# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0558 numbered 1 through 294 Created new target T0558 from T0558.a2m # command:CPU_time= 5.917 sec, elapsed time= 9.095 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nr0A/T0558-1nr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nr0A expands to /projects/compbio/data/pdb/1nr0.pdb.gz 1nr0A:# T0558 read from 1nr0A/T0558-1nr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nr0A read from 1nr0A/T0558-1nr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nr0A to template set # found chain 1nr0A in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTK 1nr0A 50 :TDTEIYTEHSHQTTVAKTSPSGYYCASGDVHGNVRIWDTTQT # choosing archetypes in rotamer library T0558 44 :EIVWEYP 1nr0A 94 :ILKTTIP T0558 52 :EKGWECNSVAATKAGEILF 1nr0A 101 :VFSGPVKDISWDSESKRIA T0558 71 :SYSKG 1nr0A 165 :SGSDD T0558 76 :AKMITRD 1nr0A 172 :VAIFEGP T0558 83 :GRELWNIAAPAGC 1nr0A 180 :FKFKSTFGEHTKF T0558 97 :MQTARILPDGNALVAWCG 1nr0A 193 :VHSVRYNPDGSLFASTGG T0558 116 :PSTILEVNMK 1nr0A 211 :DGTIVLYNGV T0558 126 :GEVLSKTEFETGIER 1nr0A 222 :GTKTGVFEDDSLKNV T0558 141 :PHAQFRQINKNKKGNYLVPLFATSEVREIAPN 1nr0A 238 :HSGSVFGLTWSPDGTKIASASADKTIKIWNVA T0558 173 :GQLLNSVKLSGT 1nr0A 271 :LKVEKTIPVGTR T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESN 1nr0A 451 :SSCVALSNDKQFVAVGGQDSKVHVYKLSGA T0558 215 :RIVRRVNAND 1nr0A 483 :SEVKTIVHPA T0558 232 :FVAQLFPLQNGGLYICNWQGH 1nr0A 493 :EITSVAFSNNGAFLVATDQSR T0558 263 :QLVEID 1nr0A 514 :KVIPYS T0558 269 :SEGKV 1nr0A 522 :NNFEL T0558 274 :VWQLNDKVKFGMI 1nr0A 539 :VACVSWSPDNVRL T0558 287 :STICPI 1nr0A 557 :DNSVIV Number of specific fragments extracted= 18 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nr0A/T0558-1nr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1nr0A/T0558-1nr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nr0A read from 1nr0A/T0558-1nr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nr0A in template set T0558 2 :KNFILLVALFL 1nr0A 50 :TDTEIYTEHSH T0558 14 :APFAQGSSPQ 1nr0A 61 :QTTVAKTSPS T0558 24 :HLLVGGSGWNKIAIINKDTKE 1nr0A 72 :YYCASGDVHGNVRIWDTTQTT T0558 45 :IVWEYP 1nr0A 95 :LKTTIP T0558 52 :EKGWECNSVAATKAGEILF 1nr0A 101 :VFSGPVKDISWDSESKRIA T0558 71 :SYSKG 1nr0A 165 :SGSDD T0558 76 :AKMIT 1nr0A 172 :VAIFE T0558 81 :RDGRELWNIA 1nr0A 178 :PPFKFKSTFG T0558 92 :PAGCEMQTARILPDGNALVAWC 1nr0A 188 :EHTKFVHSVRYNPDGSLFASTG T0558 115 :HPSTILEVNMK 1nr0A 210 :GDGTIVLYNGV T0558 126 :GEVLSKTEFE 1nr0A 222 :GTKTGVFEDD T0558 136 :TGIER 1nr0A 237 :AHSGS T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 1nr0A 242 :VFGLTWSPDGTKIASASADKTIKIWNVA T0558 173 :GQLLNSVKLSGT 1nr0A 271 :LKVEKTIPVGTR T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESN 1nr0A 451 :SSCVALSNDKQFVAVGGQDSKVHVYKLSGA T0558 215 :RIVRRVNANDI 1nr0A 483 :SEVKTIVHPAE T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1nr0A 494 :ITSVAFSNNGAFLVATDQSRKVIPYSV T0558 260 :KHPQLVE 1nr0A 522 :NNFELAH T0558 267 :IDSEGKVVWQL 1nr0A 532 :WTFHTAKVACV T0558 278 :NDKVKFGMISTICPIR 1nr0A 546 :PDNVRLATGSLDNSVI Number of specific fragments extracted= 20 number of extra gaps= 0 total=38 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nr0A/T0558-1nr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1nr0A/T0558-1nr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nr0A read from 1nr0A/T0558-1nr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nr0A in template set Warning: unaligning (T0558)R218 because of BadResidue code BAD_PEPTIDE in next template residue (1nr0A)V319 Warning: unaligning (T0558)R219 because of BadResidue code BAD_PEPTIDE at template residue (1nr0A)V319 Warning: unaligning (T0558)M285 because of BadResidue code BAD_PEPTIDE in next template residue (1nr0A)I370 Warning: unaligning (T0558)I286 because of BadResidue code BAD_PEPTIDE at template residue (1nr0A)I370 T0558 21 :SPQHLLVGGSGWNKIAIINK 1nr0A 68 :SPSGYYCASGDVHGNVRIWD T0558 41 :DTKE 1nr0A 89 :TQTT T0558 45 :IVWEYPLE 1nr0A 95 :LKTTIPVF T0558 54 :GWECNSVAATKAGEILFSY 1nr0A 103 :SGPVKDISWDSESKRIAAV T0558 73 :SKGAKMITRDG 1nr0A 169 :DNTVAIFEGPP T0558 84 :RELWNIAAPAG 1nr0A 181 :KFKSTFGEHTK T0558 96 :EMQTARILPDGNALVAWCG 1nr0A 192 :FVHSVRYNPDGSLFASTGG T0558 116 :PSTILEVNM 1nr0A 211 :DGTIVLYNG T0558 125 :KGEVLSKTEFETGIER 1nr0A 221 :DGTKTGVFEDDSLKNV T0558 141 :PHAQFRQINKNKKGNYLVPLFATSEVREIAPNGQ 1nr0A 238 :HSGSVFGLTWSPDGTKIASASADKTIKIWNVATL T0558 175 :LLNSVKLSGT 1nr0A 273 :VEKTIPVGTR T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIV 1nr0A 285 :DQQLGIIWTKQALVSISANGFINFVNPELGSID T0558 220 :VN 1nr0A 320 :RY T0558 228 :VQLFFVAQLFPLQNGGLYICNWQGH 1nr0A 322 :GHNKAITALSSSADGKTLFSADAEG T0558 263 :QLVEID 1nr0A 347 :HINSWD T0558 269 :SEGKVVW 1nr0A 354 :STGISNR T0558 279 :DKVKFG 1nr0A 363 :PDVHAT T0558 287 :STICPIRE 1nr0A 371 :TGIKTTSK Number of specific fragments extracted= 18 number of extra gaps= 2 total=56 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gnqA/T0558-2gnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gnqA expands to /projects/compbio/data/pdb/2gnq.pdb.gz 2gnqA:Skipped atom 501, because occupancy 0.5 <= existing 0.500 in 2gnqA Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1811, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1813, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1815, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1817, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1993, because occupancy 0.500 <= existing 0.500 in 2gnqA Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 2gnqA # T0558 read from 2gnqA/T0558-2gnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gnqA read from 2gnqA/T0558-2gnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gnqA to template set # found chain 2gnqA in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)L111 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (2gnqA)A169 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)A169 Warning: unaligning (T0558)S287 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)E322 T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 2gnqA 36 :ALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2gnqA 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 77 :KMITRD 2gnqA 112 :KIWDVS T0558 83 :GRELWNIAAPAGC 2gnqA 119 :GKCLKTLKGHSNY T0558 97 :MQTARILPDGNALVAWCG 2gnqA 132 :VFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVNMK 2gnqA 150 :DESVRIWDVK T0558 126 :GEVLSK 2gnqA 161 :GKCLKT T0558 134 :F 2gnqA 167 :L T0558 137 :GIERPHA 2gnqA 170 :HSDPVSA T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 2gnqA 177 :VHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSV 2gnqA 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2gnqA 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEK T0558 232 :FVAQLFPLQ 2gnqA 260 :YCIFANFSV T0558 241 :NGGLYICNWQGH 2gnqA 270 :GGKWIVSGSEDN T0558 253 :DREAGK 2gnqA 287 :NLQTKE T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2gnqA 293 :IVQKLQGHTDVVISTACHPTENII T0558 288 :TICPI 2gnqA 323 :NDKTI Number of specific fragments extracted= 17 number of extra gaps= 3 total=73 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gnqA/T0558-2gnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2gnqA/T0558-2gnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gnqA read from 2gnqA/T0558-2gnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gnqA in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)L111 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (2gnqA)A169 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)A169 Warning: unaligning (T0558)T288 because of BadResidue code BAD_PEPTIDE in next template residue (2gnqA)E322 T0558 1 :MKNFILLVALFL 2gnqA 35 :YALKFTLAGHTK T0558 14 :APFAQGSSPQ 2gnqA 47 :AVSSVKFSPN T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 2gnqA 58 :EWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2gnqA 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 77 :KMIT 2gnqA 112 :KIWD T0558 81 :RDGRELWNIA 2gnqA 117 :SSGKCLKTLK T0558 92 :PAGCEMQTARILPDGNALVAWC 2gnqA 127 :GHSNYVFCCNFNPQSNLIVSGS T0558 115 :HPSTILEVNMK 2gnqA 149 :FDESVRIWDVK T0558 126 :GEVLS 2gnqA 161 :GKCLK T0558 133 :EF 2gnqA 166 :TL T0558 137 :GIER 2gnqA 170 :HSDP T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 2gnqA 174 :VSAVHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSV 2gnqA 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 2gnqA 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKY T0558 233 :VAQLFPL 2gnqA 261 :CIFANFS T0558 240 :QNGGLYICNWQGHDREAGKG 2gnqA 269 :TGGKWIVSGSEDNLVYIWNL T0558 260 :KHPQLVEIDSEGKVVWQL 2gnqA 290 :TKEIVQKLQGHTDVVIST T0558 278 :NDKVKFGMIS 2gnqA 311 :PTENIIASAA T0558 289 :ICPI 2gnqA 324 :DKTI Number of specific fragments extracted= 19 number of extra gaps= 3 total=92 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gnqA/T0558-2gnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2gnqA/T0558-2gnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gnqA read from 2gnqA/T0558-2gnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gnqA in template set Warning: unaligning (T0558)G75 because of BadResidue code BAD_PEPTIDE in next template residue (2gnqA)L111 Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)L111 Warning: unaligning (T0558)E133 because of BadResidue code BAD_PEPTIDE in next template residue (2gnqA)A169 Warning: unaligning (T0558)F134 because of BadResidue code BAD_PEPTIDE at template residue (2gnqA)A169 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 2gnqA 55 :PNGEWLASSSADKLIKIWGAYDGKFEKTISGHKL T0558 56 :ECNSVAATKAGEILFSY 2gnqA 89 :GISDVAWSSDSNLLVSA T0558 73 :SK 2gnqA 108 :DK T0558 77 :KMITRDG 2gnqA 112 :KIWDVSS T0558 84 :RELWNIAAPAG 2gnqA 120 :KCLKTLKGHSN T0558 96 :EMQTARILPDGNALVAWCG 2gnqA 131 :YVFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVN 2gnqA 150 :DESVRIWD T0558 124 :MKGEVLSKT 2gnqA 159 :KTGKCLKTL T0558 135 :ETG 2gnqA 170 :HSD T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 2gnqA 173 :PVSAVHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSVKLS 2gnqA 203 :GQCLKTLIDD T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2gnqA 215 :PPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEK T0558 232 :FVAQLFPLQN 2gnqA 260 :YCIFANFSVT T0558 242 :GGLYICNWQGH 2gnqA 271 :GKWIVSGSEDN T0558 263 :QLVEIDSE 2gnqA 282 :LVYIWNLQ T0558 271 :GKVVWQLNDKV 2gnqA 291 :KEIVQKLQGHT T0558 284 :GMISTICPIRE 2gnqA 302 :DVVISTACHPT Number of specific fragments extracted= 17 number of extra gaps= 2 total=109 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3emhA/T0558-3emhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3emhA expands to /projects/compbio/data/pdb/3emh.pdb.gz 3emhA:Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 3emhA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 3emhA # T0558 read from 3emhA/T0558-3emhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3emhA read from 3emhA/T0558-3emhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3emhA to template set # found chain 3emhA in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 3emhA 36 :ALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3emhA 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 76 :AKMITRD 3emhA 111 :LKIWDVS T0558 83 :GRELWNIAAPAGC 3emhA 119 :GKCLKTLKGHSNY T0558 97 :MQTARILPDGNALVAWCG 3emhA 132 :VFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVNMK 3emhA 150 :DESVRIWDVK T0558 126 :GEVLSK 3emhA 161 :GKCLKT T0558 134 :FETGIERPHA 3emhA 167 :LPAHSDPVSA T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 3emhA 177 :VHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSV 3emhA 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 3emhA 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEK T0558 232 :FVAQLFPLQ 3emhA 260 :YCIFANFSV T0558 241 :NGGLYICNWQGH 3emhA 270 :GGKWIVSGSEDN T0558 253 :DREAGK 3emhA 287 :NLQTKE T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 3emhA 293 :IVQKLQGHTDVVISTACHPTENII T0558 287 :STICPI 3emhA 322 :ENDKTI Number of specific fragments extracted= 16 number of extra gaps= 0 total=125 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3emhA/T0558-3emhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3emhA/T0558-3emhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3emhA read from 3emhA/T0558-3emhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3emhA in template set T0558 1 :MKNFILLVALFL 3emhA 35 :YALKFTLAGHTK T0558 14 :APFAQGSSPQ 3emhA 47 :AVSSVKFSPN T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 3emhA 58 :EWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3emhA 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 76 :AKMIT 3emhA 111 :LKIWD T0558 81 :RDGRELWNIA 3emhA 117 :SSGKCLKTLK T0558 92 :PAGCEMQTARILPDGNALVAWC 3emhA 127 :GHSNYVFCCNFNPQSNLIVSGS T0558 115 :HPSTILEVNMK 3emhA 149 :FDESVRIWDVK T0558 126 :GEVLS 3emhA 161 :GKCLK T0558 133 :EFETGIER 3emhA 166 :TLPAHSDP T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 3emhA 174 :VSAVHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSV 3emhA 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 3emhA 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKY T0558 233 :VAQLFPL 3emhA 261 :CIFANFS T0558 240 :QNGGLYICNWQGHDREAGKG 3emhA 269 :TGGKWIVSGSEDNLVYIWNL T0558 260 :KHPQLVEIDSEGKVVWQL 3emhA 290 :TKEIVQKLQGHTDVVIST T0558 278 :NDKVKFGMIST 3emhA 311 :PTENIIASAAL T0558 289 :ICPI 3emhA 324 :DKTI Number of specific fragments extracted= 18 number of extra gaps= 0 total=143 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3emhA/T0558-3emhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3emhA/T0558-3emhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3emhA read from 3emhA/T0558-3emhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3emhA in template set T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 3emhA 55 :PNGEWLASSSADKLIKIWGAYDGKFEKTISGHKL T0558 56 :ECNSVAATKAGEILFSY 3emhA 89 :GISDVAWSSDSNLLVSA T0558 73 :SKGAKMIT 3emhA 108 :DKTLKIWD T0558 81 :RDGRELWNIAAPAG 3emhA 117 :SSGKCLKTLKGHSN T0558 96 :EMQTARILPDGNALVAWCG 3emhA 131 :YVFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVNM 3emhA 150 :DESVRIWDV T0558 125 :KGEVLSKTEFETG 3emhA 160 :TGKCLKTLPAHSD T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 3emhA 173 :PVSAVHFNRDGSLIVSSSYDGLCRIWDTA T0558 173 :GQLLNSVKLS 3emhA 203 :GQCLKTLIDD T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 3emhA 215 :PPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKY T0558 232 :FVAQLFPLQNGGLYICNWQGH 3emhA 261 :CIFANFSVTGGKWIVSGSEDN T0558 263 :QLVEID 3emhA 282 :LVYIWN T0558 269 :SEGKVVWQLNDKV 3emhA 289 :QTKEIVQKLQGHT T0558 284 :GMISTICPIRE 3emhA 302 :DVVISTACHPT Number of specific fragments extracted= 14 number of extra gaps= 0 total=157 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qc5A/T0558-2qc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qc5A expands to /projects/compbio/data/pdb/2qc5.pdb.gz 2qc5A:# T0558 read from 2qc5A/T0558-2qc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qc5A read from 2qc5A/T0558-2qc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qc5A to template set # found chain 2qc5A in template set Warning: unaligning (T0558)K34 because of BadResidue code BAD_PEPTIDE in next template residue (2qc5A)I38 Warning: unaligning (T0558)I35 because of BadResidue code BAD_PEPTIDE at template residue (2qc5A)I38 T0558 4 :FILLVALFLVAPFAQGSSPQHLLVGGSGWN 2qc5A 7 :EFNLSIPDSGPYGITSSEDGKVWFTQHKAN T0558 36 :AIINKD 2qc5A 39 :SSLDQS T0558 43 :KEIVWEYPLEKGWECNSVAATKAGEILFSYSKG 2qc5A 45 :GRIKEFEVPTPDAKVMCLIVSSLGDIWFTENGA T0558 76 :AKMITRD 2qc5A 80 :IGKLSKK T0558 83 :GRELWNIAAPAGC 2qc5A 88 :GFTEYPLPQPDSG T0558 97 :MQTARILPDGNALVAWCG 2qc5A 101 :PYGITEGLNGDIWFTQLN T0558 116 :PSTILEVNMKGEVLSKT 2qc5A 119 :GDRIGKLTADGTIYEYD T0558 134 :FETGIERPHA 2qc5A 136 :LPNKGSYPAF T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 2qc5A 146 :ITLGSDNALWFTENQNNSIGRITNT T0558 173 :GQLLNSV 2qc5A 172 :KLEEYPL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 2qc5A 180 :TNAAAPVGITSGNDGALWFVEIMGNKIGRIT T0558 212 :ESNRI 2qc5A 211 :TTGEI T0558 218 :RRVNANDIE 2qc5A 216 :SEYDIPTPN T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2qc5A 225 :ARPHAITAGKNSEIWFTEWGAN T0558 253 :DREAGK 2qc5A 252 :TNDNTI T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2qc5A 258 :QEYQLQTENAEPHGITFGKDGSVW Number of specific fragments extracted= 16 number of extra gaps= 1 total=173 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qc5A/T0558-2qc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2qc5A/T0558-2qc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qc5A read from 2qc5A/T0558-2qc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qc5A in template set Warning: unaligning (T0558)K34 because of BadResidue code BAD_PEPTIDE in next template residue (2qc5A)I38 Warning: unaligning (T0558)I35 because of BadResidue code BAD_PEPTIDE at template residue (2qc5A)I38 T0558 2 :KNFILLVALFL 2qc5A 5 :LEEFNLSIPDS T0558 14 :APFAQGSSPQ 2qc5A 16 :GPYGITSSED T0558 24 :HLLVGGSGWN 2qc5A 27 :KVWFTQHKAN T0558 36 :AIINKDTKEIVWEYP 2qc5A 39 :SSLDQSGRIKEFEVP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2qc5A 54 :TPDAKVMCLIVSSLGDIWFTENGA T0558 76 :AKMIT 2qc5A 80 :IGKLS T0558 81 :RDGRELWNIA 2qc5A 86 :KGGFTEYPLP T0558 92 :PAGCEMQTARILPDGNALVAWC 2qc5A 96 :QPDSGPYGITEGLNGDIWFTQL T0558 115 :HPSTILEVNMKGEVLS 2qc5A 118 :NGDRIGKLTADGTIYE T0558 132 :TEFETGIER 2qc5A 134 :YDLPNKGSY T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 2qc5A 143 :PAFITLGSDNALWFTENQNNSIGRITNT T0558 173 :GQLLNSV 2qc5A 172 :KLEEYPL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 2qc5A 180 :TNAAAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIPTPNAR T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 2qc5A 227 :PHAITAGKNSEIWFTEWGANQIGRITN T0558 260 :KHPQLVEIDSEGKVVWQL 2qc5A 255 :NTIQEYQLQTENAEPHGI T0558 278 :NDKVKFGMIST 2qc5A 276 :KDGSVWFALKC Number of specific fragments extracted= 16 number of extra gaps= 1 total=189 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qc5A/T0558-2qc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2qc5A/T0558-2qc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qc5A read from 2qc5A/T0558-2qc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qc5A in template set Warning: unaligning (T0558)I35 because of BadResidue code BAD_PEPTIDE in next template residue (2qc5A)I38 Warning: unaligning (T0558)A36 because of BadResidue code BAD_PEPTIDE at template residue (2qc5A)I38 T0558 21 :SPQHLLVGGSGWNK 2qc5A 23 :SEDGKVWFTQHKAN T0558 37 :IINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSY 2qc5A 39 :SSLDQSGRIKEFEVPTPDAKVMCLIVSSLGDIWFTE T0558 73 :SKGAKMITRDGRELWNIAAPAGCEMQTARILPDGNALVAWCG 2qc5A 77 :ANKIGKLSKKGGFTEYPLPQPDSGPYGITEGLNGDIWFTQLN T0558 116 :PSTILEVNMKGEV 2qc5A 119 :GDRIGKLTADGTI T0558 130 :SKTEFETG 2qc5A 132 :YEYDLPNK T0558 142 :HAQFRQINKNKKGNYLVPLFATSEVREIAPNGQLL 2qc5A 140 :GSYPAFITLGSDNALWFTENQNNSIGRITNTGKLE T0558 178 :SVKLS 2qc5A 175 :EYPLP T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVN 2qc5A 183 :AAPVGITSGNDGALWFVEIMGNKIGRITTTGEISEYDIP T0558 225 :IEGV 2qc5A 222 :TPNA T0558 232 :FVAQLFPLQNGGLYICNWQGH 2qc5A 226 :RPHAITAGKNSEIWFTEWGAN T0558 263 :QLVEIDSEGKVVW 2qc5A 247 :QIGRITNDNTIQE T0558 290 :CPIR 2qc5A 260 :YQLQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=201 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bcjB/T0558-2bcjB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bcjB expands to /projects/compbio/data/pdb/2bcj.pdb.gz 2bcjB:# T0558 read from 2bcjB/T0558-2bcjB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcjB read from 2bcjB/T0558-2bcjB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bcjB to template set # found chain 2bcjB in template set Warning: unaligning (T0558)I289 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2bcjB)L336 Warning: unaligning (T0558)C290 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2bcjB)L336 T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 2bcjB 46 :RTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2bcjB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMITRD 2bcjB 121 :CSIYNLK T0558 83 :G 2bcjB 129 :R T0558 84 :RELWNIAAPAGC 2bcjB 134 :RVSRELAGHTGY T0558 97 :MQTARILPDG 2bcjB 146 :LSCCRFLDDN T0558 108 :ALVAWCG 2bcjB 156 :QIVTSSG T0558 116 :PSTILEVNMK 2bcjB 163 :DTTCALWDIE T0558 126 :GEVLSK 2bcjB 174 :GQQTTT T0558 134 :FETGIERPHA 2bcjB 180 :FTGHTGDVMS T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 2bcjB 190 :LSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 2bcjB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 2bcjB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2bcjB 271 :CGITSVSFSKSGRLLLAGYDDF T0558 253 :DREAGK 2bcjB 298 :DALKAD T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2bcjB 304 :RAGVLAGHDNRVSCLGVTDDGMAV T0558 287 :ST 2bcjB 333 :DS T0558 291 :PI 2bcjB 337 :KI Number of specific fragments extracted= 18 number of extra gaps= 1 total=219 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bcjB/T0558-2bcjB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2bcjB/T0558-2bcjB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcjB read from 2bcjB/T0558-2bcjB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bcjB in template set Warning: unaligning (T0558)P291 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2bcjB)L336 Warning: unaligning (T0558)I292 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2bcjB)L336 T0558 1 :MKNFILLVALFL 2bcjB 45 :MRTRRTLRGHLA T0558 14 :APFAQGSSPQ 2bcjB 57 :KIYAMHWGTD T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 2bcjB 68 :RLLVSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2bcjB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMIT 2bcjB 121 :CSIYN T0558 82 :DG 2bcjB 128 :TR T0558 84 :RELWNIA 2bcjB 134 :RVSRELA T0558 92 :PAGCEMQTARILPDG 2bcjB 141 :GHTGYLSCCRFLDDN T0558 108 :ALVAWC 2bcjB 156 :QIVTSS T0558 115 :HPSTILEVNMK 2bcjB 162 :GDTTCALWDIE T0558 126 :GEVLS 2bcjB 174 :GQQTT T0558 133 :EFETGIER 2bcjB 179 :TFTGHTGD T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 2bcjB 187 :VMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 2bcjB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 2bcjB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII T0558 231 :FFVAQLFPLQNGGLYICNWQGHDREAGKG 2bcjB 271 :CGITSVSFSKSGRLLLAGYDDFNCNVWDA T0558 260 :KHPQLVEIDSEGKVVWQL 2bcjB 301 :KADRAGVLAGHDNRVSCL T0558 278 :NDKVKFGMISTIC 2bcjB 322 :DDGMAVATGSWDS T0558 293 :R 2bcjB 337 :K Number of specific fragments extracted= 19 number of extra gaps= 1 total=238 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bcjB/T0558-2bcjB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2bcjB/T0558-2bcjB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bcjB read from 2bcjB/T0558-2bcjB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bcjB in template set Warning: unaligning (T0558)K282 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2bcjB)L336 Warning: unaligning (T0558)F283 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2bcjB)L336 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 2bcjB 65 :TDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSS T0558 56 :ECNSVAATKAGEILFSY 2bcjB 99 :WVMTCAYAPSGNYVACG T0558 73 :SKGAKMITRDG 2bcjB 118 :DNICSIYNLKT T0558 84 :RELWNIAAPAG 2bcjB 134 :RVSRELAGHTG T0558 96 :EMQTARILPDG 2bcjB 145 :YLSCCRFLDDN T0558 108 :ALVAWCG 2bcjB 156 :QIVTSSG T0558 116 :PSTILEVN 2bcjB 163 :DTTCALWD T0558 124 :MKGEVLSKTEFETG 2bcjB 172 :ETGQQTTTFTGHTG T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 2bcjB 186 :DVMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSVKLS 2bcjB 216 :GMCRQTFTGH T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2bcjB 227 :SDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIIC T0558 232 :FVAQLFPLQNGGLYICNWQGHDREAGK 2bcjB 272 :GITSVSFSKSGRLLLAGYDDFNCNVWD T0558 259 :GKHPQLVEIDSEGKVVWQLNDKV 2bcjB 312 :DNRVSCLGVTDDGMAVATGSWDS Number of specific fragments extracted= 13 number of extra gaps= 1 total=251 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h14A/T0558-2h14A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h14A expands to /projects/compbio/data/pdb/2h14.pdb.gz 2h14A:Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2h14A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2h14A Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2h14A # T0558 read from 2h14A/T0558-2h14A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h14A read from 2h14A/T0558-2h14A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h14A to template set # found chain 2h14A in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)L111 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)A169 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)A169 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)C195 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)C195 T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 2h14A 36 :ALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2h14A 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 77 :KMITRD 2h14A 112 :KIWDVS T0558 83 :GRELWNIAAPAGC 2h14A 119 :GKCLKTLKGHSNY T0558 97 :MQTARILPDGNALVAWCG 2h14A 132 :VFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVNMK 2h14A 150 :DESVRIWDVK T0558 126 :GEVLSK 2h14A 161 :GKCLKT T0558 134 :F 2h14A 167 :L T0558 137 :GIERPHA 2h14A 170 :HSDPVSA T0558 148 :INKNKKGNYLVPLFATS 2h14A 177 :VHFNRDGSLIVSSSYDG T0558 167 :REIAPN 2h14A 196 :RIWDTA T0558 173 :GQLLNSV 2h14A 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2h14A 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEK T0558 232 :FVAQLFPLQ 2h14A 260 :YCIFANFSV T0558 241 :NGGLYICNWQGH 2h14A 270 :GGKWIVSGSEDN T0558 253 :DREAGK 2h14A 287 :NLQTKE T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2h14A 293 :IVQKLQGHTDVVISTACHPTENII T0558 288 :T 2h14A 323 :N Number of specific fragments extracted= 18 number of extra gaps= 3 total=269 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h14A/T0558-2h14A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2h14A/T0558-2h14A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h14A read from 2h14A/T0558-2h14A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h14A in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)L111 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)A169 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)A169 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)C195 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)C195 Warning: unaligning (T0558)T288 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)E322 T0558 1 :MKNFILLVALFL 2h14A 35 :YALKFTLAGHTK T0558 14 :APFAQGSSPQ 2h14A 47 :AVSSVKFSPN T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 2h14A 58 :EWLASSSADKLIKIWGAYDGKFEKTIS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2h14A 85 :GHKLGISDVAWSSDSNLLVSASDD T0558 77 :KMIT 2h14A 112 :KIWD T0558 81 :RDGRELWNIA 2h14A 117 :SSGKCLKTLK T0558 92 :PAGCEMQTARILPDGNALVAWC 2h14A 127 :GHSNYVFCCNFNPQSNLIVSGS T0558 115 :HPSTILEVNMK 2h14A 149 :FDESVRIWDVK T0558 126 :GEVLS 2h14A 161 :GKCLK T0558 133 :EF 2h14A 166 :TL T0558 137 :GIER 2h14A 170 :HSDP T0558 145 :FRQINKNKKGNYLVPLFATS 2h14A 174 :VSAVHFNRDGSLIVSSSYDG T0558 167 :REIAPN 2h14A 196 :RIWDTA T0558 173 :GQLLNSV 2h14A 203 :GQCLKTL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 2h14A 212 :DDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKY T0558 233 :VAQLFPL 2h14A 261 :CIFANFS T0558 240 :QNGGLYICNWQGHDREAGKG 2h14A 269 :TGGKWIVSGSEDNLVYIWNL T0558 260 :KHPQLVEIDSEGKVVWQL 2h14A 290 :TKEIVQKLQGHTDVVIST T0558 278 :NDKVKFGMIS 2h14A 311 :PTENIIASAA T0558 289 :ICPI 2h14A 324 :DKTI Number of specific fragments extracted= 20 number of extra gaps= 4 total=289 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h14A/T0558-2h14A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2h14A/T0558-2h14A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h14A read from 2h14A/T0558-2h14A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h14A in template set Warning: unaligning (T0558)G75 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)L111 Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)L111 Warning: unaligning (T0558)E133 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)A169 Warning: unaligning (T0558)F134 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)A169 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2h14A)C195 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (2h14A)C195 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 2h14A 55 :PNGEWLASSSADKLIKIWGAYDGKFEKTISGHKL T0558 56 :ECNSVAATKAGEILFSY 2h14A 89 :GISDVAWSSDSNLLVSA T0558 73 :SK 2h14A 108 :DK T0558 77 :KMIT 2h14A 112 :KIWD T0558 81 :RDGRELWNIAAPAG 2h14A 117 :SSGKCLKTLKGHSN T0558 96 :EMQTARILPDGNALVAWCG 2h14A 131 :YVFCCNFNPQSNLIVSGSF T0558 116 :PSTILEVNM 2h14A 150 :DESVRIWDV T0558 125 :KGEVLSKT 2h14A 160 :TGKCLKTL T0558 135 :ETG 2h14A 170 :HSD T0558 144 :QFRQINKNKKGNYLVPLFATS 2h14A 173 :PVSAVHFNRDGSLIVSSSYDG T0558 167 :REIAPN 2h14A 196 :RIWDTA T0558 173 :GQLLNSVKLS 2h14A 203 :GQCLKTLIDD T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 2h14A 215 :PPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKY T0558 232 :FVAQLFPLQNGGLYICNWQGH 2h14A 261 :CIFANFSVTGGKWIVSGSEDN T0558 263 :QLVEID 2h14A 282 :LVYIWN T0558 269 :SEGKVVWQLNDKV 2h14A 289 :QTKEIVQKLQGHT T0558 284 :GMISTICPIRE 2h14A 302 :DVVISTACHPT Number of specific fragments extracted= 17 number of extra gaps= 3 total=306 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gotB/T0558-1gotB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gotB expands to /projects/compbio/data/pdb/1got.pdb.gz 1gotB:# T0558 read from 1gotB/T0558-1gotB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gotB read from 1gotB/T0558-1gotB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gotB to template set # found chain 1gotB in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 1gotB 46 :RTRRTLRGHLAKIYAMHWGTDSRLLLSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1gotB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMITRD 1gotB 121 :CSIYNLK T0558 83 :GRE 1gotB 129 :REG T0558 86 :LWNIAAPAGC 1gotB 136 :SRELAGHTGY T0558 97 :MQTARILPDG 1gotB 146 :LSCCRFLDDN T0558 108 :ALVAWCG 1gotB 156 :QIVTSSG T0558 116 :PSTILEVNMK 1gotB 163 :DTTCALWDIE T0558 126 :GEVLSK 1gotB 174 :GQQTTT T0558 134 :FETGIERPHA 1gotB 180 :FTGHTGDVMS T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 1gotB 190 :LSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 1gotB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 1gotB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1gotB 271 :CGITSVSFSKSGRLLLAGYDDF T0558 253 :DREAGK 1gotB 298 :DALKAD T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 1gotB 304 :RAGVLAGHDNRVSCLGVTDDGMAV T0558 287 :STICPI 1gotB 333 :DSFLKI Number of specific fragments extracted= 17 number of extra gaps= 0 total=323 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gotB/T0558-1gotB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1gotB/T0558-1gotB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gotB read from 1gotB/T0558-1gotB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gotB in template set T0558 1 :MKNFILLVALFL 1gotB 45 :MRTRRTLRGHLA T0558 14 :APFAQGSSPQ 1gotB 57 :KIYAMHWGTD T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 1gotB 68 :RLLLSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1gotB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMIT 1gotB 121 :CSIYN T0558 81 :RDG 1gotB 127 :KTR T0558 84 :RELWNIA 1gotB 134 :RVSRELA T0558 92 :PAGCEMQTARILPDG 1gotB 141 :GHTGYLSCCRFLDDN T0558 108 :ALVAWC 1gotB 156 :QIVTSS T0558 115 :HPSTILEVNMK 1gotB 162 :GDTTCALWDIE T0558 126 :GEVLS 1gotB 174 :GQQTT T0558 133 :EFETGIER 1gotB 179 :TFTGHTGD T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 1gotB 187 :VMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 1gotB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGV 1gotB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICG T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1gotB 273 :ITSVSFSKSGRLLLAGYDDFNCNVWDA T0558 260 :KHPQLVEIDSEGKVVWQL 1gotB 301 :KADRAGVLAGHDNRVSCL T0558 278 :NDKVKFGMISTICPIR 1gotB 322 :DDGMAVATGSWDSFLK Number of specific fragments extracted= 18 number of extra gaps= 0 total=341 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gotB/T0558-1gotB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1gotB/T0558-1gotB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gotB read from 1gotB/T0558-1gotB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gotB in template set T0558 22 :PQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 1gotB 66 :DSRLLLSASQDGKLIIWDSYTTNKVHAIPLRSS T0558 56 :ECNSVAATKAGEILFSY 1gotB 99 :WVMTCAYAPSGNYVACG T0558 73 :SKGAKMITRDG 1gotB 118 :DNICSIYNLKT T0558 84 :RELWNIAAPAG 1gotB 134 :RVSRELAGHTG T0558 96 :EMQTARILPDG 1gotB 145 :YLSCCRFLDDN T0558 108 :ALVAWCG 1gotB 156 :QIVTSSG T0558 116 :PSTILEVN 1gotB 163 :DTTCALWD T0558 124 :MKGEVLSKTEFETG 1gotB 172 :ETGQQTTTFTGHTG T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 1gotB 186 :DVMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSVKLS 1gotB 216 :GMCRQTFTGH T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 1gotB 227 :SDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIIC T0558 232 :FVAQLFPLQNGGLYICNWQGH 1gotB 272 :GITSVSFSKSGRLLLAGYDDF T0558 263 :QLVEID 1gotB 293 :NCNVWD T0558 269 :SEGKVVWQLNDKVK 1gotB 300 :LKADRAGVLAGHDN T0558 285 :MISTICPIRE 1gotB 314 :RVSCLGVTDD Number of specific fragments extracted= 15 number of extra gaps= 0 total=356 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gxrA/T0558-1gxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gxrA expands to /projects/compbio/data/pdb/1gxr.pdb.gz 1gxrA:# T0558 read from 1gxrA/T0558-1gxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gxrA read from 1gxrA/T0558-1gxrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gxrA to template set # found chain 1gxrA in template set T0558 3 :NFILLVALFLVAPFAQGSSPQHLLVGGSG 1gxrA 476 :RQINTLNHGEVVCAVTISNPTRHVYTGGK T0558 33 :NKIAIINKDTK 1gxrA 505 :GCVKVWDISHP T0558 44 :EIVWEYPL 1gxrA 519 :SPVSQLDC T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1gxrA 528 :NRDNYIRSCKLLPDGCTLIVGGEA T0558 76 :AKMITR 1gxrA 554 :LSIWDL T0558 84 :RELWNIAAPAGC 1gxrA 565 :RIKAELTSSAPA T0558 97 :MQTARILPDGNALVAWCG 1gxrA 577 :CYALAISPDSKVCFSCCS T0558 116 :PSTILEVNMK 1gxrA 595 :DGNIAVWDLH T0558 126 :GEVLSK 1gxrA 606 :QTLVRQ T0558 134 :FETGIERPHA 1gxrA 612 :FQGHTDGASC T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 1gxrA 622 :IDISNDGTKLWTGGLDNTVRSWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRI 1gxrA 648 :GRQLQQHDFTSQIFSLGYCPTGEWLAVGMESSNVEVLHVNKPDK T0558 218 :RRVNAND 1gxrA 692 :YQLHLHE T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1gxrA 699 :SCVLSLKFAYCGKWFVSTGKDN T0558 263 :QLVEIDSEGKV 1gxrA 721 :LLNAWRTPYGA T0558 274 :VWQLNDKVKFGMI 1gxrA 742 :VLSCDISVDDKYI T0558 287 :STICPI 1gxrA 760 :DKKATV Number of specific fragments extracted= 17 number of extra gaps= 0 total=373 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gxrA/T0558-1gxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1gxrA/T0558-1gxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gxrA read from 1gxrA/T0558-1gxrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gxrA in template set Warning: unaligning (T0558)R81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gxrA)P564 T0558 3 :NFILLVALFL 1gxrA 476 :RQINTLNHGE T0558 14 :APFAQGSSPQ 1gxrA 486 :VVCAVTISNP T0558 24 :HLLVGGS 1gxrA 497 :RHVYTGG T0558 32 :WNKIAIINKDTKE 1gxrA 504 :KGCVKVWDISHPG T0558 45 :IVWEYP 1gxrA 522 :SQLDCL T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1gxrA 528 :NRDNYIRSCKLLPDGCTLIVGGEA T0558 76 :AKMIT 1gxrA 554 :LSIWD T0558 84 :RELWNIA 1gxrA 565 :RIKAELT T0558 92 :PAGCEMQTARILPDGNALVAWC 1gxrA 572 :SSAPACYALAISPDSKVCFSCC T0558 115 :HPSTILEVNMK 1gxrA 594 :SDGNIAVWDLH T0558 126 :GEVLS 1gxrA 606 :QTLVR T0558 133 :EFETGIER 1gxrA 611 :QFQGHTDG T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 1gxrA 619 :ASCIDISNDGTKLWTGGLDNTVRSWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIV 1gxrA 648 :GRQLQQHDFTSQIFSLGYCPTGEWLAVGMESSNVEVLHVNKPDKY T0558 219 :RVNANDIE 1gxrA 693 :QLHLHESC T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1gxrA 701 :VLSLKFAYCGKWFVSTGKDNLLNAWRT T0558 260 :KHPQLVEIDSEGKVVWQL 1gxrA 729 :YGASIFQSKESSSVLSCD T0558 278 :NDKVKFGMISTICPIR 1gxrA 749 :VDDKYIVTGSGDKKAT Number of specific fragments extracted= 18 number of extra gaps= 0 total=391 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gxrA/T0558-1gxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1gxrA/T0558-1gxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gxrA read from 1gxrA/T0558-1gxrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gxrA in template set Warning: unaligning (T0558)R81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gxrA)P564 T0558 20 :SSPQHLLVGGSGWNKIAIINKDTKEI 1gxrA 492 :ISNPTRHVYTGGKGCVKVWDISHPGN T0558 46 :VWEYPL 1gxrA 521 :VSQLDC T0558 52 :EKGWECNSVAATKAGEILFSY 1gxrA 528 :NRDNYIRSCKLLPDGCTLIVG T0558 73 :SKGAKMIT 1gxrA 551 :ASTLSIWD T0558 84 :RELWNIAAPAG 1gxrA 565 :RIKAELTSSAP T0558 96 :EMQTARILPDGNALVAWCG 1gxrA 576 :ACYALAISPDSKVCFSCCS T0558 116 :PSTILEVN 1gxrA 595 :DGNIAVWD T0558 124 :MKGEVLSKTEFETG 1gxrA 604 :HNQTLVRQFQGHTD T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 1gxrA 618 :GASCIDISNDGTKLWTGGLDNTVRSWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVN 1gxrA 648 :GRQLQQHDFTSQIFSLGYCPTGEWLAVGMESSNVEVLHVNKPDKYQLHL T0558 225 :IE 1gxrA 697 :HE T0558 231 :FFVAQLFPLQNGGLYICNWQGHDREAGK 1gxrA 699 :SCVLSLKFAYCGKWFVSTGKDNLLNAWR T0558 259 :GKHPQLVEIDSEGKVVWQLNDKVKF 1gxrA 739 :SSSVLSCDISVDDKYIVTGSGDKKA T0558 285 :MISTI 1gxrA 764 :TVYEV Number of specific fragments extracted= 14 number of extra gaps= 0 total=405 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pbiB/T0558-2pbiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pbiB expands to /projects/compbio/data/pdb/2pbi.pdb.gz 2pbiB:Skipped atom 3681, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3685, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3687, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3689, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3691, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3693, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 3695, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 4259, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 4263, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 4265, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 5000, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 5004, because occupancy 0.500 <= existing 0.500 in 2pbiB Skipped atom 5006, because occupancy 0.500 <= existing 0.500 in 2pbiB # T0558 read from 2pbiB/T0558-2pbiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pbiB read from 2pbiB/T0558-2pbiB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pbiB to template set # found chain 2pbiB in template set Warning: unaligning (T0558)I38 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)D91 Warning: unaligning (T0558)N39 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)D91 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)C263 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)C263 T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAI 2pbiB 54 :KTRRTLKGHGNKVLCMDWCKDKRRIVSSSQDGKVIV T0558 40 :KDTKEIVWEYP 2pbiB 92 :SFTTNKEHAVT T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2pbiB 103 :MPCTWVMACAYAPSGCAIACGGLD T0558 76 :AKMITRD 2pbiB 129 :CSVYPLT T0558 83 :GRE 2pbiB 137 :DKN T0558 86 :LWNIAAPAGC 2pbiB 146 :KKSVAMHTNY T0558 97 :MQTARILPDGNALVAWCG 2pbiB 156 :LSACSFTNSDMQILTASG T0558 116 :PSTILEVNMK 2pbiB 174 :DGTCALWDVE T0558 126 :GEVLSK 2pbiB 185 :GQLLQS T0558 134 :FETGIERPHA 2pbiB 191 :FHGHGADVLC T0558 148 :INKNK 2pbiB 201 :LDLAP T0558 153 :KGNYLVPLFATSEVREIAPN 2pbiB 208 :TGNTFVSGGCDKKAMVWDMR T0558 173 :GQLLNSV 2pbiB 229 :GQCVQAF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAH 2pbiB 237 :THESDVNSVRYYPSGDAFASGSDDA T0558 207 :VQLNLESNRIVRRVNANDIE 2pbiB 264 :RLYDLRADREVAIYSKESII T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2pbiB 284 :FGASSVDFSLSGRLLFAGYNDY T0558 253 :DREAGK 2pbiB 311 :DVLKGS T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2pbiB 317 :RVSILFGHENRVSTLRVSPDGTAF T0558 287 :STICPI 2pbiB 346 :DHTLRV Number of specific fragments extracted= 19 number of extra gaps= 2 total=424 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pbiB/T0558-2pbiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2pbiB/T0558-2pbiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pbiB read from 2pbiB/T0558-2pbiB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pbiB in template set Warning: unaligning (T0558)I38 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)D91 Warning: unaligning (T0558)N39 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)D91 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)C263 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)C263 T0558 1 :MKNFILLVALFL 2pbiB 53 :MKTRRTLKGHGN T0558 14 :APFAQGSSPQ 2pbiB 65 :KVLCMDWCKD T0558 24 :HLLVGGSGWNKIAI 2pbiB 76 :RRIVSSSQDGKVIV T0558 40 :KDTKEIVWEYP 2pbiB 92 :SFTTNKEHAVT T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2pbiB 103 :MPCTWVMACAYAPSGCAIACGGLD T0558 76 :AKMIT 2pbiB 129 :CSVYP T0558 81 :RDG 2pbiB 135 :TFD T0558 84 :RELWNIA 2pbiB 144 :AKKKSVA T0558 92 :PAGCEMQTARILPDGNALVAWC 2pbiB 151 :MHTNYLSACSFTNSDMQILTAS T0558 115 :HPSTILEVNMK 2pbiB 173 :GDGTCALWDVE T0558 126 :GEVLS 2pbiB 185 :GQLLQ T0558 133 :EFETGIER 2pbiB 190 :SFHGHGAD T0558 145 :FRQINKN 2pbiB 198 :VLCLDLA T0558 152 :KKGNYLVPLFATSEVREIAPN 2pbiB 207 :ETGNTFVSGGCDKKAMVWDMR T0558 173 :GQLLNSV 2pbiB 229 :GQCVQAF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAH 2pbiB 237 :THESDVNSVRYYPSGDAFASGSDDA T0558 207 :VQLNLESNRIVRRVNANDIE 2pbiB 264 :RLYDLRADREVAIYSKESII T0558 231 :FFVAQLFPLQNGGLYICNWQGHDREAGKG 2pbiB 284 :FGASSVDFSLSGRLLFAGYNDYTINVWDV T0558 260 :KHPQLVEIDSEGKVVWQL 2pbiB 314 :KGSRVSILFGHENRVSTL T0558 278 :NDKVKFGMISTICPIR 2pbiB 335 :PDGTAFCSGSWDHTLR Number of specific fragments extracted= 20 number of extra gaps= 2 total=444 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pbiB/T0558-2pbiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2pbiB/T0558-2pbiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pbiB read from 2pbiB/T0558-2pbiB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pbiB in template set Warning: unaligning (T0558)N39 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)D91 Warning: unaligning (T0558)K40 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)D91 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2pbiB)C263 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2pbiB)C263 T0558 21 :SPQHLLVGGSGWNKIAII 2pbiB 72 :CKDKRRIVSSSQDGKVIV T0558 41 :DTKEIVWEYPLEKG 2pbiB 93 :FTTNKEHAVTMPCT T0558 56 :ECNSVAATKAGEILFSY 2pbiB 107 :WVMACAYAPSGCAIACG T0558 73 :SKGAKMITRDG 2pbiB 126 :DNKCSVYPLTF T0558 84 :RELWNIAA 2pbiB 147 :KSVAMHTN T0558 96 :EMQTARILPDGNALVAWCG 2pbiB 155 :YLSACSFTNSDMQILTASG T0558 116 :PSTILEVN 2pbiB 174 :DGTCALWD T0558 124 :MKGEVLSKTEFETG 2pbiB 183 :ESGQLLQSFHGHGA T0558 144 :QFRQINK 2pbiB 197 :DVLCLDL T0558 151 :NKKGNYLVPLFATSEVREIAPN 2pbiB 206 :SETGNTFVSGGCDKKAMVWDMR T0558 173 :GQLLNSVKLS 2pbiB 229 :GQCVQAFETH T0558 183 :GTPFSSAFLDNGDCLVACGDAH 2pbiB 240 :SDVNSVRYYPSGDAFASGSDDA T0558 207 :VQLNLESNRIVRRVNANDIE 2pbiB 264 :RLYDLRADREVAIYSKESII T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2pbiB 284 :FGASSVDFSLSGRLLFAGYNDY T0558 263 :QLVEID 2pbiB 306 :TINVWD T0558 269 :SEGKVVWQLNDKVK 2pbiB 313 :LKGSRVSILFGHEN T0558 285 :MISTICPIR 2pbiB 327 :RVSTLRVSP Number of specific fragments extracted= 17 number of extra gaps= 2 total=461 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r5mA/T0558-1r5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r5mA expands to /projects/compbio/data/pdb/1r5m.pdb.gz 1r5mA:# T0558 read from 1r5mA/T0558-1r5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r5mA read from 1r5mA/T0558-1r5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r5mA to template set # found chain 1r5mA in template set Warning: unaligning (T0558)G54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r5mA)T220 Warning: unaligning (T0558)E135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)G318 Warning: unaligning (T0558)S269 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)P491 T0558 2 :KNFILLVALFLVAPFAQGSS 1r5mA 148 :VKILKEIVKLDNIVSSTWNP T0558 22 :PQHLLVGGSGWNKIAIINKD 1r5mA 169 :DESILAYGEKNSVARLARIV T0558 44 :EIVWEYPL 1r5mA 201 :TIIAELRH T0558 55 :WECNSVAATKAGEILFSYSKG 1r5mA 221 :NQVTCLAWSHDGNSIVTGVEN T0558 76 :AKMITRDGRELWNIAAPAGC 1r5mA 244 :LRLWNKTGALLNVLNFHRAP T0558 97 :MQTARILPDGNALVAWCG 1r5mA 264 :IVSVKWNKDGTHIISMDV T0558 116 :PSTILEVNMK 1r5mA 282 :ENVTILWNVI T0558 126 :GEVLSKTEF 1r5mA 293 :GTVMQHFEL T0558 138 :IERPHAQFRQINKNKKGNYLVPLFATSEVREIAPN 1r5mA 355 :LIGHHGPISVLEFNDTNKLLLSASDDGTLRIWHGG T0558 173 :GQLLNSV 1r5mA 391 :GNSQNCF T0558 180 :KLSGTPFSSAFLDNG 1r5mA 399 :GHSQSIVSASWVGDD T0558 196 :CLVACGDAHCFVQLNLESNRIVRRVNAND 1r5mA 414 :KVISCSMDGSVRLWSLKQNTLLALSIVDG T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1r5mA 443 :VPIFAGRISQDGQKYAVAFMDG T0558 263 :QLVEID 1r5mA 465 :QVNVYD T0558 274 :VWQLNDKVKFGMISTIC 1r5mA 497 :YASYQSSQDNDYIFDLS Number of specific fragments extracted= 15 number of extra gaps= 0 total=476 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r5mA/T0558-1r5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1r5mA/T0558-1r5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r5mA read from 1r5mA/T0558-1r5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r5mA in template set Warning: unaligning (T0558)K40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)Y197 Warning: unaligning (T0558)G54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r5mA)T220 Warning: unaligning (T0558)G137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)G318 Warning: unaligning (T0558)H142 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r5mA)G318 T0558 1 :MKNFILLVALFL 1r5mA 148 :VKILKEIVKLDN T0558 15 :PFAQGSSPQ 1r5mA 160 :IVSSTWNPL T0558 24 :HLLVGGSG 1r5mA 171 :SILAYGEK T0558 32 :WNKIAIIN 1r5mA 182 :ARLARIVE T0558 43 :KEIVWEYP 1r5mA 200 :LTIIAELR T0558 55 :WECNSVAATKAGEILFSYSKG 1r5mA 221 :NQVTCLAWSHDGNSIVTGVEN T0558 76 :AKMITRDGRELWNIA 1r5mA 244 :LRLWNKTGALLNVLN T0558 92 :PAGCEMQTARILPDGNALVAWC 1r5mA 259 :FHRAPIVSVKWNKDGTHIISMD T0558 115 :HPSTILEVNMK 1r5mA 281 :VENVTILWNVI T0558 126 :GEVLS 1r5mA 293 :GTVMQ T0558 133 :EFET 1r5mA 298 :HFEL T0558 143 :AQFRQINKNKKGNYLVPL 1r5mA 319 :SLGVDVEWVDDDKFVIPG T0558 162 :ATSEVREIAPN 1r5mA 337 :PKGAIFVYQIT T0558 173 :GQLLNSV 1r5mA 349 :KTPTGKL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 1r5mA 357 :GHHGPISVLEFNDTNKLLLSASDDGTLRIWHGGNGNSQNCFYGHSQS T0558 233 :VAQLFPLQNG 1r5mA 404 :IVSASWVGDD T0558 244 :LYICNWQGHDREAGKG 1r5mA 414 :KVISCSMDGSVRLWSL T0558 260 :KHPQLVEIDSEGKVVWQL 1r5mA 431 :QNTLLALSIVDGVPIFAG T0558 278 :NDKVKFGMISTICPIR 1r5mA 452 :QDGQKYAVAFMDGQVN Number of specific fragments extracted= 19 number of extra gaps= 0 total=495 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r5mA/T0558-1r5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1r5mA/T0558-1r5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r5mA read from 1r5mA/T0558-1r5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r5mA in template set Warning: unaligning (T0558)K43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)Y197 Warning: unaligning (T0558)G54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r5mA)T220 Warning: unaligning (T0558)E135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r5mA)G318 T0558 19 :GSSPQHLLVGGSGWNKIAIINKDT 1r5mA 166 :NPLDESILAYGEKNSVARLARIVE T0558 44 :EIVWEYPL 1r5mA 201 :TIIAELRH T0558 55 :WECNSVAATKAGEILFSY 1r5mA 221 :NQVTCLAWSHDGNSIVTG T0558 73 :SKGAKMITRDGRELWNIAAPAG 1r5mA 241 :NGELRLWNKTGALLNVLNFHRA T0558 96 :EMQTARILPDGNALVAWCG 1r5mA 263 :PIVSVKWNKDGTHIISMDV T0558 116 :PSTILEVN 1r5mA 282 :ENVTILWN T0558 124 :MKGEVLSKTEF 1r5mA 291 :ISGTVMQHFEL T0558 140 :RPHAQFRQINKNKKGNYLVPLFATSEVREIAPN 1r5mA 357 :GHHGPISVLEFNDTNKLLLSASDDGTLRIWHGG T0558 173 :GQLLNSVKLS 1r5mA 391 :GNSQNCFYGH T0558 183 :GTPFSSAFLDN 1r5mA 402 :QSIVSASWVGD T0558 195 :DCLVACGDAHCFVQLNLESNRIVRRVNAND 1r5mA 413 :DKVISCSMDGSVRLWSLKQNTLLALSIVDG T0558 231 :FFVAQLFPLQNGGLYICNWQGHD 1r5mA 443 :VPIFAGRISQDGQKYAVAFMDGQ T0558 254 :REAGKGKHPQLVEIDSEGKVVWQLNDKVK 1r5mA 501 :QSSQDNDYIFDLSWNCAGNKISVAYSLQE Number of specific fragments extracted= 13 number of extra gaps= 0 total=508 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pguA/T0558-1pguA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pguA expands to /projects/compbio/data/pdb/1pgu.pdb.gz 1pguA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 1pguA/T0558-1pguA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pguA read from 1pguA/T0558-1pguA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pguA to template set # found chain 1pguA in template set Warning: unaligning (T0558)F283 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1pguA)E550 T0558 2 :KNFILLVALF 1pguA 54 :PPVVQFTGHG T0558 12 :LVAPFAQGSS 1pguA 65 :SVVTTVKFSP T0558 22 :PQH 1pguA 76 :KGS T0558 25 :LLVGGSGWNKIAIINKD 1pguA 80 :YLCSGDESGKVIVWGWT T0558 42 :TKEIVWEYP 1pguA 105 :EVNVKSEFQ T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1pguA 114 :VLAGPISDISWDFEGRRLCVVGEG T0558 76 :AKMITRD 1pguA 142 :GVFISWD T0558 83 :GRELWNIAAPAGC 1pguA 150 :GNSLGEVSGHSQR T0558 97 :MQTARILPDGNA 1pguA 163 :INACHLKQSRPM T0558 109 :LVAWCG 1pguA 176 :SMTVGD T0558 116 :PSTILEVNMK 1pguA 182 :DGSVVFYQGP T0558 126 :GEVLSK 1pguA 193 :FKFSAS T0558 134 :FETGIERPHA 1pguA 199 :DRTHHKQGSF T0558 145 :FRQINKNK 1pguA 209 :VRDVEFSP T0558 153 :KGNYLVPLFATSEVREIAPN 1pguA 218 :SGEFVITVGSDRKISCFDGK T0558 173 :GQLLNSV 1pguA 239 :GEFLKYI T0558 180 :KLSGTPFSSAFL 1pguA 251 :PVQGGIFALSWL T0558 193 :NGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 1pguA 263 :DSQKFATVGADATIRVWDVTTSKCVQKWTLDKQQL T0558 228 :VQLFFVAQLFPLQNGGLYICNWQGH 1pguA 486 :PLRAKPSYISISPSETYIAAGDVMG T0558 263 :QLVEIDSEG 1pguA 511 :KILLYDLQS T0558 272 :KV 1pguA 521 :EV T0558 274 :VWQLNDKVK 1pguA 534 :INAISWKPA T0558 287 :STICPI 1pguA 551 :IEEDLV Number of specific fragments extracted= 23 number of extra gaps= 0 total=531 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pguA/T0558-1pguA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1pguA/T0558-1pguA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pguA read from 1pguA/T0558-1pguA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pguA in template set T0558 9 :ALFL 1pguA 62 :HGSS T0558 14 :APFAQGSSP 1pguA 66 :VVTTVKFSP T0558 23 :Q 1pguA 77 :G T0558 24 :HLLVGGSGWNKIAIINKDTK 1pguA 79 :QYLCSGDESGKVIVWGWTFD T0558 44 :EIVWEYP 1pguA 107 :NVKSEFQ T0558 52 :EKGWECNSVAATKAGEILF 1pguA 114 :VLAGPISDISWDFEGRRLC T0558 71 :SYSKG 1pguA 178 :TVGDD T0558 76 :AKMIT 1pguA 185 :VVFYQ T0558 81 :RDGRELWNIA 1pguA 191 :PPFKFSASDR T0558 91 :APAGCEMQTARILP 1pguA 203 :HKQGSFVRDVEFSP T0558 105 :DGNALVAWC 1pguA 218 :SGEFVITVG T0558 115 :HPSTILEVNMK 1pguA 227 :SDRKISCFDGK T0558 126 :GEVLS 1pguA 239 :GEFLK T0558 133 :EFETGIERPHAQFRQINK 1pguA 244 :YIEDDQEPVQGGIFALSW T0558 152 :KKGNYLVPLFATSEVREIAPN 1pguA 262 :LDSQKFATVGADATIRVWDVT T0558 173 :GQLLNSV 1pguA 284 :SKCVQKW T0558 180 :KLSGT 1pguA 292 :LDKQQ T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVR 1pguA 491 :PSYISISPSETYIAAGDVMGKILLYDLQSREVKT T0558 219 :RVNANDIE 1pguA 526 :RWAFRTSK T0558 233 :VAQLFPLQ 1pguA 534 :INAISWKP T0558 241 :NGGLYICNWQGHDREAGKG 1pguA 552 :EEDLVATGSLDTNIFIYSV T0558 260 :KHPQLVEI 1pguA 572 :RPMKIIKA T0558 268 :DSEGKVVWQL 1pguA 581 :NAHKDGVNNL T0558 278 :NDKVKFGMISTICPI 1pguA 593 :ETPSTLVSSGADACI Number of specific fragments extracted= 24 number of extra gaps= 0 total=555 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pguA/T0558-1pguA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1pguA/T0558-1pguA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pguA read from 1pguA/T0558-1pguA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pguA in template set T0558 19 :GSSPQHLLVGGSGWNKIAIINKDTK 1pguA 74 :PIKGSQYLCSGDESGKVIVWGWTFD T0558 44 :EIVWEYPL 1pguA 107 :NVKSEFQV T0558 53 :K 1pguA 116 :A T0558 55 :WECNSVAATKAG 1pguA 117 :GPISDISWDFEG T0558 67 :EILFSY 1pguA 130 :RLCVVG T0558 73 :SKGAKMITRDG 1pguA 139 :DNFGVFISWDS T0558 84 :RELWNIAAPAG 1pguA 151 :NSLGEVSGHSQ T0558 96 :EMQTARILPDGN 1pguA 162 :RINACHLKQSRP T0558 108 :ALVAWCG 1pguA 175 :RSMTVGD T0558 116 :PSTILEVNM 1pguA 182 :DGSVVFYQG T0558 125 :KGEVLSKTEFETGIE 1pguA 192 :PFKFSASDRTHHKQG T0558 143 :AQFRQINKNKKGN 1pguA 207 :SFVRDVEFSPDSG T0558 156 :YLVPLFATSEVREIAPN 1pguA 221 :FVITVGSDRKISCFDGK T0558 173 :GQLLNSVKLS 1pguA 239 :GEFLKYIEDD T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVN 1pguA 253 :QGGIFALSWLDSQKFATVGADATIRVWDVTTSKCVQKWT T0558 225 :IE 1pguA 292 :LD T0558 227 :GVQLFFVAQLFPLQNGGLYICNWQGH 1pguA 295 :QQLGNQQVGVVATGNGRIISLSLDGT T0558 264 :LVEIDSE 1pguA 321 :LNFYELG T0558 283 :FGMISTIC 1pguA 328 :HDEVLKTI Number of specific fragments extracted= 19 number of extra gaps= 0 total=574 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2z2nA/T0558-2z2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2z2nA expands to /projects/compbio/data/pdb/2z2n.pdb.gz 2z2nA:Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1656, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1660, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1662, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2133, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2139, because occupancy 0.500 <= existing 0.500 in 2z2nA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2288, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2292, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2z2nA Skipped atom 2296, because occupancy 0.500 <= existing 0.500 in 2z2nA # T0558 read from 2z2nA/T0558-2z2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z2nA read from 2z2nA/T0558-2z2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2z2nA to template set # found chain 2z2nA in template set Warning: unaligning (T0558)L7 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)T11 Warning: unaligning (T0558)V8 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)T11 Warning: unaligning (T0558)A9 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)Q13 Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)Q13 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)I206 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)I206 Warning: unaligning (T0558)G243 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)L238 Warning: unaligning (T0558)L244 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)L238 Warning: unaligning (T0558)D253 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)S253 Warning: unaligning (T0558)R254 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)S253 Warning: unaligning (T0558)E255 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)N254 Warning: unaligning (T0558)S269 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2z2nA)K265 Warning: unaligning (T0558)E270 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2z2nA)K265 T0558 2 :KNFIL 2z2nA 5 :LQELN T0558 11 :FLVAPFAQGSSPQHLLVGGSGWNKIAIINKD 2z2nA 14 :DTGPYGITVSDKGKVWITQHKANMISCINLD T0558 43 :KEIV 2z2nA 45 :GKIT T0558 48 :EYPL 2z2nA 49 :EYPL T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2z2nA 54 :TPDAKVMCLTISSDGEVWFTENAA T0558 76 :AKMITRD 2z2nA 80 :IGRITKK T0558 83 :GRELWNIAAPAGC 2z2nA 88 :IIKEYTLPNPDSA T0558 97 :MQTARILPDGNALVAWCG 2z2nA 101 :PYGITEGPNGDIWFTEMN T0558 116 :PSTILEVNMKGEVLSK 2z2nA 119 :GNRIGRITDDGKIREY T0558 133 :EFETGIERPHA 2z2nA 135 :ELPNKGSYPSF T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 2z2nA 146 :ITLGSDNALWFTENQNNAIGRITES T0558 173 :GQLLNSVKLSGT 2z2nA 172 :DITEFKIPTPAS T0558 185 :PFSSAFLDNGDCLVACGDAH 2z2nA 185 :PVGITKGNDDALWFVEIIGN T0558 207 :VQLNLESNRIVRRVNAND 2z2nA 207 :GRITTSGEITEFKIPTPN T0558 231 :FFVAQLFPLQNG 2z2nA 225 :ARPHAITAGAGI T0558 245 :YICNWQGH 2z2nA 239 :WFTEWGAN T0558 256 :AGK 2z2nA 255 :NII T0558 263 :QLVEID 2z2nA 258 :EEYPIQ T0558 271 :GKVVWQLNDKVKFGMI 2z2nA 266 :SAEPHGICFDGETIWF Number of specific fragments extracted= 19 number of extra gaps= 5 total=593 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2z2nA/T0558-2z2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2z2nA/T0558-2z2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z2nA read from 2z2nA/T0558-2z2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2z2nA in template set Warning: unaligning (T0558)L7 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)T11 Warning: unaligning (T0558)V8 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)T11 Warning: unaligning (T0558)A9 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)Q13 Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)Q13 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)I206 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)I206 Warning: unaligning (T0558)G243 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)L238 Warning: unaligning (T0558)L244 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)L238 Warning: unaligning (T0558)K258 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)S253 Warning: unaligning (T0558)G259 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)S253 Warning: unaligning (T0558)S269 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2z2nA)K265 Warning: unaligning (T0558)E270 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2z2nA)K265 T0558 3 :NFIL 2z2nA 6 :QELN T0558 11 :FL 2z2nA 14 :DT T0558 14 :APFAQGSSPQ 2z2nA 16 :GPYGITVSDK T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 2z2nA 27 :KVWITQHKANMISCINLDGKITEYPLP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2z2nA 54 :TPDAKVMCLTISSDGEVWFTENAA T0558 76 :AKMIT 2z2nA 80 :IGRIT T0558 81 :RDGRELWNIA 2z2nA 86 :KGIIKEYTLP T0558 92 :PAGCEMQTARILPDGNALVAWC 2z2nA 96 :NPDSAPYGITEGPNGDIWFTEM T0558 115 :HPSTILEVNMKGEVLS 2z2nA 118 :NGNRIGRITDDGKIRE T0558 132 :TEFETGIER 2z2nA 134 :YELPNKGSY T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 2z2nA 143 :PSFITLGSDNALWFTENQNNAIGRITES T0558 173 :GQLLNSV 2z2nA 172 :DITEFKI T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAH 2z2nA 180 :TPASGPVGITKGNDDALWFVEIIGN T0558 207 :VQLNLESNRIVRRVNANDIE 2z2nA 207 :GRITTSGEITEFKIPTPNAR T0558 233 :VAQLFPLQNG 2z2nA 227 :PHAITAGAGI T0558 245 :YICNWQGHDREAG 2z2nA 239 :WFTEWGANKIGRL T0558 260 :KHPQLVEID 2z2nA 255 :NIIEEYPIQ T0558 271 :GKVVWQL 2z2nA 266 :SAEPHGI T0558 278 :NDKVKFGMISTICPI 2z2nA 275 :DGETIWFAMECDKIG Number of specific fragments extracted= 19 number of extra gaps= 5 total=612 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2z2nA/T0558-2z2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2z2nA/T0558-2z2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z2nA read from 2z2nA/T0558-2z2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2z2nA in template set Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)I206 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)I206 Warning: unaligning (T0558)G243 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)L238 Warning: unaligning (T0558)L244 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)L238 Warning: unaligning (T0558)D268 because of BadResidue code BAD_PEPTIDE in next template residue (2z2nA)S253 Warning: unaligning (T0558)S269 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)S253 Warning: unaligning (T0558)E270 because of BadResidue code BAD_PEPTIDE at template residue (2z2nA)N254 Warning: unaligning (T0558)K280 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (2z2nA)K265 Warning: unaligning (T0558)V281 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (2z2nA)K265 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSY 2z2nA 23 :SDKGKVWITQHKANMISCINLDGKITEYPLPTPDAKVMCLTISSDGEVWFTE T0558 73 :SKGAKMITRDGRELWNIAAPAGCEMQTARILPDGNALVAWCG 2z2nA 77 :ANKIGRITKKGIIKEYTLPNPDSAPYGITEGPNGDIWFTEMN T0558 116 :PSTILEVNMKGEV 2z2nA 119 :GNRIGRITDDGKI T0558 130 :SKTEFETG 2z2nA 132 :REYELPNK T0558 142 :HAQFRQINKNKKGNYLVPLFATSEVREIAPNGQL 2z2nA 140 :GSYPSFITLGSDNALWFTENQNNAIGRITESGDI T0558 177 :NSVKLS 2z2nA 174 :TEFKIP T0558 183 :GTPFSSAFLDNGDCLVACGDAH 2z2nA 183 :SGPVGITKGNDDALWFVEIIGN T0558 207 :VQLN 2z2nA 207 :GRIT T0558 212 :ESNRI 2z2nA 211 :TSGEI T0558 217 :VRRVNAND 2z2nA 217 :EFKIPTPN T0558 231 :FFVAQLFPLQNG 2z2nA 225 :ARPHAITAGAGI T0558 245 :YICNWQGH 2z2nA 239 :WFTEWGAN T0558 263 :QLVEI 2z2nA 247 :KIGRL T0558 271 :GKVVWQLND 2z2nA 255 :NIIEEYPIQ T0558 282 :KF 2z2nA 266 :SA T0558 285 :MISTICPIRE 2z2nA 268 :EPHGICFDGE Number of specific fragments extracted= 16 number of extra gaps= 4 total=628 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei4B/T0558-3ei4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ei4B expands to /projects/compbio/data/pdb/3ei4.pdb.gz 3ei4B:# T0558 read from 3ei4B/T0558-3ei4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei4B read from 3ei4B/T0558-3ei4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ei4B to template set # found chain 3ei4B in template set Warning: unaligning (T0558)A9 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)F110 Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)F110 Warning: unaligning (T0558)K77 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)L183 Warning: unaligning (T0558)M78 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L183 Warning: unaligning (T0558)Q98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)S206 Warning: unaligning (T0558)T99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)S206 Warning: unaligning (T0558)A100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L207 Warning: unaligning (T0558)R101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)D208 Warning: unaligning (T0558)S130 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)N237 Warning: unaligning (T0558)K131 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)N237 Warning: unaligning (T0558)K272 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)K381 Warning: unaligning (T0558)V273 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)M382 T0558 2 :KNFILLV 3ei4B 102 :RILQKAA T0558 11 :FLVAPFAQGSSPQH 3ei4B 111 :DRRATSLAWHPTHP T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPL 3ei4B 126 :TVAVGSKGGDIMLWNFGIKDKPTFIKG T0558 52 :EKGWECNSVAATK 3ei4B 154 :GAGGSITGLKFNP T0558 65 :AGEILFSYSKG 3ei4B 168 :NTNQFYASSME T0558 76 :A 3ei4B 181 :T T0558 79 :ITRD 3ei4B 184 :QDFK T0558 83 :GRELWNIAAPAGCE 3ei4B 189 :NILRVFASSDTINI T0558 97 :M 3ei4B 204 :F T0558 102 :ILPDGNALVAWCG 3ei4B 209 :VSASSRMVVTGDN T0558 116 :PSTILEVNMKGEVL 3ei4B 222 :VGNVILLNMDGKEL T0558 134 :FETGIERPHA 3ei4B 238 :LRMHKKKVTH T0558 148 :INKNK 3ei4B 248 :VALNP T0558 153 :KGNYLVPLFATSEVREIAPN 3ei4B 254 :CDWFLATASVDQTVKIWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESN 3ei4B 279 :ASFLYSLPHRHPVNAACFSPDGARLLTTDQKSEIRVYSASQW T0558 215 :RIVRRVNANDIEG 3ei4B 324 :LGLIPHPHRHFQH T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3ei4B 337 :LTPIKAAWHPRYNLIVVGRYPD T0558 254 :REAGKG 3ei4B 365 :TPYELR T0558 263 :QLVEIDSEG 3ei4B 371 :TIDVFDGNS T0558 274 :VWQLNDKVKFGMI 3ei4B 383 :MCQLYDPESSGIS Number of specific fragments extracted= 20 number of extra gaps= 5 total=648 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei4B/T0558-3ei4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3ei4B/T0558-3ei4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei4B read from 3ei4B/T0558-3ei4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ei4B in template set Warning: unaligning (T0558)A9 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)F110 Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)F110 Warning: unaligning (T0558)K77 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)L183 Warning: unaligning (T0558)M78 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L183 Warning: unaligning (T0558)Q98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)S206 Warning: unaligning (T0558)T99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)S206 Warning: unaligning (T0558)A100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L207 Warning: unaligning (T0558)R101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)D208 Warning: unaligning (T0558)S130 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)N237 Warning: unaligning (T0558)E133 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)N237 Warning: unaligning (T0558)H261 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)K381 Warning: unaligning (T0558)P262 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)K381 Warning: unaligning (T0558)Q263 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)M382 Warning: unaligning (T0558)N278 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)P402 T0558 2 :KNFILLV 3ei4B 102 :RILQKAA T0558 11 :FL 3ei4B 111 :DR T0558 14 :APFAQGSSPQ 3ei4B 113 :RATSLAWHPT T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 3ei4B 125 :STVAVGSKGGDIMLWNFGIKDKPTFIK T0558 51 :LEKGWECNSVAATK 3ei4B 153 :IGAGGSITGLKFNP T0558 65 :AGEILFSYSKG 3ei4B 168 :NTNQFYASSME T0558 76 :A 3ei4B 181 :T T0558 79 :IT 3ei4B 184 :QD T0558 81 :RDG 3ei4B 187 :KGN T0558 84 :RELWNIA 3ei4B 192 :RVFASSD T0558 92 :PAGCEM 3ei4B 199 :TINIWF T0558 102 :ILPDGNALVAWC 3ei4B 209 :VSASSRMVVTGD T0558 115 :HPSTILEVNMKGEVL 3ei4B 221 :NVGNVILLNMDGKEL T0558 134 :FETGIER 3ei4B 238 :LRMHKKK T0558 145 :FRQINKNKKGN 3ei4B 245 :VTHVALNPCCD T0558 156 :YLVPLFATSEVREIAPNG 3ei4B 257 :FLATASVDQTVKIWDLRQ T0558 174 :QLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNR 3ei4B 280 :SFLYSLPHRHPVNAACFSPDGARLLTTDQKSEIRVYSASQWD T0558 216 :IVRRVNANDIEGV 3ei4B 325 :GLIPHPHRHFQHL T0558 232 :FVAQLFPLQNGGLYICNW 3ei4B 338 :TPIKAAWHPRYNLIVVGR T0558 250 :QGHDREAGKG 3ei4B 368 :ELRTIDVFDG T0558 260 :K 3ei4B 379 :S T0558 264 :LVEI 3ei4B 383 :MCQL T0558 268 :DSEGKVVWQL 3ei4B 389 :PESSGISSLN T0558 279 :DKVKFGMISTIC 3ei4B 403 :MGDTLASAMGYH Number of specific fragments extracted= 24 number of extra gaps= 6 total=672 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei4B/T0558-3ei4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3ei4B/T0558-3ei4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei4B read from 3ei4B/T0558-3ei4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ei4B in template set Warning: unaligning (T0558)K77 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)L183 Warning: unaligning (T0558)M78 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L183 Warning: unaligning (T0558)Q98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)S206 Warning: unaligning (T0558)T99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)S206 Warning: unaligning (T0558)A100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)L207 Warning: unaligning (T0558)R101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)D208 Warning: unaligning (T0558)S130 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)N237 Warning: unaligning (T0558)K131 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)N237 Warning: unaligning (T0558)G284 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ei4B)K381 Warning: unaligning (T0558)M285 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)K381 Warning: unaligning (T0558)I286 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ei4B)M382 T0558 19 :GSSPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 3ei4B 120 :HPTHPSTVAVGSKGGDIMLWNFGIKDKPTFIKG T0558 52 :EKGWECNSVAATK 3ei4B 154 :GAGGSITGLKFNP T0558 65 :AGEILFSY 3ei4B 169 :TNQFYASS T0558 73 :SKGA 3ei4B 178 :EGTT T0558 79 :ITRDGRELWN 3ei4B 184 :QDFKGNILRV T0558 89 :IAA 3ei4B 195 :ASS T0558 92 :PAGCEM 3ei4B 199 :TINIWF T0558 102 :ILPDGNALVAWCG 3ei4B 209 :VSASSRMVVTGDN T0558 116 :PSTILEVNMKGEVL 3ei4B 222 :VGNVILLNMDGKEL T0558 132 :TEFETG 3ei4B 238 :LRMHKK T0558 144 :QFRQINKNKKG 3ei4B 244 :KVTHVALNPCC T0558 155 :NYLVPLFATSEVREIA 3ei4B 256 :WFLATASVDQTVKIWD T0558 171 :PNGQ 3ei4B 273 :RQVR T0558 175 :LLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNR 3ei4B 281 :FLYSLPHRHPVNAACFSPDGARLLTTDQKSEIRVYSASQWD T0558 216 :IVRRVNANDIEGV 3ei4B 325 :GLIPHPHRHFQHL T0558 232 :FVAQLFPLQNGGLYICNWQGHDREAGKGKH 3ei4B 338 :TPIKAAWHPRYNLIVVGRYPDPNFKSCTPY T0558 262 :PQLVEI 3ei4B 370 :RTIDVF T0558 280 :KVKF 3ei4B 376 :DGNS T0558 287 :STICPIRE 3ei4B 383 :MCQLYDPE Number of specific fragments extracted= 19 number of extra gaps= 4 total=691 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hxjA/T0558-3hxjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hxjA expands to /projects/compbio/data/pdb/3hxj.pdb.gz 3hxjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 3hxjA/T0558-3hxjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hxjA read from 3hxjA/T0558-3hxjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hxjA to template set # found chain 3hxjA in template set Warning: unaligning (T0558)D268 because last residue in template chain is (3hxjA)N322 T0558 2 :KNFILLVALFLVAPFAQGSSPQH 3hxjA 50 :SVKWFFKSGEIIECRPSIGKDGT T0558 25 :LLVGGSGWNKIAIINKD 3hxjA 109 :ILYVTSMDGHLYAINTD T0558 43 :KEIVWEYPLEKG 3hxjA 126 :GTEKWRFKTKKA T0558 57 :CNSVAATKAGEILFSYSKG 3hxjA 138 :IYATPIVSEDGTIYVGSND T0558 76 :AKMITRDGRELWNIAAPAGC 3hxjA 159 :LYAINPDGTEKWRFKTNDAI T0558 97 :MQTARILPDGNALVA 3hxjA 179 :TSAASIGKDGTIYFG T0558 116 :PSTILEVNMKGEVLSKTEFET 3hxjA 194 :SDKVYAINPDGTEKWNFYAGY T0558 139 :ERPHA 3hxjA 215 :WTVTR T0558 148 :INKNKKGNYLV 3hxjA 220 :PAISEDGTIYV T0558 160 :LFATSEVREIAPNGQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 3hxjA 231 :TSLDGHLYAINPDGTEKWRFKTGKRIESSPVIGNTDTIYFGSYDGHLYAIN T0558 212 :ESNRIVRRVNAND 3hxjA 282 :PDGTEKWNFETGS T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3hxjA 295 :WIIATPVIDENGTIYFGTRNGK T0558 263 :QLVEI 3hxjA 317 :FYALF Number of specific fragments extracted= 13 number of extra gaps= 0 total=704 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hxjA/T0558-3hxjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3hxjA/T0558-3hxjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hxjA read from 3hxjA/T0558-3hxjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hxjA in template set T0558 15 :PFAQGSSPQHLLVGGSGWNKIAIINKD 3hxjA 22 :DSSPILAKNGTIYLGSSNKNLYAINTD T0558 43 :KEIVWEYP 3hxjA 49 :GSVKWFFK T0558 52 :EKGWECNSVAATKAGE 3hxjA 57 :SGEIIECRPSIGKDGT T0558 68 :IL 3hxjA 80 :VY T0558 71 :SYSKG 3hxjA 112 :VTSMD T0558 76 :AKMITRDGRELWNIA 3hxjA 119 :LYAINTDGTEKWRFK T0558 92 :PAGCEMQTARILPDG 3hxjA 134 :TKKAIYATPIVSEDG T0558 108 :ALVAWC 3hxjA 149 :TIYVGS T0558 115 :HPSTILEVNMKGEVLS 3hxjA 155 :NDNYLYAINPDGTEKW T0558 133 :EFETGIER 3hxjA 171 :RFKTNDAI T0558 145 :FRQINKNKKGNYLVPL 3hxjA 179 :TSAASIGKDGTIYFGS T0558 164 :SEVREIAPNGQLLNSV 3hxjA 195 :DKVYAINPDGTEKWNF T0558 180 :KLSGTPFSSAFLDNG 3hxjA 212 :AGYWTVTRPAISEDG T0558 196 :CLVACGDAHCFVQLN 3hxjA 227 :TIYVTSLDGHLYAIN T0558 212 :ESNRIVRRVNANDI 3hxjA 242 :PDGTEKWRFKTGKR T0558 232 :FVAQLFPLQNG 3hxjA 256 :IESSPVIGNTD T0558 244 :LYICNWQGHDREAGKGKHPQLVEIDSEGKVVWQL 3hxjA 267 :TIYFGSYDGHLYAINPDGTEKWNFETGSWIIATP T0558 278 :NDKVKFGMISTICPI 3hxjA 303 :DENGTIYFGTRNGKF Number of specific fragments extracted= 18 number of extra gaps= 0 total=722 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hxjA/T0558-3hxjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3hxjA/T0558-3hxjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hxjA read from 3hxjA/T0558-3hxjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hxjA in template set Warning: unaligning (T0558)S269 because last residue in template chain is (3hxjA)N322 T0558 26 :LVGGSGWNKIAIINKDTKEIVWEYPLEKGWECN 3hxjA 109 :ILYVTSMDGHLYAINTDGTEKWRFKTKKAIYAT T0558 60 :VAATKAGEILFSY 3hxjA 142 :PIVSEDGTIYVGS T0558 73 :SKGAKMITRDGRELWNIAAPAGC 3hxjA 156 :DNYLYAINPDGTEKWRFKTNDAI T0558 97 :MQTARIL 3hxjA 179 :TSAASIG T0558 105 :DGNALVAWCG 3hxjA 186 :KDGTIYFGSD T0558 118 :TILEVNMKGEVLSKTEFETG 3hxjA 196 :KVYAINPDGTEKWNFYAGYW T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPNGQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 3hxjA 216 :TVTRPAISEDGTIYVTSLDGHLYAINPDGTEKWRFKTGKRIESSPVIGNTDTIYFGSYDGHLYAIN T0558 212 :ESNRIVRRVN 3hxjA 282 :PDGTEKWNFE T0558 225 :IEGV 3hxjA 292 :TGSW T0558 232 :FVAQLFPLQNGGLYICNWQGH 3hxjA 296 :IIATPVIDENGTIYFGTRNGK T0558 264 :LVEID 3hxjA 317 :FYALF Number of specific fragments extracted= 11 number of extra gaps= 0 total=733 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a0rB/T0558-1a0rB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a0rB expands to /projects/compbio/data/pdb/1a0r.pdb.gz 1a0rB:# T0558 read from 1a0rB/T0558-1a0rB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a0rB read from 1a0rB/T0558-1a0rB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a0rB to template set # found chain 1a0rB in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 1a0rB 46 :RTRRTLRGHLAKIYAMHWGTDSRLLLSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1a0rB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMITRD 1a0rB 121 :CSIYNLK T0558 83 :GRE 1a0rB 129 :REG T0558 86 :LWNIAAPAGC 1a0rB 136 :SRELAGHTGY T0558 97 :MQTARIL 1a0rB 146 :LSCCRFL T0558 105 :DGNALVAWCG 1a0rB 153 :DDNQIVTSSG T0558 116 :PSTILEVNMK 1a0rB 163 :DTTCALWDIE T0558 126 :GEVLSK 1a0rB 174 :GQQTTT T0558 134 :FETGIERPHA 1a0rB 180 :FTGHTGDVMS T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 1a0rB 190 :LSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 1a0rB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 1a0rB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1a0rB 271 :CGITSVSFSKSGRLLLAGYDDF T0558 253 :DREAGK 1a0rB 298 :DALKAD T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 1a0rB 304 :RAGVLAGHDNRVSCLGVTDDGMAV T0558 287 :STICPI 1a0rB 333 :DSFLKI Number of specific fragments extracted= 17 number of extra gaps= 0 total=750 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a0rB/T0558-1a0rB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1a0rB/T0558-1a0rB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a0rB read from 1a0rB/T0558-1a0rB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a0rB in template set T0558 1 :MKNFILLVALFL 1a0rB 45 :MRTRRTLRGHLA T0558 14 :APFAQGSSPQ 1a0rB 57 :KIYAMHWGTD T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 1a0rB 68 :RLLLSASQDGKLIIWDSYTTNKVHAIP T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1a0rB 95 :LRSSWVMTCAYAPSGNYVACGGLD T0558 76 :AKMIT 1a0rB 121 :CSIYN T0558 81 :RDG 1a0rB 128 :TRE T0558 84 :RELWNIA 1a0rB 134 :RVSRELA T0558 92 :PAGCEMQTARILPDG 1a0rB 141 :GHTGYLSCCRFLDDN T0558 108 :ALVAWC 1a0rB 156 :QIVTSS T0558 115 :HPSTILEVNMK 1a0rB 162 :GDTTCALWDIE T0558 126 :GEVLS 1a0rB 174 :GQQTT T0558 133 :EFETGIER 1a0rB 179 :TFTGHTGD T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 1a0rB 187 :VMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSV 1a0rB 216 :GMCRQTF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 1a0rB 224 :GHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII T0558 231 :FFVAQLFPLQNGGLYICNWQGHDREAGKG 1a0rB 271 :CGITSVSFSKSGRLLLAGYDDFNCNVWDA T0558 260 :KHPQLVEIDSEGKVVWQL 1a0rB 301 :KADRAGVLAGHDNRVSCL T0558 278 :NDKVKFGMISTICPIR 1a0rB 322 :DDGMAVATGSWDSFLK Number of specific fragments extracted= 18 number of extra gaps= 0 total=768 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a0rB/T0558-1a0rB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1a0rB/T0558-1a0rB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a0rB read from 1a0rB/T0558-1a0rB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a0rB in template set T0558 22 :PQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 1a0rB 66 :DSRLLLSASQDGKLIIWDSYTTNKVHAIPLRSS T0558 56 :ECNSVAATKAGEILFSY 1a0rB 99 :WVMTCAYAPSGNYVACG T0558 73 :SKGAKMITRDG 1a0rB 118 :DNICSIYNLKT T0558 84 :RELWNIAAPAG 1a0rB 134 :RVSRELAGHTG T0558 96 :EMQTARILPDG 1a0rB 145 :YLSCCRFLDDN T0558 108 :ALVAWCG 1a0rB 156 :QIVTSSG T0558 116 :PSTILEVN 1a0rB 163 :DTTCALWD T0558 124 :MKGEVLSKTEFETG 1a0rB 172 :ETGQQTTTFTGHTG T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPN 1a0rB 186 :DVMSLSLAPDTRLFVSGACDASAKLWDVR T0558 173 :GQLLNSVKLS 1a0rB 216 :GMCRQTFTGH T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 1a0rB 227 :SDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIIC T0558 232 :FVAQLFPLQNGGLYICNWQGH 1a0rB 272 :GITSVSFSKSGRLLLAGYDDF T0558 263 :QLVEID 1a0rB 293 :NCNVWD T0558 269 :SEGKVVWQLNDKVK 1a0rB 300 :LKADRAGVLAGHDN T0558 285 :MISTICPI 1a0rB 314 :RVSCLGVT Number of specific fragments extracted= 15 number of extra gaps= 0 total=783 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oajA/T0558-2oajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2oajA expands to /projects/compbio/data/pdb/2oaj.pdb.gz 2oajA:# T0558 read from 2oajA/T0558-2oajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oajA read from 2oajA/T0558-2oajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oajA to template set # found chain 2oajA in template set T0558 3 :NFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 2oajA 69 :AETNKYGMSSKPIAAAFDFTQNLLAIATVTGEVHIYGQQQVEVVIKLE T0558 53 :KGWECNSVAATKAGEILFSYSKG 2oajA 117 :DRSAIKEMRFVKGIYLVVINAKD T0558 76 :AKMITRD 2oajA 141 :VYVLSLY T0558 83 :GRELWNIAAPAG 2oajA 149 :QKVLTTVFVPGK T0558 97 :MQTARILPDGNALVAWCG 2oajA 161 :ITSIDTDASLDWMLIGLQ T0558 116 :PSTILEVNMK 2oajA 179 :NGSMIVYDID T0558 126 :GEVLSKTE 2oajA 190 :DQLSSFKL T0558 134 :FETGIERPHA 2oajA 207 :PAARLSPIVS T0558 148 :INKNK 2oajA 217 :IQWNP T0558 153 :KGNYLVPLFA 2oajA 223 :DIGTVLISYE T0558 164 :SEVREIAPN 2oajA 233 :YVTLTYSLV T0558 173 :GQLLNSV 2oajA 243 :NEIKQSF T0558 180 :KLSGT 2oajA 252 :ELPPF T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2oajA 274 :VIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMARTVFETEI T0558 228 :VQLFFVAQLFPLQNG 2oajA 633 :ANKGKTSAINNSNIG T0558 244 :LYICNWQGH 2oajA 648 :FVGIAYAAG T0558 263 :QLVEIDSEG 2oajA 657 :SLMLIDRRG T0558 272 :KV 2oajA 667 :AI T0558 274 :VWQLNDKVKFGMI 2oajA 716 :TYKILPASGGKFD T0558 287 :STICPI 2oajA 732 :MDITNV Number of specific fragments extracted= 20 number of extra gaps= 0 total=803 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oajA/T0558-2oajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2oajA/T0558-2oajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oajA read from 2oajA/T0558-2oajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oajA in template set T0558 4 :FILLVALFL 2oajA 70 :ETNKYGMSS T0558 14 :APFAQGSSPQ 2oajA 79 :KPIAAAFDFT T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEY 2oajA 90 :NLLAIATVTGEVHIYGQQQVEVVIKL T0558 52 :EKGWECNSVAATK 2oajA 116 :EDRSAIKEMRFVK T0558 66 :GEILFSYSKG 2oajA 129 :GIYLVVINAK T0558 76 :AKMIT 2oajA 141 :VYVLS T0558 81 :RDGRELWNIA 2oajA 147 :YSQKVLTTVF T0558 93 :AGCEMQTARILPDGNALVAWC 2oajA 157 :VPGKITSIDTDASLDWMLIGL T0558 115 :HPSTILEVNMK 2oajA 178 :QNGSMIVYDID T0558 126 :GEVLS 2oajA 190 :DQLSS T0558 132 :TEFETG 2oajA 195 :FKLDNL T0558 138 :I 2oajA 271 :T T0558 143 :AQFRQINKNKKGNYLVPLFATSEVREIAPN 2oajA 272 :PKVIQSLYHPNSLHIITIHEDNSLVFWDAN T0558 173 :GQLLNSV 2oajA 303 :GHMIMAR T0558 180 :KLSGT 2oajA 311 :VFETE T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLN 2oajA 551 :VDKISFAAETLELAVSIETGDVVLFK T0558 211 :LESN 2oajA 621 :VRQG T0558 215 :RIVRRVNANDIE 2oajA 626 :MPSTAVHANKGK T0558 233 :VAQLFPLQNG 2oajA 638 :TSAINNSNIG T0558 244 :LYICNWQGHDREAGKGKHPQLVEI 2oajA 648 :FVGIAYAAGSLMLIDRRGPAIIYM T0558 268 :DSEGKVVWQL 2oajA 679 :GAQSACVTCI T0558 278 :NDK 2oajA 697 :DDG T0558 281 :VKFGMISTICPI 2oajA 703 :ILMVCGTDMGEV Number of specific fragments extracted= 23 number of extra gaps= 0 total=826 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oajA/T0558-2oajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2oajA/T0558-2oajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oajA read from 2oajA/T0558-2oajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2oajA in template set T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYPLEK 2oajA 90 :NLLAIATVTGEVHIYGQQQVEVVIKLEDRS T0558 56 :ECNSVAATKAGEILFSY 2oajA 120 :AIKEMRFVKGIYLVVIN T0558 73 :SKGAKMITRDG 2oajA 138 :KDTVYVLSLYS T0558 84 :RELWNIAAPAG 2oajA 150 :KVLTTVFVPGK T0558 97 :MQTARILPDGNALVAWCG 2oajA 161 :ITSIDTDASLDWMLIGLQ T0558 116 :PSTILEVNMKGEVLSKTEFET 2oajA 179 :NGSMIVYDIDRDQLSSFKLDN T0558 137 :GIERPHAQFRQINKNKK 2oajA 206 :FPAARLSPIVSIQWNPR T0558 154 :GNYLVPLFATSEVREIAPNGQLLNSVKLS 2oajA 224 :IGTVLISYEYVTLTYSLVENEIKQSFIYE T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVN 2oajA 272 :PKVIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMART T0558 222 :ANDIE 2oajA 317 :NVPQP T0558 227 :GVQLFFVAQLFPL 2oajA 328 :STNAAKISKVYWM T0558 240 :QNG 2oajA 343 :NNP T0558 243 :GLYICNWQGH 2oajA 348 :TSLLISHKSI T0558 255 :E 2oajA 358 :S T0558 258 :KGKHPQLVEID 2oajA 359 :RGDNQSLTMID Number of specific fragments extracted= 15 number of extra gaps= 0 total=841 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3frxA/T0558-3frxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3frxA expands to /projects/compbio/data/pdb/3frx.pdb.gz 3frxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 3frxA/T0558-3frxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3frxA read from 3frxA/T0558-3frxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3frxA to template set # found chain 3frxA in template set Warning: unaligning (T0558)D105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3frxA)S166 Warning: unaligning (T0558)N223 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3frxA)G280 Warning: unaligning (T0558)D224 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3frxA)G280 Warning: unaligning (T0558)I225 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3frxA)Y281 Warning: unaligning (T0558)K272 because last residue in template chain is (3frxA)A318 T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 3frxA 56 :VPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFV T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3frxA 105 :GHKSDVMSVDIDKKASMIISGSRD T0558 76 :AKMITRDGRELWNIAAPAGC 3frxA 131 :IKVWTIKGQCLATLLGHNDW T0558 97 :MQTARILP 3frxA 151 :VSQVRVVP T0558 108 :ALVAWCG 3frxA 168 :TIISAGN T0558 116 :PSTILEVNMK 3frxA 175 :DKMVKAWNLN T0558 126 :GEVLSK 3frxA 186 :FQIEAD T0558 134 :FETGIERPHA 3frxA 192 :FIGHNSNINT T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 3frxA 202 :LTASPDGTLIASAGKDGEIMLWNLA T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAH 3frxA 228 :KKAMYTLSAQDEVFSLAFSPNRYWLAAATATG T0558 206 :FVQLNLESNRIVRRVN 3frxA 260 :IKVFSLDPQYLVDDLR T0558 222 :A 3frxA 278 :F T0558 226 :EGVQLFFVAQLFPLQNGGLYICNWQGH 3frxA 282 :SKAAEPHAVSLAWSADGQTLFAGYTDN T0558 263 :QLVEIDSEG 3frxA 309 :VIRVWQVMT Number of specific fragments extracted= 14 number of extra gaps= 1 total=855 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3frxA/T0558-3frxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3frxA/T0558-3frxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3frxA read from 3frxA/T0558-3frxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3frxA in template set Warning: unaligning (T0558)G154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3frxA)S166 T0558 2 :KNFILLVALFL 3frxA 8 :VLRGTLEGHNG T0558 14 :APFAQGSSPQ 3frxA 19 :WVTSLATSAG T0558 24 :HLLVGGSGWNKIAIINKDT 3frxA 31 :NLLLSASRDKTLISWKLTG T0558 43 :KEIVWEYP 3frxA 55 :GVPVRSFK T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3frxA 63 :GHSHIVQDCTLTADGAYALSASWD T0558 76 :AKMIT 3frxA 89 :LRLWD T0558 81 :RDGRELWNIA 3frxA 95 :ATGETYQRFV T0558 92 :PAGCEMQTARILPDGNALVAWC 3frxA 105 :GHKSDVMSVDIDKKASMIISGS T0558 115 :HPSTILEVNMKGEVLS 3frxA 127 :RDKTIKVWTIKGQCLA T0558 133 :EFETGIER 3frxA 143 :TLLGHNDW T0558 145 :FRQINKNK 3frxA 151 :VSQVRVVP T0558 155 :NYLVPLFATSEVREIAPN 3frxA 167 :VTIISAGNDKMVKAWNLN T0558 173 :GQLLNSV 3frxA 186 :FQIEADF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDI 3frxA 194 :GHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDE T0558 233 :VAQLFPLQNGGLYICNWQG 3frxA 240 :VFSLAFSPNRYWLAAATAT T0558 253 :DREAGKG 3frxA 259 :GIKVFSL T0558 260 :KHPQLVEI 3frxA 267 :PQYLVDDL T0558 268 :DSEGKVVWQL 3frxA 283 :KAAEPHAVSL T0558 278 :NDKVKFGMISTICPI 3frxA 296 :ADGQTLFAGYTDNVI Number of specific fragments extracted= 19 number of extra gaps= 0 total=874 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3frxA/T0558-3frxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3frxA/T0558-3frxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3frxA read from 3frxA/T0558-3frxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3frxA in template set Warning: unaligning (T0558)G154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3frxA)S166 T0558 20 :SSPQHLLVGGSGWNKIAIINKDTKE 3frxA 27 :AGQPNLLLSASRDKTLISWKLTGDD T0558 45 :IVWEYPLE 3frxA 57 :PVRSFKGH T0558 54 :GWECNSVAATKAGEILFSY 3frxA 65 :SHIVQDCTLTADGAYALSA T0558 73 :SKGAKMIT 3frxA 86 :DKTLRLWD T0558 81 :RDGRELWNIAAPAG 3frxA 95 :ATGETYQRFVGHKS T0558 96 :EMQTARILPDGNALVAWCG 3frxA 109 :DVMSVDIDKKASMIISGSR T0558 116 :PSTILEVNMKGEVLSKTEFETG 3frxA 128 :DKTIKVWTIKGQCLATLLGHND T0558 144 :QFRQINKN 3frxA 150 :WVSQVRVV T0558 155 :NYLVPLFATSEVREIAPN 3frxA 167 :VTIISAGNDKMVKAWNLN T0558 173 :GQLLNSVKLS 3frxA 186 :FQIEADFIGH T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 3frxA 197 :SNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQD T0558 232 :FVAQLFPLQNGGLYICNWQGH 3frxA 239 :EVFSLAFSPNRYWLAAATATG T0558 262 :PQLVEI 3frxA 260 :IKVFSL T0558 269 :SEGKVVWQLN 3frxA 266 :DPQYLVDDLR T0558 279 :DKVKFGMISTICPIRE 3frxA 282 :SKAAEPHAVSLAWSAD Number of specific fragments extracted= 15 number of extra gaps= 0 total=889 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fvzA/T0558-3fvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3fvzA expands to /projects/compbio/data/pdb/3fvz.pdb.gz 3fvzA:Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2447, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2449, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2451, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2453, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2455, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2457, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2459, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2461, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2463, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2666, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2668, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2670, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2672, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2674, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2676, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2678, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2680, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2682, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2684, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2686, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2688, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2690, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2692, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2694, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2696, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2698, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2700, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2702, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2704, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2706, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2708, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2710, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2712, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2714, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2716, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2718, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2720, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2722, because occupancy 0.500 <= existing 0.500 in 3fvzA Skipped atom 2724, because occupancy 0.500 <= existing 0.500 in 3fvzA # T0558 read from 3fvzA/T0558-3fvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fvzA read from 3fvzA/T0558-3fvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fvzA to template set # found chain 3fvzA in template set Warning: unaligning (T0558)C113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)Y654 Warning: unaligning (T0558)G114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)Y654 Warning: unaligning (T0558)L176 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)R723 Warning: unaligning (T0558)N177 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)R723 Warning: unaligning (T0558)T184 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)V734 Warning: unaligning (T0558)P185 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)V734 Warning: unaligning (T0558)F190 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)I740 Warning: unaligning (T0558)L191 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)I740 T0558 6 :LLVALFLVAPFAQGSSPQHLLVGGSGWNK 3fvzA 509 :GVYLLPGQVSGVALDSKNNLVIFHRGDHV T0558 35 :IAIINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSYSKG 3fvzA 562 :ILVIDPNNAEILQSSGKNLFYLPHGLSIDTDGNYWVTDVAL T0558 76 :AKMITRD 3fvzA 605 :VFKLDPH T0558 83 :GRE 3fvzA 613 :KEG T0558 87 :WNIAAPAGCE 3fvzA 617 :LLILGRSMQP T0558 97 :MQTARILP 3fvzA 636 :PTDVAVEP T0558 105 :DGNALVAW 3fvzA 645 :TGAVFVSD T0558 115 :HPSTILEVNMKGEVLSKTEFETGIERPHAQ 3fvzA 655 :CNSRIVQFSPSGKFVTQWGEESSGSSPRPG T0558 145 :FRQINKNKKG 3fvzA 689 :PHSLALVPHL T0558 155 :NYLVPLFATSEVREIAPN 3fvzA 700 :QLCVADRENGRIQCFKTD T0558 173 :GQL 3fvzA 719 :KEF T0558 178 :SV 3fvzA 724 :EI T0558 180 :KLSG 3fvzA 729 :SFGR T0558 186 :FSSA 3fvzA 735 :FAIS T0558 193 :NG 3fvzA 741 :PG T0558 197 :LVACGDAH 3fvzA 743 :FLFAVNGK T0558 205 :CFVQLNLESNRIVRRVNANDIEG 3fvzA 760 :QGFVMNFSSGEIIDVFKPVRKHF T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3fvzA 783 :DMPHDIVASEDGTVYIGDAHTN T0558 263 :QLVEID 3fvzA 805 :TVWKFT T0558 277 :LNDKVK 3fvzA 811 :LTEKME Number of specific fragments extracted= 20 number of extra gaps= 4 total=909 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fvzA/T0558-3fvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3fvzA/T0558-3fvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fvzA read from 3fvzA/T0558-3fvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fvzA in template set Warning: unaligning (T0558)C113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)Y654 Warning: unaligning (T0558)G114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)Y654 Warning: unaligning (T0558)L176 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)R723 Warning: unaligning (T0558)N177 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)R723 Warning: unaligning (T0558)T184 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)V734 Warning: unaligning (T0558)P185 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)V734 Warning: unaligning (T0558)F190 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)I740 Warning: unaligning (T0558)L191 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)I740 T0558 10 :LFL 3fvzA 513 :LPG T0558 14 :APFAQGSSPQ 3fvzA 516 :QVSGVALDSK T0558 24 :HLLVG 3fvzA 527 :NLVIF T0558 29 :GSGWNKIAIINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSYSKG 3fvzA 556 :PIEEDTILVIDPNNAEILQSSGKNLFYLPHGLSIDTDGNYWVTDVAL T0558 76 :AKMITRDG 3fvzA 605 :VFKLDPHS T0558 84 :RELWNIA 3fvzA 615 :GPLLILG T0558 91 :APAGCEMQTARILP 3fvzA 630 :QNHFCQPTDVAVEP T0558 105 :DGNALVAW 3fvzA 645 :TGAVFVSD T0558 115 :HPSTILEVNMKGEVLSKT 3fvzA 655 :CNSRIVQFSPSGKFVTQW T0558 133 :EFETGIER 3fvzA 681 :PRPGQFSV T0558 145 :FRQINKN 3fvzA 689 :PHSLALV T0558 152 :KKGNYLVPLFATSEVREIAPN 3fvzA 697 :HLDQLCVADRENGRIQCFKTD T0558 173 :GQL 3fvzA 719 :KEF T0558 178 :SVKLS 3fvzA 724 :EIKHA T0558 183 :G 3fvzA 732 :R T0558 186 :FSSA 3fvzA 735 :FAIS T0558 192 :DN 3fvzA 741 :PG T0558 196 :CLVACG 3fvzA 743 :FLFAVN T0558 202 :DAHCFVQLNLESNRIVRRVNANDIE 3fvzA 757 :EPVQGFVMNFSSGEIIDVFKPVRKH T0558 230 :LFFVAQLFPLQNGGLYICNWQGHDREAGKG 3fvzA 782 :FDMPHDIVASEDGTVYIGDAHTNTVWKFTL T0558 260 :KHP 3fvzA 813 :EKM Number of specific fragments extracted= 21 number of extra gaps= 4 total=930 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fvzA/T0558-3fvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3fvzA/T0558-3fvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fvzA read from 3fvzA/T0558-3fvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fvzA in template set Warning: unaligning (T0558)C113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)Y654 Warning: unaligning (T0558)G114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)Y654 Warning: unaligning (T0558)N177 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fvzA)R723 Warning: unaligning (T0558)S178 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fvzA)R723 Warning: unaligning (T0558)T184 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)V734 Warning: unaligning (T0558)P185 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)V734 Warning: unaligning (T0558)F190 because of BadResidue code BAD_PEPTIDE in next template residue (3fvzA)I740 Warning: unaligning (T0558)L191 because of BadResidue code BAD_PEPTIDE at template residue (3fvzA)I740 T0558 14 :APFAQGSSPQHLLVGGSG 3fvzA 550 :QQRGLGPIEEDTILVIDP T0558 41 :DTKEIVWEYPLEKGWECNSVAATKAGEILFSY 3fvzA 568 :NNAEILQSSGKNLFYLPHGLSIDTDGNYWVTD T0558 73 :SKGAKMITRDGRELWNIAA 3fvzA 602 :LHQVFKLDPHSKEGPLLIL T0558 92 :PAG 3fvzA 629 :DQN T0558 95 :CEMQTARILP 3fvzA 634 :CQPTDVAVEP T0558 105 :DGNALVAW 3fvzA 645 :TGAVFVSD T0558 115 :HPSTILEVNMKGEVLSKTEFETGIERPHAQ 3fvzA 655 :CNSRIVQFSPSGKFVTQWGEESSGSSPRPG T0558 145 :FRQINKN 3fvzA 689 :PHSLALV T0558 152 :KKGNYLVPLFATSEVREIAPNGQLL 3fvzA 697 :HLDQLCVADRENGRIQCFKTDTKEF T0558 179 :VKLS 3fvzA 724 :EIKH T0558 183 :G 3fvzA 732 :R T0558 186 :FSSA 3fvzA 735 :FAIS T0558 192 :DN 3fvzA 741 :PG T0558 195 :DCLVACGD 3fvzA 743 :FLFAVNGK T0558 203 :AHCFVQLNLESNRIVRRVN 3fvzA 758 :PVQGFVMNFSSGEIIDVFK T0558 225 :IEGVQLFFVAQLFPLQNGGLYICNWQGH 3fvzA 777 :PVRKHFDMPHDIVASEDGTVYIGDAHTN T0558 261 :HPQLVEIDS 3fvzA 805 :TVWKFTLTE Number of specific fragments extracted= 17 number of extra gaps= 4 total=947 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fm0A/T0558-3fm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3fm0A expands to /projects/compbio/data/pdb/3fm0.pdb.gz 3fm0A:# T0558 read from 3fm0A/T0558-3fm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fm0A read from 3fm0A/T0558-3fm0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fm0A to template set # found chain 3fm0A in template set Warning: unaligning (T0558)A14 because of BadResidue code BAD_PEPTIDE at template residue (3fm0A)C19 Warning: unaligning (T0558)R81 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3fm0A)D94 Warning: unaligning (T0558)D82 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3fm0A)D94 T0558 2 :KNFILLVALFLV 3fm0A 6 :VLLGRVPAHPDS T0558 15 :PFAQGSSPQHLLVGGSGWNKIAIINKDTK 3fm0A 20 :WFLAWNPAGTLLASCGGDRRIRIWGTEGD T0558 44 :EIVWEYPLEKGWECNSVAATKAGEILFSYSKG 3fm0A 51 :ICKSVLSEGHQRTVRKVAWSPCGNYLASASFD T0558 76 :AKMI 3fm0A 85 :TCIW T0558 80 :T 3fm0A 91 :N T0558 83 :GRELWNIAAPAGC 3fm0A 95 :FECVTTLEGHENE T0558 97 :MQTARILPDGNALVAWCG 3fm0A 108 :VKSVAWAPSGNLLATCSR T0558 116 :PSTILEVNMK 3fm0A 126 :DKSVWVWEVD T0558 126 :GEVLSKTEFETGIERPHA 3fm0A 138 :DEYECVSVLNSHTQDVKH T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 3fm0A 156 :VVWHPSQELLASASYDDTVKLYREE T0558 173 :GQL 3fm0A 182 :DDW T0558 176 :LNSV 3fm0A 187 :CATL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNL 3fm0A 192 :GHESTVWSLAFDPSGQRLASCSDDRTVRIWRQ T0558 212 :ES 3fm0A 226 :PG T0558 214 :NRIVRRVN 3fm0A 241 :WKCICTLS T0558 222 :AND 3fm0A 250 :FHS T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3fm0A 253 :RTIYDIAWCQLTGALATACGDD T0558 263 :QLVEID 3fm0A 275 :AIRVFQ T0558 269 :SEGKV 3fm0A 282 :DPNSD T0558 274 :VWQLNDKVKFGMI 3fm0A 306 :VNCVAWNPKEPGL T0558 287 :STICP 3fm0A 325 :DGEVA Number of specific fragments extracted= 21 number of extra gaps= 2 total=968 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fm0A/T0558-3fm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3fm0A/T0558-3fm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fm0A read from 3fm0A/T0558-3fm0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fm0A in template set Warning: unaligning (T0558)A14 because of BadResidue code BAD_PEPTIDE in next template residue (3fm0A)C19 Warning: unaligning (T0558)P15 because of BadResidue code BAD_PEPTIDE at template residue (3fm0A)C19 Warning: unaligning (T0558)R81 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3fm0A)D94 Warning: unaligning (T0558)E212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3fm0A)P239 T0558 2 :KNFILLVALFLV 3fm0A 6 :VLLGRVPAHPDS T0558 16 :FAQGSSPQ 3fm0A 20 :WFLAWNPA T0558 24 :HLLVGGSGWNKIAIINKDTKE 3fm0A 29 :TLLASCGGDRRIRIWGTEGDS T0558 45 :IVWEYPLEKGWECNSVAATKAGEILFSYSKG 3fm0A 52 :CKSVLSEGHQRTVRKVAWSPCGNYLASASFD T0558 76 :AKMIT 3fm0A 85 :TCIWK T0558 83 :GRELWNIA 3fm0A 95 :FECVTTLE T0558 92 :PAGCEMQTARILPDGNALVAWC 3fm0A 103 :GHENEVKSVAWAPSGNLLATCS T0558 115 :HPSTILEVNMK 3fm0A 125 :RDKSVWVWEVD T0558 126 :G 3fm0A 137 :E T0558 127 :EVLS 3fm0A 141 :ECVS T0558 133 :EFETGIER 3fm0A 145 :VLNSHTQD T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 3fm0A 153 :VKHVVWHPSQELLASASYDDTVKLYREE T0558 173 :GQ 3fm0A 182 :DD T0558 175 :LLNSV 3fm0A 186 :CCATL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 3fm0A 192 :GHESTVWSLAFDPSGQRLASCSDDRTVRIWR T0558 213 :SNRIVRRVNANDIE 3fm0A 240 :SWKCICTLSGFHSR T0558 232 :FVAQLFPLQNGGLYICNWQGHDREAGKG 3fm0A 254 :TIYDIAWCQLTGALATACGDDAIRVFQE T0558 260 :KH 3fm0A 283 :PN T0558 262 :PQLVEI 3fm0A 293 :SLTAHL T0558 268 :DSEGKVVWQL 3fm0A 300 :QAHSQDVNCV T0558 278 :NDKVKFGMISTICPIR 3fm0A 314 :KEPGLLASCSDDGEVA Number of specific fragments extracted= 21 number of extra gaps= 1 total=989 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fm0A/T0558-3fm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3fm0A/T0558-3fm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fm0A read from 3fm0A/T0558-3fm0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fm0A in template set Warning: unaligning (T0558)G83 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3fm0A)D94 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 3fm0A 26 :PAGTLLASCGGDRRIRIWGTEGDSWICKSVL T0558 52 :EKGWECNSVAATKAGEILFSY 3fm0A 59 :GHQRTVRKVAWSPCGNYLASA T0558 73 :SKGAKMITRD 3fm0A 82 :DATTCIWKKN T0558 84 :RELWNIAAPAG 3fm0A 96 :ECVTTLEGHEN T0558 96 :EMQTARILPDGNALVAWCG 3fm0A 107 :EVKSVAWAPSGNLLATCSR T0558 116 :PS 3fm0A 126 :DK T0558 118 :TILEVNMKGEVLSKTEFETGIE 3fm0A 130 :WVWEVDEEDEYECVSVLNSHTQ T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAP 3fm0A 152 :DVKHVVWHPSQELLASASYDDTVKLYRE T0558 172 :NGQLLNSVKLS 3fm0A 181 :EDDWVCCATLE T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESN 3fm0A 195 :STVWSLAFDPSGQRLASCSDDRTVRIWRQYLP T0558 216 :IVRRVN 3fm0A 243 :CICTLS T0558 223 :NDIE 3fm0A 249 :GFHS T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3fm0A 253 :RTIYDIAWCQLTGALATACGDD T0558 261 :HPQLVEIDSEG 3fm0A 275 :AIRVFQEDPNS T0558 273 :VVWQLNDKVKF 3fm0A 292 :FSLTAHLHQAH T0558 284 :GMISTICPI 3fm0A 304 :QDVNCVAWN Number of specific fragments extracted= 16 number of extra gaps= 1 total=1005 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i2nA/T0558-3i2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i2nA expands to /projects/compbio/data/pdb/3i2n.pdb.gz 3i2nA:Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 3i2nA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 3i2nA Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 3i2nA Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 3i2nA Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 3i2nA Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 3i2nA # T0558 read from 3i2nA/T0558-3i2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i2nA read from 3i2nA/T0558-3i2nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i2nA to template set # found chain 3i2nA in template set Warning: unaligning (T0558)S30 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)R41 Warning: unaligning (T0558)C95 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)I114 Warning: unaligning (T0558)M97 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)I114 Warning: unaligning (T0558)D105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)G128 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)P158 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)P158 Warning: unaligning (T0558)K152 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)E179 Warning: unaligning (T0558)K153 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)E179 Warning: unaligning (T0558)D253 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)K298 Warning: unaligning (T0558)V273 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)I324 Warning: unaligning (T0558)V274 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)I324 Warning: unaligning (T0558)I289 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)V346 Warning: unaligning (T0558)C290 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)V346 T0558 2 :KNFILLVALFLVAPFAQGSS 3i2nA 9 :IIAHIQKGFNYTVFDCKWVP T0558 22 :PQHLLVGG 3i2nA 30 :SAKFVTMG T0558 31 :GWNKIAIINKDTKEIVWEYPLEKGWECNSVAA 3i2nA 42 :GTGVIQLYEIQHGDLKLLREIEKAKPIKCGTF T0558 63 :TKAGEILFSYSKG 3i2nA 77 :SLQQRYLATGDFG T0558 76 :AKMITRD 3i2nA 92 :LHIWNLE T0558 83 :GRELWNIAAPAG 3i2nA 101 :EMPVYSVKGHKE T0558 98 :QTARILP 3i2nA 115 :NAIDGIG T0558 106 :GNALVAWCG 3i2nA 129 :APEIVTGSR T0558 116 :PSTILEVNMK 3i2nA 138 :DGTVKVWDPR T0558 126 :GEVLSK 3i2nA 150 :DDPVAN T0558 134 :F 3i2nA 156 :M T0558 137 :GIERPHAQFRQINK 3i2nA 159 :VQGENKRDCWTVAF T0558 151 :N 3i2nA 177 :N T0558 154 :GNYLVPLFATSEVREIAPN 3i2nA 180 :ERVVCAGYDNGDIKLFDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNG 3i2nA 200 :MALRWETNIKNGVCSLEFDRKD T0558 195 :DCLVACGDAHCFVQLNL 3i2nA 225 :NKLVATSLEGKFHVFDM T0558 212 :ESNRIVRRVNAND 3i2nA 247 :TKGFASVSEKAHK T0558 231 :FFVAQLFPLQNG 3i2nA 260 :STVWQVRHLPQN T0558 243 :GLYICNWQGH 3i2nA 273 :ELFLTAGGAG T0558 254 :REAGK 3i2nA 299 :DSEGI T0558 259 :GKHPQLVEIDSE 3i2nA 306 :GVAGSVSLLQNV T0558 271 :GK 3i2nA 321 :TQ T0558 275 :WQLNDKVKFGMI 3i2nA 325 :SSLDWSPDKRGL T0558 287 :ST 3i2nA 343 :DQ Number of specific fragments extracted= 24 number of extra gaps= 6 total=1029 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i2nA/T0558-3i2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3i2nA/T0558-3i2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i2nA read from 3i2nA/T0558-3i2nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i2nA in template set Warning: unaligning (T0558)G31 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)R41 Warning: unaligning (T0558)E96 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)I114 Warning: unaligning (T0558)M97 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)I114 Warning: unaligning (T0558)P104 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)G128 Warning: unaligning (T0558)D105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)G128 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)P158 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)P158 Warning: unaligning (T0558)K152 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)E179 Warning: unaligning (T0558)K153 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)E179 Warning: unaligning (T0558)V273 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)I324 Warning: unaligning (T0558)V274 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)I324 Warning: unaligning (T0558)P291 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)V346 Warning: unaligning (T0558)I292 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)V346 T0558 2 :KNFILLVALFL 3i2nA 9 :IIAHIQKGFNY T0558 14 :APFAQGSSPQ 3i2nA 20 :TVFDCKWVPC T0558 24 :HLLVGGS 3i2nA 31 :AKFVTMG T0558 33 :NKIAIINKDTKEIVWEYPLEKGWECNSVAA 3i2nA 44 :GVIQLYEIQHGDLKLLREIEKAKPIKCGTF T0558 63 :TKAGEILFSYSKG 3i2nA 77 :SLQQRYLATGDFG T0558 76 :AKMIT 3i2nA 92 :LHIWN T0558 81 :RDGR 3i2nA 98 :EAPE T0558 85 :ELWNIA 3i2nA 103 :PVYSVK T0558 92 :PAGC 3i2nA 109 :GHKE T0558 98 :QTARI 3i2nA 115 :NAIDG T0558 103 :L 3i2nA 126 :G T0558 106 :GNALVAWC 3i2nA 129 :APEIVTGS T0558 115 :HPSTILEVNMK 3i2nA 137 :RDGTVKVWDPR T0558 126 :GEVLS 3i2nA 150 :DDPVA T0558 133 :EF 3i2nA 155 :NM T0558 137 :GIERPHAQFRQINKN 3i2nA 159 :VQGENKRDCWTVAFG T0558 154 :GNYLVPLFATSEVREIAPN 3i2nA 180 :ERVVCAGYDNGDIKLFDLR T0558 173 :GQLLNSVKLSGTPFSSAFLDNG 3i2nA 200 :MALRWETNIKNGVCSLEFDRKD T0558 195 :DCLVACGDAHCFVQLNLESNR 3i2nA 225 :NKLVATSLEGKFHVFDMRTQH T0558 216 :IVRRVNANDIE 3i2nA 251 :ASVSEKAHKST T0558 233 :VAQLFPLQN 3i2nA 262 :VWQVRHLPQ T0558 242 :GGLYICNWQGHDREAGKG 3i2nA 272 :RELFLTAGGAGGLHLWKY T0558 260 :KH 3i2nA 291 :YP T0558 262 :PQLVEIDSEGK 3i2nA 312 :SLLQNVTLSTQ T0558 275 :WQL 3i2nA 325 :SSL T0558 278 :NDKV 3i2nA 331 :PDKR T0558 282 :KFGMISTIC 3i2nA 336 :LCVCSSFDQ Number of specific fragments extracted= 27 number of extra gaps= 6 total=1056 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i2nA/T0558-3i2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3i2nA/T0558-3i2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i2nA read from 3i2nA/T0558-3i2nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i2nA in template set Warning: unaligning (T0558)G31 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)R41 Warning: unaligning (T0558)K34 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)R41 Warning: unaligning (T0558)E96 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)I114 Warning: unaligning (T0558)M97 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)I114 Warning: unaligning (T0558)D105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)G128 Warning: unaligning (T0558)E133 because of BadResidue code BAD_PEPTIDE in next template residue (3i2nA)P158 Warning: unaligning (T0558)F134 because of BadResidue code BAD_PEPTIDE at template residue (3i2nA)P158 Warning: unaligning (T0558)K152 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)E179 Warning: unaligning (T0558)K153 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3i2nA)E179 Warning: unaligning (T0558)F283 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3i2nA)K298 T0558 20 :SSPQHLLVGGS 3i2nA 27 :VPCSAKFVTMG T0558 35 :IAIINKDTKEI 3i2nA 46 :IQLYEIQHGDL T0558 46 :VWEYPLEK 3i2nA 59 :LREIEKAK T0558 56 :ECNSVAAT 3i2nA 67 :PIKCGTFG T0558 64 :KAGEILFSY 3i2nA 79 :QQRYLATGD T0558 73 :SKGAKMITRDG 3i2nA 89 :GGNLHIWNLEA T0558 86 :LWNIAAPAG 3i2nA 104 :VYSVKGHKE T0558 98 :QTARILP 3i2nA 115 :NAIDGIG T0558 106 :GNALVAWCG 3i2nA 129 :APEIVTGSR T0558 116 :PSTILEVNMKGE 3i2nA 138 :DGTVKVWDPRQK T0558 128 :VLSKT 3i2nA 152 :PVANM T0558 135 :ETGIER 3i2nA 159 :VQGENK T0558 141 :PHAQFRQINKN 3i2nA 167 :CWTVAFGNAYN T0558 154 :GNYLVPLFATSEVREIA 3i2nA 180 :ERVVCAGYDNGDIKLFD T0558 171 :PNGQLLNSVKLS 3i2nA 198 :RNMALRWETNIK T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNR 3i2nA 213 :CSLEFDRKDISMNKLVATSLEGKFHVFDMRTQH T0558 216 :IVRRVN 3i2nA 251 :ASVSEK T0558 232 :FVAQLFPLQNG 3i2nA 261 :TVWQVRHLPQN T0558 243 :GLYICNWQGH 3i2nA 273 :ELFLTAGGAG T0558 263 :QL 3i2nA 283 :GL T0558 273 :VVWQLNDKVK 3i2nA 285 :HLWKYEYPIQ Number of specific fragments extracted= 21 number of extra gaps= 4 total=1077 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7fA/T0558-1q7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q7fA expands to /projects/compbio/data/pdb/1q7f.pdb.gz 1q7fA:# T0558 read from 1q7fA/T0558-1q7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7fA read from 1q7fA/T0558-1q7fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q7fA to template set # found chain 1q7fA in template set T0558 9 :ALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKD 1q7fA 778 :GQFTEPSGVAVNAQNDIIVADTNNHRIQIFDKE T0558 43 :KEIVWEYPL 1q7fA 811 :GRFKFQFGE T0558 52 :EKGWECNSVAATKAG 1q7fA 825 :SQLLYPNRVAVVRNS T0558 67 :EILFSYSKG 1q7fA 841 :DIIVTERSP T0558 76 :AKMITRDGRELWNIAAPAGCEMQTARILPDGNALVAWCG 1q7fA 853 :IQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVECK T0558 116 :PSTILEVNMKGEVLSKTEFETGIERPHA 1q7fA 892 :VMRVIIFDQNGNVLHKFGCSKHLEFPNG T0558 148 :INKNKKGNYLVPLFATSEVREIAPNGQLLNSV 1q7fA 920 :VVVNDKQEIFISDNRAHCVKVFNYEGQYLRQI T0558 180 :KLSGTPFSSAFLDNGDCLVACGD 1q7fA 955 :GITNYPIGVGINSNGEILIADNH T0558 203 :AHCFVQLN 1q7fA 979 :NFNLTIFT T0558 212 :ESNRIVRRVNAND 1q7fA 987 :QDGQLISALESKV T0558 229 :QLFFVAQLFPLQNGGLYICNWQG 1q7fA 1000 :KHAQCFDVALMDDGSVVLASKDY T0558 263 :QLVEIDSEGK 1q7fA 1023 :RLYIYRYVQL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1089 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7fA/T0558-1q7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1q7fA/T0558-1q7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7fA read from 1q7fA/T0558-1q7fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7fA in template set T0558 8 :VALFL 1q7fA 777 :EGQFT T0558 14 :APFAQGSSPQ 1q7fA 782 :EPSGVAVNAQ T0558 24 :HLLVGGSGWNKIAIINKD 1q7fA 793 :DIIVADTNNHRIQIFDKE T0558 43 :KEIVWEYP 1q7fA 811 :GRFKFQFG T0558 51 :LEKGWECNSVAATKA 1q7fA 824 :DSQLLYPNRVAVVRN T0558 66 :GEILFSYSKG 1q7fA 840 :GDIIVTERSP T0558 76 :AKMITRDGRELWNIAAPAGCEMQTARILPDGNALVAWC 1q7fA 853 :IQIYNQYGQFVRKFGATILQHPRGVTVDNKGRIIVVEC T0558 115 :HPSTILEVNMKGEVLSKTEFETGIER 1q7fA 891 :KVMRVIIFDQNGNVLHKFGCSKHLEF T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPNGQLLNSV 1q7fA 917 :PNGVVVNDKQEIFISDNRAHCVKVFNYEGQYLRQI T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAH 1q7fA 955 :GITNYPIGVGINSNGEILIADNHNN T0558 205 :CFVQLNL 1q7fA 981 :NLTIFTQ T0558 213 :SNRIVRR 1q7fA 988 :DGQLISA T0558 220 :VNANDIE 1q7fA 997 :SKVKHAQ T0558 233 :VAQLFPLQNGGLYICN 1q7fA 1004 :CFDVALMDDGSVVLAS T0558 250 :QGHDREAGKG 1q7fA 1020 :KDYRLYIYRY T0558 260 :KHP 1q7fA 1031 :QLA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1105 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7fA/T0558-1q7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1q7fA/T0558-1q7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7fA read from 1q7fA/T0558-1q7fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7fA in template set T0558 52 :EKGWECNSVAATKAGEILFSY 1q7fA 778 :GQFTEPSGVAVNAQNDIIVAD T0558 73 :SKGAKMITRDGRELWNIAA 1q7fA 801 :NHRIQIFDKEGRFKFQFGE T0558 92 :PAG 1q7fA 823 :RDS T0558 95 :CEMQTARIL 1q7fA 828 :LYPNRVAVV T0558 104 :PDGNALVAWCGHPSTILEVNMKGEVL 1q7fA 838 :NSGDIIVTERSPTHQIQIYNQYGQFV T0558 131 :KTEFETGIE 1q7fA 864 :RKFGATILQ T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIAPNGQLLNSVKLS 1q7fA 873 :HPRGVTVDNKGRIIVVECKVMRVIIFDQNGNVLHKFGCS T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLN 1q7fA 915 :EFPNGVVVNDKQEIFISDNRAHCVKVFN T0558 212 :ESNRIVRRVNAND 1q7fA 943 :YEGQYLRQIGGEG T0558 229 :QLFFVAQLFPLQNGGLYICNWQGH 1q7fA 956 :ITNYPIGVGINSNGEILIADNHNN T0558 262 :PQLVEIDSEGKVVWQLNDKVKFGMISTICPIRE 1q7fA 980 :FNLTIFTQDGQLISALESKVKHAQCFDVALMDD Number of specific fragments extracted= 11 number of extra gaps= 0 total=1116 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dxkC/T0558-3dxkC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dxkC expands to /projects/compbio/data/pdb/3dxk.pdb.gz 3dxkC:# T0558 read from 3dxkC/T0558-3dxkC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dxkC read from 3dxkC/T0558-3dxkC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dxkC to template set # found chain 3dxkC in template set Warning: unaligning (T0558)S182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dxkC)C202 T0558 6 :LLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTK 3dxkC 3 :YHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGN T0558 44 :EIVWEYP 3dxkC 43 :VQVHELK T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3dxkC 50 :EHNGQVTGIDWAPDSNRIVTCGTD T0558 76 :AKMITRD 3dxkC 76 :AYVWTLK T0558 83 :GRE 3dxkC 84 :RTW T0558 86 :LWNIAAPAGC 3dxkC 89 :TLVILRINRA T0558 97 :MQTARILPDGNALVAWCG 3dxkC 99 :ARCVRWAPNEKKFAVGSG T0558 116 :PSTILEVNMK 3dxkC 117 :SRVISICYFE T0558 126 :GEVLSKTEFETGIERPHA 3dxkC 130 :DWWVCKHIKKPIRSTVLS T0558 148 :INKNKKGNYLVPLFATSEVREIAP 3dxkC 148 :LDWHPNSVLLAAGSCDFKCRIFSA T0558 173 :GQLLNSV 3dxkC 192 :GELMFES T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 3dxkC 203 :GWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASET T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3dxkC 245 :LPLLAVTFITESSLVAAGHDCF T0558 263 :QLVEIDSEG 3dxkC 268 :VLFTYDSAA T0558 272 :KV 3dxkC 280 :SF Number of specific fragments extracted= 15 number of extra gaps= 0 total=1131 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dxkC/T0558-3dxkC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dxkC/T0558-3dxkC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dxkC read from 3dxkC/T0558-3dxkC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dxkC in template set Warning: unaligning (T0558)V179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dxkC)C202 Warning: unaligning (T0558)S182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dxkC)C202 T0558 6 :LLVALFL 3dxkC 3 :YHSFLVE T0558 14 :APFAQGSSPQ 3dxkC 10 :PISCHAWNKD T0558 24 :HLLVGGSGWNKIAIINKDTKE 3dxkC 21 :TQIAICPNNHEVHIYEKSGNK T0558 45 :IVWEYP 3dxkC 44 :QVHELK T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3dxkC 50 :EHNGQVTGIDWAPDSNRIVTCGTD T0558 76 :AKMIT 3dxkC 76 :AYVWT T0558 81 :RDGRE 3dxkC 82 :KGRTW T0558 86 :LWNIAAPAGCEMQTARILPDGNALVAWC 3dxkC 88 :PTLVILRINRAARCVRWAPNEKKFAVGS T0558 115 :HPSTILEVNMK 3dxkC 116 :GSRVISICYFE T0558 126 :G 3dxkC 128 :E T0558 127 :EVLS 3dxkC 133 :VCKH T0558 133 :EFETGIER 3dxkC 137 :IKKPIRST T0558 145 :FRQINKNKKGNYLVPLFATSEVREIA 3dxkC 145 :VLSLDWHPNSVLLAAGSCDFKCRIFS T0558 171 :PNGQLLNS 3dxkC 191 :FGELMFES T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDI 3dxkC 203 :GWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETL T0558 232 :FVAQLFPLQNGGLYICN 3dxkC 246 :PLLAVTFITESSLVAAG T0558 250 :QGHDREAGKG 3dxkC 263 :HDCFPVLFTY T0558 260 :KHP 3dxkC 274 :SAA T0558 263 :QLVEIDS 3dxkC 278 :KLSFGGR T0558 270 :EGKVVWQL 3dxkC 325 :HKNSVSQI T0558 278 :NDKV 3dxkC 336 :SGGK T0558 282 :KFGMISTICPIR 3dxkC 344 :QFCTTGMDGGMS Number of specific fragments extracted= 22 number of extra gaps= 0 total=1153 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dxkC/T0558-3dxkC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dxkC/T0558-3dxkC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dxkC read from 3dxkC/T0558-3dxkC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dxkC in template set T0558 20 :SSPQHLLVGGSGWNKIAIINK 3dxkC 16 :WNKDRTQIAICPNNHEVHIYE T0558 41 :DTKEIVWEYPL 3dxkC 38 :SGNKWVQVHEL T0558 52 :EKGWECNSVAATKAGEILFSY 3dxkC 50 :EHNGQVTGIDWAPDSNRIVTC T0558 73 :SKGAKMIT 3dxkC 73 :DRNAYVWT T0558 81 :RDGRELWNIAA 3dxkC 82 :KGRTWKPTLVI T0558 92 :PAG 3dxkC 95 :INR T0558 96 :EMQTARILPDGNALVAWCG 3dxkC 98 :AARCVRWAPNEKKFAVGSG T0558 116 :PSTILEVN 3dxkC 117 :SRVISICY T0558 124 :MKGEVLSKTEF 3dxkC 126 :EQENDWWVCKH T0558 135 :ETGIE 3dxkC 138 :KKPIR T0558 143 :AQFRQINKNKKGNYLVPLFATSEVREIA 3dxkC 143 :STVLSLDWHPNSVLLAAGSCDFKCRIFS T0558 179 :VKLS 3dxkC 171 :AYIK T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 3dxkC 203 :GWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASET T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3dxkC 245 :LPLLAVTFITESSLVAAGHDCF T0558 262 :PQLVEIDSEG 3dxkC 267 :PVLFTYDSAA Number of specific fragments extracted= 15 number of extra gaps= 0 total=1168 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei3B/T0558-3ei3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ei3B expands to /projects/compbio/data/pdb/3ei3.pdb.gz 3ei3B:# T0558 read from 3ei3B/T0558-3ei3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei3B read from 3ei3B/T0558-3ei3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ei3B to template set # found chain 3ei3B in template set Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)D147 Warning: unaligning (T0558)F11 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)D147 Warning: unaligning (T0558)S30 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)K168 Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)K168 Warning: unaligning (T0558)I267 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)N453 Warning: unaligning (T0558)D268 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)N453 T0558 2 :KNFILLVA 3ei3B 138 :KLHRTASP T0558 12 :LVAPFAQGSSPQH 3ei3B 148 :RRVTSLEWHPTHP T0558 25 :LLVGG 3ei3B 162 :TVAVG T0558 32 :WNKIAIINKDTKEIVWEYPL 3ei3B 169 :GGDIILWDYDVQNKTSFIQG T0558 52 :EKGWECNSVAATK 3ei3B 190 :GPGDAITGMKFNQ T0558 65 :AGEILFSYSKG 3ei3B 204 :NTNQLFVSSIR T0558 76 :AKMITRDGRE 3ei3B 217 :TTLRDFSGSV T0558 86 :LWNIAAPAGC 3ei3B 230 :FAKTDSWDYW T0558 97 :MQTARILPDGNALVAWCG 3ei3B 240 :YCCVDVSVSRQMLATGDS T0558 116 :PSTILEVNMKGEVLSK 3ei3B 258 :TGRLLLLGLDGHEIFK T0558 134 :FETGIERPHA 3ei3B 274 :EKLHKAKVTH T0558 148 :INKNK 3ei3B 284 :AEFNP T0558 153 :KGNYLVPLFATSEVREIAPN 3ei3B 290 :CDWLMATSSVDATVKLWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLD 3ei3B 315 :NSYIAEMPHEKPVNAAYFNP T0558 193 :NGDCLVACGDAH 3ei3B 336 :DSTKLLTTDQRN T0558 205 :CFVQLNLESNRIVRRVNANDIE 3ei3B 405 :TIDIYDANSGGLVHQLRDPNAA T0558 231 :FFVAQLFPLQNGGLYICNWQG 3ei3B 427 :GIISLNKFSPTGDVLASGMGF T0558 263 :QLVE 3ei3B 448 :NILI T0558 269 :S 3ei3B 454 :R Number of specific fragments extracted= 19 number of extra gaps= 3 total=1187 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei3B/T0558-3ei3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3ei3B/T0558-3ei3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei3B read from 3ei3B/T0558-3ei3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ei3B in template set Warning: unaligning (T0558)L10 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)D147 Warning: unaligning (T0558)F11 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)D147 Warning: unaligning (T0558)S30 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)K168 Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)K168 T0558 1 :MKNFILLVA 3ei3B 137 :YKLHRTASP T0558 12 :L 3ei3B 148 :R T0558 14 :APFAQGSSPQ 3ei3B 149 :RVTSLEWHPT T0558 24 :HLLVGG 3ei3B 161 :TTVAVG T0558 32 :WNKIAIINKDTKEIVWEYP 3ei3B 169 :GGDIILWDYDVQNKTSFIQ T0558 51 :LEKGWECNSVAATK 3ei3B 189 :MGPGDAITGMKFNQ T0558 65 :AGEILFSYSKG 3ei3B 204 :NTNQLFVSSIR T0558 76 :AKMITRDGRELWNIA 3ei3B 217 :TTLRDFSGSVIQVFA T0558 91 :APAGCEMQTARILPDGNALVAWC 3ei3B 234 :DSWDYWYCCVDVSVSRQMLATGD T0558 115 :HPSTILEVNMKGEVLS 3ei3B 257 :STGRLLLLGLDGHEIF T0558 133 :EFETGIER 3ei3B 273 :KEKLHKAK T0558 145 :FRQINKNKKG 3ei3B 281 :VTHAEFNPRC T0558 155 :NYLVPLFATSEVREIAPN 3ei3B 292 :WLMATSSVDATVKLWDLR T0558 173 :GQLLNSVKLSGTPFSSAFLD 3ei3B 315 :NSYIAEMPHEKPVNAAYFNP T0558 193 :NGDCLVACGDAHCFVQLNLES 3ei3B 336 :DSTKLLTTDQRNEIRVYSSYD T0558 214 :NRIVRRVNAND 3ei3B 361 :DQIIIHPHRQF T0558 226 :EGV 3ei3B 372 :QHL T0558 232 :FVAQLFPLQNGGLYICNW 3ei3B 375 :TPIKATWHPMYDLIVAGR T0558 250 :QGHDREAGKG 3ei3B 402 :DKRTIDIYDA T0558 260 :KHPQLVEI 3ei3B 413 :SGGLVHQL T0558 268 :DSEGKVVWQL 3ei3B 423 :PNAAGIISLN T0558 278 :NDKVKFGMISTIC 3ei3B 436 :PTGDVLASGMGFN Number of specific fragments extracted= 22 number of extra gaps= 2 total=1209 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ei3B/T0558-3ei3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3ei3B/T0558-3ei3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ei3B read from 3ei3B/T0558-3ei3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ei3B in template set Warning: unaligning (T0558)S30 because of BadResidue code BAD_PEPTIDE in next template residue (3ei3B)K168 Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE at template residue (3ei3B)K168 T0558 19 :GSSPQHLLVGG 3ei3B 156 :HPTHPTTVAVG T0558 32 :WNKIAIINKDTKEIVWEYPL 3ei3B 169 :GGDIILWDYDVQNKTSFIQG T0558 52 :EKGWECNSVAATKA 3ei3B 190 :GPGDAITGMKFNQF T0558 66 :GEILFSY 3ei3B 206 :NQLFVSS T0558 73 :SKGAKMITRDG 3ei3B 214 :RGATTLRDFSG T0558 84 :RELWNIAAPAGC 3ei3B 228 :QVFAKTDSWDYW T0558 97 :MQTARILPDGNALVAWCG 3ei3B 240 :YCCVDVSVSRQMLATGDS T0558 116 :PSTILEVNMKGEVLSKTEFETG 3ei3B 258 :TGRLLLLGLDGHEIFKEKLHKA T0558 144 :QFRQINKNK 3ei3B 280 :KVTHAEFNP T0558 153 :KGNYLVPLFATSEVREIA 3ei3B 290 :CDWLMATSSVDATVKLWD T0558 171 :PNGQ 3ei3B 309 :RNIK T0558 175 :LLNSVKLSGTPFSSAFLD 3ei3B 317 :YIAEMPHEKPVNAAYFNP T0558 193 :NGDCLVACGDAHCFVQLNLESNR 3ei3B 336 :DSTKLLTTDQRNEIRVYSSYDWS T0558 216 :IVRRVNANDIEGV 3ei3B 362 :QIIIHPHRQFQHL T0558 232 :FVAQLFPLQNGGLYICNWQGHDREAGKGKHPQLVEIDSEGKVVWQLNDKVKFGMISTICPIRE 3ei3B 375 :TPIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFSPT Number of specific fragments extracted= 15 number of extra gaps= 1 total=1224 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dwlC/T0558-3dwlC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dwlC expands to /projects/compbio/data/pdb/3dwl.pdb.gz 3dwlC:# T0558 read from 3dwlC/T0558-3dwlC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dwlC read from 3dwlC/T0558-3dwlC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dwlC to template set # found chain 3dwlC in template set Warning: unaligning (T0558)K2 because first residue in template chain is (3dwlC)A2 Warning: unaligning (T0558)I79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)T89 Warning: unaligning (T0558)M124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)W135 Warning: unaligning (T0558)E127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)W135 Warning: unaligning (T0558)Q208 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)A232 Warning: unaligning (T0558)L209 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)A232 Warning: unaligning (T0558)G271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)A285 T0558 3 :NFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 3dwlC 3 :TSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTF T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3dwlC 53 :DHDKIVTCVDWAPKSNRIVTCSQD T0558 76 :AKM 3dwlC 79 :AYV T0558 83 :GRELWNIAAPAGC 3dwlC 90 :WKQTLVLLRLNRA T0558 97 :MQTARILPDGNALVAWCG 3dwlC 103 :ATFVRWSPNEDKFAVGSG T0558 116 :PSTILEVN 3dwlC 121 :ARVISVCY T0558 128 :VLSKTEFETGIERPHA 3dwlC 136 :WVSKHLKRPLRSTILS T0558 148 :INKNKKGNYLVPLFATSEVREIAP 3dwlC 152 :LDWHPNNVLLAAGCADRKAYVLSA T0558 172 :N 3dwlC 194 :P T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFV 3dwlC 196 :NTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVT T0558 210 :NLESN 3dwlC 233 :YPSAP T0558 215 :RIVRRVNAND 3dwlC 242 :RALITVKLSQ T0558 231 :FFVAQLFPLQNG 3dwlC 252 :LPLRSLLWANES T0558 244 :LYICNWQGH 3dwlC 264 :AIVAAGYNY T0558 263 :QLVEIDSE 3dwlC 273 :SPILLQGN T0558 274 :VWQLNDKVKFGM 3dwlC 351 :RPYAGTPGNITA T0558 287 :STI 3dwlC 369 :DGR Number of specific fragments extracted= 17 number of extra gaps= 1 total=1241 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dwlC/T0558-3dwlC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dwlC/T0558-3dwlC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dwlC read from 3dwlC/T0558-3dwlC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dwlC in template set Warning: unaligning (T0558)K2 because first residue in template chain is (3dwlC)A2 Warning: unaligning (T0558)I79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)T89 Warning: unaligning (T0558)E85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)T89 Warning: unaligning (T0558)M124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)W135 Warning: unaligning (T0558)G126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)W135 Warning: unaligning (T0558)Q208 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)A232 Warning: unaligning (T0558)L209 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)A232 Warning: unaligning (T0558)P262 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)S337 T0558 3 :NFILLVALFL 3dwlC 3 :TSQVLHILPK T0558 14 :APFAQGSSPQ 3dwlC 13 :PSYEHAFNSQ T0558 24 :HLLVGGSGWNKIAIINKDTKEIVW 3dwlC 24 :TEFVTTTATNQVELYEQDGNGWKH T0558 48 :EYP 3dwlC 50 :TFS T0558 52 :EKGWECNSVAATKAGEILFSYSKG 3dwlC 53 :DHDKIVTCVDWAPKSNRIVTCSQD T0558 76 :AKM 3dwlC 79 :AYV T0558 86 :LWNIAAPAGCEMQTARILPDGNALVAWC 3dwlC 92 :QTLVLLRLNRAATFVRWSPNEDKFAVGS T0558 115 :HPSTILEVN 3dwlC 120 :GARVISVCY T0558 127 :EVLS 3dwlC 136 :WVSK T0558 133 :EFETGIERP 3dwlC 140 :HLKRPLRST T0558 145 :FRQINKNKKGNYLVPLFATSEVREIA 3dwlC 149 :ILSLDWHPNNVLLAAGCADRKAYVLS T0558 171 :PNGQLLNSV 3dwlC 191 :SRLPFNTVC T0558 180 :KLS 3dwlC 201 :EYP T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFV 3dwlC 206 :GWVHAVGFSPSGNALAYAGHDSSVT T0558 210 :NLESN 3dwlC 233 :YPSAP T0558 215 :RIVRRVNANDIE 3dwlC 242 :RALITVKLSQLP T0558 233 :VAQLFPLQNGGLYICNW 3dwlC 254 :LRSLLWANESAIVAAGY T0558 251 :GHDREAGKGK 3dwlC 271 :NYSPILLQGN T0558 261 :H 3dwlC 310 :E T0558 271 :GKVVWQL 3dwlC 344 :QNMIATL T0558 278 :NDKV 3dwlC 356 :TPGN T0558 282 :KFGMISTICPI 3dwlC 362 :AFTSSGTDGRV Number of specific fragments extracted= 22 number of extra gaps= 1 total=1263 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dwlC/T0558-3dwlC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dwlC/T0558-3dwlC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dwlC read from 3dwlC/T0558-3dwlC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dwlC in template set Warning: unaligning (T0558)I79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)T89 Warning: unaligning (T0558)N88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)T89 Warning: unaligning (T0558)M124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)W135 Warning: unaligning (T0558)K131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)W135 Warning: unaligning (T0558)Q208 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dwlC)A232 Warning: unaligning (T0558)L209 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dwlC)A232 T0558 20 :SSPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 3dwlC 20 :NSQRTEFVTTTATNQVELYEQDGNGWKHARTF T0558 52 :EKGWECNSVAATKAGEILFSY 3dwlC 53 :DHDKIVTCVDWAPKSNRIVTC T0558 73 :SKGAKM 3dwlC 76 :DRNAYV T0558 89 :IAA 3dwlC 90 :WKQ T0558 92 :P 3dwlC 99 :L T0558 94 :GCEMQTARILPDGNALVAWCG 3dwlC 100 :NRAATFVRWSPNEDKFAVGSG T0558 116 :PSTILEVN 3dwlC 121 :ARVISVCY T0558 132 :TEFETGIERPHAQFRQINKNKKGNYLVPLFATSEVR 3dwlC 136 :WVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAY T0558 176 :LNSVKLS 3dwlC 172 :VLSAYVR T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFV 3dwlC 206 :GWVHAVGFSPSGNALAYAGHDSSVT T0558 210 :NLESNR 3dwlC 233 :YPSAPE T0558 225 :IEGVQLF 3dwlC 239 :QPPRALI T0558 232 :FVAQLFPLQNGGLYICNWQGH 3dwlC 253 :PLRSLLWANESAIVAAGYNYS T0558 264 :LVEID 3dwlC 274 :PILLQ Number of specific fragments extracted= 14 number of extra gaps= 1 total=1277 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3acpA/T0558-3acpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3acpA expands to /projects/compbio/data/pdb/3acp.pdb.gz 3acpA:# T0558 read from 3acpA/T0558-3acpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3acpA read from 3acpA/T0558-3acpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3acpA to template set # found chain 3acpA in template set Warning: unaligning (T0558)K258 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)S365 Warning: unaligning (T0558)G259 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)S365 Warning: unaligning (T0558)K260 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)E366 T0558 4 :FILLVALF 3acpA 78 :FLFNTIIR T0558 14 :APFAQGSS 3acpA 96 :YTAVDTAK T0558 22 :PQHLLVGGSGWNKIAIINKD 3acpA 105 :QMRRFILGTTEGDIKVLDSN T0558 43 :KEIVWEYPLEKGWECNSVAATKAGEILFSYSKG 3acpA 125 :FNLQREIDQAHVSEITKLKFFPSGEALISSSQD T0558 76 :AKMITRD 3acpA 160 :LKIWSVK T0558 83 :GRELWNIAAPAGC 3acpA 168 :GSNPRTLIGHRAT T0558 97 :MQTARILPDGNALVAWCG 3acpA 181 :VTDIAIIDRGRNVLSASL T0558 116 :PSTILEVNMK 3acpA 199 :DGTIRLWECG T0558 126 :GEVLSKTEFE 3acpA 210 :GTTIHTFNRK T0558 139 :ERPHAQFRQINKNK 3acpA 220 :ENPHDGVNSIALFV T0558 153 :K 3acpA 235 :T T0558 154 :GNYLVPLFATSEVREIAPN 3acpA 256 :GKYVIAGHVSGVITVHNVF T0558 173 :GQLLNSV 3acpA 276 :KEQTIQL T0558 180 :KLSGTPFSSAFLDNG 3acpA 285 :KFTCSCNSLTVDGNN T0558 195 :DCLVACGDAHCFVQLNLESN 3acpA 301 :NYIYAGYENGMLAQWDLRSP T0558 215 :RIVRRVNANDI 3acpA 322 :CPVGEFLINEG T0558 231 :FFVAQLFPLQNG 3acpA 333 :TPINNVYFAAGA T0558 244 :LYICNWQGH 3acpA 345 :LFVSSGFDT T0558 253 :DREAG 3acpA 359 :IISDP T0558 261 :HPQL 3acpA 367 :RPAI T0558 265 :VEIDSEGKVVWQLN 3acpA 376 :TFLVSNDDEVSQFC T0558 279 :DKVKFGMI 3acpA 394 :DESNGEVL T0558 287 :STICP 3acpA 406 :NNFCA Number of specific fragments extracted= 23 number of extra gaps= 1 total=1300 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3acpA/T0558-3acpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3acpA/T0558-3acpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3acpA read from 3acpA/T0558-3acpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3acpA in template set Warning: unaligning (T0558)N155 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)Q238 Warning: unaligning (T0558)H261 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)S365 Warning: unaligning (T0558)P262 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)S365 Warning: unaligning (T0558)Q263 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)E366 T0558 4 :FILLVALFLVAPFAQGSSP 3acpA 85 :RDGSKMLKRADYTAVDTAK T0558 23 :Q 3acpA 105 :Q T0558 24 :HLLVGGSGWNKIAIINKD 3acpA 107 :RRFILGTTEGDIKVLDSN T0558 43 :KEIVWEYPLEKGWECNSVAATKAGEILFSYSKG 3acpA 125 :FNLQREIDQAHVSEITKLKFFPSGEALISSSQD T0558 76 :AKMIT 3acpA 160 :LKIWS T0558 81 :RDGRELWNIA 3acpA 166 :KDGSNPRTLI T0558 92 :PAGCEMQTARILPDGNALVAWC 3acpA 176 :GHRATVTDIAIIDRGRNVLSAS T0558 115 :HPSTILEVNMK 3acpA 198 :LDGTIRLWECG T0558 126 :GEVLS 3acpA 210 :GTTIH T0558 133 :EFETGIER 3acpA 215 :TFNRKENP T0558 142 :HAQFRQINKN 3acpA 223 :HDGVNSIALF T0558 152 :KKG 3acpA 234 :GTD T0558 156 :YLVPLFATSEVREIAPN 3acpA 258 :YVIAGHVSGVITVHNVF T0558 173 :GQLLNSV 3acpA 276 :KEQTIQL T0558 180 :KLSGTPFSSAFL 3acpA 285 :KFTCSCNSLTVD T0558 192 :DNGDCLVACGDAHCFVQLNLESNR 3acpA 298 :NNANYIYAGYENGMLAQWDLRSPE T0558 217 :VRRVNANDI 3acpA 325 :GEFLINEGT T0558 232 :FVAQLFPLQ 3acpA 334 :PINNVYFAA T0558 242 :GGLYICNWQGHDREAGKG 3acpA 343 :GALFVSSGFDTSIKLDII T0558 260 :K 3acpA 363 :P T0558 264 :LVEIDSEG 3acpA 367 :RPAIEFET T0558 272 :KVVWQL 3acpA 384 :EVSQFC T0558 278 :NDKVKFGMI 3acpA 396 :SNGEVLEVG T0558 288 :TICPI 3acpA 405 :KNNFC Number of specific fragments extracted= 24 number of extra gaps= 2 total=1324 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3acpA/T0558-3acpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3acpA/T0558-3acpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3acpA read from 3acpA/T0558-3acpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3acpA in template set Warning: unaligning (T0558)H142 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)S245 Warning: unaligning (T0558)A143 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)S245 Warning: unaligning (T0558)Q144 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)K247 Warning: unaligning (T0558)F145 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)K247 Warning: unaligning (T0558)H261 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3acpA)S365 Warning: unaligning (T0558)P262 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)S365 Warning: unaligning (T0558)Q263 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3acpA)E366 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSY 3acpA 103 :KLQMRRFILGTTEGDIKVLDSNFNLQREIDQAHVSEITKLKFFPSGEALISS T0558 73 :SKGAKMITRDG 3acpA 157 :DMQLKIWSVKD T0558 84 :RELWNIAAPAG 3acpA 169 :SNPRTLIGHRA T0558 96 :EMQTARILPDGNALVAWCG 3acpA 180 :TVTDIAIIDRGRNVLSASL T0558 116 :PSTILEVNMK 3acpA 199 :DGTIRLWECG T0558 126 :GEVLSKTEFET 3acpA 210 :GTTIHTFNRKE T0558 141 :P 3acpA 243 :S T0558 146 :RQINKNKKGNYLVPLFATSEVREIA 3acpA 248 :NNLEFGTYGKYVIAGHVSGVITVHN T0558 171 :PNGQLLNSVKLS 3acpA 274 :FSKEQTIQLPSK T0558 183 :GTPFSSAFLDNG 3acpA 288 :CSCNSLTVDGNN T0558 195 :DCLVACGDAHCFVQLNLESNR 3acpA 301 :NYIYAGYENGMLAQWDLRSPE T0558 227 :GVQLF 3acpA 324 :VGEFL T0558 232 :FVAQLFPLQNGGLYICNWQGHD 3acpA 333 :TPINNVYFAAGALFVSSGFDTS T0558 254 :REAGKGK 3acpA 357 :LDIISDP T0558 264 :LVEIDSE 3acpA 367 :RPAIEFE Number of specific fragments extracted= 15 number of extra gaps= 2 total=1339 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2j04B/T0558-2j04B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2j04B expands to /projects/compbio/data/pdb/2j04.pdb.gz 2j04B:# T0558 read from 2j04B/T0558-2j04B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j04B read from 2j04B/T0558-2j04B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2j04B to template set # found chain 2j04B in template set Warning: unaligning (T0558)P15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)D368 Warning: unaligning (T0558)F16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)D368 Warning: unaligning (T0558)H24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)A377 Warning: unaligning (T0558)L25 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)L384 Warning: unaligning (T0558)L26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)L384 Warning: unaligning (T0558)A108 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)V481 Warning: unaligning (T0558)L109 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)V481 Warning: unaligning (T0558)A111 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)T484 Warning: unaligning (T0558)W112 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)T484 Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)G511 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)G511 Warning: unaligning (T0558)N151 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)P521 Warning: unaligning (T0558)K152 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)P521 Warning: unaligning (T0558)E212 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)A583 Warning: unaligning (T0558)S213 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)A583 Warning: unaligning (T0558)N214 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)R585 Warning: unaligning (T0558)R215 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)R585 Warning: unaligning (T0558)A222 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)S608 Warning: unaligning (T0558)N223 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)S608 Warning: unaligning (T0558)D224 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)I609 Warning: unaligning (T0558)Q229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)H638 Warning: unaligning (T0558)P238 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)N648 Warning: unaligning (T0558)L239 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)N648 Warning: unaligning (T0558)G271 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)E674 Warning: unaligning (T0558)K272 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)E674 Warning: unaligning (T0558)V273 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)H675 T0558 2 :KNFILLVALFLVA 2j04B 354 :VKVQTIVHSFGEV T0558 17 :AQGSSPQ 2j04B 369 :LKWHEGC T0558 27 :VGGSGWNKIAIINKD 2j04B 385 :SFVSQEGTINFLEII T0558 51 :L 2j04B 400 :D T0558 52 :EKGWECNSVAATKAGEILFSYSKG 2j04B 420 :LADSLITTFDFLSPTTVVCGFKNG T0558 76 :AKMITRD 2j04B 445 :VAEFDLT T0558 83 :GRELWNI 2j04B 453 :PEVPSFY T0558 90 :AAPAGC 2j04B 461 :QVHDSY T0558 97 :MQTARI 2j04B 467 :ILSVST T0558 103 :LPDGN 2j04B 475 :SDFED T0558 110 :V 2j04B 482 :V T0558 113 :CGHPSTILEVNMK 2j04B 485 :VAVDGYFYIFNPK T0558 126 :GEVLSKTEF 2j04B 501 :TTKTTVSRF T0558 139 :ERPHA 2j04B 512 :SNLVP T0558 148 :INK 2j04B 517 :VVY T0558 153 :KGNYLVPLFA 2j04B 523 :IYSYIYSDGA T0558 164 :SEVREIAPN 2j04B 533 :SSLRAVPSR T0558 173 :GQLLNSV 2j04B 543 :AFAVHPL T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 2j04B 551 :SRETTITAIGVSRLHPMVLAGSADGSLIITN T0558 216 :IVRRVN 2j04B 601 :RLWKWD T0558 225 :IEG 2j04B 610 :KDD T0558 230 :LFFVAQLF 2j04B 639 :GINITCTK T0558 240 :Q 2j04B 649 :E T0558 241 :NGGLYICNWQGH 2j04B 653 :GGKCYAFSNSAG T0558 263 :QLVEIDSE 2j04B 665 :LLTLEYLS Number of specific fragments extracted= 25 number of extra gaps= 11 total=1364 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2j04B/T0558-2j04B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2j04B/T0558-2j04B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j04B read from 2j04B/T0558-2j04B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j04B in template set Warning: unaligning (T0558)S21 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)G307 Warning: unaligning (T0558)W32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)S338 Warning: unaligning (T0558)N58 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)D368 Warning: unaligning (T0558)S59 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)D368 Warning: unaligning (T0558)E67 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)A377 Warning: unaligning (T0558)I68 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)L384 Warning: unaligning (T0558)L69 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)L384 Warning: unaligning (T0558)R81 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)T403 Warning: unaligning (T0558)D82 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)T403 Warning: unaligning (T0558)N155 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)V481 Warning: unaligning (T0558)Y156 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)V481 Warning: unaligning (T0558)V158 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)T484 Warning: unaligning (T0558)P159 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)T484 Warning: unaligning (T0558)K180 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)G511 Warning: unaligning (T0558)L191 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)P521 Warning: unaligning (T0558)D192 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)P521 Warning: unaligning (T0558)G259 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)A583 Warning: unaligning (T0558)K260 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)R585 Warning: unaligning (T0558)H261 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)R585 Warning: unaligning (T0558)P262 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)L600 Warning: unaligning (T0558)S269 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)S608 Warning: unaligning (T0558)E270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)H638 T0558 22 :PQ 2j04B 308 :KD T0558 24 :HLLVGGSG 2j04B 311 :QYLAVAVS T0558 33 :NKIAIINKDTK 2j04B 339 :SCIQIFKMNTS T0558 44 :EIVWEYP 2j04B 354 :VKVQTIV T0558 52 :EKGWEC 2j04B 361 :HSFGEV T0558 60 :VAATKAG 2j04B 369 :LKWHEGC T0558 70 :FSYSKG 2j04B 385 :SFVSQE T0558 76 :AKMIT 2j04B 393 :INFLE T0558 83 :G 2j04B 404 :D T0558 84 :RELWNIA 2j04B 413 :KPSLTLS T0558 92 :PAGCEMQTARILP 2j04B 420 :LADSLITTFDFLS T0558 106 :GNALVAWC 2j04B 433 :PTTVVCGF T0558 115 :HPSTILEVNMK 2j04B 441 :KNGFVAEFDLT T0558 126 :GEVLSK 2j04B 453 :PEVPSF T0558 133 :EFETGIER 2j04B 459 :YDQVHDSY T0558 145 :FRQINKN 2j04B 467 :ILSVSTA T0558 152 :KKG 2j04B 477 :FED T0558 157 :L 2j04B 482 :V T0558 160 :LFATSEVREIAPN 2j04B 485 :VAVDGYFYIFNPK T0558 173 :GQLLNSV 2j04B 503 :KTTVSRF T0558 181 :LS 2j04B 512 :SN T0558 185 :PFSSAF 2j04B 514 :LVPVVY T0558 193 :NGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 2j04B 522 :QIYSYIYSDGASSLRAVPSRAAFAVHPLVSRETT T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGK 2j04B 556 :ITAIGVSRLHPMVLAGSADGSLIITN T0558 263 :QLVEID 2j04B 601 :RLWKWD T0558 271 :GKVVWQL 2j04B 639 :GINITCT T0558 278 :NDKVKFGMISTICPI 2j04B 652 :AGGKCYAFSNSAGLL Number of specific fragments extracted= 27 number of extra gaps= 13 total=1391 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2j04B/T0558-2j04B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2j04B/T0558-2j04B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j04B read from 2j04B/T0558-2j04B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j04B in template set Warning: unaligning (T0558)G19 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)A377 Warning: unaligning (T0558)S20 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)A377 Warning: unaligning (T0558)P22 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)L380 Warning: unaligning (T0558)Q23 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)L380 Warning: unaligning (T0558)H24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)V381 Warning: unaligning (T0558)L26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)L384 Warning: unaligning (T0558)V27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)L384 Warning: unaligning (T0558)D41 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)T403 Warning: unaligning (T0558)T42 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)T403 Warning: unaligning (T0558)A108 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)V481 Warning: unaligning (T0558)L109 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)V481 Warning: unaligning (T0558)A111 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)T484 Warning: unaligning (T0558)W112 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)T484 Warning: unaligning (T0558)E133 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)G511 Warning: unaligning (T0558)F134 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)G511 Warning: unaligning (T0558)N151 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)P521 Warning: unaligning (T0558)K152 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)P521 Warning: unaligning (T0558)E212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)H638 Warning: unaligning (T0558)E226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)H638 Warning: unaligning (T0558)Q235 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2j04B)N648 Warning: unaligning (T0558)L236 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2j04B)N648 T0558 15 :PFAQ 2j04B 372 :HEGC T0558 21 :S 2j04B 378 :P T0558 25 :L 2j04B 382 :G T0558 28 :GGSGWNKIAIIN 2j04B 385 :SFVSQEGTINFL T0558 40 :K 2j04B 401 :N T0558 43 :KEIV 2j04B 404 :DVHV T0558 47 :WEYPLEKG 2j04B 416 :LTLSLADS T0558 56 :ECNSVAATKAGEILFSY 2j04B 424 :LITTFDFLSPTTVVCGF T0558 73 :SKGAKMITRDG 2j04B 442 :NGFVAEFDLTD T0558 87 :WNIAAPAG 2j04B 458 :FYDQVHDS T0558 96 :EMQTARI 2j04B 466 :YILSVST T0558 103 :LPDGN 2j04B 475 :SDFED T0558 110 :V 2j04B 482 :V T0558 113 :CGHPSTILEVNMKG 2j04B 485 :VAVDGYFYIFNPKD T0558 127 :EVLSKT 2j04B 504 :TTVSRF T0558 143 :AQFRQINK 2j04B 512 :SNLVPVVY T0558 153 :KGNYLVPLFATSEVREIAPN 2j04B 522 :QIYSYIYSDGASSLRAVPSR T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAH 2j04B 544 :FAVHPLVSRETTITAIGVSRLHPMVLAGSADG T0558 227 :GVQLFFVA 2j04B 639 :GINITCTK T0558 237 :FPLQNGGLYICNWQGH 2j04B 649 :ETSAGGKCYAFSNSAG T0558 263 :QLVEID 2j04B 665 :LLTLEY Number of specific fragments extracted= 21 number of extra gaps= 9 total=1412 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k8kC/T0558-1k8kC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k8kC expands to /projects/compbio/data/pdb/1k8k.pdb.gz 1k8kC:# T0558 read from 1k8kC/T0558-1k8kC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k8kC read from 1k8kC/T0558-1k8kC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k8kC to template set # found chain 1k8kC in template set Warning: unaligning (T0558)V13 because of BadResidue code BAD_PEPTIDE in next template residue (1k8kC)I11 Warning: unaligning (T0558)A14 because of BadResidue code BAD_PEPTIDE at template residue (1k8kC)I11 Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE in next template residue (1k8kC)N29 Warning: unaligning (T0558)W32 because of BadResidue code BAD_PEPTIDE at template residue (1k8kC)N29 T0558 6 :LLVALFL 1k8kC 3 :YHSFLVE T0558 15 :PFAQGSSPQHLLVGGS 1k8kC 12 :SCHAWNKDRTQIAICP T0558 33 :NKIAIINKDTK 1k8kC 30 :HEVHIYEKSGN T0558 44 :EIVWEYP 1k8kC 43 :VQVHELK T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1k8kC 50 :EHNGQVTGVDWAPDSNRIVTCGTD T0558 76 :AKMITRD 1k8kC 76 :AYVWTLK T0558 83 :GRE 1k8kC 84 :RTW T0558 86 :LWNIAAPAGC 1k8kC 89 :TLVILRINRA T0558 97 :MQTARILPDGNALVAWCG 1k8kC 99 :ARCVRWAPNEKKFAVGSG T0558 116 :PSTILEVNMK 1k8kC 117 :SRVISICYFE T0558 126 :GEVLSKTE 1k8kC 128 :ENDWWVCK T0558 134 :FETGIERPHA 1k8kC 138 :KKPIRSTVLS T0558 148 :INKNKKGNYLVPLFATSEVREIAP 1k8kC 148 :LDWHPNSVLLAAGSCDFKCRIFSA T0558 172 :N 1k8kC 190 :P T0558 173 :GQLLNSV 1k8kC 192 :GELMFES T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 1k8kC 200 :SSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASET T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1k8kC 245 :LPLLAVTFITESSLVAAGHDCF T0558 263 :QLVEIDSEG 1k8kC 268 :VLFTYDSAA T0558 272 :KV 1k8kC 278 :KL T0558 274 :VWQLNDK 1k8kC 329 :VSQISVL Number of specific fragments extracted= 20 number of extra gaps= 2 total=1432 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k8kC/T0558-1k8kC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1k8kC/T0558-1k8kC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k8kC read from 1k8kC/T0558-1k8kC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k8kC in template set Warning: unaligning (T0558)A14 because of BadResidue code BAD_PEPTIDE in next template residue (1k8kC)I11 Warning: unaligning (T0558)P15 because of BadResidue code BAD_PEPTIDE at template residue (1k8kC)I11 Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE in next template residue (1k8kC)N29 Warning: unaligning (T0558)W32 because of BadResidue code BAD_PEPTIDE at template residue (1k8kC)N29 T0558 6 :LL 1k8kC 5 :SF T0558 10 :LFL 1k8kC 7 :LVE T0558 16 :FAQGSSPQ 1k8kC 12 :SCHAWNKD T0558 24 :HLLVGGS 1k8kC 21 :TQIAICP T0558 33 :NKIAIINKDTKE 1k8kC 30 :HEVHIYEKSGNK T0558 45 :IVWEYP 1k8kC 44 :QVHELK T0558 52 :EKGWECNSVAATKAGEILFSYSKG 1k8kC 50 :EHNGQVTGVDWAPDSNRIVTCGTD T0558 76 :AKMIT 1k8kC 76 :AYVWT T0558 81 :RDGREL 1k8kC 82 :KGRTWK T0558 87 :WNIAAPAGCEMQTARILPDGNALVAWC 1k8kC 89 :TLVILRINRAARCVRWAPNEKKFAVGS T0558 115 :HPSTILEVNMK 1k8kC 116 :GSRVISICYFE T0558 126 :G 1k8kC 128 :E T0558 127 :EVLS 1k8kC 133 :VCKH T0558 133 :EFETGIER 1k8kC 137 :IKKPIRST T0558 145 :FRQINKNKKGNYLVPLFATSEVREIA 1k8kC 145 :VLSLDWHPNSVLLAAGSCDFKCRIFS T0558 171 :PNGQLLNSV 1k8kC 190 :PFGELMFES T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 1k8kC 200 :SSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASETLP T0558 233 :VAQLFPLQNGGLYICN 1k8kC 247 :LLAVTFITESSLVAAG T0558 250 :QGHDREAGKG 1k8kC 263 :HDCFPVLFTY T0558 260 :KHPQLVEID 1k8kC 274 :SAAGKLSFG T0558 269 :SEGKVVWQL 1k8kC 324 :LHKNSVSQI T0558 278 :NDKVKFGMISTICPI 1k8kC 340 :AKCSQFCTTGMDGGM Number of specific fragments extracted= 22 number of extra gaps= 2 total=1454 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k8kC/T0558-1k8kC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1k8kC/T0558-1k8kC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k8kC read from 1k8kC/T0558-1k8kC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k8kC in template set Warning: unaligning (T0558)G31 because of BadResidue code BAD_PEPTIDE in next template residue (1k8kC)N29 Warning: unaligning (T0558)W32 because of BadResidue code BAD_PEPTIDE at template residue (1k8kC)N29 T0558 21 :SPQHLLVGGS 1k8kC 18 :KDRTQIAICP T0558 33 :NKIAIINKDTKEIVWEYPL 1k8kC 30 :HEVHIYEKSGNKWVQVHEL T0558 52 :EKGWECNSVAATKAGEILFSY 1k8kC 50 :EHNGQVTGVDWAPDSNRIVTC T0558 73 :SKGAKMIT 1k8kC 73 :DRNAYVWT T0558 81 :RDGRELWN 1k8kC 82 :KGRTWKPT T0558 89 :IAAPAGCEMQTARILPDGNALVAWCG 1k8kC 91 :VILRINRAARCVRWAPNEKKFAVGSG T0558 116 :PS 1k8kC 117 :SR T0558 118 :TILEVNMKGEVLSKTEFETGIER 1k8kC 121 :SICYFEQENDWWVCKHIKKPIRS T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIA 1k8kC 144 :TVLSLDWHPNSVLLAAGSCDFKCRIFS T0558 171 :PNGQLLNSVKLS 1k8kC 190 :PFGELMFESSSS T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 1k8kC 203 :GWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATLASET T0558 231 :FFVAQLFPLQNGGLYICNWQGH 1k8kC 245 :LPLLAVTFITESSLVAAGHDCF T0558 262 :PQLVEIDSEG 1k8kC 267 :PVLFTYDSAA Number of specific fragments extracted= 13 number of extra gaps= 1 total=1467 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kb0A/T0558-1kb0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kb0A expands to /projects/compbio/data/pdb/1kb0.pdb.gz 1kb0A:Skipped atom 156, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 158, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 160, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 162, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 164, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 166, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 168, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 170, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 172, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 174, because occupancy 0.440 <= existing 0.560 in 1kb0A Skipped atom 5023, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5025, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5027, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5029, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5031, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5033, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5035, because occupancy 0.430 <= existing 0.520 in 1kb0A Skipped atom 5037, because occupancy 0.430 <= existing 0.520 in 1kb0A # T0558 read from 1kb0A/T0558-1kb0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kb0A read from 1kb0A/T0558-1kb0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kb0A to template set # found chain 1kb0A in template set Warning: unaligning (T0558)F11 because of BadResidue code BAD_PEPTIDE in next template residue (1kb0A)C117 Warning: unaligning (T0558)L12 because of BadResidue code BAD_PEPTIDE at template residue (1kb0A)C117 Warning: unaligning (T0558)V217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kb0A)E513 Warning: unaligning (T0558)R219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kb0A)E513 Warning: unaligning (T0558)F283 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kb0A)T579 T0558 7 :LVAL 1kb0A 112 :GFKG T0558 13 :VAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 1kb0A 118 :DVVNRGVALWKGKVYVGAWDGRLIALDAATGKEVWHQNT T0558 52 :EKGWECNSVAATK 1kb0A 158 :EGQKGSLTITGAP T0558 65 :AGEILFSYSKG 1kb0A 174 :KGKVIIGNGGA T0558 76 :AKMITRD 1kb0A 192 :ITAYDAE T0558 83 :GRELWNIA 1kb0A 200 :GERKWRWF T0558 91 :APAGC 1kb0A 310 :TSTQP T0558 97 :MQTARILPDG 1kb0A 315 :MILADIKIAG T0558 107 :NALVAWCG 1kb0A 328 :KVILHAPK T0558 116 :PSTILEVNMK 1kb0A 336 :NGFFFVLDRT T0558 126 :GEVLSKTE 1kb0A 347 :GKFISAKN T0558 134 :FETG 1kb0A 364 :YDKH T0558 138 :IERPHA 1kb0A 392 :AHNWHP T0558 148 :INKNKKGNYLVPLFA 1kb0A 398 :MSFNPQTGLVYLPAQ T0558 164 :S 1kb0A 413 :N T0558 165 :EVREIAPN 1kb0A 458 :RLLAWDPV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRI 1kb0A 467 :QKAAWSVEHVSPWNGGTLTTAGNVVFQGTADGRLVAYHAATGEK T0558 220 :VNAND 1kb0A 514 :APTGT T0558 231 :FFVAQLFP 1kb0A 519 :GVVAAPST T0558 239 :LQNGGLYICNWQGH 1kb0A 528 :MVDGRQYVSVAVGW T0558 253 :DREAGKGKHPQLVEIDSEGKV 1kb0A 549 :ARATERQGPGTVYTFVVGGKA T0558 284 :GMISTI 1kb0A 580 :GQLLQG Number of specific fragments extracted= 22 number of extra gaps= 1 total=1489 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kb0A/T0558-1kb0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1kb0A/T0558-1kb0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kb0A read from 1kb0A/T0558-1kb0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kb0A in template set Warning: unaligning (T0558)F11 because of BadResidue code BAD_PEPTIDE in next template residue (1kb0A)C117 Warning: unaligning (T0558)L12 because of BadResidue code BAD_PEPTIDE at template residue (1kb0A)C117 Warning: unaligning (T0558)G114 because of BadResidue code BAD_PEPTIDE in next template residue (1kb0A)Y281 Warning: unaligning (T0558)H115 because of BadResidue code BAD_PEPTIDE at template residue (1kb0A)Y281 Warning: unaligning (T0558)L264 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kb0A)E513 Warning: unaligning (T0558)E266 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kb0A)E513 T0558 3 :NFILLVAL 1kb0A 108 :DRSTGFKG T0558 14 :APFAQGSSPQ 1kb0A 118 :DVVNRGVALW T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 1kb0A 129 :GKVYVGAWDGRLIALDAATGKEVWHQN T0558 51 :LEKGWECN 1kb0A 158 :EGQKGSLT T0558 59 :SVAAT 1kb0A 169 :APRVF T0558 65 :AGEILFSYSKG 1kb0A 174 :KGKVIIGNGGA T0558 76 :AKMIT 1kb0A 192 :ITAYD T0558 81 :RDGRELWNIA 1kb0A 198 :ETGERKWRWF T0558 95 :CEMQTARILPDGNALVAWC 1kb0A 243 :TMWDSMTFDAELNTMYVGT T0558 116 :PSTILEVNMK 1kb0A 282 :LASIVALDPD T0558 126 :GEVLSKTEFETGIERPHAQFRQINKNK 1kb0A 293 :GKYKWHYQETPGDNWDYTSTQPMILAD T0558 153 :KGN 1kb0A 323 :AGK T0558 156 :YLVPLFATSEVREIAPN 1kb0A 329 :VILHAPKNGFFFVLDRT T0558 173 :GQLLNSV 1kb0A 347 :GKFISAK T0558 180 :KLSGT 1kb0A 355 :FVPVN T0558 185 :PFSSAFLDNGDCLVACGDAH 1kb0A 395 :WHPMSFNPQTGLVYLPAQNV T0558 205 :CFVQLNLESNRIVRRVNANDI 1kb0A 458 :RLLAWDPVAQKAAWSVEHVSP T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1kb0A 479 :WNGGTLTTAGNVVFQGTADGRLVAYHA T0558 260 :KHPQ 1kb0A 507 :TGEK T0558 267 :IDSEGKVV 1kb0A 514 :APTGTGVV T0558 275 :WQL 1kb0A 525 :STY T0558 278 :NDKVKFGMIST 1kb0A 529 :VDGRQYVSVAV Number of specific fragments extracted= 22 number of extra gaps= 2 total=1511 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kb0A/T0558-1kb0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1kb0A/T0558-1kb0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kb0A read from 1kb0A/T0558-1kb0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kb0A in template set Warning: unaligning (T0558)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kb0A)E513 Warning: unaligning (T0558)Q276 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kb0A)E513 T0558 23 :QHLLVGGSGWNKIAIINKDTKEIVWEYPLEKGWE 1kb0A 77 :DGIMYVSASWSVVHAIDTRTGNRIWTYDPQIDRS T0558 57 :CN 1kb0A 113 :FK T0558 59 :SVAATKAGEILFSY 1kb0A 122 :RGVALWKGKVYVGA T0558 73 :SKGAKMIT 1kb0A 137 :DGRLIALD T0558 81 :RDGRELWNIAAPAG 1kb0A 146 :ATGKEVWHQNTFEG T0558 95 :CEMQ 1kb0A 164 :LTIT T0558 105 :DGNALVAWCGH 1kb0A 174 :KGKVIIGNGGA T0558 116 :PSTILEVNMK 1kb0A 189 :RGYITAYDAE T0558 126 :GEVLSKTEFET 1kb0A 200 :GERKWRWFSVP T0558 153 :KG 1kb0A 323 :AG T0558 155 :NYLVPLFATSEVREIAPN 1kb0A 328 :KVILHAPKNGFFFVLDRT T0558 173 :GQLLNSVKLS 1kb0A 347 :GKFISAKNFV T0558 183 :GTPFSSAFLDNGDCLVACGDAH 1kb0A 393 :HNWHPMSFNPQTGLVYLPAQNV T0558 205 :CFVQLNLESNRIVRRVNAND 1kb0A 458 :RLLAWDPVAQKAAWSVEHVS T0558 231 :FFVAQLFPLQNGGLYICNWQG 1kb0A 478 :PWNGGTLTTAGNVVFQGTADG T0558 263 :QLVEID 1kb0A 499 :RLVAYH T0558 269 :SEGKV 1kb0A 506 :ATGEK T0558 277 :LN 1kb0A 514 :AP Number of specific fragments extracted= 18 number of extra gaps= 0 total=1529 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l0qA/T0558-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l0qA expands to /projects/compbio/data/pdb/1l0q.pdb.gz 1l0qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OZ1 for alphabet: pdb_atoms Bad short name: NZ2 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 1l0qA/T0558-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0558-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l0qA to template set # found chain 1l0qA in template set Warning: unaligning (T0558)Q250 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l0qA)N266 Warning: unaligning (T0558)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l0qA)N266 T0558 3 :NFILLVALFLVAPFAQGSSPQH 1l0qA 23 :KVTATIPVGSNPMGAVISPDGT T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPLEKG 1l0qA 46 :VYVANAHSNDVSIIDTATNNVIATVPAGSS T0558 57 :CNSVAATKAGEILFSYSKG 1l0qA 76 :PQGVAVSPDGKQVYVTNMA T0558 76 :AKMITRD 1l0qA 98 :LSVIDTT T0558 83 :GRELWNIAAPAG 1l0qA 106 :NTVAGTVKTGKS T0558 97 :MQTARILPDGNALVAWCGHPSTILEVNMK 1l0qA 118 :PLGLALSPDGKKLYVTNNGDKTVSVINTV T0558 126 :GEVLSKTEFE 1l0qA 148 :KAVINTVSVG T0558 139 :ERPHA 1l0qA 158 :RSPKG T0558 148 :INKNKKG 1l0qA 163 :IAVTPDG T0558 155 :NYLVPLFATSEVREIAPN 1l0qA 171 :KVYVANFDSMSISVIDTV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 1l0qA 190 :NSVIDTVKVEAAPSGIAVNPEGTKAYVTNV T0558 203 :AH 1l0qA 221 :KY T0558 205 :CFVQLNLESNRIVRRVNAND 1l0qA 225 :TVSMIDTGTNKITARIPVGP T0558 232 :FVAQLFPLQNG 1l0qA 245 :DPAGIAVTPDG T0558 243 :GLYICNW 1l0qA 257 :KVYVALS T0558 263 :QLVEIDSEG 1l0qA 267 :TVSVIDTAT T0558 272 :KV 1l0qA 277 :TI T0558 274 :VWQLNDKVKFGMI 1l0qA 295 :IGSIPVQPVYPSA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1547 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l0qA/T0558-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1l0qA/T0558-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0558-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l0qA in template set Warning: unaligning (T0558)Q23 because first residue in template chain is (1l0qA)S1 Warning: unaligning (T0558)I289 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l0qA)N266 T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 1l0qA 3 :FAYIANSESDNISVIDVTSNKVTATIP T0558 53 :KGWECNSVAATKAGEILFSYSKG 1l0qA 30 :VGSNPMGAVISPDGTKVYVANAH T0558 76 :AKMIT 1l0qA 56 :VSIID T0558 81 :RDGRELWNIA 1l0qA 62 :ATNNVIATVP T0558 93 :AGCEMQTARILPDGNALVAWCGHPSTILEVNMK 1l0qA 72 :AGSSPQGVAVSPDGKQVYVTNMASSTLSVIDTT T0558 126 :GEVLS 1l0qA 106 :NTVAG T0558 133 :EFETG 1l0qA 111 :TVKTG T0558 139 :ER 1l0qA 116 :KS T0558 145 :FRQINKNKKG 1l0qA 118 :PLGLALSPDG T0558 155 :NYLVPLFATSEVREIAPN 1l0qA 129 :KLYVTNNGDKTVSVINTV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 1l0qA 148 :KAVINTVSVGRSPKGIAVTPDGTKVYVANF T0558 203 :AHCFVQLNLESNRIVRRVNANDI 1l0qA 179 :SMSISVIDTVTNSVIDTVKVEAA T0558 233 :VAQLFPLQNGGLYICNWQG 1l0qA 202 :PSGIAVNPEGTKAYVTNVD T0558 252 :HDREAGKG 1l0qA 224 :NTVSMIDT T0558 260 :KHPQLVEIDSEGKVVWQL 1l0qA 233 :TNKITARIPVGPDPAGIA T0558 278 :NDKVKFGMIST 1l0qA 253 :PDGKKVYVALS Number of specific fragments extracted= 16 number of extra gaps= 0 total=1563 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l0qA/T0558-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1l0qA/T0558-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0558-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l0qA in template set T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPLEK 1l0qA 4 :AYIANSESDNISVIDVTSNKVTATIPVGS T0558 56 :ECNSVAATKAG 1l0qA 33 :NPMGAVISPDG T0558 67 :EILFSY 1l0qA 45 :KVYVAN T0558 73 :SKGAKMITRDGRELWN 1l0qA 53 :SNDVSIIDTATNNVIA T0558 89 :IAAPAG 1l0qA 70 :VPAGSS T0558 97 :MQTARILPDGNALVAWCGHPSTILEVNMK 1l0qA 76 :PQGVAVSPDGKQVYVTNMASSTLSVIDTT T0558 126 :GEVLSKTEFETG 1l0qA 106 :NTVAGTVKTGKS T0558 145 :FRQINKNKKGNYLVPL 1l0qA 118 :PLGLALSPDGKKLYVT T0558 161 :FATSEVREIAPN 1l0qA 135 :NGDKTVSVINTV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 1l0qA 148 :KAVINTVSVGRSPKGIAVTPDGTKVYVANF T0558 203 :AHCFVQLNLESNRIVRRVNAND 1l0qA 179 :SMSISVIDTVTNSVIDTVKVEA T0558 232 :FVAQLFPLQNGGLYICNWQGH 1l0qA 201 :APSGIAVNPEGTKAYVTNVDK T0558 260 :KHPQLVEID 1l0qA 222 :YFNTVSMID T0558 269 :SEGKVVWQLND 1l0qA 232 :GTNKITARIPV T0558 283 :FGMISTICPI 1l0qA 243 :GPDPAGIAVT Number of specific fragments extracted= 15 number of extra gaps= 0 total=1578 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfqA/T0558-1yfqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1yfqA/T0558-1yfqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfqA read from 1yfqA/T0558-1yfqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yfqA in training set Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)S144 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)S144 Warning: unaligning (T0558)G137 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)N145 Warning: unaligning (T0558)R140 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)V149 Warning: unaligning (T0558)P141 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)V149 Warning: unaligning (T0558)H142 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)K150 Warning: unaligning (T0558)R218 because of BadResidue code BAD_PEPTIDE in next template residue (1yfqA)N288 Warning: unaligning (T0558)R219 because of BadResidue code BAD_PEPTIDE at template residue (1yfqA)N288 Warning: unaligning (T0558)K258 because of BadResidue code BAD_PEPTIDE in next template residue (1yfqA)I326 Warning: unaligning (T0558)G259 because of BadResidue code BAD_PEPTIDE at template residue (1yfqA)I326 T0558 4 :FILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTK 1yfqA 4 :VQIEQAPKDYISDIKIIPSKSLLLITSWDGSLTVYKFDIQ T0558 44 :EIVWEYPLEKG 1yfqA 48 :DLLQSLRYKHP T0558 57 :CNSVAATKAG 1yfqA 59 :LLCCNFIDNT T0558 67 :EILFSYSKG 1yfqA 70 :LQIYVGTVQ T0558 76 :AKMITRD 1yfqA 81 :ILKVDLI T0558 83 :GRELWNIA 1yfqA 89 :SPSFQALT T0558 91 :APAGC 1yfqA 100 :ANLGI T0558 97 :MQTARI 1yfqA 105 :CRICKY T0558 105 :DGNALVAWCG 1yfqA 111 :GDDKLIAASW T0558 116 :PSTILEVNM 1yfqA 121 :DGLIEVIDP T0558 125 :KGEVLSKTEF 1yfqA 133 :GDGVIAVKNL T0558 138 :IE 1yfqA 146 :NT T0558 143 :AQFRQINKN 1yfqA 151 :NKIFTMDTN T0558 154 :GNYLVPLFATSEVREIAPN 1yfqA 160 :SSRLIVGMNNSQVQWFRLP T0558 173 :GQLLNSV 1yfqA 181 :EDDNGTI T0558 180 :KLSGT 1yfqA 191 :GLKYQ T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIV 1yfqA 254 :VNSIEFSPRHKFLYTAGSDGIISCWNLQTRKKI T0558 220 :VN 1yfqA 289 :FA T0558 222 :AND 1yfqA 292 :FNE T0558 231 :FFVAQLFPLQN 1yfqA 295 :DSVVKIACSDN T0558 244 :LYICNWQGH 1yfqA 306 :ILCLATSDD T0558 253 :DREAG 1yfqA 320 :AAIDQ T0558 260 :KHP 1yfqA 327 :ELN T0558 263 :QLVEI 1yfqA 332 :SIYII Number of specific fragments extracted= 24 number of extra gaps= 4 total=1602 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfqA/T0558-1yfqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1yfqA/T0558-1yfqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfqA read from 1yfqA/T0558-1yfqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yfqA in training set Warning: unaligning (T0558)E135 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)S144 Warning: unaligning (T0558)T136 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)S144 Warning: unaligning (T0558)G137 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)N145 Warning: unaligning (T0558)R140 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)V149 Warning: unaligning (T0558)P141 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)V149 Warning: unaligning (T0558)H142 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)K150 Warning: unaligning (T0558)V265 because of BadResidue code BAD_PEPTIDE in next template residue (1yfqA)N288 Warning: unaligning (T0558)E266 because of BadResidue code BAD_PEPTIDE at template residue (1yfqA)N288 T0558 2 :KNFILLVALFL 1yfqA 2 :QIVQIEQAPKD T0558 14 :APFAQGSSPQ 1yfqA 13 :YISDIKIIPS T0558 24 :HLLVGGSGWNKIAIINKD 1yfqA 24 :SLLLITSWDGSLTVYKFD T0558 42 :TKEIVWEYP 1yfqA 46 :NVDLLQSLR T0558 53 :KGWECNSVAATKAGE 1yfqA 55 :YKHPLLCCNFIDNTD T0558 68 :ILFSYSKG 1yfqA 71 :QIYVGTVQ T0558 76 :AKMIT 1yfqA 81 :ILKVD T0558 81 :RDGRELWNIA 1yfqA 87 :IGSPSFQALT T0558 92 :PAGCEMQTARILP 1yfqA 97 :NNEANLGICRICK T0558 105 :DGNALVAWC 1yfqA 111 :GDDKLIAAS T0558 115 :HPSTILEVNMK 1yfqA 120 :WDGLIEVIDPR T0558 126 :G 1yfqA 133 :G T0558 127 :EVLS 1yfqA 137 :IAVK T0558 133 :EF 1yfqA 141 :NL T0558 138 :IE 1yfqA 146 :NT T0558 143 :AQFRQINKN 1yfqA 151 :NKIFTMDTN T0558 154 :GNYLVPLFATSEVREIAPN 1yfqA 160 :SSRLIVGMNNSQVQWFRLP T0558 173 :GQ 1yfqA 181 :ED T0558 175 :LLNSVKLSGTPFSSAFLD 1yfqA 186 :TIEESGLKYQIRDVALLP T0558 193 :NGDCLVACGDAHCFVQL 1yfqA 205 :EQEGYACSSIDGRVAVE T0558 210 :NLESN 1yfqA 224 :DDQGD T0558 216 :IVRRVNANDIEGV 1yfqA 234 :KRFAFRCHRLNLK T0558 229 :QLFFVAQLFPLQNGGLYICNWQGHDREAGKG 1yfqA 250 :LAYPVNSIEFSPRHKFLYTAGSDGIISCWNL T0558 260 :KHPQL 1yfqA 282 :TRKKI T0558 267 :IDS 1yfqA 289 :FAK T0558 270 :EGKVVWQL 1yfqA 293 :NEDSVVKI T0558 278 :NDKVKFGMIST 1yfqA 304 :DNILCLATSDD Number of specific fragments extracted= 27 number of extra gaps= 3 total=1629 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yfqA/T0558-1yfqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1yfqA/T0558-1yfqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yfqA read from 1yfqA/T0558-1yfqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yfqA in training set Warning: unaligning (T0558)A90 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)S144 Warning: unaligning (T0558)A91 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)S144 Warning: unaligning (T0558)G94 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1yfqA)V149 Warning: unaligning (T0558)C95 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)V149 Warning: unaligning (T0558)E96 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1yfqA)K150 Warning: unaligning (T0558)R218 because of BadResidue code BAD_PEPTIDE in next template residue (1yfqA)N288 Warning: unaligning (T0558)R219 because of BadResidue code BAD_PEPTIDE at template residue (1yfqA)N288 T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPL 1yfqA 67 :NTDLQIYVGTVQGEILKVDLIGSPSFQALTN T0558 52 :EKGWECNSVAATKAGEILFSYS 1yfqA 99 :EANLGICRICKYGDDKLIAASW T0558 74 :KGAKMIT 1yfqA 122 :GLIEVID T0558 83 :GRELWNI 1yfqA 136 :VIAVKNL T0558 92 :PA 1yfqA 146 :NT T0558 97 :MQTARILPDGNALVAWCG 1yfqA 151 :NKIFTMDTNSSRLIVGMN T0558 116 :PSTILEVNM 1yfqA 169 :NSQVQWFRL T0558 125 :KGEVLSKTEFETG 1yfqA 181 :EDDNGTIEESGLK T0558 143 :AQFRQINKNK 1yfqA 194 :YQIRDVALLP T0558 153 :KGNYLVPLFATSEVREIAP 1yfqA 205 :EQEGYACSSIDGRVAVEFF T0558 172 :NGQ 1yfqA 225 :DQG T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIV 1yfqA 252 :YPVNSIEFSPRHKFLYTAGSDGIISCWNLQTRKKI T0558 220 :VNA 1yfqA 289 :FAK T0558 228 :VQLFFVAQLFPLQNGGLYICNWQGHDREAGKGK 1yfqA 292 :FNEDSVVKIACSDNILCLATSDDTFKTNAAIDQ T0558 261 :HPQLVEIDS 1yfqA 330 :ASSIYIIFD Number of specific fragments extracted= 15 number of extra gaps= 3 total=1644 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3greA/T0558-3greA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3greA expands to /projects/compbio/data/pdb/3gre.pdb.gz 3greA:Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2374, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2378, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2380, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2382, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2384, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2386, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2790, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2794, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2796, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2798, because occupancy 0.500 <= existing 0.500 in 3greA Skipped atom 2800, because occupancy 0.500 <= existing 0.500 in 3greA # T0558 read from 3greA/T0558-3greA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3greA read from 3greA/T0558-3greA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3greA to template set # found chain 3greA in template set Warning: unaligning (T0558)L230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3greA)H1424 T0558 2 :KNFILLVALF 3greA 1070 :KLIATLMENE T0558 12 :LVAPFAQGSS 3greA 1081 :NSITSSAVSP T0558 22 :PQHLLVGGSGWNKIAIIN 3greA 1092 :ETPYLITGSDQGVIKIWN T0558 40 :KDTKEIVWEYPLEKG 3greA 1116 :GEVYSSSLTYDCSST T0558 57 :CNSVAATKAGEILFSYSKG 3greA 1131 :VTQITMIPNFDAFAVSSKD T0558 76 :AKMITRD 3greA 1152 :IIVLKVN T0558 83 :GRE 3greA 1160 :YQQ T0558 86 :LWNIAAPAGCE 3greA 1174 :IRKINLKNFGK T0558 97 :MQTARILP 3greA 1188 :AVRMRAFV T0558 105 :DGNALVAWCG 3greA 1198 :EKSLLVALTN T0558 116 :PSTILEVNMK 3greA 1208 :LSRVIIFDIR T0558 126 :GEVLSKTEFETGIERPHA 3greA 1219 :LERLQIIENSPRHGAVSS T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 3greA 1237 :ICIDEECCVLILGTTRGIIDIWDIR T0558 173 :GQLLNSV 3greA 1263 :NVLIRSW T0558 180 :KLSG 3greA 1272 :GDHA T0558 185 :PFSSAFLD 3greA 1277 :ITHVEVCQ T0558 193 :NGDCLVACGDAHC 3greA 1288 :KNSVIVVGGSSKT T0558 206 :FVQLNLESNRIVRRVNANDIEG 3greA 1302 :LTIWNFVKGHCQYAFINSDEQP T0558 231 :FFVAQLFPLQ 3greA 1425 :DIINSISTCE T0558 241 :NG 3greA 1436 :DE T0558 243 :GLYICNWQGH 3greA 1439 :PLLVACDNSG T0558 263 :QLVEI 3greA 1449 :LIGIF Number of specific fragments extracted= 22 number of extra gaps= 0 total=1666 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3greA/T0558-3greA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3greA/T0558-3greA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3greA read from 3greA/T0558-3greA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3greA in template set Warning: unaligning (T0558)G227 because of BadResidue code BAD_PEPTIDE in next template residue (3greA)R1344 Warning: unaligning (T0558)V228 because of BadResidue code BAD_PEPTIDE at template residue (3greA)R1344 Warning: unaligning (T0558)E270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3greA)H1424 T0558 2 :KNFILLVALFLVAPFAQGSSPQ 3greA 1070 :KLIATLMENEPNSITSSAVSPG T0558 24 :HLLVGGSGWNKIAIIN 3greA 1094 :PYLITGSDQGVIKIWN T0558 40 :KDTKEIVWEYP 3greA 1116 :GEVYSSSLTYD T0558 53 :KGWECNSVAATKAGEILFSYSKG 3greA 1127 :CSSTVTQITMIPNFDAFAVSSKD T0558 76 :AKMI 3greA 1152 :IIVL T0558 80 :T 3greA 1167 :K T0558 81 :RDGRELWNIA 3greA 1169 :LNCECIRKIN T0558 91 :APAGCEMQ 3greA 1182 :FGKNEYAV T0558 99 :TARILPDGNALVAWCGHPSTILEVNMK 3greA 1191 :MRAFVNEEKSLLVALTNLSRVIIFDIR T0558 126 :GEVLSKTEFETGIER 3greA 1219 :LERLQIIENSPRHGA T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 3greA 1234 :VSSICIDEECCVLILGTTRGIIDIWDIR T0558 173 :GQLLNSVKLSGTPFSSAFL 3greA 1263 :NVLIRSWSFGDHAPITHVE T0558 192 :DNGDCLVACGDAHC 3greA 1287 :GKNSVIVVGGSSKT T0558 206 :FVQLNLESNRIVRRVNAN 3greA 1302 :LTIWNFVKGHCQYAFINS T0558 224 :DIE 3greA 1340 :FCG T0558 229 :QLFFVAQLFPLQNGGLYICNWQGHDR 3greA 1345 :SLNALSTISVSNDKILLTDEATSSIV T0558 255 :EAGKG 3greA 1394 :IPTQV T0558 260 :KHPQLVEIDS 3greA 1400 :ANLTMLLRKM T0558 272 :KVVWQL 3greA 1428 :NSISTC T0558 278 :NDKVKFGMISTICPIR 3greA 1436 :DETPLLVACDNSGLIG Number of specific fragments extracted= 20 number of extra gaps= 1 total=1686 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3greA/T0558-3greA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3greA/T0558-3greA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3greA read from 3greA/T0558-3greA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3greA in template set T0558 44 :EIVWEYPLEKGWECNSVAATKAG 3greA 1070 :KLIATLMENEPNSITSSAVSPGE T0558 67 :EILFSY 3greA 1094 :PYLITG T0558 73 :SKGAKMIT 3greA 1102 :QGVIKIWN T0558 87 :WNIAAPAG 3greA 1123 :LTYDCSST T0558 97 :MQTARILPDGNALVAWCG 3greA 1131 :VTQITMIPNFDAFAVSSK T0558 116 :PSTILEVN 3greA 1149 :DGQIIVLK T0558 128 :VLSKTEFETGIERPHAQFRQINKNKKGNYLVPLFATSEVREIAPN 3greA 1173 :CIRKINLKNFGKNEYAVRMRAFVNEEKSLLVALTNLSRVIIFDIR T0558 173 :GQLLNSVKLS 3greA 1219 :LERLQIIENS T0558 183 :GTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVN 3greA 1232 :GAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWS T0558 227 :GVQLFFVAQLFPLQ 3greA 1271 :FGDHAPITHVEVCQ T0558 241 :NGGLYICNWQGH 3greA 1289 :NSVIVVGGSSKT T0558 263 :QLVEID 3greA 1301 :FLTIWN T0558 269 :SEGKVVWQLNDKVKF 3greA 1308 :VKGHCQYAFINSDEQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=1699 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aq5A/T0558-2aq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aq5A expands to /projects/compbio/data/pdb/2aq5.pdb.gz 2aq5A:Bad short name: OD for alphabet: pdb_atoms Bad short name: OD for alphabet: pdb_atoms Bad short name: OD for alphabet: pdb_atoms Bad short name: OD for alphabet: pdb_atoms # T0558 read from 2aq5A/T0558-2aq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aq5A read from 2aq5A/T0558-2aq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aq5A to template set # found chain 2aq5A in template set Warning: unaligning (T0558)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)E52 Warning: unaligning (T0558)E52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)G79 Warning: unaligning (T0558)A62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)P91 Warning: unaligning (T0558)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)P91 Warning: unaligning (T0558)C113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)D153 Warning: unaligning (T0558)P116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)D153 Warning: unaligning (T0558)T288 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)E333 T0558 5 :ILLVALFLVAPFAQGSSPQHLLVG 2aq5A 26 :EDVRVSQTTWDSGFCAVNPKFMAL T0558 31 :GWNKIAIINKDTKEI 2aq5A 55 :GGGAFLVLPLGKTGR T0558 53 :KGWECNSVA 2aq5A 80 :HTAPVLDIA T0558 65 :AGEILFSYSKG 2aq5A 93 :NDNVIASGSED T0558 76 :AKMITRD 2aq5A 106 :VMVWEIP T0558 83 :GRE 2aq5A 114 :GGL T0558 86 :LWNIAAPAGC 2aq5A 124 :VITLEGHTKR T0558 97 :MQTARILPDG 2aq5A 134 :VGIVAWHPTA T0558 107 :NALVAW 2aq5A 145 :NVLLSA T0558 117 :STILEVNMK 2aq5A 154 :NVILVWDVG T0558 126 :GEVLSKTEFETGIERPHA 2aq5A 164 :GAAVLTLGPDVHPDTIYS T0558 148 :INKNKKGNYLVPLFATSEVREIAPN 2aq5A 182 :VDWSRDGALICTSCRDKRVRVIEPR T0558 173 :GQLLNSV 2aq5A 208 :GTVVAEK T0558 180 :KLSGT 2aq5A 217 :PHEGT T0558 185 :PFSSAFLDNGDCLVACGD 2aq5A 223 :PVHAVFVSEGKILTTGFS T0558 203 :AHCFVQLNLESNR 2aq5A 244 :ERQVALWDTKHLE T0558 216 :IVRRVNAND 2aq5A 260 :SLQELDTSS T0558 232 :FVAQLFPLQNG 2aq5A 269 :GVLLPFFDPDT T0558 243 :GLYICNWQGHDR 2aq5A 281 :IVYLCGKGDSSI T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMI 2aq5A 293 :RYFEITSEAPFLHYLSMFSSKESQ T0558 289 :ICPI 2aq5A 334 :IARF Number of specific fragments extracted= 21 number of extra gaps= 0 total=1720 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aq5A/T0558-2aq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2aq5A/T0558-2aq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aq5A read from 2aq5A/T0558-2aq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aq5A in template set Warning: unaligning (T0558)G28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)E52 Warning: unaligning (T0558)E52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)G79 Warning: unaligning (T0558)A62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)P91 Warning: unaligning (T0558)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)P91 Warning: unaligning (T0558)C113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)D153 Warning: unaligning (T0558)P116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)D153 Warning: unaligning (T0558)N278 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)E333 Warning: unaligning (T0558)K280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)E333 T0558 6 :LLVALFL 2aq5A 29 :RVSQTTW T0558 14 :APFAQGSSPQHLLV 2aq5A 36 :DSGFCAVNPKFMAL T0558 29 :GSGWNKIAIINKDTK 2aq5A 53 :ASGGGAFLVLPLGKT T0558 50 :P 2aq5A 68 :G T0558 53 :KGWECNSVA 2aq5A 80 :HTAPVLDIA T0558 65 :AGEILFSYSKG 2aq5A 93 :NDNVIASGSED T0558 76 :AKMIT 2aq5A 106 :VMVWE T0558 81 :RDG 2aq5A 112 :PDG T0558 84 :RELWNIA 2aq5A 122 :EPVITLE T0558 92 :PAGCEMQTARILPDG 2aq5A 129 :GHTKRVGIVAWHPTA T0558 107 :NALVAW 2aq5A 145 :NVLLSA T0558 117 :STILEVNMK 2aq5A 154 :NVILVWDVG T0558 126 :GEVLSKTEFETGIER 2aq5A 164 :GAAVLTLGPDVHPDT T0558 145 :FRQINKNKKGNYLVPLFATSEVREIAPN 2aq5A 179 :IYSVDWSRDGALICTSCRDKRVRVIEPR T0558 173 :GQLLNSV 2aq5A 208 :GTVVAEK T0558 180 :KLS 2aq5A 217 :PHE T0558 183 :GTPFSSAFLDNGDCLVACGDAH 2aq5A 221 :TRPVHAVFVSEGKILTTGFSRM T0558 205 :CFVQLNLESNR 2aq5A 246 :QVALWDTKHLE T0558 216 :IVRRVNANDI 2aq5A 260 :SLQELDTSSG T0558 233 :VAQLFPLQNGG 2aq5A 270 :VLLPFFDPDTN T0558 244 :LYICNWQGHDREAGKG 2aq5A 282 :VYLCGKGDSSIRYFEI T0558 260 :KHP 2aq5A 299 :SEA T0558 263 :QLVEIDSEGK 2aq5A 306 :YLSMFSSKES T0558 273 :VVW 2aq5A 318 :GMG T0558 281 :V 2aq5A 334 :I T0558 282 :KFGMIST 2aq5A 336 :RFYKLHE Number of specific fragments extracted= 26 number of extra gaps= 0 total=1746 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aq5A/T0558-2aq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2aq5A/T0558-2aq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aq5A read from 2aq5A/T0558-2aq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aq5A in template set Warning: unaligning (T0558)G28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)E52 Warning: unaligning (T0558)S30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)E52 Warning: unaligning (T0558)A62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)P91 Warning: unaligning (T0558)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)P91 Warning: unaligning (T0558)C113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2aq5A)D153 Warning: unaligning (T0558)P116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2aq5A)D153 T0558 20 :SSPQHLLV 2aq5A 42 :VNPKFMAL T0558 31 :GWNKIAIINKDTKE 2aq5A 53 :ASGGGAFLVLPLGK T0558 54 :GWECNSVA 2aq5A 81 :TAPVLDIA T0558 65 :AGEILFSY 2aq5A 94 :DNVIASGS T0558 73 :SKGAKMIT 2aq5A 103 :DCTVMVWE T0558 81 :RDGRE 2aq5A 112 :PDGGL T0558 86 :LWNIAAPAG 2aq5A 124 :VITLEGHTK T0558 96 :EMQTARILP 2aq5A 133 :RVGIVAWHP T0558 105 :DGNALVAW 2aq5A 143 :AQNVLLSA T0558 117 :STILEVN 2aq5A 154 :NVILVWD T0558 124 :MKGEVLSKTEFETGIE 2aq5A 162 :GTGAAVLTLGPDVHPD T0558 144 :QFRQINKNKKGNYLVPLFATSEVREIA 2aq5A 178 :TIYSVDWSRDGALICTSCRDKRVRVIE T0558 171 :PNGQLLNSVKLS 2aq5A 206 :RKGTVVAEKDRP T0558 183 :GTPFSSAFLDNGDCLVACGDAH 2aq5A 221 :TRPVHAVFVSEGKILTTGFSRM T0558 205 :CFVQLNLESNR 2aq5A 246 :QVALWDTKHLE T0558 216 :IVRRVNAND 2aq5A 260 :SLQELDTSS T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2aq5A 269 :GVLLPFFDPDTNIVYLCGKGDS T0558 261 :HP 2aq5A 291 :SI T0558 273 :VVWQLNDKVKFGMISTICPIR 2aq5A 293 :RYFEITSEAPFLHYLSMFSSK Number of specific fragments extracted= 19 number of extra gaps= 0 total=1765 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bwsA/T0558-3bwsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bwsA expands to /projects/compbio/data/pdb/3bws.pdb.gz 3bwsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 3bwsA/T0558-3bwsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwsA read from 3bwsA/T0558-3bwsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bwsA to template set # found chain 3bwsA in template set Warning: unaligning (T0558)S59 because of BadResidue code BAD_PEPTIDE in next template residue (3bwsA)I198 Warning: unaligning (T0558)V60 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)I198 Warning: unaligning (T0558)A203 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)C347 T0558 3 :NFILLVALFLVAPFAQGS 3bwsA 137 :RFISRFKTGFQPKSVRFI T0558 22 :PQHLLVGGS 3bwsA 155 :DNTRLAIPL T0558 31 :GWNKIAIINKDTKEIV 3bwsA 165 :EDEGMDVLDINSGQTV T0558 48 :EYPL 3bwsA 181 :RLSP T0558 52 :EKGWECN 3bwsA 190 :KKLGFVE T0558 61 :AATKAGEILFSYSKG 3bwsA 199 :SIPEHNELWVSQMQA T0558 76 :AKMITRD 3bwsA 216 :VHVFDLK T0558 83 :GRELWNIAAPAGC 3bwsA 224 :LAYKATVDLTGKW T0558 97 :MQTARILPDGNALVAWCGHPSTILEVNMK 3bwsA 237 :SKILLYDPIRDLVYCSNWISEDISVIDRK T0558 126 :GEVLSK 3bwsA 267 :KLEIRK T0558 134 :FETG 3bwsA 273 :TDKI T0558 139 :ERPHA 3bwsA 277 :GLPRG T0558 148 :INKNKKG 3bwsA 282 :LLLSKDG T0558 155 :NYLVPLFAT 3bwsA 290 :ELYIAQFSA T0558 164 :SEVREIAPN 3bwsA 306 :GRLGIYSMD T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 3bwsA 316 :EKLIDTIGPPGNKRHIVSGNTENKIYVSDM T0558 204 :HCFVQLNLESNRIVRRVNAND 3bwsA 348 :SKIEVYDLKEKKVQKSIPVFD T0558 232 :FVAQLFPLQNG 3bwsA 369 :KPNTIALSPDG T0558 243 :GLYICNWQGH 3bwsA 381 :YLYVSCRGPN T0558 253 :DREAGKGKHPQLVEIDSEG 3bwsA 395 :GYLKKGLVLGKVYVIDTTT T0558 272 :KV 3bwsA 415 :TV T0558 274 :VWQLNDKVKFGMI 3bwsA 426 :PTGLDVSPDNRYL Number of specific fragments extracted= 22 number of extra gaps= 2 total=1787 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bwsA/T0558-3bwsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3bwsA/T0558-3bwsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwsA read from 3bwsA/T0558-3bwsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwsA in template set Warning: unaligning (T0558)V60 because of BadResidue code BAD_PEPTIDE in next template residue (3bwsA)I198 Warning: unaligning (T0558)A61 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)I198 Warning: unaligning (T0558)D202 because of BadResidue code BAD_PEPTIDE in next template residue (3bwsA)C347 Warning: unaligning (T0558)A203 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)C347 T0558 2 :KNFILLVALF 3bwsA 137 :RFISRFKTGF T0558 14 :APFAQGSSPQHLLVGG 3bwsA 147 :QPKSVRFIDNTRLAIP T0558 30 :SGWNKIAIINKDTKEIVWEYP 3bwsA 164 :LEDEGMDVLDINSGQTVRLSP T0558 52 :E 3bwsA 185 :P T0558 54 :GWECNS 3bwsA 191 :KLGFVE T0558 62 :ATKAGE 3bwsA 199 :SIPEHN T0558 68 :ILFSYSKG 3bwsA 206 :LWVSQMQA T0558 76 :AKMIT 3bwsA 216 :VHVFD T0558 81 :RDGRELWNIA 3bwsA 222 :KTLAYKATVD T0558 92 :PAGCEMQTARILPDGNALVAWCGHPSTILEVNMK 3bwsA 232 :LTGKWSKILLYDPIRDLVYCSNWISEDISVIDRK T0558 126 :GEVLS 3bwsA 267 :KLEIR T0558 133 :EFETGIE 3bwsA 272 :KTDKIGL T0558 145 :FRQINKNKKGNYLVP 3bwsA 279 :PRGLLLSKDGKELYI T0558 160 :LFATSEVREIAPN 3bwsA 302 :ESGGGRLGIYSMD T0558 173 :GQLLNSV 3bwsA 316 :EKLIDTI T0558 180 :KL 3bwsA 324 :PP T0558 183 :GTPFSSAFLDNGD 3bwsA 326 :GNKRHIVSGNTEN T0558 196 :CLVACG 3bwsA 340 :IYVSDM T0558 204 :HCFVQLNLESNRIVRRVNANDI 3bwsA 348 :SKIEVYDLKEKKVQKSIPVFDK T0558 233 :VAQLFPLQNGG 3bwsA 370 :PNTIALSPDGK T0558 244 :LYICNWQGH 3bwsA 382 :LYVSCRGPN T0558 253 :DREAGKG 3bwsA 405 :KVYVIDT T0558 260 :KHPQLVEIDSEGKVVWQL 3bwsA 413 :TDTVKEFWEAGNQPTGLD T0558 278 :NDKVKFGMISTIC 3bwsA 433 :PDNRYLVISDFLD Number of specific fragments extracted= 24 number of extra gaps= 2 total=1811 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bwsA/T0558-3bwsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3bwsA/T0558-3bwsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwsA read from 3bwsA/T0558-3bwsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwsA in template set Warning: unaligning (T0558)V60 because of BadResidue code BAD_PEPTIDE in next template residue (3bwsA)I198 Warning: unaligning (T0558)A61 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)I198 Warning: unaligning (T0558)A203 because of BadResidue code BAD_PEPTIDE at template residue (3bwsA)C347 T0558 17 :AQGSSPQHLLVGGSGWNKIAIINK 3bwsA 150 :SVRFIDNTRLAIPLLEDEGMDVLD T0558 41 :DTKEIVWEYPL 3bwsA 175 :NSGQTVRLSPP T0558 52 :EKGWECNS 3bwsA 189 :KKKLGFVE T0558 62 :ATKAG 3bwsA 199 :SIPEH T0558 67 :EILFSY 3bwsA 205 :ELWVSQ T0558 73 :SKGAKMITRDG 3bwsA 213 :ANAVHVFDLKT T0558 84 :RELWNIAAPAG 3bwsA 225 :AYKATVDLTGK T0558 96 :EMQTARILPDGNALVAWCGHPSTILEVNMK 3bwsA 236 :WSKILLYDPIRDLVYCSNWISEDISVIDRK T0558 126 :GEVLSKTEFET 3bwsA 267 :KLEIRKTDKIG T0558 144 :QFRQINKNKKGNYLVPLFATS 3bwsA 278 :LPRGLLLSKDGKELYIAQFSA T0558 165 :EVREIAPN 3bwsA 307 :RLGIYSMD T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 3bwsA 316 :EKLIDTIGPPGNKRHIVSGNTENKIYVSDM T0558 204 :HCFVQLNLESNRIVRRVNAN 3bwsA 348 :SKIEVYDLKEKKVQKSIPVF T0558 231 :FFVAQLFPLQNGG 3bwsA 368 :DKPNTIALSPDGK T0558 244 :LYICNWQGHDREAGKGKH 3bwsA 382 :LYVSCRGPNHPTEGYLKK T0558 262 :PQLVEIDSE 3bwsA 404 :GKVYVIDTT T0558 271 :GKVVWQLND 3bwsA 414 :DTVKEFWEA T0558 283 :FGMISTICPI 3bwsA 423 :GNQPTGLDVS Number of specific fragments extracted= 18 number of extra gaps= 2 total=1829 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dsmA/T0558-3dsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dsmA expands to /projects/compbio/data/pdb/3dsm.pdb.gz 3dsmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0558 read from 3dsmA/T0558-3dsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dsmA read from 3dsmA/T0558-3dsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dsmA to template set # found chain 3dsmA in template set T0558 10 :LFLVAPFAQG 3dsmA 56 :LGDVAQSMVI T0558 21 :SPQHLLVGGSGWNKIAIINKDTKEIVWEYPLEKG 3dsmA 66 :RDGIGWIVVNNSHVIFAIDINTFKEVGRITGFTS T0558 57 :CNSVAATKAGEILFSYSKG 3dsmA 100 :PRYIHFLSDEKAYVTQIWD T0558 76 :AKMITRD 3dsmA 121 :IFIINPK T0558 83 :GRELWNIAAPAGCE 3dsmA 129 :YEITGYIECPDMDM T0558 97 :MQTARIL 3dsmA 147 :TEQMVQY T0558 105 :DGNALVAWCGHPSTILEVNMK 3dsmA 154 :GKYVYVNCWSYQNRILKIDTE T0558 126 :GEVLSKTEFE 3dsmA 176 :DKVVDELTIG T0558 139 :ERPHA 3dsmA 186 :IQPTS T0558 148 :INKNKKGNYLVPLFAT 3dsmA 191 :LVMDKYNKMWTITDGG T0558 164 :SEVREIAPN 3dsmA 217 :PSLYRIDAE T0558 173 :GQLLNSV 3dsmA 227 :FTVEKQF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDA 3dsmA 236 :KLGDWPSEVQLNGTRDTLYWINND T0558 206 :FVQLNLESNR 3dsmA 260 :IWRMPVEADR T0558 222 :ANDIEG 3dsmA 275 :FLEFRD T0558 231 :FFVAQLFPLQNG 3dsmA 281 :TKYYGLTVNPNN T0558 243 :GLYICNWQGH 3dsmA 294 :EVYVADAIDY T0558 258 :KGKH 3dsmA 304 :QQQG T0558 263 :QLVEIDSEGKV 3dsmA 308 :IVYRYSPQGKL T0558 274 :VWQLNDKVKFGMI 3dsmA 321 :EFYVGIIPGAFCW T0558 287 :ST 3dsmA 336 :EH Number of specific fragments extracted= 21 number of extra gaps= 0 total=1850 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dsmA/T0558-3dsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dsmA/T0558-3dsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dsmA read from 3dsmA/T0558-3dsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dsmA in template set T0558 8 :VALFL 3dsmA 54 :FKLGD T0558 14 :APFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 3dsmA 59 :VAQSMVIRDGIGWIVVNNSHVIFAIDINTFKEVGRIT T0558 52 :EK 3dsmA 96 :GF T0558 55 :WECNSVAATKAGEILFSYSKG 3dsmA 98 :TSPRYIHFLSDEKAYVTQIWD T0558 76 :AKMIT 3dsmA 121 :IFIIN T0558 81 :RDGRELWNIA 3dsmA 127 :KTYEITGYIE T0558 91 :APAGCEMQTARILPD 3dsmA 141 :DMESGSTEQMVQYGK T0558 108 :ALVAWC 3dsmA 156 :YVYVNC T0558 114 :GHPSTILEVNMK 3dsmA 163 :SYQNRILKIDTE T0558 126 :GEVLS 3dsmA 176 :DKVVD T0558 133 :EF 3dsmA 181 :EL T0558 136 :TGIER 3dsmA 183 :TIGIQ T0558 145 :FRQINKNKKGNYLVPLFAT 3dsmA 188 :PTSLVMDKYNKMWTITDGG T0558 164 :SEVREIAPN 3dsmA 217 :PSLYRIDAE T0558 173 :GQLLNSV 3dsmA 227 :FTVEKQF T0558 180 :KLSGTPFSSAFLDNGDCLVACGDA 3dsmA 236 :KLGDWPSEVQLNGTRDTLYWINND T0558 206 :FVQLNLESNRIV 3dsmA 260 :IWRMPVEADRVP T0558 220 :VNANDIE 3dsmA 276 :LEFRDTK T0558 233 :VAQLFPLQNGG 3dsmA 283 :YYGLTVNPNNG T0558 244 :LYICNWQG 3dsmA 295 :VYVADAID T0558 252 :HDREAGKGKHPQLVEIDS 3dsmA 307 :GIVYRYSPQGKLIDEFYV T0558 271 :GKVVWQL 3dsmA 325 :GIIPGAF Number of specific fragments extracted= 22 number of extra gaps= 0 total=1872 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dsmA/T0558-3dsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3dsmA/T0558-3dsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dsmA read from 3dsmA/T0558-3dsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dsmA in template set T0558 24 :HLLVGGSGWN 3dsmA 16 :SGLFITNEGN T0558 34 :KIAIINKDTKEIV 3dsmA 32 :TLSYYDPATCEVE T0558 54 :GWECNSVAATKAGEILFSYS 3dsmA 57 :GDVAQSMVIRDGIGWIVVNN T0558 74 :KGAKMITRDG 3dsmA 78 :HVIFAIDINT T0558 84 :RELWNIAAPAG 3dsmA 89 :KEVGRITGFTS T0558 97 :MQTARILPDGNALVAWCG 3dsmA 100 :PRYIHFLSDEKAYVTQIW T0558 116 :PSTILEVNM 3dsmA 118 :DYRIFIINP T0558 125 :KGEVLSKTEFETGIE 3dsmA 128 :TYEITGYIECPDMDM T0558 141 :PHAQFRQINKNKKGNYLVPLFATSEVREIAPN 3dsmA 143 :ESGSTEQMVQYGKYVYVNCWSYQNRILKIDTE T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGD 3dsmA 176 :DKVVDELTIGIQPTSLVMDKYNKMWTITDG T0558 205 :CFVQLNLESNRIVRRVNANDIEGVQLF 3dsmA 218 :SLYRIDAETFTVEKQFKFKLGDWPSEV T0558 233 :VAQLFPLQN 3dsmA 283 :YYGLTVNPN T0558 242 :GGLYICNWQGH 3dsmA 293 :GEVYVADAIDY T0558 259 :GKHPQLVEIDSEGKVVWQ 3dsmA 304 :QQQGIVYRYSPQGKLIDE T0558 281 :VKFGM 3dsmA 322 :FYVGI T0558 286 :ISTICPIRE 3dsmA 328 :PGAFCWKLE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1888 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ovrB/T0558-2ovrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ovrB expands to /projects/compbio/data/pdb/2ovr.pdb.gz 2ovrB:# T0558 read from 2ovrB/T0558-2ovrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ovrB read from 2ovrB/T0558-2ovrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ovrB to template set # found chain 2ovrB in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQH 2ovrB 2371 :KSPKVLKGHDDHVITCLQFCGNR T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYP 2ovrB 2433 :IIISGSTDRTLKVWNAETGECIHTLY T0558 52 :EKGWECNSVAATKA 2ovrB 2459 :GHTSTVRCMHLHEK T0558 68 :ILFSYSKG 2ovrB 2473 :RVVSGSRD T0558 76 :AKMITRD 2ovrB 2483 :LRVWDIE T0558 83 :GRELWNIAAPAGC 2ovrB 2491 :GQCLHVLMGHVAA T0558 97 :MQTARI 2ovrB 2504 :VRCVQY T0558 105 :DGNALVAWCG 2ovrB 2510 :DGRRVVSGAY T0558 116 :PSTILEVNMK 2ovrB 2520 :DFMVKVWDPE T0558 126 :GEVLSK 2ovrB 2531 :ETCLHT T0558 134 :FETGIERPHA 2ovrB 2537 :LQGHTNRVYS T0558 148 :INKN 2ovrB 2547 :LQFD T0558 154 :GNYLVPLFATSEVREIAPN 2ovrB 2551 :GIHVVSGSLDTSIRVWDVE T0558 173 :GQLLNSV 2ovrB 2571 :GNCIHTL T0558 180 :KLSGTPFSSAFL 2ovrB 2579 :GHQSLTSGMELK T0558 194 :GDCLVACGDAHCFVQLNLESNRIVRRVNANDIEG 2ovrB 2591 :DNILVSGNADSTVKIWDIKTGQCLQTLQGPNKHQ T0558 231 :FFVAQLFPLQN 2ovrB 2625 :SAVTCLQFNKN T0558 244 :LYICNWQGH 2ovrB 2636 :FVITSSDDG T0558 263 :QLVEIDSEG 2ovrB 2645 :TVKLWDLKT T0558 272 :KV 2ovrB 2655 :EF T0558 274 :VWQLNDKVKFGMI 2ovrB 2672 :VWRIRASNTKLVC T0558 287 :ST 2ovrB 2690 :NG Number of specific fragments extracted= 22 number of extra gaps= 0 total=1910 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ovrB/T0558-2ovrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2ovrB/T0558-2ovrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ovrB read from 2ovrB/T0558-2ovrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ovrB in template set T0558 2 :KNFILLVALFL 2ovrB 2412 :KCLRTLVGHTG T0558 14 :APFAQGS 2ovrB 2423 :GVWSSQM T0558 22 :PQHLLVGGSGWNKIAIINKDTKEIVWEYP 2ovrB 2430 :RDNIIISGSTDRTLKVWNAETGECIHTLY T0558 52 :EKGWECNSVAATKA 2ovrB 2459 :GHTSTVRCMHLHEK T0558 68 :ILFSYSKG 2ovrB 2473 :RVVSGSRD T0558 76 :AKMIT 2ovrB 2483 :LRVWD T0558 81 :RDGRELWNIA 2ovrB 2489 :ETGQCLHVLM T0558 92 :PAGCEMQTARIL 2ovrB 2499 :GHVAAVRCVQYD T0558 106 :GNALVAWC 2ovrB 2511 :GRRVVSGA T0558 115 :HPSTILEVNMK 2ovrB 2519 :YDFMVKVWDPE T0558 126 :GEVLS 2ovrB 2531 :ETCLH T0558 133 :EFETGIER 2ovrB 2536 :TLQGHTNR T0558 145 :FRQINKNKK 2ovrB 2544 :VYSLQFDGI T0558 156 :YLVPLFATSEVREIAPN 2ovrB 2553 :HVVSGSLDTSIRVWDVE T0558 173 :GQLLNSV 2ovrB 2571 :GNCIHTL T0558 180 :KLSGTPFSSAFLDN 2ovrB 2579 :GHQSLTSGMELKDN T0558 196 :CLVACGDAHCFVQLNLESNRIVRRVNANDIEGVQ 2ovrB 2593 :ILVSGNADSTVKIWDIKTGQCLQTLQGPNKHQSA T0558 233 :VAQLFPLQN 2ovrB 2627 :VTCLQFNKN T0558 244 :LYICNWQGHDREAGKG 2ovrB 2636 :FVITSSDDGTVKLWDL T0558 260 :KHPQLVEI 2ovrB 2653 :TGEFIRNL T0558 268 :DSEGKVVWQL 2ovrB 2666 :GGSGGVVWRI T0558 278 :NDKVKFGMISTICPIR 2ovrB 2679 :NTKLVCAVGSRNGTEE Number of specific fragments extracted= 22 number of extra gaps= 0 total=1932 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ovrB/T0558-2ovrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2ovrB/T0558-2ovrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ovrB read from 2ovrB/T0558-2ovrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ovrB in template set T0558 22 :PQHLLVGGSGWNKIAIINKDTKEIVWEYPLEK 2ovrB 2430 :RDNIIISGSTDRTLKVWNAETGECIHTLYGHT T0558 55 :WECNSVAATKAGEILFSYSKGAKMIT 2ovrB 2462 :STVRCMHLHEKRVVSGSRDATLRVWD T0558 81 :RDGRELWNIAAPAG 2ovrB 2489 :ETGQCLHVLMGHVA T0558 96 :EMQTARI 2ovrB 2503 :AVRCVQY T0558 105 :DGNALVAWCG 2ovrB 2510 :DGRRVVSGAY T0558 116 :PSTILEVN 2ovrB 2520 :DFMVKVWD T0558 124 :MKGEVLSKTEFETG 2ovrB 2529 :ETETCLHTLQGHTN T0558 144 :QFRQINK 2ovrB 2543 :RVYSLQF T0558 153 :KGNYLVPLFATSEVREIAPN 2ovrB 2550 :DGIHVVSGSLDTSIRVWDVE T0558 173 :GQLLNSVKLS 2ovrB 2571 :GNCIHTLTGH T0558 183 :GTPFSSAFL 2ovrB 2582 :SLTSGMELK T0558 194 :GDCLVACGDAHCFVQLNLESNRIVRRVNANDIEGVQLFFVA 2ovrB 2591 :DNILVSGNADSTVKIWDIKTGQCLQTLQGPNKHQSAVTCLQ T0558 240 :QNGGLYICNWQGH 2ovrB 2632 :FNKNFVITSSDDG T0558 263 :QLVEID 2ovrB 2645 :TVKLWD T0558 269 :SEGKVVWQLND 2ovrB 2652 :KTGEFIRNLVT Number of specific fragments extracted= 15 number of extra gaps= 0 total=1947 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pm7B/T0558-2pm7B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pm7B expands to /projects/compbio/data/pdb/2pm7.pdb.gz 2pm7B:# T0558 read from 2pm7B/T0558-2pm7B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pm7B read from 2pm7B/T0558-2pm7B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pm7B to template set # found chain 2pm7B in template set Warning: unaligning (T0558)L12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)I12 Warning: unaligning (T0558)A14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)I12 Warning: unaligning (T0558)Q18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)D18 Warning: unaligning (T0558)S20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)D18 Warning: unaligning (T0558)L25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)A25 Warning: unaligning (T0558)V27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)A25 Warning: unaligning (T0558)A76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)I81 Warning: unaligning (T0558)M78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)I81 Warning: unaligning (T0558)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)L116 Warning: unaligning (T0558)L109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)L116 Warning: unaligning (T0558)G154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)S170 Warning: unaligning (T0558)C196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pm7B)A223 Warning: unaligning (T0558)V198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pm7B)A223 Warning: unaligning (T0558)L277 because last residue in template chain is (2pm7B)A292 T0558 8 :VALF 2pm7B 6 :NAHN T0558 15 :PFA 2pm7B 13 :HDA T0558 21 :SPQH 2pm7B 19 :YYGK T0558 28 :GGSGWNKIAIINKDTK 2pm7B 26 :TCSSDKTIKIFEVEGE T0558 44 :EIVWEYP 2pm7B 44 :KLIDTLT T0558 52 :EKGWECNSVAATK 2pm7B 51 :GHEGPVWRVDWAH T0558 65 :AG 2pm7B 65 :KF T0558 67 :EILFSYSKG 2pm7B 68 :TILASCSYD T0558 79 :ITRD 2pm7B 82 :WKEE T0558 83 :GRE 2pm7B 87 :GRW T0558 86 :LWNIAAPAGC 2pm7B 92 :IAVHAVHSAS T0558 97 :MQTARILP 2pm7B 102 :VNSVQWAP T0558 105 :DG 2pm7B 112 :YG T0558 110 :VAWCG 2pm7B 117 :LVASS T0558 116 :PSTILEVNMK 2pm7B 122 :DGKVSVVEFK T0558 126 :GEVLSKTEFETGIERPHA 2pm7B 133 :NGTTSPIIIDAHAIGVNS T0558 148 :INKNKK 2pm7B 151 :ASWAPA T0558 155 :NYLVPLFATSEVREIAPN 2pm7B 171 :RKFVTGGADNLVKIWKYN T0558 173 :G 2pm7B 190 :D T0558 174 :QLLNSV 2pm7B 195 :VLESTL T0558 180 :KLSGTPFSSAFLD 2pm7B 202 :GHSDWVRDVAWSP T0558 193 :NGD 2pm7B 218 :LRS T0558 199 :ACGDAHCFVQLNL 2pm7B 224 :SVSQDRTCIIWTQ T0558 212 :ESNRIVRRVNANDIEG 2pm7B 239 :EQGPWKKTLLKEEKFP T0558 231 :FFVAQLFPLQNGGLYICNWQGH 2pm7B 255 :DVLWRASWSLSGNVLALSGGDN T0558 263 :QLVEID 2pm7B 277 :KVTLWK T0558 269 :SEGKVVWQ 2pm7B 284 :NLEGKWEP Number of specific fragments extracted= 27 number of extra gaps= 0 total=1974 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pm7B/T0558-2pm7B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2pm7B/T0558-2pm7B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pm7B read from 2pm7B/T0558-2pm7B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pm7B in template set Warning: unaligning (T0558)F4 because first residue in template chain is (2pm7B)V2 Warning: unaligning (T0558)L12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)I12 Warning: unaligning (T0558)P15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)I12 Warning: unaligning (T0558)G19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)D18 Warning: unaligning (T0558)S21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)D18 Warning: unaligning (T0558)L25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)A25 Warning: unaligning (T0558)V27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)A25 Warning: unaligning (T0558)A76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)I81 Warning: unaligning (T0558)M78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)I81 Warning: unaligning (T0558)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)L116 Warning: unaligning (T0558)L109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)L116 Warning: unaligning (T0558)G154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)S170 Warning: unaligning (T0558)C196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pm7B)A223 Warning: unaligning (T0558)V198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pm7B)A223 Warning: unaligning (T0558)I267 because last residue in template chain is (2pm7B)A292 T0558 5 :ILLVALF 2pm7B 3 :VIANAHN T0558 16 :FAQ 2pm7B 13 :HDA T0558 22 :PQ 2pm7B 19 :YY T0558 24 :H 2pm7B 22 :K T0558 28 :GGSGWNKIAIINKDTKEI 2pm7B 26 :TCSSDKTIKIFEVEGETH T0558 46 :VWEYP 2pm7B 46 :IDTLT T0558 52 :EKGWECNSVAATKA 2pm7B 51 :GHEGPVWRVDWAHP T0558 66 :GEILFSYSKG 2pm7B 67 :GTILASCSYD T0558 79 :IT 2pm7B 82 :WK T0558 81 :RDGRE 2pm7B 85 :ENGRW T0558 86 :LWNIA 2pm7B 92 :IAVHA T0558 92 :PAGCEMQTARILPD 2pm7B 97 :VHSASVNSVQWAPH T0558 106 :G 2pm7B 113 :G T0558 110 :VAWC 2pm7B 117 :LVAS T0558 115 :HPSTILEVNMK 2pm7B 121 :SDGKVSVVEFK T0558 126 :GEVLSKTEFETGIER 2pm7B 133 :NGTTSPIIIDAHAIG T0558 145 :FRQINKNK 2pm7B 148 :VNSASWAP T0558 155 :NYLVPLFATSEVREI 2pm7B 171 :RKFVTGGADNLVKIW T0558 170 :APN 2pm7B 190 :DAQ T0558 173 :GQLLNSV 2pm7B 194 :YVLESTL T0558 180 :KLSGTPFSSAFLDN 2pm7B 202 :GHSDWVRDVAWSPT T0558 194 :GD 2pm7B 219 :RS T0558 199 :ACGDAHCFVQLNL 2pm7B 224 :SVSQDRTCIIWTQ T0558 212 :ESNRIVRRVNANDIEGV 2pm7B 239 :EQGPWKKTLLKEEKFPD T0558 232 :FVAQLFPLQNGGLYICNWQGHDREAGKG 2pm7B 256 :VLWRASWSLSGNVLALSGGDNKVTLWKE T0558 260 :KHPQLVE 2pm7B 285 :LEGKWEP Number of specific fragments extracted= 26 number of extra gaps= 0 total=2000 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pm7B/T0558-2pm7B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2pm7B/T0558-2pm7B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pm7B read from 2pm7B/T0558-2pm7B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pm7B in template set Warning: unaligning (T0558)L25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)A25 Warning: unaligning (T0558)V27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)A25 Warning: unaligning (T0558)A76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)I81 Warning: unaligning (T0558)M78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)I81 Warning: unaligning (T0558)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)L116 Warning: unaligning (T0558)L109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)L116 Warning: unaligning (T0558)P141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2pm7B)S170 Warning: unaligning (T0558)G154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2pm7B)S170 Warning: unaligning (T0558)C196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pm7B)A223 Warning: unaligning (T0558)V198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pm7B)A223 T0558 21 :SPQH 2pm7B 19 :YYGK T0558 28 :GGSGWNKIAIINKDTKEI 2pm7B 26 :TCSSDKTIKIFEVEGETH T0558 46 :VWEYPLE 2pm7B 46 :IDTLTGH T0558 54 :GWECNSVAAT 2pm7B 53 :EGPVWRVDWA T0558 64 :KAGEILFSY 2pm7B 65 :KFGTILASC T0558 73 :SKG 2pm7B 76 :DGK T0558 79 :IT 2pm7B 82 :WK T0558 81 :RDGRE 2pm7B 85 :ENGRW T0558 86 :LWNIAAPAG 2pm7B 92 :IAVHAVHSA T0558 96 :EMQTARILP 2pm7B 101 :SVNSVQWAP T0558 105 :DG 2pm7B 112 :YG T0558 110 :VAWCG 2pm7B 117 :LVASS T0558 116 :PSTILEVNMKGE 2pm7B 122 :DGKVSVVEFKEN T0558 128 :VLSKTEFET 2pm7B 137 :SPIIIDAHA T0558 138 :IER 2pm7B 154 :APA T0558 155 :NYLVPLFATSEVREIAP 2pm7B 171 :RKFVTGGADNLVKIWKY T0558 172 :NGQ 2pm7B 189 :SDA T0558 175 :LLNSVKLS 2pm7B 196 :LESTLEGH T0558 183 :GTPFSSAFLD 2pm7B 205 :DWVRDVAWSP T0558 193 :NGD 2pm7B 218 :LRS T0558 199 :ACGDAHCFVQLNLESNR 2pm7B 224 :SVSQDRTCIIWTQDNEQ T0558 216 :IVRRVNANDIEG 2pm7B 244 :KKTLLKEEKFPD T0558 232 :FVAQLFPLQNGGLYICNWQGH 2pm7B 256 :VLWRASWSLSGNVLALSGGDN T0558 261 :HPQLVEIDSEGKVV 2pm7B 277 :KVTLWKENLEGKWE Number of specific fragments extracted= 24 number of extra gaps= 0 total=2024 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e0cA/T0558-3e0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3e0cA expands to /projects/compbio/data/pdb/3e0c.pdb.gz 3e0cA:Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1887, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1889, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1891, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1897, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1908, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1910, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1914, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1916, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1918, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1920, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1922, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1924, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1926, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3163, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3165, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3167, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3169, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3171, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 3173, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4947, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4949, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4951, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4953, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4955, because occupancy 0.500 <= existing 0.500 in 3e0cA Skipped atom 4957, because occupancy 0.500 <= existing 0.500 in 3e0cA # T0558 read from 3e0cA/T0558-3e0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e0cA read from 3e0cA/T0558-3e0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e0cA to template set # found chain 3e0cA in template set Warning: unaligning (T0558)H24 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)K74 Warning: unaligning (T0558)D41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)S97 Warning: unaligning (T0558)K43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)S97 Warning: unaligning (T0558)C57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)G119 Warning: unaligning (T0558)A108 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)L602 Warning: unaligning (T0558)L109 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)L602 Warning: unaligning (T0558)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)K627 Warning: unaligning (T0558)T132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)K627 Warning: unaligning (T0558)G154 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)S645 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)I848 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)I848 Warning: unaligning (T0558)P171 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)G856 Warning: unaligning (T0558)G173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)G856 T0558 4 :FILLVALFLVAPFAQGSSPQ 3e0cA 51 :PVKEVGMYGKIAVMELFRPK T0558 25 :LLVGGSGWNKIAIINK 3e0cA 76 :LLFILTAKYNACILEY T0558 44 :EIVWEYPL 3e0cA 98 :IDIITRAH T0558 58 :NSVAATKAGEILF 3e0cA 120 :IIGIIDPECRMIG T0558 71 :SYSKG 3e0cA 558 :IGLWT T0558 76 :AKMITRD 3e0cA 566 :ARILKLP T0558 83 :GRELWNIAAPAGCEMQTARILP 3e0cA 574 :FELLHKEMLGGEIIPRSILMTT T0558 105 :DGN 3e0cA 598 :SSH T0558 110 :VAWCG 3e0cA 603 :LCALG T0558 116 :PSTILEVNMK 3e0cA 608 :DGALFYFGLN T0558 126 :GEVL 3e0cA 621 :GLLS T0558 134 :FETGIERPHA 3e0cA 628 :KVTLGTQPTV T0558 148 :INKNK 3e0cA 638 :LRTFR T0558 155 :NYLVPLFATS 3e0cA 646 :TTNVFACSDR T0558 167 :REIA 3e0cA 849 :VVFQ T0558 174 :QLLNSV 3e0cA 857 :KLQTVA T0558 180 :KLSGTPFSSAFLDN 3e0cA 865 :EVKGAVYSMVEFNG T0558 196 :CLVACGDAH 3e0cA 879 :KLLASINST T0558 206 :FVQLNLESNRIVRRVNAND 3e0cA 888 :VRLYEWTTEKELRTECNHY T0558 231 :FFVAQLFPLQNGGLYICNWQGHDR 3e0cA 907 :NNIMALYLKTKGDFILVGDLMRSV T0558 263 :QLVEIDSEGKV 3e0cA 931 :LLLAYKPMEGN T0558 274 :VWQLNDKVKFGMI 3e0cA 954 :MSAVEILDDDNFL T0558 287 :STICPI 3e0cA 971 :AFNLFV Number of specific fragments extracted= 23 number of extra gaps= 2 total=2047 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e0cA/T0558-3e0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3e0cA/T0558-3e0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e0cA read from 3e0cA/T0558-3e0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3e0cA in template set Warning: unaligning (T0558)L103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)G551 Warning: unaligning (T0558)P104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)G551 Warning: unaligning (T0558)Y156 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)L602 Warning: unaligning (T0558)L157 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)L602 Warning: unaligning (T0558)N177 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)K627 Warning: unaligning (T0558)V179 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)K627 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)I848 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)I848 Warning: unaligning (T0558)L211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3e0cA)G856 Warning: unaligning (T0558)N214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)G856 T0558 2 :KNFILLV 3e0cA 50 :RPVKEVG T0558 10 :LFL 3e0cA 57 :MYG T0558 14 :APFAQGS 3e0cA 60 :KIAVMEL T0558 21 :SPQ 3e0cA 463 :VAH T0558 24 :HLLVGG 3e0cA 467 :QLIQIT T0558 32 :WNKIAIINKDTKEIVWEYPLEKGWECNS 3e0cA 473 :SASVRLVSQEPKALVSEWKEPQAKNISV T0558 62 :ATKAGEILFSYSKG 3e0cA 501 :ASCNSSQVVVAVGR T0558 76 :AKMIT 3e0cA 516 :LYYLQ T0558 81 :RDGR 3e0cA 522 :HPQE T0558 85 :ELWNIAAPAGCEMQTARI 3e0cA 528 :QISHTEMEHEVACLDITP T0558 106 :GNALVAWCGHPSTILEVNMK 3e0cA 553 :SPLCAIGLWTDISARILKLP T0558 126 :GEVLSKTEF 3e0cA 574 :FELLHKEML T0558 136 :TGIER 3e0cA 583 :GGEII T0558 145 :FRQINKN 3e0cA 588 :PRSILMT T0558 152 :KKGN 3e0cA 597 :ESSH T0558 158 :VPLFATSEVREI 3e0cA 603 :LCALGDGALFYF T0558 170 :APN 3e0cA 617 :NIE T0558 173 :GQLL 3e0cA 621 :GLLS T0558 180 :KLSGT 3e0cA 629 :VTLGT T0558 185 :PFSSAFLDNGDCLVACGDAH 3e0cA 721 :PRKICYQEVSQCFGVLSSRI T0558 207 :VQLN 3e0cA 849 :VVFQ T0558 215 :RIVRRVNANDI 3e0cA 859 :QTVAEKEVKGA T0558 233 :VAQLFPLQN 3e0cA 870 :VYSMVEFNG T0558 243 :G 3e0cA 879 :K T0558 245 :YICNW 3e0cA 880 :LLASI T0558 251 :GHDREAGKG 3e0cA 885 :NSTVRLYEW T0558 260 :KHPQLVEIDSEGKVVWQL 3e0cA 895 :TEKELRTECNHYNNIMAL T0558 278 :NDKVKFGMISTICPI 3e0cA 916 :TKGDFILVGDLMRSV Number of specific fragments extracted= 28 number of extra gaps= 3 total=2075 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3e0cA/T0558-3e0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3e0cA/T0558-3e0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e0cA read from 3e0cA/T0558-3e0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3e0cA in template set Warning: unaligning (T0558)Y156 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)F829 Warning: unaligning (T0558)L157 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)F829 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (3e0cA)I848 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (3e0cA)I848 Warning: unaligning (T0558)N172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3e0cA)G856 T0558 23 :QHLLVGGSGWNKIAIINKDTKEIVWEYPLEKGWECNSVAATKAGEILFSYSKGAKMITRDG 3e0cA 464 :AHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQ T0558 84 :RELWNIAAPAG 3e0cA 527 :RQISHTEMEHE T0558 97 :MQTARILP 3e0cA 538 :VACLDITP T0558 105 :DGNALVAWCGHPSTILEVN 3e0cA 552 :LSPLCAIGLWTDISARILK T0558 124 :MKGEVLSKTEFET 3e0cA 572 :PSFELLHKEMLGG T0558 148 :INKNKKG 3e0cA 818 :SCKLGKD T0558 155 :N 3e0cA 827 :T T0558 158 :VPLFATS 3e0cA 830 :IVGTAMV T0558 167 :REIA 3e0cA 849 :VVFQ T0558 174 :QLLNSVKLSGTPFSSAFL 3e0cA 859 :QTVAEKEVKGAVYSMVEF T0558 193 :NGDCLVACGDAHCFVQLN 3e0cA 877 :NGKLLASINSTVRLYEWT T0558 212 :ESNRIVRRVNAN 3e0cA 895 :TEKELRTECNHY T0558 229 :QLFFVAQLFPLQN 3e0cA 907 :NNIMALYLKTKGD T0558 244 :LYICNWQGH 3e0cA 921 :ILVGDLMRS T0558 262 :PQLVEIDSE 3e0cA 930 :VLLLAYKPM T0558 271 :GKVVWQLNDKVKF 3e0cA 940 :GNFEEIARDFNPN T0558 285 :MISTICPIRE 3e0cA 953 :WMSAVEILDD Number of specific fragments extracted= 17 number of extra gaps= 2 total=2092 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kv9A/T0558-1kv9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kv9A expands to /projects/compbio/data/pdb/1kv9.pdb.gz 1kv9A:# T0558 read from 1kv9A/T0558-1kv9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kv9A read from 1kv9A/T0558-1kv9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kv9A to template set # found chain 1kv9A in template set T0558 4 :FILLVALFLVAPFAQGSSPQH 1kv9A 87 :KELWRYDPEVAKVKARTSCCD T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPL 1kv9A 119 :KVYVGTLDGRLIALDAKTGKAIWSQQT T0558 53 :KGWECN 1kv9A 148 :PAKPYS T0558 59 :SVAAT 1kv9A 157 :APRVV T0558 65 :AGEILFSY 1kv9A 162 :KGKVIIGN T0558 73 :SKG 1kv9A 172 :AEY T0558 76 :AKMITRD 1kv9A 180 :VSAYDAD T0558 83 :GRELWNIA 1kv9A 188 :GKLAWRFY T0558 91 :APAGC 1kv9A 297 :TATQQ T0558 97 :MQTARILPDG 1kv9A 302 :ITLAELNIDG T0558 107 :NALVAWCG 1kv9A 315 :KVLMQAPK T0558 116 :PSTILEVNMK 1kv9A 323 :NGFFYVLDRT T0558 126 :GEVLSKTEFETG 1kv9A 334 :GKLISAEKFGKV T0558 138 :IERPHA 1kv9A 380 :AHNWHS T0558 148 :INKNKKGNYLVPLFATS 1kv9A 386 :MSFNPGTGLVYIPYQEV T0558 165 :EVREIAPN 1kv9A 439 :ALLAWDPV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 1kv9A 448 :QKAAWKVPYPTHWNGGTLSTAGNLVFQGTAAGQMHAYSADKGEALWQFEAQS T0558 231 :FFVAQLFP 1kv9A 500 :GIVAAPMT T0558 239 :LQNGGLYICNWQGH 1kv9A 509 :ELAGRQYVAIMAGW T0558 253 :DREAGK 1kv9A 538 :GMKNRS T0558 263 :QLVEIDSEGKV 1kv9A 544 :RLLVFALDGKA T0558 274 :VWQLNDKVKFGMI 1kv9A 556 :LPPPAPAPAKVER Number of specific fragments extracted= 22 number of extra gaps= 0 total=2114 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kv9A/T0558-1kv9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1kv9A/T0558-1kv9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kv9A read from 1kv9A/T0558-1kv9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kv9A in template set Warning: unaligning (T0558)G114 because of BadResidue code BAD_PEPTIDE in next template residue (1kv9A)Y268 Warning: unaligning (T0558)H115 because of BadResidue code BAD_PEPTIDE at template residue (1kv9A)Y268 T0558 3 :NFILLVALFL 1kv9A 97 :AKVKARTSCC T0558 14 :APFAQGSSPQ 1kv9A 107 :DAVNRGVALW T0558 24 :HLLVGGSGWNKIAIINKDTKEIVWEYP 1kv9A 118 :DKVYVGTLDGRLIALDAKTGKAIWSQQ T0558 51 :LEKGWEC 1kv9A 148 :PAKPYSI T0558 58 :NSVAAT 1kv9A 156 :GAPRVV T0558 65 :AGEILFSYSKG 1kv9A 162 :KGKVIIGNGGA T0558 76 :AKMIT 1kv9A 180 :VSAYD T0558 81 :RDGRELWNIA 1kv9A 186 :DTGKLAWRFY T0558 95 :CEMQTARILPDGNALVAWC 1kv9A 230 :TVWDSMAYDPELDLLYVGT T0558 116 :PSTILEVNMK 1kv9A 269 :LSSILAIRPD T0558 126 :GEVLSKTEFETG 1kv9A 280 :GKLAWHYQVTPG T0558 138 :IER 1kv9A 299 :TQQ T0558 145 :FRQINKNKKGN 1kv9A 302 :ITLAELNIDGK T0558 156 :YLVPLFATSEVREIAPN 1kv9A 316 :VLMQAPKNGFFYVLDRT T0558 173 :GQLLNSVKLSGT 1kv9A 334 :GKLISAEKFGKV T0558 185 :PFSSAFLDNGDCLVACGDAH 1kv9A 383 :WHSMSFNPGTGLVYIPYQEV T0558 205 :CFVQLNLESNRIVRRVNANDI 1kv9A 439 :ALLAWDPVKQKAAWKVPYPTH T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1kv9A 460 :WNGGTLSTAGNLVFQGTAAGQMHAYSA T0558 260 :KHPQLVEIDSEGKVV 1kv9A 488 :KGEALWQFEAQSGIV T0558 275 :WQL 1kv9A 506 :MTF T0558 278 :NDKVKFGMIST 1kv9A 510 :LAGRQYVAIMA Number of specific fragments extracted= 21 number of extra gaps= 1 total=2135 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kv9A/T0558-1kv9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1kv9A/T0558-1kv9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kv9A read from 1kv9A/T0558-1kv9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kv9A in template set T0558 23 :QHLLVGGSGWNKIAIINKDTKEIVWEYPL 1kv9A 66 :DGVIYTSMSWSRVIAVDAASGKELWRYDP T0558 52 :EKGWECN 1kv9A 97 :AKVKART T0558 59 :SVAATKAGEILFSY 1kv9A 111 :RGVALWGDKVYVGT T0558 73 :SKGAKMITRDG 1kv9A 126 :DGRLIALDAKT T0558 84 :RELWNIAA 1kv9A 138 :KAIWSQQT T0558 92 :PAGCEMQTARILPDGNALVAWCGH 1kv9A 149 :AKPYSITGAPRVVKGKVIIGNGGA T0558 116 :PSTILEVNMK 1kv9A 177 :RGFVSAYDAD T0558 126 :GEVLSKTEFET 1kv9A 188 :GKLAWRFYTVP T0558 145 :FRQINKNKKGNYLVPLFATS 1kv9A 232 :WDSMAYDPELDLLYVGTGNG T0558 165 :EVREIAPN 1kv9A 271 :SILAIRPD T0558 173 :GQLLNSVKLS 1kv9A 280 :GKLAWHYQVT T0558 183 :GTPFSSAFLDNGDCLVACGDAH 1kv9A 313 :PRKVLMQAPKNGFFYVLDRTNG T0558 205 :CFVQLNLESNRIVRRVNA 1kv9A 439 :ALLAWDPVKQKAAWKVPY T0558 229 :QLFFVAQLFPLQNGGLYICNWQG 1kv9A 457 :PTHWNGGTLSTAGNLVFQGTAAG T0558 263 :QLVEID 1kv9A 480 :QMHAYS T0558 269 :SEGKVVWQLNDKVKFGMISTICPIRE 1kv9A 487 :DKGEALWQFEAQSGIVAAPMTFELAG Number of specific fragments extracted= 16 number of extra gaps= 0 total=2151 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiqA/T0558-1yiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yiqA expands to /projects/compbio/data/pdb/1yiq.pdb.gz 1yiqA:# T0558 read from 1yiqA/T0558-1yiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiqA read from 1yiqA/T0558-1yiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yiqA to template set # found chain 1yiqA in template set T0558 14 :APFAQGSSPQH 1yiqA 62 :VEATPIVVDGV T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPL 1yiqA 123 :KVYVGVLDGRLEAIDAKTGQRAWSVDT T0558 52 :EKGWECN 1yiqA 154 :KRSYTIT T0558 59 :SVAAT 1yiqA 162 :APRVV T0558 65 :AGEILFSY 1yiqA 167 :NGKVVIGN T0558 73 :SKG 1yiqA 177 :AEF T0558 76 :AKMITRD 1yiqA 185 :VTAYDAE T0558 83 :GRELWNIA 1yiqA 193 :GKEAWRFY T0558 97 :MQTARILPDG 1yiqA 307 :MILAELPIDG T0558 107 :NALVAWCG 1yiqA 320 :KVLMQAPK T0558 116 :PSTILEVNMK 1yiqA 328 :NGFFYVIDRA T0558 126 :GEVLSKTEFETG 1yiqA 339 :GELLSAKGIVPQ T0558 138 :IERPHA 1yiqA 388 :AHDWQP T0558 148 :INKNKKGNYLVPLFATS 1yiqA 394 :MSYNPDTGLVYIPAHIM T0558 165 :EVREIAPN 1yiqA 456 :KLIAWDPV T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 1yiqA 465 :QQAAWEVPYVTIFNGGTLSTAGNLVFEGSADGRVIAYAADTGEKLWEQPAAS T0558 231 :FFVAQLFPLQ 1yiqA 517 :GVMAAPVTYS T0558 241 :NGGLYICNWQGH 1yiqA 528 :DGEQYVTFMAGW T0558 253 :DREAGK 1yiqA 555 :GVQPYA T0558 263 :QLVEIDSEGKV 1yiqA 561 :QVLTYKLGGTA T0558 274 :VWQLNDKVKFG 1yiqA 573 :LQEPAPRPDTP T0558 291 :P 1yiqA 584 :K Number of specific fragments extracted= 22 number of extra gaps= 0 total=2173 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiqA/T0558-1yiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1yiqA/T0558-1yiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiqA read from 1yiqA/T0558-1yiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yiqA in template set T0558 2 :KNFILLVALFLVAPFAQGSSPQHLLVGGSGWNKIAIINKDTKEIVWEYP 1yiqA 49 :GLAWSYKLDLDRGVEATPIVVDGVMYTTGPFSVVYALDARDGRLIWKYD T0558 51 :LEKGWECNSVAATK 1yiqA 108 :ACCDAVNRGVAVWK T0558 66 :GEILFSYSKG 1yiqA 122 :GKVYVGVLDG T0558 76 :AKMIT 1yiqA 133 :LEAID T0558 81 :RDGRELWNIA 1yiqA 139 :KTGQRAWSVD T0558 91 :APAGCEMQTARILPDGNALVAWC 1yiqA 153 :HKRSYTITGAPRVVNGKVVIGNG T0558 114 :GHPSTILEVNMK 1yiqA 180 :GVRGYVTAYDAE T0558 126 :GEVLS 1yiqA 193 :GKEAW T0558 133 :EFETG 1yiqA 198 :RFYTV T0558 138 :IER 1yiqA 304 :TQH T0558 145 :FRQINKNKKGN 1yiqA 307 :MILAELPIDGK T0558 156 :YLVPLFATSEVREIAPN 1yiqA 321 :VLMQAPKNGFFYVIDRA T0558 173 :GQLLNSV 1yiqA 339 :GELLSAK T0558 180 :KLSGT 1yiqA 347 :IVPQS T0558 185 :PFSSAFLDNGDCLVACGDAH 1yiqA 391 :WQPMSYNPDTGLVYIPAHIM T0558 205 :CFVQLNLESNRIVRRVNANDIE 1yiqA 456 :KLIAWDPVKQQAAWEVPYVTIF T0558 234 :AQLFPLQNGGLYICNWQGHDREAGKG 1yiqA 478 :NGGTLSTAGNLVFEGSADGRVIAYAA T0558 260 :KHPQLVEIDSEGKVV 1yiqA 505 :TGEKLWEQPAASGVM T0558 275 :WQL 1yiqA 523 :VTY T0558 278 :NDKVKFGMISTI 1yiqA 527 :VDGEQYVTFMAG Number of specific fragments extracted= 20 number of extra gaps= 0 total=2193 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yiqA/T0558-1yiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1yiqA/T0558-1yiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yiqA read from 1yiqA/T0558-1yiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yiqA in template set T0558 23 :QHLLVGGSGWNKIAIINKDTKEIVWEYPL 1yiqA 70 :DGVMYTTGPFSVVYALDARDGRLIWKYDP T0558 52 :EKGWECN 1yiqA 101 :DRHRAGE T0558 59 :SVAATKAGEILFSY 1yiqA 115 :RGVAVWKGKVYVGV T0558 73 :SKGAKMIT 1yiqA 130 :DGRLEAID T0558 81 :RDGRELWNIAA 1yiqA 139 :KTGQRAWSVDT T0558 92 :PAG 1yiqA 152 :DHK T0558 95 :CEMQTARILPDGNALVAW 1yiqA 157 :YTITGAPRVVNGKVVIGN T0558 116 :PSTILEVNMK 1yiqA 182 :RGYVTAYDAE T0558 126 :GEVLSKTEFET 1yiqA 193 :GKEAWRFYTVP T0558 154 :G 1yiqA 316 :G T0558 155 :NYLVPLFATSEVREIAPN 1yiqA 320 :KVLMQAPKNGFFYVIDRA T0558 173 :GQLLNSVKLS 1yiqA 339 :GELLSAKGIV T0558 183 :GTPFSSAFLDNGDCLVACGD 1yiqA 389 :HDWQPMSYNPDTGLVYIPAH T0558 205 :CFVQLNLESNRIVRRVN 1yiqA 456 :KLIAWDPVKQQAAWEVP T0558 228 :VQLFFVAQLFPLQNGGLYICNWQG 1yiqA 473 :YVTIFNGGTLSTAGNLVFEGSADG T0558 263 :QLVEID 1yiqA 497 :RVIAYA T0558 269 :SEGKVVWQLN 1yiqA 504 :DTGEKLWEQP Number of specific fragments extracted= 17 number of extra gaps= 0 total=2210 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2agyA/T0558-2agyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2agyA expands to /projects/compbio/data/pdb/2agy.pdb.gz 2agyA:Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 2agyA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 2agyA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 2agyA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 2agyA # T0558 read from 2agyA/T0558-2agyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2agyA read from 2agyA/T0558-2agyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2agyA to template set # found chain 2agyA in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)V155 Warning: unaligning (T0558)H115 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)P201 Warning: unaligning (T0558)P116 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)P201 Warning: unaligning (T0558)F186 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)L330 Warning: unaligning (T0558)S187 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)L330 T0558 19 :GSSPQHLLVGGS 2agyA 83 :SAPQENRIYVMD T0558 31 :GWNKIAIINKDTKEIVWEYPLE 2agyA 101 :TESRVHVYDYTNGKFLGMVPTA T0558 56 :ECNSVAATKAGEILFSYSKG 2agyA 123 :FNGHVQVSNDGKKIYTMTTY T0558 77 :KMITRD 2agyA 156 :EVWDAD T0558 83 :GRELWNIAAPAGC 2agyA 163 :LTFEKEISLPPKR T0558 97 :MQT 2agyA 176 :VQG T0558 100 :ARILPDGNALVAWCG 2agyA 185 :FRQTTDGKFIVLQNA T0558 117 :ST 2agyA 202 :AT T0558 119 :ILEVNMK 2agyA 205 :IGIVDVA T0558 126 :GEVLSKTE 2agyA 213 :GDYVEDVT T0558 137 :GIERPHA 2agyA 221 :AAAGCWS T0558 148 :INKNKKG 2agyA 228 :VIPQPNR T0558 155 :NYLVPLFATSEVREIAPN 2agyA 236 :RSFMTICGDGGLLTINLG T0558 173 :GQLLNSV 2agyA 256 :GKVASQS T0558 180 :KLSGT 2agyA 269 :SVKDD T0558 185 :P 2agyA 328 :Y T0558 188 :SAFLD 2agyA 331 :VGLHR T0558 193 :NGDCLVACGDAH 2agyA 337 :SGRMYVFMHPDG T0558 205 :CFVQLNLESNRIVRRVNAND 2agyA 359 :EIWVMDTKTKQRVARIPGRD T0558 233 :VAQLFPLQNGGLYICNWQG 2agyA 379 :ALSMTIDQQRNLMLTLDGG T0558 263 :QLVEIDSEG 2agyA 398 :NVNVYDISQ T0558 272 :KV 2agyA 410 :KL T0558 274 :VWQLNDKVKF 2agyA 422 :SLQVQFHPVG Number of specific fragments extracted= 23 number of extra gaps= 3 total=2233 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2agyA/T0558-2agyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2agyA/T0558-2agyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2agyA read from 2agyA/T0558-2agyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2agyA in template set Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)V155 Warning: unaligning (T0558)H115 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)P201 Warning: unaligning (T0558)P116 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)P201 Warning: unaligning (T0558)P185 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)L330 T0558 18 :QGSSPQ 2agyA 82 :VSAPQE T0558 24 :HLLVGGS 2agyA 89 :RIYVMDS T0558 31 :GWNKIAIINKDTKEIVWEYP 2agyA 101 :TESRVHVYDYTNGKFLGMVP T0558 54 :GWECNSVAATKAGEILFSYS 2agyA 121 :TAFNGHVQVSNDGKKIYTMT T0558 77 :KMIT 2agyA 156 :EVWD T0558 81 :RDGRELWNIA 2agyA 161 :DKLTFEKEIS T0558 94 :GCEMQT 2agyA 173 :PKRVQG T0558 100 :ARILPDGNALVAWCG 2agyA 185 :FRQTTDGKFIVLQNA T0558 117 :ST 2agyA 202 :AT T0558 119 :ILEVNMK 2agyA 205 :IGIVDVA T0558 126 :GEVLS 2agyA 213 :GDYVE T0558 133 :EFETGIE 2agyA 218 :DVTAAAG T0558 145 :FRQINKNKKGN 2agyA 225 :CWSVIPQPNRP T0558 156 :YLVPLFATSEVREIA 2agyA 237 :SFMTICGDGGLLTIN T0558 171 :PNGQLLNS 2agyA 254 :EDGKVASQ T0558 179 :V 2agyA 267 :M T0558 180 :KLSGT 2agyA 269 :SVKDD T0558 186 :FSSAFLDNGDCLVACG 2agyA 331 :VGLHRASGRMYVFMHP T0558 202 :DAHCFVQLNLESNRIVRRVNAND 2agyA 356 :PAAEIWVMDTKTKQRVARIPGRD T0558 233 :VAQLFPLQNGGLYICNWQG 2agyA 379 :ALSMTIDQQRNLMLTLDGG T0558 253 :DREAGKG 2agyA 398 :NVNVYDI T0558 260 :KHPQLVEIDSEGKVVWQL 2agyA 408 :EPKLLRTIEGAAEASLQV T0558 278 :NDK 2agyA 429 :PVG Number of specific fragments extracted= 23 number of extra gaps= 3 total=2256 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2agyA/T0558-2agyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2agyA/T0558-2agyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2agyA read from 2agyA/T0558-2agyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2agyA in template set Warning: unaligning (T0558)G75 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)V155 Warning: unaligning (T0558)A76 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)V155 Warning: unaligning (T0558)H115 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)P201 Warning: unaligning (T0558)P116 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)P201 Warning: unaligning (T0558)P185 because of BadResidue code BAD_PEPTIDE in next template residue (2agyA)L330 Warning: unaligning (T0558)F186 because of BadResidue code BAD_PEPTIDE at template residue (2agyA)L330 T0558 18 :QGSSPQHLLVGGS 2agyA 82 :VSAPQENRIYVMD T0558 31 :GWNKIAIINKDTKEIVWEYPLE 2agyA 101 :TESRVHVYDYTNGKFLGMVPTA T0558 56 :ECNSVAATKAG 2agyA 123 :FNGHVQVSNDG T0558 67 :EILFSY 2agyA 135 :KIYTMT T0558 73 :SK 2agyA 152 :SD T0558 77 :KMITRDG 2agyA 156 :EVWDADK T0558 84 :RELWNIAAPAG 2agyA 164 :TFEKEISLPPK T0558 95 :CEMQTARILPDGNALVAWCG 2agyA 180 :NYDGLFRQTTDGKFIVLQNA T0558 117 :ST 2agyA 202 :AT T0558 119 :ILEVNMK 2agyA 205 :IGIVDVA T0558 126 :GEVLSKT 2agyA 213 :GDYVEDV T0558 143 :AQFRQINKN 2agyA 220 :TAAAGCWSV T0558 152 :KKGNYLVPLFATSEVR 2agyA 233 :NRPRSFMTICGDGGLL T0558 168 :EIAPNGQLLNSVKLS 2agyA 251 :NLGEDGKVASQSRSK T0558 183 :GT 2agyA 327 :GY T0558 187 :SSAFLDN 2agyA 331 :VGLHRAS T0558 242 :GGLYICNWQGHDREAGKGKHPQLVEID 2agyA 338 :GRMYVFMHPDGKEGTHKFPAAEIWVMD T0558 282 :KFGMISTICPIRE 2agyA 366 :KTKQRVARIPGRD Number of specific fragments extracted= 18 number of extra gaps= 3 total=2274 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3li3A/T0558-3li3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3li3A expands to /projects/compbio/data/pdb/3li3.pdb.gz 3li3A:# T0558 read from 3li3A/T0558-3li3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3li3A read from 3li3A/T0558-3li3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3li3A to template set # found chain 3li3A in template set T0558 3 :NFILLVALFLVAPFAQGSSPQHLLVGGS 3li3A 9 :LFTKVTEDIPGAEGPVFDKNGDFYIVAP T0558 31 :GWNKIAIINKDTKEIVWEYPL 3li3A 44 :PAGEILRIDLKTGKKTVICKP T0558 52 :EKGWECNSVAATKAG 3li3A 68 :GYGGIPAGCQCDRDA T0558 67 :EILFSYSKG 3li3A 84 :QLFVADMRL T0558 76 :AKMITRDGRELWNI 3li3A 94 :LLVVQTDGTFEEIA T0558 90 :AAPAGCE 3li3A 109 :KDSEGRR T0558 97 :MQTARILPDGNALVAWC 3li3A 119 :CNECAFDYEGNLWITAP T0558 114 :GHPSTILEVNMKGEVLSKT 3li3A 150 :EKFGSIYCFTTDGQMIQVD T0558 135 :ETG 3li3A 169 :TAF T0558 139 :ERPHA 3li3A 172 :QFPNG T0558 148 :INK 3li3A 177 :IAV T0558 151 :NKKG 3li3A 182 :MNDG T0558 155 :NYLVPLFATSEVREIAPN 3li3A 189 :QLIVAETPTKKLWSYDIK T0558 173 :GQL 3li3A 209 :AKI T0558 176 :LNSV 3li3A 214 :KKVW T0558 180 :KLSGT 3li3A 219 :HIPGT T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 3li3A 228 :ADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPF T0558 231 :FFVAQLFPLQNG 3li3A 268 :EKPSNLHFKPQT T0558 243 :GLYICNWQGH 3li3A 281 :TIFVTEHENN T0558 263 :QLVEIDSEGKV 3li3A 291 :AVWKFEWQRNG T0558 274 :VWQLNDKVKF 3li3A 303 :KQYCETLKFG Number of specific fragments extracted= 21 number of extra gaps= 0 total=2295 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3li3A/T0558-3li3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3li3A/T0558-3li3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3li3A read from 3li3A/T0558-3li3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3li3A in template set T0558 3 :NFILLVALFL 3li3A 9 :LFTKVTEDIP T0558 14 :APFAQGSSPQ 3li3A 19 :GAEGPVFDKN T0558 24 :HLLVGGSG 3li3A 30 :DFYIVAPE T0558 32 :WNKIAIINKDTKEIVWEYP 3li3A 45 :AGEILRIDLKTGKKTVICK T0558 51 :LEKGWECNSVAATKAGEILFSYSKG 3li3A 67 :NGYGGIPAGCQCDRDANQLFVADMR T0558 76 :AKMITRDGRELWNIA 3li3A 94 :LLVVQTDGTFEEIAK T0558 91 :APAG 3li3A 112 :EGRR T0558 95 :CEMQTARILPDGNALVAWC 3li3A 117 :QGCNECAFDYEGNLWITAP T0558 114 :GHPSTILEVNMKGEVLS 3li3A 150 :EKFGSIYCFTTDGQMIQ T0558 134 :FETGIER 3li3A 167 :VDTAFQF T0558 145 :FRQINKN 3li3A 174 :PNGIAVR T0558 152 :KKGN 3li3A 183 :NDGR T0558 156 :YLVPLFATSEVREIAPN 3li3A 190 :LIVAETPTKKLWSYDIK T0558 173 :G 3li3A 208 :P T0558 174 :QLLNSV 3li3A 212 :ENKKVW T0558 180 :KLSGT 3li3A 219 :HIPGT T0558 185 :PFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNANDIE 3li3A 228 :ADGMDFDEDNNLLVANWGSSHIEVFGPDGGQPKMRIRCPFEK T0558 233 :VAQLFPLQNGG 3li3A 270 :PSNLHFKPQTK T0558 244 :LYICNWQGHDREAGKGK 3li3A 282 :IFVTEHENNAVWKFEWQ Number of specific fragments extracted= 19 number of extra gaps= 0 total=2314 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3li3A/T0558-3li3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 3li3A/T0558-3li3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3li3A read from 3li3A/T0558-3li3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3li3A in template set T0558 57 :CNSVAATKAGEILFSY 3li3A 20 :AEGPVFDKNGDFYIVA T0558 73 :SKGAKMITRDGRELWNIAA 3li3A 45 :AGEILRIDLKTGKKTVICK T0558 92 :PAG 3li3A 66 :VNG T0558 95 :CEMQTARILPDGNALVAWCG 3li3A 71 :GIPAGCQCDRDANQLFVADM T0558 116 :PSTILEVNMKGEVLS 3li3A 91 :RLGLLVVQTDGTFEE T0558 132 :TEFETGIERPHAQFRQINKNKKGNYLVPLFATS 3li3A 106 :IAKKDSEGRRMQGCNECAFDYEGNLWITAPAGE T0558 165 :EVREIAPNGQLLNSVKLSGTPFSSAFL 3li3A 154 :SIYCFTTDGQMIQVDTAFQFPNGIAVR T0558 192 :DNGDCLVACGDAHCFVQLNLESN 3li3A 186 :RPYQLIVAETPTKKLWSYDIKGP T0558 215 :RIVRRVNAN 3li3A 215 :KVWGHIPGT T0558 225 :IE 3li3A 224 :HE T0558 231 :FFVAQLFPLQNGGLYICNWQGH 3li3A 226 :GGADGMDFDEDNNLLVANWGSS T0558 263 :QLVEIDSEGK 3li3A 248 :HIEVFGPDGG T0558 282 :KFGMIST 3li3A 258 :QPKMRIR Number of specific fragments extracted= 13 number of extra gaps= 0 total=2327 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2p4oA/T0558-2p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2p4oA expands to /projects/compbio/data/pdb/2p4o.pdb.gz 2p4oA:Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2p4oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2p4oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2063, because occupancy 0.500 <= existing 0.500 in 2p4oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2067, because occupancy 0.500 <= existing 0.500 in 2p4oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2069, because occupancy 0.500 <= existing 0.500 in 2p4oA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2073, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2194, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2198, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2200, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2202, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2204, because occupancy 0.500 <= existing 0.500 in 2p4oA Skipped atom 2206, because occupancy 0.500 <= existing 0.500 in 2p4oA # T0558 read from 2p4oA/T0558-2p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p4oA read from 2p4oA/T0558-2p4oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2p4oA to template set # found chain 2p4oA in template set Warning: unaligning (T0558)G29 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)H49 Warning: unaligning (T0558)S30 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)H49 Warning: unaligning (T0558)G126 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)P147 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)L190 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)L190 Warning: unaligning (T0558)Q263 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)V292 Warning: unaligning (T0558)L264 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)V292 T0558 3 :NFILLVALFLVAPFAQGSSPQHLLVG 2p4oA 22 :KIITSFPVNTFLENLASAPDGTIFVT T0558 31 :GWNKIAIINKD 2p4oA 50 :EVGEIVSITPD T0558 43 :KEIVWEYPLEKG 2p4oA 61 :GNQQIHATVEGK T0558 57 :CNSVAATKAGEILFSYSKG 2p4oA 73 :VSGLAFTSNGDLVATGWNA T0558 76 :AKMITRD 2p4oA 96 :VVSLVKS T0558 83 :GRELWNIAAPAGCEMQTARILPDGNALVAWCG 2p4oA 104 :GTVETLLTLPDAIFLNGITPLSDTQYLTADSY T0558 116 :PSTILEVNMK 2p4oA 136 :RGAIWLIDVV T0558 127 :EVLSKTEFETG 2p4oA 148 :SGSIWLEHPML T0558 138 :IERPHAQFRQINKNKK 2p4oA 163 :SESVFPAANGLKRFGN T0558 155 :NYLVPLFATS 2p4oA 179 :FLYVSNTEKM T0558 167 :REIAPN 2p4oA 191 :LRIPVD T0558 173 :GQLLNSV 2p4oA 198 :TDKPGEP T0558 180 :KLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESN 2p4oA 208 :VEQTNIDDFAFDVEGNLYGATHIYNSVVRIAPDRS T0558 215 :RIVRRVNAND 2p4oA 244 :TIIAQAEQGV T0558 231 :FFVAQLFP 2p4oA 254 :IGSTAVAF T0558 239 :LQNG 2p4oA 265 :EGDC T0558 243 :GLYICNWQGH 2p4oA 270 :AIYVVTNGGM T0558 253 :DREA 2p4oA 282 :PPPT T0558 258 :KGKHP 2p4oA 286 :GVVPA T0558 265 :VEIDSEGKV 2p4oA 293 :VRLEVGKPG Number of specific fragments extracted= 20 number of extra gaps= 4 total=2347 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2p4oA/T0558-2p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2p4oA/T0558-2p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p4oA read from 2p4oA/T0558-2p4oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p4oA in template set Warning: unaligning (T0558)G29 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)H49 Warning: unaligning (T0558)S30 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)H49 Warning: unaligning (T0558)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)L190 Warning: unaligning (T0558)V166 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)L190 Warning: unaligning (T0558)K282 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)V292 Warning: unaligning (T0558)F283 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)V292 T0558 3 :NF 2p4oA 23 :II T0558 6 :LLVALFL 2p4oA 25 :TSFPVNT T0558 14 :APFAQGSSPQ 2p4oA 32 :FLENLASAPD T0558 24 :HLLVG 2p4oA 43 :TIFVT T0558 31 :GWNKIAIINKD 2p4oA 50 :EVGEIVSITPD T0558 43 :KEIVWEYPLEK 2p4oA 61 :GNQQIHATVEG T0558 56 :ECNSVAATKAGEILFSYSKG 2p4oA 72 :KVSGLAFTSNGDLVATGWNA T0558 76 :AKMIT 2p4oA 94 :IPVVS T0558 81 :RDGRELWNIAAPAGCEMQTARILPDGNALVAWC 2p4oA 102 :SDGTVETLLTLPDAIFLNGITPLSDTQYLTADS T0558 115 :HPSTILEVNMK 2p4oA 135 :YRGAIWLIDVV T0558 126 :GEVLSKT 2p4oA 149 :GSIWLEH T0558 136 :TG 2p4oA 156 :PM T0558 138 :IERPHAQFRQINKNKK 2p4oA 163 :SESVFPAANGLKRFGN T0558 155 :NYLVPLFATS 2p4oA 179 :FLYVSNTEKM T0558 167 :REIAPN 2p4oA 191 :LRIPVD T0558 173 :GQL 2p4oA 199 :DKP T0558 176 :LNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLN 2p4oA 204 :PEIFVEQTNIDDFAFDVEGNLYGATHIYNSVVRIA T0558 212 :ESNRIVRRVNANDI 2p4oA 239 :PDRSTTIIAQAEQG T0558 230 :LFFVAQLFPL 2p4oA 253 :VIGSTAVAFG T0558 240 :QNGG 2p4oA 266 :GDCT T0558 244 :LYICNWQGHDREAGKG 2p4oA 271 :IYVVTNGGMFLPPPTG T0558 279 :DKV 2p4oA 288 :VPA T0558 284 :GMISTICPI 2p4oA 293 :VRLEVGKPG Number of specific fragments extracted= 23 number of extra gaps= 3 total=2370 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2p4oA/T0558-2p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 2p4oA/T0558-2p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p4oA read from 2p4oA/T0558-2p4oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p4oA in template set Warning: unaligning (T0558)Y72 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)H49 Warning: unaligning (T0558)G173 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)P147 Warning: unaligning (T0558)C205 because of BadResidue code BAD_PEPTIDE in next template residue (2p4oA)L190 Warning: unaligning (T0558)F206 because of BadResidue code BAD_PEPTIDE at template residue (2p4oA)L190 T0558 51 :LEKGWECNSVAATKAGEILFS 2p4oA 27 :FPVNTFLENLASAPDGTIFVT T0558 73 :SKGAKMITRDG 2p4oA 51 :VGEIVSITPDG T0558 84 :RELWN 2p4oA 64 :QIHAT T0558 91 :APA 2p4oA 69 :VEG T0558 96 :EMQTARILPDGNALVAWCGHPS 2p4oA 72 :KVSGLAFTSNGDLVATGWNADS T0558 118 :TILEVNMKGEVLSKTEFETG 2p4oA 96 :VVSLVKSDGTVETLLTLPDA T0558 143 :AQFRQINKNKKGNYLVPLFATSEVREIAPN 2p4oA 116 :IFLNGITPLSDTQYLTADSYRGAIWLIDVV T0558 174 :QLLNSVKLS 2p4oA 148 :SGSIWLEHP T0558 183 :GTPFSSAFLDNG 2p4oA 166 :VFPAANGLKRFG T0558 195 :DCLVACGDAH 2p4oA 179 :FLYVSNTEKM T0558 207 :VQLNLESNR 2p4oA 191 :LRIPVDSTD T0558 224 :DIEGVQLF 2p4oA 200 :KPGEPEIF T0558 232 :FVAQLFPLQNGGLYICNWQGH 2p4oA 212 :NIDDFAFDVEGNLYGATHIYN T0558 263 :QLVEIDSEGKVVWQLNDKVKFGMISTICPIR 2p4oA 233 :SVVRIAPDRSTTIIAQAEQGVIGSTAVAFGQ Number of specific fragments extracted= 14 number of extra gaps= 3 total=2384 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrwA/T0558-1lrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lrwA expands to /projects/compbio/data/pdb/1lrw.pdb.gz 1lrwA:# T0558 read from 1lrwA/T0558-1lrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrwA read from 1lrwA/T0558-1lrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lrwA to template set # found chain 1lrwA in template set T0558 16 :FAQGSSPQH 1lrwA 56 :GTPLVVGDR T0558 25 :LLVGGSGWNKIAIINKDTKEIVWEYPL 1lrwA 123 :LIFRTQLDGHIVAMDAETGETRWIMEN T0558 53 :KGWECN 1lrwA 154 :VGSTLT T0558 59 :SVAATKA 1lrwA 161 :APYVIKD T0558 68 :ILFSYSKG 1lrwA 168 :LVLVGSSG T0558 76 :AKMITRD 1lrwA 184 :VTAYDVK T0558 83 :GRELWNIA 1lrwA 192 :GEMRWRAF T0558 97 :MQTARILPDGNALVAWC 1lrwA 243 :WGWYAYDPEVDLFYYGS T0558 114 :GHPSTILEVNMK 1lrwA 330 :DRNGIVYTLDRT T0558 126 :GEVLSKTEFETG 1lrwA 343 :GDLISADKMDDT T0558 165 :EVREIAPN 1lrwA 454 :QIKAYDAI T0558 173 :GQLLNSVKLSGTPFSSAFLDNGDCLVACGDAHCFVQLNLESNRIVRRVNAND 1lrwA 463 :GEMKWEKMERFSVWGGTMATAGGLTFYATLDGFIKARDSDTGDLLWKFKLPS T0558 231 :FFVAQLFPLQ 1lrwA 515 :GVIGHPMTYK T0558 241 :NGGLYICNWQGH 1lrwA 526 :DGRQYVAIMYGV T0558 253 :DREAGKGKHPQLVEIDSEGKVV 1lrwA 564 :RLQEFTQMGGGVMVFSLDGESP T0558 277 :LNDKVKFG 1lrwA 586 :YSDPNVGE Number of specific fragments extracted= 16 number of extra gaps= 0 total=2400 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrwA/T0558-1lrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1lrwA/T0558-1lrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrwA read from 1lrwA/T0558-1lrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lrwA in template set T0558 4 :FILLVALFL 1lrwA 45 :SFSTGVLHG T0558 14 :APFAQGSSPQHLLVGGSGWNKIAIINKD 1lrwA 54 :HEGTPLVVGDRMFIHTPFPNTTFALDLN T0558 42 :TKEIVWEYP 1lrwA 83 :PGKILWQNK T0558 55 :WECNSVAATKAGE 1lrwA 106 :VVNRGLAYWPGDD T0558 68 :ILFSYSKG 1lrwA 123 :LIFRTQLD T0558 76 :AKMIT 1lrwA 133 :IVAMD T0558 81 :RDGRELWNIAAPAGCEMQTARILP 1lrwA 139 :ETGETRWIMENSDIKVGSTLTIAP T0558 105 :DGNALVAWC 1lrwA 166 :KDLVLVGSS T0558 114 :GHPSTILEVNMK 1lrwA 179 :GVRGYVTAYDVK T0558 126 :GEVLSKTEFETG 1lrwA 192 :GEMRWRAFATGP T0558 138 :IER 1lrwA 304 :YAG T0558 145 :FRQINKN 1lrwA 307 :VNVMMLS T0558 152 :KKGN 1lrwA 318 :KQGQ T0558 156 :YLVPLFATSEVREIAPN 1lrwA 325 :LLTHPDRNGIVYTLDRT T0558 173 :GQLLNSVKLSGT 1lrwA 343 :GDLISADKMDDT T0558 185 :PFSSAFLDNGDCLVACGDAH 1lrwA 395 :QGHDSYDPERKVFMLGINHI T0558 205 :CFVQLNLESNRIVRRVNANDI 1lrwA 454 :QIKAYDAISGEMKWEKMERFS T0558 233 :VAQLFPLQNGGLYICNWQGHDREAGKG 1lrwA 475 :VWGGTMATAGGLTFYATLDGFIKARDS T0558 260 :KHPQLVEIDSEGKVVWQL 1lrwA 503 :TGDLLWKFKLPSGVIGHP T0558 278 :NDKVKFGMIST 1lrwA 525 :HDGRQYVAIMY Number of specific fragments extracted= 20 number of extra gaps= 0 total=2420 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrwA/T0558-1lrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0558 read from 1lrwA/T0558-1lrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrwA read from 1lrwA/T0558-1lrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lrwA in template set T0558 23 :QHLLVGGSGWNKIAIINK 1lrwA 62 :GDRMFIHTPFPNTTFALD T0558 41 :DTKEIVWEYPLEKGWECN 1lrwA 82 :EPGKILWQNKPKQNPTAR T0558 59 :SVAATKA 1lrwA 109 :RGLAYWP T0558 66 :GEILFSY 1lrwA 122 :PLIFRTQ T0558 73 :SKGAKMITRDG 1lrwA 130 :DGHIVAMDAET T0558 84 :RELWNIAA 1lrwA 142 :ETRWIMEN T0558 92 :PAGCEMQTARILPDGNALVAW 1lrwA 153 :KVGSTLTIAPYVIKDLVLVGS T0558 113 :CGHPSTILEVNM 1lrwA 178 :LGVRGYVTAYDV T0558 125 :KGEVLSKTEFET 1lrwA 191 :SGEMRWRAFATG T0558 152 :KKG 1lrwA 318 :KQG T0558 155 :NYLVPLFATSEVREIAPN 1lrwA 324 :KLLTHPDRNGIVYTLDRT T0558 173 :GQLLNSVKLS 1lrwA 343 :GDLISADKMD T0558 183 :GTPFSSAFLDNGDCLVACGDA 1lrwA 394 :NQGHDSYDPERKVFMLGINHI T0558 205 :CFVQLNLESNRIVRRVN 1lrwA 454 :QIKAYDAISGEMKWEKM T0558 228 :VQLFFVAQLFPLQNGGLYICNWQG 1lrwA 471 :ERFSVWGGTMATAGGLTFYATLDG T0558 263 :QLVEID 1lrwA 495 :FIKARD T0558 269 :SEGKVVWQLN 1lrwA 502 :DTGDLLWKFK Number of specific fragments extracted= 17 number of extra gaps= 0 total=2437 Will force an alignment to be made, even if fragment is small Number of alignments=129 # command:CPU_time= 52.391 sec, elapsed time= 94.492 sec. # command:DEBUG: alignment library has 129 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 129 # Adding 5626 constraints to all_contacts Done adding distance constraints # command:CPU_time= 52.628 sec, elapsed time= 94.738 sec. # command:Reading probabilities from T0558.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 123.200 Optimizing... Probability sum: -553.572, CN propb: -553.572 weights: 0.330 constraints: 1244 # command:CPU_time= 1425.363 sec, elapsed time= 1468.045 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 1244 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 1244 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 4382 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 4382 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 1425.459 sec, elapsed time= 1469.010 sec. # command: