYFAYGSN 2fh7A 1741 :IDGYRQQKAYIATQGPL T0342 26 :LLTERIHLRN 2fh7A 1759 :ETTEDFWRML T0342 41 :F 2fh7A 1779 :L T0342 44 :ARLQDFKLDFGNSQGKTSQTWHGGIATIFQSPG 2fh7A 1782 :LREMGREKCHQYWPAERSARYQYFVVDPMAEYN T0342 102 :SGMYVVIEVKV 2fh7A 1815 :MPQYILREFKV T0342 113 :ATQEGKEITCRSYLMTNYESAPPSP 2fh7A 1827 :DARDGQSRTVRQFQFTDWPEQGVPK T0342 138 :QYKKIICMGAK 2fh7A 1858 :DFIGQVHKTKE T0342 152 :LP 2fh7A 1872 :QD Number of specific fragments extracted= 8 number of extra gaps= 2 total=435 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t5hX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t5hX expands to /projects/compbio/data/pdb/1t5h.pdb.gz 1t5hX:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 1t5hX/merged-good-all-a2m # 1t5hX read from 1t5hX/merged-good-all-a2m # adding 1t5hX to template set # found chain 1t5hX in template set T0342 3 :N 1t5hX 266 :G T0342 9 :VTGPDEESFLYFAYGSNLLTERI 1t5hX 267 :SSLKLDSLRHVTFAGATMPDAVL T0342 75 :PGDE 1t5hX 347 :NGEE T0342 81 :G 1t5hX 351 :G T0342 82 :VVWKMN 1t5hX 353 :LIVAAS T0342 88 :KSNLN 1t5hX 369 :PQATA T0342 102 :SGMYVVIEVKVATQEG 1t5hX 378 :DGWYRTSDVAVWTPEG T0342 118 :KE 1t5hX 441 :GQ T0342 121 :TCRSYLMTNYESAPPSPQYKKII 1t5hX 443 :SVTACVVPRLGETLSADALDTFC T0342 148 :KENGLPL 1t5hX 466 :RSSELAD T0342 163 :IEPNDYTGKVSEEIEDII 1t5hX 485 :LPKNALNKVLRRQLVQQV Number of specific fragments extracted= 11 number of extra gaps= 0 total=446 Number of alignments=48 # 1t5hX read from 1t5hX/merged-good-all-a2m # found chain 1t5hX in template set T0342 6 :CKDVTGPDEESFLYFAYGSNLLTE 1t5hX 264 :HAGSSLKLDSLRHVTFAGATMPDA T0342 30 :RIHLRNPSAAFFCVAR 1t5hX 291 :TVHQHLPGEKVNIYGT T0342 48 :DFKLDFGNSQGKTSQTWHG 1t5hX 309 :AMNSLYMRQPKTGTEMAPG T0342 67 :GIATIFQSPGDE 1t5hX 330 :SEVRIVRIGGGV T0342 85 :KM 1t5hX 396 :RI T0342 87 :NKSN 1t5hX 400 :RVDD T0342 91 :LNSLDEQEGVKSGMYVVIEVKVATQEGKE 1t5hX 414 :PSEIERVLGTAPGVTEVVVIGLADQRWGQ T0342 121 :TCRSYLMTNYESAPPSPQYKKI 1t5hX 443 :SVTACVVPRLGETLSADALDTF T0342 147 :AKENGLPL 1t5hX 465 :CRSSELAD T0342 163 :IEPNDYTGKVSEEIEDII 1t5hX 485 :LPKNALNKVLRRQLVQQV Number of specific fragments extracted= 10 number of extra gaps= 0 total=456 Number of alignments=49 # 1t5hX read from 1t5hX/merged-good-all-a2m # found chain 1t5hX in template set T0342 18 :LYFAYGSNLLTER 1t5hX 276 :HVTFAGATMPDAV T0342 31 :IHLRN 1t5hX 292 :VHQHL T0342 36 :PSAAFFCVARLQDF 1t5hX 316 :RQPKTGTEMAPGFF T0342 50 :KLDFGNSQGKTSQTW 1t5hX 331 :EVRIVRIGGGVDEIV T0342 66 :GGIATIFQSPGDEVW 1t5hX 382 :RTSDVAVWTPEGTVR T0342 81 :G 1t5hX 399 :G T0342 87 :NKSN 1t5hX 400 :RVDD T0342 91 :LNSLDEQEGVKSGMYVVIEVKVATQEGKEITCRSYLMTNYESAP 1t5hX 414 :PSEIERVLGTAPGVTEVVVIGLADQRWGQSVTACVVPRLGETLS T0342 137 :P 1t5hX 458 :A T0342 154 :LEYQEKLKAIEPND 1t5hX 459 :DALDTFCRSSELAD Number of specific fragments extracted= 10 number of extra gaps= 0 total=466 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cjxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cjxA expands to /projects/compbio/data/pdb/1cjx.pdb.gz 1cjxA:Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2047, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2049, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2051, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2459, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2461, because occupancy 0.500 <= existing 0.500 in 1cjxA Skipped atom 2464, because occupancy 0.500 <= existing 0.500 in 1cjxA # T0342 read from 1cjxA/merged-good-all-a2m # 1cjxA read from 1cjxA/merged-good-all-a2m # adding 1cjxA to template set # found chain 1cjxA in template set Warning: unaligning (T0342)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1cjxA)E132 Warning: unaligning (T0342)S102 because of BadResidue code BAD_PEPTIDE at template residue (1cjxA)E132 Warning: unaligning (T0342)G103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cjxA)G133 T0342 16 :SFLYFAYGSN 1cjxA 12 :GFEFIEFASP T0342 26 :LLTERIHLRN 1cjxA 25 :TLEPIFEIMG T0342 38 :AAFFCVARLQDFKL 1cjxA 35 :FTKVATHRSKNVHL T0342 62 :QTWHGGIATIFQSPGD 1cjxA 49 :YRQGEINLILNNEPNS T0342 79 :VWGVVWKM 1cjxA 77 :VCGMAFRV T0342 87 :N 1cjxA 86 :D T0342 88 :KSNLNSLDEQ 1cjxA 88 :QKAYNRALEL T0342 99 :GV 1cjxA 98 :GA T0342 104 :M 1cjxA 134 :S T0342 112 :VATQEG 1cjxA 141 :FVYLEG T0342 122 :CRSYLMTN 1cjxA 240 :HVAFLTDD T0342 143 :ICMGAKENG 1cjxA 251 :TWDALKKIG T0342 152 :LPLEYQEKL 1cjxA 266 :PPDTYYEML T0342 161 :KAIEPNDYT 1cjxA 276 :GRLPDHGEP T0342 173 :SEEIEDI 1cjxA 285 :VDQLQAR Number of specific fragments extracted= 15 number of extra gaps= 1 total=481 Number of alignments=51 # 1cjxA read from 1cjxA/merged-good-all-a2m # found chain 1cjxA in template set Warning: unaligning (T0342)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1cjxA)E132 Warning: unaligning (T0342)S102 because of BadResidue code BAD_PEPTIDE at template residue (1cjxA)E132 Warning: unaligning (T0342)G103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cjxA)G133 T0342 14 :E 1cjxA 7 :P T0342 15 :ESFLYFAYGS 1cjxA 11 :MGFEFIEFAS T0342 34 :RNPS 1cjxA 21 :PTPG T0342 38 :AAFFCVARLQDFKLD 1cjxA 35 :FTKVATHRSKNVHLY T0342 63 :TWHGGIATIFQSPGDE 1cjxA 50 :RQGEINLILNNEPNSI T0342 79 :VWGVVWKM 1cjxA 77 :VCGMAFRV T0342 87 :N 1cjxA 86 :D T0342 88 :KSNLNSLDEQE 1cjxA 88 :QKAYNRALELG T0342 99 :GV 1cjxA 129 :RF T0342 104 :M 1cjxA 134 :S T0342 112 :VATQEG 1cjxA 141 :FVYLEG T0342 123 :RSYLMTN 1cjxA 241 :VAFLTDD T0342 139 :YKK 1cjxA 248 :LVK T0342 143 :ICMGAKENG 1cjxA 251 :TWDALKKIG T0342 152 :LPLEYQEKL 1cjxA 266 :PPDTYYEML T0342 161 :KAIEPNDYT 1cjxA 276 :GRLPDHGEP T0342 173 :SEEIEDI 1cjxA 285 :VDQLQAR Number of specific fragments extracted= 17 number of extra gaps= 1 total=498 Number of alignments=52 # 1cjxA read from 1cjxA/merged-good-all-a2m # found chain 1cjxA in template set T0342 16 :SFLYFAYGSN 1cjxA 12 :GFEFIEFASP T0342 26 :LLTERIHLRN 1cjxA 25 :TLEPIFEIMG T0342 40 :FFCVARLQDF 1cjxA 35 :FTKVATHRSK T0342 50 :KLDF 1cjxA 47 :HLYR T0342 64 :WHGGIATIFQSPGD 1cjxA 51 :QGEINLILNNEPNS T0342 79 :VWGVVWKMN 1cjxA 77 :VCGMAFRVK T0342 88 :KSNLNSLDEQ 1cjxA 88 :QKAYNRALEL T0342 103 :GMYV 1cjxA 98 :GAQP T0342 110 :VKVATQEGKEIT 1cjxA 102 :IHIDTGPMELNL T0342 122 :CRSYLMTN 1cjxA 240 :HVAFLTDD T0342 140 :KKIICMGAKENGL 1cjxA 248 :LVKTWDALKKIGM T0342 153 :PLEYQEKLKAI 1cjxA 267 :PDTYYEMLEGR T0342 165 :PNDYTGKVSEEIE 1cjxA 278 :LPDHGEPVDQLQA Number of specific fragments extracted= 13 number of extra gaps= 0 total=511 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v30A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0342 read from 1v30A/merged-good-all-a2m # 1v30A read from 1v30A/merged-good-all-a2m # found chain 1v30A in training set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDF 1v30A 8 :VRIAVYGTLRKGKPLHWYLKGAKFLGEDWIEGYQLYF T0342 62 :QTW 1v30A 45 :EYL T0342 69 :ATIFQSPG 1v30A 48 :PYAVKGKG T0342 78 :EVWGVVWKMNKSNLNSLDEQEG 1v30A 56 :KLKVEVYEVDKETFERINEIEI T0342 102 :SGMYVVIEVK 1v30A 78 :GTGYRLVEVS T0342 114 :TQEGK 1v30A 88 :TKFGK T0342 122 :CRSYLMTN 1v30A 93 :AFLWEWGS Number of specific fragments extracted= 7 number of extra gaps= 0 total=518 Number of alignments=54 # 1v30A read from 1v30A/merged-good-all-a2m # found chain 1v30A in training set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNLLTERIHLRNPSAAFFCVARLQDFKLDFGNS 1v30A 8 :VRIAVYGTLRKGKPLHWYLKGAKFLGEDWIEGYQLYFEYL T0342 69 :ATIFQSPG 1v30A 48 :PYAVKGKG T0342 78 :EVWGVVWKMNKSNLNSLDEQEGV 1v30A 56 :KLKVEVYEVDKETFERINEIEIG T0342 102 :SG 1v30A 79 :TG T0342 105 :YVVIEVK 1v30A 81 :YRLVEVS T0342 114 :TQEGK 1v30A 88 :TKFGK T0342 122 :CRSYLMTN 1v30A 93 :AFLWEWGS Number of specific fragments extracted= 7 number of extra gaps= 0 total=525 Number of alignments=55 # 1v30A read from 1v30A/merged-good-all-a2m # found chain 1v30A in training set Warning: unaligning (T0342)S16 because first residue in template chain is (1v30A)S7 T0342 17 :FLYFAYGSNL 1v30A 8 :VRIAVYGTLR T0342 32 :HLRNPSAAFFCVARLQDFKLDFG 1v30A 23 :HWYLKGAKFLGEDWIEGYQLYFE T0342 58 :GK 1v30A 46 :YL T0342 69 :ATIFQS 1v30A 48 :PYAVKG T0342 76 :GDEVWGVVWKMNKSNLNSLDEQEGV 1v30A 54 :KGKLKVEVYEVDKETFERINEIEIG T0342 103 :GMYV 1v30A 79 :TGYR T0342 109 :EVKVATQEGK 1v30A 83 :LVEVSTKFGK T0342 121 :TCRSYLMTNYES 1v30A 93 :AFLWEWGSKPRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=533 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fvgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fvgA expands to /projects/compbio/data/pdb/2fvg.pdb.gz 2fvgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 2fvgA/merged-good-all-a2m # 2fvgA read from 2fvgA/merged-good-all-a2m # adding 2fvgA to template set # found chain 2fvgA in template set T0342 14 :EES 2fvgA 51 :SSK T0342 18 :LYFAYGSNLL 2fvgA 54 :KLLVSAHMDE T0342 38 :AAFFCVARLQDFKLDFGNSQGKTSQTWHGGIATI 2fvgA 64 :VGFVVSKIEKDGKVSFLPVGGVDPRILPGKVVQV T0342 72 :FQS 2fvgA 100 :LKG T0342 75 :PGDEV 2fvgA 123 :ENLRI T0342 91 :LNSLDEQ 2fvgA 134 :ADEAKKY T0342 100 :VKSGMYVVIEVKVATQEG 2fvgA 141 :VSIGDYVSFVSDYIEKNG T0342 126 :LMTN 2fvgA 243 :AITF T0342 130 :YESAPPSPQYKKIICMGAKENGLP 2fvgA 248 :HRGYVIPKEIFQTIVDTAKNNDIP Number of specific fragments extracted= 9 number of extra gaps= 0 total=542 Number of alignments=57 # 2fvgA read from 2fvgA/merged-good-all-a2m # found chain 2fvgA in template set Warning: unaligning (T0342)N87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fvgA)P120 T0342 15 :ESFLYFAYGSNLL 2fvgA 51 :SSKKLLVSAHMDE T0342 41 :F 2fvgA 64 :V T0342 43 :VARLQD 2fvgA 65 :GFVVSK T0342 49 :FKLDFGNSQGKTSQTWHGGIATI 2fvgA 75 :GKVSFLPVGGVDPRILPGKVVQV T0342 75 :PG 2fvgA 98 :KN T0342 79 :VWGVVWKM 2fvgA 100 :LKGVIGYR T0342 99 :GVKSGMYVVIEVKVATQEG 2fvgA 140 :YVSIGDYVSFVSDYIEKNG T0342 126 :LMTN 2fvgA 243 :AITF T0342 130 :YESAPPSPQYKKIICMGAKENGLP 2fvgA 248 :HRGYVIPKEIFQTIVDTAKNNDIP Number of specific fragments extracted= 9 number of extra gaps= 0 total=551 Number of alignments=58 # 2fvgA read from 2fvgA/merged-good-all-a2m # found chain 2fvgA in template set Warning: unaligning (T0342)Q57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fvgA)P120 T0342 39 :AFFCVARLQDFKLDFGNS 2fvgA 90 :LPGKVVQVKNLKGVIGYR T0342 65 :HGGIATIFQS 2fvgA 123 :ENLRIDFGFS T0342 87 :NKSN 2fvgA 133 :SADE T0342 94 :LDE 2fvgA 137 :AKK T0342 99 :GVKSGMYVVIEVKVATQEGKEIT 2fvgA 140 :YVSIGDYVSFVSDYIEKNGRAVG T0342 124 :SYLMTNYESAPPSPQYKKIICMGAKENGLP 2fvgA 242 :PAITFYHRGYVIPKEIFQTIVDTAKNNDIP Number of specific fragments extracted= 6 number of extra gaps= 0 total=557 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0342/1xhsA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0342/1xhsA/merged-good-all-a2m.gz for input Trying 1xhsA/merged-good-all-a2m Error: Couldn't open file 1xhsA/merged-good-all-a2m or 1xhsA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yqgA expands to /projects/compbio/data/pdb/1yqg.pdb.gz 1yqgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0342 read from 1yqgA/merged-good-all-a2m # 1yqgA read from 1yqgA/merged-good-all-a2m # adding 1yqgA to template set # found chain 1yqgA in template set T0342 14 :EESFLYFAYGSNLLTERIHLRNPSAAFFCVA 1yqgA 79 :TNGALVLSVAAGLSVGTLSRYLGGTRRIVRV T0342 53 :FGN 1yqgA 110 :MPN T0342 60 :TSQTWHGGIATIFQSPG 1yqgA 113 :TPGKIGLGVSGMYAEAE T0342 86 :MNKSNLNSLDEQEG 1yqgA 130 :VSETDRRIADRIMK T0342 103 :GM 1yqgA 144 :SV T0342 126 :LMTNY 1yqgA 150 :WLDDE T0342 137 :PQ 1yqgA 155 :EK T0342 143 :ICMGAKENGLPLEYQEKL 1yqgA 157 :MHGITGISGSGPAYVFYL T0342 161 :KAIE 1yqgA 176 :DALQ T0342 165 :PNDYTGKVSEEIEDIIKK 1yqgA 184 :RQGFDMAEARALSLATFK Number of specific fragments extracted= 10 number of extra gaps= 0 total=567 Number of alignments=60 # 1yqgA read from 1yqgA/merged-good-all-a2m # found chain 1yqgA in template set T0342 15 :ESFLYFAYGSNLLTERIHLRNPSAAFFCV 1yqgA 80 :NGALVLSVAAGLSVGTLSRYLGGTRRIVR T0342 52 :DFGN 1yqgA 109 :VMPN T0342 61 :SQTWHG 1yqgA 113 :TPGKIG T0342 67 :GIATIFQSPG 1yqgA 120 :GVSGMYAEAE T0342 86 :MNKSNLNSLDEQEGV 1yqgA 130 :VSETDRRIADRIMKS T0342 102 :SG 1yqgA 145 :VG T0342 111 :KVATQEG 1yqgA 147 :LTVWLDD T0342 137 :PQ 1yqgA 155 :EK T0342 143 :ICMGAKENGLPLEYQEKL 1yqgA 157 :MHGITGISGSGPAYVFYL T0342 161 :KAIEPN 1yqgA 176 :DALQNA T0342 167 :DYTGKVSEEIEDIIKK 1yqgA 186 :GFDMAEARALSLATFK Number of specific fragments extracted= 11 number of extra gaps= 0 total=578 Number of alignments=61 # 1yqgA read from 1yqgA/merged-good-all-a2m # found chain 1yqgA in template set T0342 15 :ESFLYFAYGSNLLTERIHLRNPSAAFFCVAR 1yqgA 80 :NGALVLSVAAGLSVGTLSRYLGGTRRIVRVM T0342 58 :GKTSQTWHGGIATIFQSPG 1yqgA 111 :PNTPGKIGLGVSGMYAEAE T0342 86 :MNKSNLNSLDEQEGVK 1yqgA 130 :VSETDRRIADRIMKSV T0342 108 :IEVKVATQEG 1yqgA 146 :GLTVWLDDEE T0342 136 :SPQY 1yqgA 167 :GPAY T0342 140 :KKIICMGAKENGLPLEYQEKLKA 1yqgA 175 :LDALQNAAIRQGFDMAEARALSL T0342 174 :EEIEDIIKK 1yqgA 198 :ATFKGAVAL Number of specific fragments extracted= 7 number of extra gaps= 0 total=585 Number of alignments=62 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 62 Adding 2927 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -341.0051, CN propb: -341.0051 weights: 0.1831 constraints: 678 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 678 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 678 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 2249 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 2249 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 2927 # command: