# 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 T0628 numbered 1 through 295 Created new target T0628 from T0628.a2m # command:CPU_time= 5.758 sec, elapsed time= 14.869 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2e2oA/T0628-2e2oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2e2oA expands to /projects/compbio/data/pdb/2e2o.pdb.gz 2e2oA:# T0628 read from 2e2oA/T0628-2e2oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e2oA read from 2e2oA/T0628-2e2oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2e2oA to template set # found chain 2e2oA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQ 2e2oA 2 :MIIVGVDAGGTKTKAVAYD # choosing archetypes in rotamer library T0628 25 :GEECLESRQSEA 2e2oA 22 :EGNFIGEGSSGP T0628 37 :GVTRLNGRSPAAVLAEITQHWRDGA 2e2oA 35 :NYHNVGLTRAIENIKEAVKIAAKGE T0628 62 :TPVVMAGM 2e2oA 61 :DVVGMGVA T0628 84 :LPAAFS 2e2oA 69 :GLDSKF T0628 90 :DIGQQLTAVGDNIWIIP 2e2oA 78 :NFTPLASLIAPKVIIQH T0628 122 :EETQLLGARALAPSSVYVMPGTHCKWVLADRRQIHDFR 2e2oA 95 :DGVIALFAETLGEPGVVVIAGTGSVVEGYNGKEFLRVG T0628 160 :TVLTGELHHLLLQL 2e2oA 145 :YWVGRKALRKVLKM T0628 176 :VGAGLP 2e2oA 159 :MDGLEN T0628 182 :PQETSAAAFAAGLQRGINNPAVLPQLFEVRASHVLGAL 2e2oA 176 :INVKDLDELVMWSYTSSCQIDLVASIAKAVDEAANEGD T0628 222 :EQVSEFLSGLL 2e2oA 214 :TVAMDILKQGA T0628 233 :IGAEVATLSDTF 2e2oA 227 :LASQAVYLARKI T0628 246 :GQQAISLVA 2e2oA 239 :GTNKVYLKG T0628 255 :GSSLTSRYQQAFAAIGREVSAVAGD 2e2oA 252 :SNIYHKFFTLYLEKEGIISDLGKRS T0628 281 :AFQTGIRSIAYAV 2e2oA 277 :PEIGAVILAYKEV Number of specific fragments extracted= 15 number of extra gaps= 0 total=15 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 2e2oA/T0628-2e2oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2e2oA/T0628-2e2oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e2oA read from 2e2oA/T0628-2e2oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e2oA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQ 2e2oA 2 :MIIVGVDAGGTKTKAVAYD T0628 25 :GEECLESRQSEA 2e2oA 22 :EGNFIGEGSSGP T0628 37 :GVTRLNGRSPAAVLAEITQHWRDGATPVVMAGMVG 2e2oA 35 :NYHNVGLTRAIENIKEAVKIAAKGEADVVGMGVAG T0628 85 :PAA 2e2oA 70 :LDS T0628 88 :FSDIGQQLTAVGDNIWIIP 2e2oA 76 :WENFTPLASLIAPKVIIQH T0628 122 :EETQLLGARALAPSSVYVMPGTHCKWVLADRRQIHD 2e2oA 95 :DGVIALFAETLGEPGVVVIAGTGSVVEGYNGKEFLR T0628 158 :FRTVLTGELHHLLLQL 2e2oA 143 :SAYWVGRKALRKVLKM T0628 176 :VGAGLPPQ 2e2oA 159 :MDGLENKT T0628 184 :ETSAAAFAAGLQRGINNPAVLPQLFEVRASHVLGAL 2e2oA 178 :VKDLDELVMWSYTSSCQIDLVASIAKAVDEAANEGD T0628 222 :EQVSEFLSGLL 2e2oA 214 :TVAMDILKQGA T0628 233 :IGAEVATLSDT 2e2oA 227 :LASQAVYLARK T0628 245 :AGQQAISLVAG 2e2oA 238 :IGTNKVYLKGG T0628 256 :SSLTSRYQQAFAAIGREVSAVAG 2e2oA 253 :NIYHKFFTLYLEKEGIISDLGKR T0628 280 :TAFQTGIRSIAYAVA 2e2oA 276 :SPEIGAVILAYKEVG Number of specific fragments extracted= 14 number of extra gaps= 0 total=29 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 2e2oA/T0628-2e2oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2e2oA/T0628-2e2oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e2oA read from 2e2oA/T0628-2e2oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e2oA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQGEE 2e2oA 2 :MIIVGVDAGGTKTKAVAYDCEG T0628 28 :CLESRQSEAGVTRL 2e2oA 25 :FIGEGSSGPGNYHN T0628 42 :NGRSPAAVLAEITQHWRDGATPVVMAGMVGSNV 2e2oA 40 :GLTRAIENIKEAVKIAAKGEADVVGMGVAGLDS T0628 85 :PAAFSDIGQQLTAVGDNIWIIP 2e2oA 73 :KFDWENFTPLASLIAPKVIIQH T0628 123 :ETQLLGARALAP 2e2oA 95 :DGVIALFAETLG T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 2e2oA 108 :PGVVVIAGTGSVVEGYNGKEFLR T0628 158 :FRTVLTGELHHLLLQ 2e2oA 143 :SAYWVGRKALRKVLK T0628 175 :LVGAGLPP 2e2oA 158 :MMDGLENK T0628 183 :QETSAAAFAAGLQRGINNPAVLPQLFEVRASHVLGAL 2e2oA 177 :NVKDLDELVMWSYTSSCQIDLVASIAKAVDEAANEGD T0628 222 :EQVSEFLSGLL 2e2oA 214 :TVAMDILKQGA T0628 233 :IGAEVATLSDTFA 2e2oA 227 :LASQAVYLARKIG T0628 247 :QQAISLVAG 2e2oA 240 :TNKVYLKGG T0628 256 :SSLTSRYQQAFAAIGREVSAVAGD 2e2oA 253 :NIYHKFFTLYLEKEGIISDLGKRS T0628 281 :AFQTGIRSIAYAVA 2e2oA 277 :PEIGAVILAYKEVG Number of specific fragments extracted= 14 number of extra gaps= 0 total=43 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 2aa4A/T0628-2aa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aa4A expands to /projects/compbio/data/pdb/2aa4.pdb.gz 2aa4A:Skipped atom 1038, because occupancy 0.5 <= existing 0.500 in 2aa4A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1544, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1546, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1548, because occupancy 0.500 <= existing 0.500 in 2aa4A Skipped atom 1550, because occupancy 0.500 <= existing 0.500 in 2aa4A # T0628 read from 2aa4A/T0628-2aa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aa4A read from 2aa4A/T0628-2aa4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aa4A to template set # found chain 2aa4A in template set Warning: unaligning (T0628)Q172 because of BadResidue code BAD_PEPTIDE at template residue (2aa4A)A151 T0628 7 :RYIAIDWGSTNLRAWLYQ 2aa4A 2 :TTLAIDIGGTKLAAALIG T0628 25 :GEECLESRQSEA 2aa4A 21 :DGQIRDRRELPT T0628 42 :NG 2aa4A 33 :PA T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMV 2aa4A 39 :EALRDALSALVSPLQAHAQRVAIASTG T0628 77 :KIAPYLPLPAAFSDI 2aa4A 66 :IIRDGSLLALNPHNL T0628 93 :QQLTAV 2aa4A 81 :GGLLHF T0628 99 :GDNIWIIP 2aa4A 97 :NLPTIAIN T0628 122 :EETQLLGARALAP 2aa4A 107 :QAAAWAEFQALDG T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2aa4A 123 :DMVFITVSTGVGGGVVSGCKLL T0628 173 :LSLVGAGLPPQ 2aa4A 152 :GHIGHTLADPH T0628 187 :AAAFAAGLQRGINNP 2aa4A 176 :AIASGRGIAAAAQGE T0628 203 :VLPQLFEVR 2aa4A 195 :DAKTIFTRA T0628 216 :LGAL 2aa4A 204 :GQGD T0628 222 :EQVSEFL 2aa4A 208 :EQAQQLI T0628 229 :SGLLIGAEVATLSDTF 2aa4A 217 :SARTLARLIADIKATT T0628 246 :GQQAISLVA 2aa4A 233 :DCQCVVVGG T0628 255 :GSSLTSRYQQAFAAIG 2aa4A 246 :AEGYLALVETYLAQEP T0628 271 :REVSAVA 2aa4A 266 :VDLLAAH T0628 278 :GDTAFQTGIRSIAY 2aa4A 274 :RHDAGLLGAALLAQ Number of specific fragments extracted= 19 number of extra gaps= 1 total=62 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 2aa4A/T0628-2aa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2aa4A/T0628-2aa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aa4A read from 2aa4A/T0628-2aa4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aa4A in template set Warning: unaligning (T0628)Q172 because of BadResidue code BAD_PEPTIDE at template residue (2aa4A)A151 T0628 7 :RYIAIDWGSTNLRAWLYQ 2aa4A 2 :TTLAIDIGGTKLAAALIG T0628 25 :GEECLESRQSEA 2aa4A 21 :DGQIRDRRELPT T0628 42 :NG 2aa4A 33 :PA T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMV 2aa4A 39 :EALRDALSALVSPLQAHAQRVAIASTG T0628 77 :KIAPYLPLPAAFSDI 2aa4A 66 :IIRDGSLLALNPHNL T0628 93 :QQLTAV 2aa4A 81 :GGLLHF T0628 99 :GDNIWIIP 2aa4A 97 :NLPTIAIN T0628 122 :EETQLLGARALAP 2aa4A 106 :AQAAAWAEFQALD T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2aa4A 123 :DMVFITVSTGVGGGVVSGCKLL T0628 173 :LSLVGAGLPPQETS 2aa4A 152 :GHIGHTLADPHGPV T0628 187 :AAAFAAGLQRGINNPA 2aa4A 176 :AIASGRGIAAAAQGEL T0628 203 :VLPQLFEV 2aa4A 195 :DAKTIFTR T0628 215 :VLGAL 2aa4A 203 :AGQGD T0628 222 :EQVSEFLSGL 2aa4A 208 :EQAQQLIHRS T0628 232 :LIGAEVATLSDTF 2aa4A 220 :TLARLIADIKATT T0628 246 :GQQAISLVA 2aa4A 233 :DCQCVVVGG T0628 255 :GSSLTSRYQQAFAAI 2aa4A 246 :AEGYLALVETYLAQE T0628 270 :GREVSAVA 2aa4A 265 :HVDLLAAH T0628 278 :GDTAFQTGIRSIAY 2aa4A 274 :RHDAGLLGAALLAQ Number of specific fragments extracted= 19 number of extra gaps= 1 total=81 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 2aa4A/T0628-2aa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2aa4A/T0628-2aa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aa4A read from 2aa4A/T0628-2aa4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aa4A in template set T0628 7 :RYIAIDWGSTNLRAWLYQGEECLE 2aa4A 2 :TTLAIDIGGTKLAAALIGADGQIR T0628 31 :SRQ 2aa4A 27 :RRE T0628 39 :TRLNGRSPAAVLAEITQHWRD 2aa4A 30 :LPTPASQTPEALRDALSALVS T0628 60 :GATPVVMAGM 2aa4A 55 :HAQRVAIAST T0628 76 :WKIAPYLPLPAAFSDIGQ 2aa4A 65 :GIIRDGSLLALNPHNLGG T0628 95 :LTAV 2aa4A 83 :LLHF T0628 99 :GDNIWIIPG 2aa4A 97 :NLPTIAIND T0628 122 :EETQLLGARALAP 2aa4A 106 :AQAAAWAEFQALD T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2aa4A 123 :DMVFITVSTGVGGGVVSGCKLL T0628 173 :LSLVGAGLPPQETS 2aa4A 152 :GHIGHTLADPHGPV T0628 187 :AAAFAAGLQRGINNPA 2aa4A 176 :AIASGRGIAAAAQGEL T0628 204 :LPQLFEV 2aa4A 196 :AKTIFTR T0628 215 :VLGAL 2aa4A 203 :AGQGD T0628 222 :EQVSEFLSGL 2aa4A 208 :EQAQQLIHRS T0628 232 :LIGAEVATLSDTFA 2aa4A 220 :TLARLIADIKATTD T0628 247 :QQAISLVA 2aa4A 234 :CQCVVVGG T0628 255 :GSSLTSRYQQAFAAI 2aa4A 246 :AEGYLALVETYLAQE T0628 270 :GREVSAVA 2aa4A 265 :HVDLLAAH T0628 278 :GDTAFQTGIRSIAY 2aa4A 274 :RHDAGLLGAALLAQ Number of specific fragments extracted= 19 number of extra gaps= 0 total=100 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 2ap1A/T0628-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0628 read from 2ap1A/T0628-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0628-2ap1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ap1A to template set # found chain 2ap1A in template set Warning: unaligning (T0628)T5 because first residue in template chain is (2ap1A)N-1 T0628 6 :ARYIAIDWGSTNLRAWLYQ 2ap1A 0 :AMYYGFDIGGTKIALGVFD T0628 25 :GEECLESRQ 2ap1A 20 :TRRLQWEKR T0628 39 :TRLNGRSPAAV 2ap1A 29 :VPTPHTSYSAF T0628 50 :LAEITQHWRD 2ap1A 43 :VCELVEEADQ T0628 60 :GATPVVMA 2ap1A 56 :VKGSVGIG T0628 68 :GMVGSNVGWKIAPYLP 2ap1A 66 :GMPETEDGTLYAANVP T0628 86 :AA 2ap1A 86 :KP T0628 91 :IGQQLTAV 2ap1A 88 :LRADLSAR T0628 99 :GDNIWIIP 2ap1A 97 :DRDVRLDN T0628 122 :EETQLLGARALAP 2ap1A 105 :DANCFALSEAWDD T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2ap1A 124 :LVMGLILGTGVGGGLVLNGKPI T0628 169 :LLL 2ap1A 163 :DAL T0628 174 :SLVGAGLPP 2ap1A 166 :TLMGFDFPL T0628 183 :QE 2ap1A 180 :GQ T0628 187 :AAAFAAGLQRGINNPAVLPQLFEVR 2ap1A 191 :GRGFAWLYQHYYDQSLQAPEIIALW T0628 216 :LGA 2ap1A 216 :EQG T0628 221 :REQVSEFLSGL 2ap1A 219 :DEQAHAHVERY T0628 232 :LIGAEVATLSDTFAGQ 2ap1A 232 :LLAVCLGNILTIVDPD T0628 250 :ISLVAGSSLT 2ap1A 248 :LLVIGGGLSN T0628 264 :QAFA 2ap1A 260 :AITT T0628 270 :GR 2ap1A 276 :VA T0628 272 :EVSAV 2ap1A 281 :RIERA T0628 278 :GDTAFQTGIRS 2ap1A 288 :GDAGGMRGAAF Number of specific fragments extracted= 23 number of extra gaps= 0 total=123 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 2ap1A/T0628-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2ap1A/T0628-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0628-2ap1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set Warning: unaligning (T0628)T5 because first residue in template chain is (2ap1A)N-1 T0628 6 :ARYIAIDWGSTNLRAWLYQ 2ap1A 0 :AMYYGFDIGGTKIALGVFD T0628 25 :GEECLESRQSE 2ap1A 20 :TRRLQWEKRVP T0628 41 :LNGRSPAAV 2ap1A 31 :TPHTSYSAF T0628 50 :LAEITQHWRD 2ap1A 43 :VCELVEEADQ T0628 60 :GATPVVMA 2ap1A 56 :VKGSVGIG T0628 68 :GMVGSNVGWKIAPYLP 2ap1A 66 :GMPETEDGTLYAANVP T0628 86 :AA 2ap1A 86 :KP T0628 91 :IGQQLTAV 2ap1A 88 :LRADLSAR T0628 99 :GDNIWIIP 2ap1A 97 :DRDVRLDN T0628 122 :EETQLLGARALAP 2ap1A 106 :ANCFALSEAWDDE T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRT 2ap1A 124 :LVMGLILGTGVGGGLVLNGKPITGQS T0628 164 :GELHH 2ap1A 162 :VDALT T0628 175 :LVGAGLP 2ap1A 167 :LMGFDFP T0628 182 :PQE 2ap1A 179 :CGQ T0628 187 :AAAFAAGLQRGINNPAVLPQLFEVR 2ap1A 191 :GRGFAWLYQHYYDQSLQAPEIIALW T0628 216 :LGA 2ap1A 216 :EQG T0628 221 :REQVSEFLSGL 2ap1A 219 :DEQAHAHVERY T0628 232 :LIGAEVATLSDTF 2ap1A 232 :LLAVCLGNILTIV T0628 246 :GQQ 2ap1A 245 :DPD T0628 250 :ISLVAGSSLT 2ap1A 248 :LLVIGGGLSN T0628 264 :QAFA 2ap1A 260 :AITT T0628 270 :GREVSAVA 2ap1A 279 :APRIERAR T0628 278 :GDTAFQTGIRS 2ap1A 288 :GDAGGMRGAAF Number of specific fragments extracted= 23 number of extra gaps= 0 total=146 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 2ap1A/T0628-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2ap1A/T0628-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ap1A read from 2ap1A/T0628-2ap1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ap1A in template set Warning: unaligning (T0628)T5 because first residue in template chain is (2ap1A)N-1 T0628 6 :ARYIAIDWGSTNLRAWLYQGEECLESR 2ap1A 0 :AMYYGFDIGGTKIALGVFDSTRRLQWE T0628 37 :GVTRLNGRSPAA 2ap1A 27 :KRVPTPHTSYSA T0628 49 :VLAEITQHWRD 2ap1A 42 :AVCELVEEADQ T0628 60 :GATPVVMA 2ap1A 56 :VKGSVGIG T0628 68 :GMVGSNVGWKIAPYL 2ap1A 66 :GMPETEDGTLYAANV T0628 83 :PLP 2ap1A 85 :GKP T0628 91 :IGQQLTAV 2ap1A 88 :LRADLSAR T0628 99 :GDNIWIIP 2ap1A 97 :DRDVRLDN T0628 122 :EETQLLGARALAP 2ap1A 105 :DANCFALSEAWDD T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 2ap1A 124 :LVMGLILGTGVGGGLVLNGKPIT T0628 171 :LQLSLVGAGLPPQETS 2ap1A 163 :DALTLMGFDFPLRRCG T0628 187 :AAAFAAGLQRGINNPAVLPQLFEVR 2ap1A 191 :GRGFAWLYQHYYDQSLQAPEIIALW T0628 216 :LGAL 2ap1A 216 :EQGD T0628 222 :EQVSEFLSGL 2ap1A 220 :EQAHAHVERY T0628 232 :LIGAEVATLSDTF 2ap1A 232 :LLAVCLGNILTIV T0628 247 :QQAISLVAGS 2ap1A 245 :DPDLLVIGGG Number of specific fragments extracted= 16 number of extra gaps= 0 total=162 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 1zbsA/T0628-1zbsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zbsA expands to /projects/compbio/data/pdb/1zbs.pdb.gz 1zbsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 1zbsA/T0628-1zbsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zbsA read from 1zbsA/T0628-1zbsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zbsA to template set # found chain 1zbsA in template set Warning: unaligning (T0628)R7 because first residue in template chain is (1zbsA)M1 T0628 8 :YIAIDWGSTNLRAWLYQGEECLESRQSEA 1zbsA 2 :ILIGDSGSTKTDWCIAKEGKSLGRFQTSG T0628 39 :TRLNGRSPAAVLAEITQHW 1zbsA 31 :INPFQQDRNEIDTALRSEV T0628 58 :RD 1zbsA 54 :GQ T0628 60 :GATPVVMAGMVGSNV 1zbsA 59 :SIRAVYFYGAGCTPA T0628 87 :AFSDIGQQLTAV 1zbsA 74 :KAPMLNEALDSM T0628 99 :GDNIWIIP 1zbsA 89 :CDRIEVAG T0628 123 :ETQLLGARALAP 1zbsA 97 :DMLGAARALCGD T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 1zbsA 110 :EGIACILGTGSNSCLFDGREIKANV T0628 160 :TVLTGELHHLLL 1zbsA 148 :AVLGRLFIGSLL T0628 177 :GAGLPPQ 1zbsA 160 :KGQMPEG T0628 184 :ETSAAAFAA 1zbsA 176 :GLTSADIIE T0628 196 :RGINNPAVLPQLFEV 1zbsA 185 :SVYRKPFPNRFLAGF T0628 212 :ASHVLGALPREQVSEFLSGLLIGAEVATLSDTFAGQQAISLVAG 1zbsA 200 :SPFIAQHLDIPAVYSLVQNSFDDFLVRNVLRYNRPDLPLHFIGS T0628 256 :SSLTSRYQQAFAAIGREVSAVAG 1zbsA 246 :FHYREVLSSVIKKRGLTLGSVLQ T0628 283 :QTGIRSIAYAVAN 1zbsA 271 :MEGLIQYHHNNHV Number of specific fragments extracted= 15 number of extra gaps= 0 total=177 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 1zbsA/T0628-1zbsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1zbsA/T0628-1zbsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zbsA read from 1zbsA/T0628-1zbsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zbsA in template set Warning: unaligning (T0628)R7 because first residue in template chain is (1zbsA)M1 T0628 8 :YIAIDWGSTNLRAWLYQGEECLESRQSEA 1zbsA 2 :ILIGDSGSTKTDWCIAKEGKSLGRFQTSG T0628 39 :TRLNGRSPAAV 1zbsA 31 :INPFQQDRNEI T0628 51 :AEITQHW 1zbsA 42 :DTALRSE T0628 58 :RD 1zbsA 54 :GQ T0628 60 :GATPVVMA 1zbsA 59 :SIRAVYFY T0628 69 :MVGS 1zbsA 67 :GAGC T0628 84 :LPAAFSDIGQQLTAV 1zbsA 71 :TPAKAPMLNEALDSM T0628 99 :GDNIWII 1zbsA 89 :CDRIEVA T0628 122 :EETQLLGARALAP 1zbsA 96 :GDMLGAARALCGD T0628 135 :SSVYVMPGTHCKWVLADRRQIHDF 1zbsA 110 :EGIACILGTGSNSCLFDGREIKAN T0628 159 :RTVLTGELHHL 1zbsA 148 :AVLGRLFIGSL T0628 176 :VGAGLPPQ 1zbsA 159 :LKGQMPEG T0628 184 :ETSAAAFAAGLQR 1zbsA 176 :GLTSADIIESVYR T0628 200 :NPAVLPQLFE 1zbsA 189 :KPFPNRFLAG T0628 212 :ASHVLGALPREQVSEFLSGLLIGAEVATLSDTFAGQQAISLVAG 1zbsA 200 :SPFIAQHLDIPAVYSLVQNSFDDFLVRNVLRYNRPDLPLHFIGS T0628 256 :SSLTSRYQQAFAAIGREVSAVAG 1zbsA 246 :FHYREVLSSVIKKRGLTLGSVLQ T0628 279 :DTAFQTGIR 1zbsA 271 :MEGLIQYHH Number of specific fragments extracted= 17 number of extra gaps= 0 total=194 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 1zbsA/T0628-1zbsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1zbsA/T0628-1zbsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zbsA read from 1zbsA/T0628-1zbsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zbsA in template set Warning: unaligning (T0628)R7 because first residue in template chain is (1zbsA)M1 T0628 8 :YIAIDWGSTNLRAWLYQGEECLESRQSEAGV 1zbsA 2 :ILIGDSGSTKTDWCIAKEGKSLGRFQTSGIN T0628 41 :LNGRSPAAVLAEITQHWRD 1zbsA 33 :PFQQDRNEIDTALRSEVLP T0628 60 :GATPVVMAGM 1zbsA 59 :SIRAVYFYGA T0628 73 :NVG 1zbsA 69 :GCT T0628 85 :PAAFSDIGQQLTAV 1zbsA 72 :PAKAPMLNEALDSM T0628 99 :GDNIWIIP 1zbsA 89 :CDRIEVAG T0628 121 :GEETQLLGARAL 1zbsA 97 :DMLGAARALCGD T0628 134 :PSSVYVMPGTHCKWVLADRRQIHDFR 1zbsA 109 :SEGIACILGTGSNSCLFDGREIKANV T0628 163 :TGELHHLLLQLSLVGAGLPPQ 1zbsA 146 :SGAVLGRLFIGSLLKGQMPEG T0628 184 :ETSAAAFAAGLQRG 1zbsA 176 :GLTSADIIESVYRK T0628 200 :NPAVLPQL 1zbsA 190 :PFPNRFLA T0628 212 :ASHVLGALPREQVSEFLSGLLIGAEVATLSDTFAGQQAISLVAG 1zbsA 200 :SPFIAQHLDIPAVYSLVQNSFDDFLVRNVLRYNRPDLPLHFIGS T0628 256 :SSLTSRYQQAFAAIGREVSAVAGD 1zbsA 246 :FHYREVLSSVIKKRGLTLGSVLQS T0628 283 :QTGIRSIAYA 1zbsA 271 :MEGLIQYHHN Number of specific fragments extracted= 14 number of extra gaps= 0 total=208 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 3htvA/T0628-3htvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3htvA expands to /projects/compbio/data/pdb/3htv.pdb.gz 3htvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 138, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 785, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1103, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1286, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1290, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1294, because occupancy 0.370 <= existing 0.380 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 3htvA Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 3htvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 3htvA/T0628-3htvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3htvA read from 3htvA/T0628-3htvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3htvA to template set # found chain 3htvA in template set Warning: unaligning (T0628)P182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3htvA)E185 T0628 7 :RYIAIDWGSTNLRAWLYQ 3htvA 7 :VVAGVDMGATHIRFCLRT T0628 25 :GEECL 3htvA 26 :EGETL T0628 30 :ESRQSEA 3htvA 33 :EKKRTAE T0628 41 :LNGRSPAAVLAEITQHWRD 3htvA 40 :VIAPGLVSGIGEMIDEQLR T0628 60 :GA 3htvA 61 :NA T0628 62 :TPVVMA 3htvA 65 :HGLVMG T0628 68 :GMVGSNVG 3htvA 73 :ALVSKDKR T0628 77 :KIAPYLPLPAA 3htvA 81 :TIISTPNLPLT T0628 88 :FSDIGQQLTAV 3htvA 95 :LYDLADKLENT T0628 99 :GDNIWIIP 3htvA 107 :NCPVEFSR T0628 122 :EETQLLGARALA 3htvA 117 :NLQLSWDVVENR T0628 135 :SSVYVMPGTHCKWVLADRRQIH 3htvA 133 :LVLAAYLGTGMGFAVWMNGAPW T0628 183 :QETSAAAFAAGLQR 3htvA 186 :TNCSGMALRRWYEQ T0628 201 :PA 3htvA 200 :QP T0628 203 :VLPQLFEV 3htvA 205 :PLRDLFVH T0628 215 :V 3htvA 213 :A T0628 217 :GAL 3htvA 214 :ENA T0628 222 :EQVSEFLSG 3htvA 217 :PFVQSLLEN T0628 233 :IGAEVATLSDTF 3htvA 226 :AARAIATSINLF T0628 246 :GQQAISLVAG 3htvA 238 :DPDAVILGGG T0628 256 :SSLTSRYQQAFAAI 3htvA 253 :AFPRETLVAMTQKY T0628 270 :GREVSAVA 3htvA 275 :VVRFIAAS T0628 278 :GDTAFQTGIRSIAYAV 3htvA 284 :SDFNGAQGAAILAHQR Number of specific fragments extracted= 23 number of extra gaps= 0 total=231 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 3htvA/T0628-3htvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3htvA/T0628-3htvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3htvA read from 3htvA/T0628-3htvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3htvA in template set Warning: unaligning (T0628)P182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3htvA)E185 T0628 6 :ARYIAIDWGSTNLRAWLYQ 3htvA 6 :NVVAGVDMGATHIRFCLRT T0628 25 :GEECLESRQSEA 3htvA 26 :EGETLHCEKKRT T0628 40 :RLNGRSPAAVLAEITQHWRD 3htvA 39 :EVIAPGLVSGIGEMIDEQLR T0628 60 :GATPVVMA 3htvA 63 :RCHGLVMG T0628 68 :GMVGSNVG 3htvA 73 :ALVSKDKR T0628 77 :KIAPYLPLPAA 3htvA 81 :TIISTPNLPLT T0628 88 :FSDIGQQLTAV 3htvA 95 :LYDLADKLENT T0628 99 :GDNIWIIP 3htvA 107 :NCPVEFSR T0628 122 :EETQLLGARALAP 3htvA 116 :VNLQLSWDVVENR T0628 135 :SSVYVMPGTHCKWVLADRRQIH 3htvA 133 :LVLAAYLGTGMGFAVWMNGAPW T0628 183 :QETSAAAFAAGLQR 3htvA 186 :TNCSGMALRRWYEQ T0628 201 :P 3htvA 200 :Q T0628 202 :A 3htvA 203 :N T0628 203 :VLPQLFE 3htvA 205 :PLRDLFV T0628 215 :VLGAL 3htvA 212 :HAENA T0628 222 :EQVSEFLS 3htvA 217 :PFVQSLLE T0628 232 :LIGAEVATLSDTF 3htvA 225 :NAARAIATSINLF T0628 246 :GQQAISLVAG 3htvA 238 :DPDAVILGGG T0628 256 :SSLTSRYQQAFAAI 3htvA 253 :AFPRETLVAMTQKY T0628 270 :GREVSAVAG 3htvA 275 :VVRFIAASS T0628 279 :DTAFQTGIRSIAYAV 3htvA 285 :DFNGAQGAAILAHQR Number of specific fragments extracted= 21 number of extra gaps= 0 total=252 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 3htvA/T0628-3htvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3htvA/T0628-3htvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3htvA read from 3htvA/T0628-3htvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3htvA in template set Warning: unaligning (T0628)P182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3htvA)E185 T0628 5 :TARYIAIDWGSTNLRAWLYQGEE 3htvA 5 :HNVVAGVDMGATHIRFCLRTAEG T0628 28 :CLESRQSE 3htvA 29 :TLHCEKKR T0628 40 :RLNGRSPAAVLAEITQHWRD 3htvA 39 :EVIAPGLVSGIGEMIDEQLR T0628 60 :GATPVVMA 3htvA 63 :RCHGLVMG T0628 68 :GMVGSNVGW 3htvA 73 :ALVSKDKRT T0628 78 :IAPYLPLPAA 3htvA 82 :IISTPNLPLT T0628 88 :FSDIGQQLTAV 3htvA 95 :LYDLADKLENT T0628 99 :GDNIWIIP 3htvA 107 :NCPVEFSR T0628 122 :EETQLLGARALAP 3htvA 116 :VNLQLSWDVVENR T0628 135 :SSVYVMPGTHCKWVLADRRQIH 3htvA 133 :LVLAAYLGTGMGFAVWMNGAPW T0628 183 :QETSAAAFAAGLQR 3htvA 186 :TNCSGMALRRWYEQ T0628 197 :GINNPA 3htvA 203 :NYPLRD T0628 211 :RASHVLGA 3htvA 209 :LFVHAENA T0628 222 :EQVSEFLSG 3htvA 217 :PFVQSLLEN T0628 233 :IGAEVATLSDTFA 3htvA 226 :AARAIATSINLFD T0628 247 :QQAISLVAG 3htvA 239 :PDAVILGGG T0628 256 :SSLTSRYQQAFAAI 3htvA 253 :AFPRETLVAMTQKY T0628 270 :GREVSAVA 3htvA 275 :VVRFIAAS T0628 278 :GDTAFQTGIRSIAYAV 3htvA 284 :SDFNGAQGAAILAHQR Number of specific fragments extracted= 19 number of extra gaps= 0 total=271 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 2gupA/T0628-2gupA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gupA expands to /projects/compbio/data/pdb/2gup.pdb.gz 2gupA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 2gupA/T0628-2gupA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gupA read from 2gupA/T0628-2gupA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gupA to template set # found chain 2gupA in template set Warning: unaligning (T0628)A6 because first residue in template chain is (2gupA)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)G126 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)G126 Warning: unaligning (T0628)V203 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2gupA)D186 Warning: unaligning (T0628)R271 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)V263 Warning: unaligning (T0628)E272 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)V263 T0628 7 :RYIAIDWGSTNLRAWLYQ 2gupA 2 :TIATIDIGGTGIKFASLT T0628 25 :GEECLESRQSE 2gupA 21 :DGKILDKTSIS T0628 43 :GRSPAAVLAEITQHWRD 2gupA 32 :TPENLEDLLAWLDQRLS T0628 60 :GA 2gupA 50 :QD T0628 62 :TPVVMA 2gupA 53 :SGIAMS T0628 68 :GMVGSNVGWKI 2gupA 61 :GAVNQETGVID T0628 84 :LPAAFSD 2gupA 72 :GFSAVPY T0628 91 :IGQQLTAVGDNIWIIP 2gupA 84 :WYEALSSYQLPVHLEN T0628 122 :EETQLLGARALAP 2gupA 102 :NCVGLSELLAHPE T0628 135 :SSVYVMPG 2gupA 117 :NAACVVIG T0628 145 :CKWVLADRRQIH 2gupA 127 :IGGAMIINGRLH T0628 172 :QLSLVGAGLPPQ 2gupA 145 :GGEFGYMTTLAP T0628 184 :ETS 2gupA 158 :EKL T0628 187 :AAAFAAGLQRGINNPA 2gupA 169 :TGNMVRYVIEKSGHTD T0628 204 :LPQLFEVR 2gupA 187 :GRKIYQEA T0628 216 :LGAL 2gupA 195 :AAGN T0628 222 :EQVSEFL 2gupA 199 :ILCQEAI T0628 229 :SGLLIGAEVATLSDTF 2gupA 208 :MNRNLAQGLLNIQYLI T0628 246 :GQQAISLVA 2gupA 224 :DPGVISLGG T0628 255 :GSSLTSRYQQAFAAI 2gupA 237 :NPDFIQGVKKAVEDF T0628 270 :G 2gupA 261 :A T0628 273 :VSAVAG 2gupA 264 :IQACTY T0628 279 :DTAFQTGIRSIAYAVAN 2gupA 271 :ADANLYGALVNWLQEEK Number of specific fragments extracted= 23 number of extra gaps= 3 total=294 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 2gupA/T0628-2gupA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2gupA/T0628-2gupA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gupA read from 2gupA/T0628-2gupA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gupA in template set Warning: unaligning (T0628)A6 because first residue in template chain is (2gupA)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)G126 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)G126 Warning: unaligning (T0628)V203 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2gupA)D186 Warning: unaligning (T0628)R271 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)V263 Warning: unaligning (T0628)E272 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)V263 T0628 7 :RYIAIDWGSTNLRAWLYQ 2gupA 2 :TIATIDIGGTGIKFASLT T0628 25 :GEECLESRQSE 2gupA 21 :DGKILDKTSIS T0628 42 :NGRSPAA 2gupA 32 :TPENLED T0628 50 :LAEITQHWRD 2gupA 39 :LLAWLDQRLS T0628 60 :GATPVVMAGMVG 2gupA 50 :QDYSGIAMSVPG T0628 72 :SNVGW 2gupA 65 :QETGV T0628 82 :LPLPAAFSD 2gupA 70 :IDGFSAVPY T0628 91 :IGQQLTAVGDNIWIIP 2gupA 84 :WYEALSSYQLPVHLEN T0628 122 :EETQLLGARALAP 2gupA 101 :ANCVGLSELLAHP T0628 135 :SSVYVMPG 2gupA 117 :NAACVVIG T0628 145 :CKWVLADRRQIH 2gupA 127 :IGGAMIINGRLH T0628 172 :QLSLVGAGLPPQE 2gupA 145 :GGEFGYMTTLAPA T0628 185 :TS 2gupA 160 :LN T0628 187 :AAAFAAGLQRGINNPA 2gupA 169 :TGNMVRYVIEKSGHTD T0628 204 :LPQLFEVR 2gupA 187 :GRKIYQEA T0628 216 :LGAL 2gupA 195 :AAGN T0628 222 :EQVSEFLSGL 2gupA 199 :ILCQEAIERM T0628 232 :LIGAEVATLSDT 2gupA 211 :NLAQGLLNIQYL T0628 245 :AGQQAISLVA 2gupA 223 :IDPGVISLGG T0628 255 :GSSLTSRYQQAFAAI 2gupA 237 :NPDFIQGVKKAVEDF T0628 270 :G 2gupA 261 :A T0628 273 :VSAVAG 2gupA 264 :IQACTY T0628 279 :DTAFQTGIRSIAYAVAN 2gupA 271 :ADANLYGALVNWLQEEK Number of specific fragments extracted= 23 number of extra gaps= 3 total=317 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 2gupA/T0628-2gupA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2gupA/T0628-2gupA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gupA read from 2gupA/T0628-2gupA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gupA in template set Warning: unaligning (T0628)A6 because first residue in template chain is (2gupA)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)G126 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)G126 Warning: unaligning (T0628)A202 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2gupA)D186 Warning: unaligning (T0628)V203 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2gupA)D186 Warning: unaligning (T0628)R271 because of BadResidue code BAD_PEPTIDE in next template residue (2gupA)V263 Warning: unaligning (T0628)E272 because of BadResidue code BAD_PEPTIDE at template residue (2gupA)V263 T0628 7 :RYIAIDWGSTNLRAWLYQGEECLESRQS 2gupA 2 :TIATIDIGGTGIKFASLTPDGKILDKTS T0628 40 :RLNGRSPAAVLAEITQHWRDGATPVVMAGMVG 2gupA 30 :ISTPENLEDLLAWLDQRLSEQDYSGIAMSVPG T0628 72 :SNVGWKIAPYLPLPAAFSDIGQQLTAVGDNIWIIP 2gupA 65 :QETGVIDGFSAVPYIHGFSWYEALSSYQLPVHLEN T0628 122 :EETQLLGARALAP 2gupA 101 :ANCVGLSELLAHP T0628 135 :SSVYVMPG 2gupA 117 :NAACVVIG T0628 145 :CKWVLADRRQIHD 2gupA 127 :IGGAMIINGRLHR T0628 172 :QLSLVGAGLPPQETS 2gupA 145 :GGEFGYMTTLAPAEK T0628 187 :AAAFAAGLQR 2gupA 169 :TGNMVRYVIE T0628 197 :GINNP 2gupA 180 :SGHTD T0628 204 :LPQLFEVR 2gupA 187 :GRKIYQEA T0628 212 :ASHVL 2gupA 201 :CQEAI T0628 222 :EQVSEFL 2gupA 206 :ERMNRNL T0628 234 :GAEVATLSDTFA 2gupA 213 :AQGLLNIQYLID T0628 247 :QQAISLVA 2gupA 225 :PGVISLGG T0628 255 :GSSLTSRYQQAFAAI 2gupA 237 :NPDFIQGVKKAVEDF T0628 270 :G 2gupA 261 :A T0628 273 :VSAVA 2gupA 264 :IQACT T0628 278 :GDTAFQTGIRSIAYAV 2gupA 270 :HADANLYGALVNWLQE Number of specific fragments extracted= 18 number of extra gaps= 3 total=335 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 1sz2A/T0628-1sz2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sz2A expands to /projects/compbio/data/pdb/1sz2.pdb.gz 1sz2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 533, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 652, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1311, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1825, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 1sz2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 1sz2A Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 1sz2A # T0628 read from 1sz2A/T0628-1sz2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz2A read from 1sz2A/T0628-1sz2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sz2A to template set # found chain 1sz2A in template set Warning: unaligning (T0628)A6 because first residue in template chain is (1sz2A)K3 Warning: unaligning (T0628)P83 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1sz2A)W79 Warning: unaligning (T0628)L84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1sz2A)W79 T0628 7 :RYIAIDWGSTNLRAWLYQ 1sz2A 4 :YALVGDVGGTNARLALCD T0628 25 :GEECLESRQ 1sz2A 23 :ASGEISQAK T0628 38 :VTRLNG 1sz2A 32 :TYSGLD T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMVGSNVGWKIAPYL 1sz2A 39 :PSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNH T0628 85 :PAAFSDIGQQL 1sz2A 80 :AFSIAEMKKNL T0628 99 :GDNIWIIPG 1sz2A 91 :GFSHLEIIN T0628 122 :EETQLLGARALAP 1sz2A 100 :DFTAVSMAIPMLK T0628 135 :SS 1sz2A 127 :GK T0628 137 :VYVMPGTHCKWVLAD 1sz2A 131 :AVYGAGTGLGVAHLV T0628 152 :RRQIH 1sz2A 148 :DKRWV T0628 158 :FRTVL 1sz2A 173 :ILEIL T0628 163 :TGELHHLLLQL 1sz2A 195 :LVNLYRAIVKA T0628 178 :AGLPPQETS 1sz2A 206 :DNRLPENLK T0628 187 :AAAFAAGLQ 1sz2A 216 :KDITERALA T0628 199 :NNPAVLPQLFEVRAS 1sz2A 225 :DSCTDCRRALSLFCV T0628 232 :LIGAEVATLSDTFAGQQAISLVAG 1sz2A 240 :IMGRFGGNLALNLGTFGGVFIAGG T0628 256 :SSLTSRYQQ 1sz2A 266 :PRFLEFFKA T0628 265 :AF 1sz2A 280 :AF T0628 268 :AIGREVSAVAGDTAFQTGIRSIAYAVAN 1sz2A 291 :VHDIPVYLIVHDNPGLLGSGAHLRQTLG Number of specific fragments extracted= 19 number of extra gaps= 1 total=354 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 1sz2A/T0628-1sz2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1sz2A/T0628-1sz2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz2A read from 1sz2A/T0628-1sz2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sz2A in template set Warning: unaligning (T0628)A6 because first residue in template chain is (1sz2A)K3 Warning: unaligning (T0628)P83 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1sz2A)W79 Warning: unaligning (T0628)L84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1sz2A)W79 T0628 7 :RYIAIDWGSTNLRAWLYQ 1sz2A 4 :YALVGDVGGTNARLALCD T0628 25 :GEECLESRQ 1sz2A 23 :ASGEISQAK T0628 38 :VTRLNG 1sz2A 32 :TYSGLD T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMVGSNVGWKIAPYL 1sz2A 39 :PSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNH T0628 85 :PAAFSDIGQQL 1sz2A 80 :AFSIAEMKKNL T0628 99 :GDNIWIIPG 1sz2A 91 :GFSHLEIIN T0628 121 :GEETQLLGARALAP 1sz2A 100 :DFTAVSMAIPMLKK T0628 135 :SSVYVMPGTHCKWVLAD 1sz2A 129 :PIAVYGAGTGLGVAHLV T0628 152 :RRQIH 1sz2A 148 :DKRWV T0628 158 :FRT 1sz2A 153 :SLP T0628 163 :TGELHHLLLQLS 1sz2A 170 :EAIILEILRAEI T0628 178 :AGLPPQE 1sz2A 182 :GHVSAER T0628 185 :TSAAAFAAGLQRGINNPA 1sz2A 190 :LSGPGLVNLYRAIVKADN T0628 203 :VLPQLFEVRA 1sz2A 214 :KPKDITERAL T0628 217 :GAL 1sz2A 224 :ADS T0628 221 :REQVSEFLSGL 1sz2A 227 :CTDCRRALSLF T0628 232 :LIGAEVATLSDTFAGQQAISLVAG 1sz2A 240 :IMGRFGGNLALNLGTFGGVFIAGG T0628 256 :SSLTSRYQQ 1sz2A 266 :PRFLEFFKA T0628 265 :AF 1sz2A 280 :AF T0628 267 :AAIGREVSAVAGDTAFQTGIRSIAYAVAN 1sz2A 290 :YVHDIPVYLIVHDNPGLLGSGAHLRQTLG Number of specific fragments extracted= 20 number of extra gaps= 1 total=374 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 1sz2A/T0628-1sz2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1sz2A/T0628-1sz2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz2A read from 1sz2A/T0628-1sz2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sz2A in template set Warning: unaligning (T0628)A6 because first residue in template chain is (1sz2A)K3 Warning: unaligning (T0628)P83 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1sz2A)W79 Warning: unaligning (T0628)L84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1sz2A)W79 T0628 7 :RYIAIDWGSTNLRAWLYQGEE 1sz2A 4 :YALVGDVGGTNARLALCDIAS T0628 28 :CLESRQ 1sz2A 26 :EISQAK T0628 38 :VTRLNG 1sz2A 32 :TYSGLD T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMVGSNVGWKIAPYL 1sz2A 39 :PSLEAVIRVYLEEHKVEVKDGCIAIACPITGDWVAMTNH T0628 85 :PAAFSDIGQQLTA 1sz2A 80 :AFSIAEMKKNLGF T0628 100 :DNIWIIP 1sz2A 93 :SHLEIIN T0628 121 :GEETQLLGARALAP 1sz2A 100 :DFTAVSMAIPMLKK T0628 135 :SSVYVMPGTHCKWVLAD 1sz2A 129 :PIAVYGAGTGLGVAHLV T0628 152 :RRQIH 1sz2A 148 :DKRWV T0628 174 :SLVGAGLPPQETSAAAFAAGLQRGINNPAVLP 1sz2A 157 :EGGHVDFAPNSEEEAIILEILRAEIGHVSAER T0628 206 :QLFE 1sz2A 193 :PGLV T0628 210 :VRASHVLGA 1sz2A 199 :YRAIVKADN T0628 219 :LPREQVSEF 1sz2A 213 :LKPKDITER T0628 228 :LSGLLIGAEVATLSDTFAGQQAISLVAG 1sz2A 236 :LFCVIMGRFGGNLALNLGTFGGVFIAGG T0628 256 :SSLTSRYQQ 1sz2A 266 :PRFLEFFKA T0628 265 :AF 1sz2A 280 :AF T0628 267 :AAIGREVSAVAGDTAFQTGIRSIAYAVAN 1sz2A 290 :YVHDIPVYLIVHDNPGLLGSGAHLRQTLG Number of specific fragments extracted= 17 number of extra gaps= 1 total=391 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 1zc6A/T0628-1zc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zc6A expands to /projects/compbio/data/pdb/1zc6.pdb.gz 1zc6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 1zc6A/T0628-1zc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zc6A read from 1zc6A/T0628-1zc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zc6A to template set # found chain 1zc6A in template set T0628 5 :T 1zc6A 11 :R T0628 7 :RYIAIDWGSTNLRAWLYQ 1zc6A 12 :YLIGVDGGGTGTRIRLHA T0628 25 :GEECLESRQSEAGVTRLNGRSPAAVLAEITQHWRD 1zc6A 31 :DGTPLAMAEGGASALSQGIAKSWQAVLSTLEAAFQ T0628 60 :G 1zc6A 68 :G T0628 62 :TPVVMAGMVGSNV 1zc6A 77 :CAIGLGLSGVHNR T0628 86 :AAFSDIGQQLTA 1zc6A 90 :QWAGEFESQAPG T0628 99 :GDNIWIIP 1zc6A 102 :FARLSLAT T0628 123 :ETQLLGARALAP 1zc6A 110 :DGYTTLLGAHGG T0628 135 :SSVYVMPGTHCKWVLAD 1zc6A 123 :PGIIVALGTGSIGEALY T0628 152 :RRQIHD 1zc6A 141 :DGSHRE T0628 158 :FRTVLTGELHHLLLQL 1zc6A 159 :SGAWLGQRAAQLTQMA T0628 176 :VGAGLPP 1zc6A 175 :LDGRHSH T0628 187 :AAAFAAGLQRGINNPAV 1zc6A 182 :SPLTRAVLDFVGGDWQA T0628 212 :ASHVLGALPREQVSEF 1zc6A 199 :MMAWNGRATPAQFARL T0628 234 :GAEVATLSD 1zc6A 215 :APLVLSAAR T0628 246 :GQ 1zc6A 224 :VD T0628 256 :SSLTSRYQQAFAA 1zc6A 226 :PEADALLRQAGED T0628 286 :IRSIAYAVA 1zc6A 239 :AWAIARALD Number of specific fragments extracted= 18 number of extra gaps= 0 total=409 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 1zc6A/T0628-1zc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1zc6A/T0628-1zc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zc6A read from 1zc6A/T0628-1zc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zc6A in template set T0628 6 :ARYIAIDWGSTNLRAWLYQ 1zc6A 11 :RYLIGVDGGGTGTRIRLHA T0628 25 :GEECLESRQSEAGVTRLNGRSPAAVLAEITQHWRD 1zc6A 31 :DGTPLAMAEGGASALSQGIAKSWQAVLSTLEAAFQ T0628 61 :AT 1zc6A 68 :GL T0628 63 :PVVMAGM 1zc6A 78 :AIGLGLS T0628 71 :G 1zc6A 85 :G T0628 86 :AAFSDIGQQLTAV 1zc6A 86 :VHNRQWAGEFESQ T0628 99 :GDNIWIIP 1zc6A 102 :FARLSLAT T0628 123 :ETQLLGARALAP 1zc6A 110 :DGYTTLLGAHGG T0628 135 :SSVYVMPGTHCKWVLAD 1zc6A 123 :PGIIVALGTGSIGEALY T0628 152 :RRQIHDF 1zc6A 141 :DGSHREA T0628 161 :VLTGELHHLLLQLSLVGAGLPPQ 1zc6A 160 :GAWLGQRAAQLTQMALDGRHSHS T0628 188 :AAFAAGLQRGINNPAVLPQLFE 1zc6A 183 :PLTRAVLDFVGGDWQAMMAWNG T0628 211 :RASHVLGAL 1zc6A 217 :LVLSAARVD T0628 222 :EQVSEFLSGL 1zc6A 226 :PEADALLRQA T0628 234 :GAEVATLSD 1zc6A 236 :GEDAWAIAR T0628 243 :TFAGQQAISLVA 1zc6A 247 :DPQDELPVALCG Number of specific fragments extracted= 16 number of extra gaps= 0 total=425 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 1zc6A/T0628-1zc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1zc6A/T0628-1zc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zc6A read from 1zc6A/T0628-1zc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zc6A in template set T0628 4 :MTARYIAIDWGSTNLRAWLYQGEE 1zc6A 9 :SIRYLIGVDGGGTGTRIRLHASDG T0628 28 :CLESRQSEAGVTRLNGRSPAAVLAEITQHWRD 1zc6A 34 :PLAMAEGGASALSQGIAKSWQAVLSTLEAAFQ T0628 60 :GATPVVMAGMVG 1zc6A 75 :SACAIGLGLSGV T0628 87 :AFSDIGQQLTAV 1zc6A 87 :HNRQWAGEFESQ T0628 99 :GDNIWIIP 1zc6A 102 :FARLSLAT T0628 124 :TQLLGARALAP 1zc6A 110 :DGYTTLLGAHG T0628 135 :SSVYVMPGTHCKWVLAD 1zc6A 123 :PGIIVALGTGSIGEALY T0628 152 :RRQIHD 1zc6A 141 :DGSHRE T0628 158 :FRTVLTGELHHLLLQL 1zc6A 159 :SGAWLGQRAAQLTQMA T0628 176 :VGAGLPP 1zc6A 175 :LDGRHSH T0628 187 :A 1zc6A 182 :S T0628 189 :AFAAGLQR 1zc6A 183 :PLTRAVLD T0628 197 :GINNPAVLPQLFE 1zc6A 192 :VGGDWQAMMAWNG T0628 211 :RASHVLGAL 1zc6A 217 :LVLSAARVD T0628 222 :EQVSEFLSG 1zc6A 226 :PEADALLRQ T0628 233 :IGAEVATLSDTFAGQ 1zc6A 235 :AGEDAWAIARALDPQ T0628 248 :QAISLVA 1zc6A 252 :LPVALCG T0628 257 :SLTS 1zc6A 259 :GLGQ Number of specific fragments extracted= 18 number of extra gaps= 0 total=443 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 2qm1A/T0628-2qm1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qm1A expands to /projects/compbio/data/pdb/2qm1.pdb.gz 2qm1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 219, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 260, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 262, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 264, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 266, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 268, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 270, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2qm1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 528, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 2qm1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 648, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 773, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 775, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 777, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 779, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 781, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 783, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 785, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1090, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1096, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1098, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1100, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1102, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1423, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1536, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1538, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1540, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1542, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1544, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1546, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1548, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1550, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1552, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1554, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1556, because occupancy 0.400 <= existing 0.600 in 2qm1A Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1795, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1797, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1799, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1801, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1803, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1805, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1879, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1881, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 2qm1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2081, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2085, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2087, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2089, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2091, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2213, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2215, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2217, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2219, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2221, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2223, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2225, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2227, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2416, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2418, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2424, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2426, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2428, because occupancy 0.500 <= existing 0.500 in 2qm1A Skipped atom 2430, because occupancy 0.500 <= existing 0.500 in 2qm1A # T0628 read from 2qm1A/T0628-2qm1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qm1A read from 2qm1A/T0628-2qm1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qm1A to template set # found chain 2qm1A in template set Warning: unaligning (T0628)W21 because of BadResidue code BAD_PEPTIDE in next template residue (2qm1A)I19 Warning: unaligning (T0628)L22 because of BadResidue code BAD_PEPTIDE at template residue (2qm1A)I19 T0628 1 :SNAMTARYIAIDWGSTNLRA 2qm1A -2 :SNAMDKKIIGIDLGGTTIKF T0628 23 :YQ 2qm1A 20 :LT T0628 25 :GEECLESRQSEAGVT 2qm1A 23 :DGVVQQKWSIETNIL T0628 43 :G 2qm1A 38 :E T0628 44 :RSPAAVLAEITQHW 2qm1A 45 :PSIIESIRHRIDLY T0628 58 :RDGATPVVMAGMVG 2qm1A 62 :KEDFVGIGMGTPGS T0628 72 :SNVG 2qm1A 78 :IEKG T0628 76 :WKIAPYLPL 2qm1A 83 :VVGAYNLNW T0628 85 :PAAF 2qm1A 94 :VQPV T0628 92 :GQQLTAV 2qm1A 98 :KEQIESA T0628 99 :GDNIWIIP 2qm1A 106 :GIPFALDN T0628 122 :EETQLLGARALAP 2qm1A 117 :VAALGERWKGAGE T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2qm1A 133 :DVIFITLGTGVGGGIVAAGKLL T0628 158 :FRTVLTGELHHLLLQL 2qm1A 184 :LETVSSATGVVRVARH T0628 176 :VGAGLPPQ 2qm1A 200 :LSEEFAGD T0628 184 :ETS 2qm1A 219 :DVS T0628 190 :FAAGLQRGINNPAVLPQLFEVRAS 2qm1A 222 :SKDVFEFAEKGDHFALMVVDRVCF T0628 232 :LIGAEVATLSDTF 2qm1A 246 :YLGLATGNLGNTL T0628 246 :GQQAISLVAG 2qm1A 259 :NPDSVVIGGG T0628 256 :SSLTSRYQQAFAAI 2qm1A 274 :EFLRSRVEKYFQEF T0628 270 :GREVSAVA 2qm1A 295 :STKIKLAE T0628 278 :GDTAFQTGIRSIAYAVAN 2qm1A 304 :GNEAGVIGAASLALQFSK Number of specific fragments extracted= 22 number of extra gaps= 1 total=465 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 2qm1A/T0628-2qm1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2qm1A/T0628-2qm1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qm1A read from 2qm1A/T0628-2qm1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qm1A in template set Warning: unaligning (T0628)W21 because of BadResidue code BAD_PEPTIDE in next template residue (2qm1A)I19 Warning: unaligning (T0628)L22 because of BadResidue code BAD_PEPTIDE at template residue (2qm1A)I19 T0628 1 :SNAMTARYIAIDWGSTNLRA 2qm1A -2 :SNAMDKKIIGIDLGGTTIKF T0628 23 :YQ 2qm1A 20 :LT T0628 25 :GEECLESRQ 2qm1A 23 :DGVVQQKWS T0628 34 :SEAGVTR 2qm1A 36 :ILEDGKH T0628 44 :RSPAAVLAEITQHW 2qm1A 45 :PSIIESIRHRIDLY T0628 58 :RDGATPVVMAGMV 2qm1A 62 :KEDFVGIGMGTPG T0628 71 :GSNVG 2qm1A 77 :DIEKG T0628 76 :WKIAPYLPLPAAF 2qm1A 83 :VVGAYNLNWTTVQ T0628 90 :DIGQQLTAV 2qm1A 96 :PVKEQIESA T0628 99 :GDNIWIIP 2qm1A 106 :GIPFALDN T0628 122 :EETQLLGARALAP 2qm1A 115 :ANVAALGERWKGA T0628 135 :SSVYVMPGTHCKWVLADRRQIH 2qm1A 133 :DVIFITLGTGVGGGIVAAGKLL T0628 172 :QLSLVGAGLPPQ 2qm1A 161 :AGEVGHVTVDPN T0628 184 :E 2qm1A 180 :K T0628 187 :AAAFAAGLQRGIN 2qm1A 190 :ATGVVRVARHLSE T0628 202 :A 2qm1A 205 :A T0628 203 :VLPQL 2qm1A 209 :ELKQA T0628 208 :FEVRASHVLGALP 2qm1A 222 :SKDVFEFAEKGDH T0628 223 :QVSEFLSGL 2qm1A 235 :FALMVVDRV T0628 232 :LIGAEVATLSDT 2qm1A 246 :YLGLATGNLGNT T0628 245 :AGQQAISLVAG 2qm1A 258 :LNPDSVVIGGG T0628 256 :SSLTSRYQQAFAAI 2qm1A 274 :EFLRSRVEKYFQEF T0628 270 :GREVSAVAG 2qm1A 295 :STKIKLAEL T0628 279 :DTAFQTGIRSIAYAVAN 2qm1A 305 :NEAGVIGAASLALQFSK Number of specific fragments extracted= 24 number of extra gaps= 1 total=489 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 2qm1A/T0628-2qm1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2qm1A/T0628-2qm1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qm1A read from 2qm1A/T0628-2qm1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qm1A in template set Warning: unaligning (T0628)W21 because of BadResidue code BAD_PEPTIDE in next template residue (2qm1A)I19 Warning: unaligning (T0628)L22 because of BadResidue code BAD_PEPTIDE at template residue (2qm1A)I19 T0628 2 :NAMTARYIAIDWGSTNLRA 2qm1A -1 :NAMDKKIIGIDLGGTTIKF T0628 23 :YQGEECLESRQS 2qm1A 20 :LTTDGVVQQKWS T0628 40 :RLNGRSPAAVLAEITQHWRD 2qm1A 37 :LEDGKHIVPSIIESIRHRID T0628 60 :GATPVVMAGM 2qm1A 64 :DFVGIGMGTP T0628 70 :VGSNVG 2qm1A 76 :VDIEKG T0628 76 :WKIAPYLPLPAAF 2qm1A 83 :VVGAYNLNWTTVQ T0628 90 :DIGQQLTAV 2qm1A 96 :PVKEQIESA T0628 99 :GDNIWIIP 2qm1A 106 :GIPFALDN T0628 122 :EETQLLGARALAP 2qm1A 117 :VAALGERWKGAGE T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 2qm1A 133 :DVIFITLGTGVGGGIVAAGKLLH T0628 172 :QLSLVGAGLPPQETS 2qm1A 161 :AGEVGHVTVDPNGFD T0628 187 :AAAFAAGLQRGI 2qm1A 190 :ATGVVRVARHLS T0628 199 :NNPAVLPQL 2qm1A 206 :GDSELKQAI T0628 208 :FEVRASHVLGAL 2qm1A 222 :SKDVFEFAEKGD T0628 222 :EQVSEFLSGL 2qm1A 234 :HFALMVVDRV T0628 232 :LIGAEVATLSDTFA 2qm1A 246 :YLGLATGNLGNTLN T0628 247 :QQAISLVAG 2qm1A 260 :PDSVVIGGG T0628 256 :SSLTSRYQQAF 2qm1A 274 :EFLRSRVEKYF T0628 267 :AAIGREVSAVA 2qm1A 292 :VRNSTKIKLAE T0628 278 :GDTAFQTGIRSIA 2qm1A 304 :GNEAGVIGAASLA Number of specific fragments extracted= 20 number of extra gaps= 1 total=509 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 2ch5A/T0628-2ch5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ch5A expands to /projects/compbio/data/pdb/2ch5.pdb.gz 2ch5A:# T0628 read from 2ch5A/T0628-2ch5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ch5A read from 2ch5A/T0628-2ch5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ch5A to template set # found chain 2ch5A in template set Warning: unaligning (T0628)M4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ch5A)M1 Warning: unaligning (T0628)T16 because of BadResidue code BAD_PEPTIDE in next template residue (2ch5A)R14 Warning: unaligning (T0628)N17 because of BadResidue code BAD_PEPTIDE at template residue (2ch5A)R14 Warning: unaligning (T0628)G270 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2ch5A)F299 T0628 5 :TARYIAIDWGS 2ch5A 2 :AAIYGGVEGGG T0628 18 :LRAWLYQ 2ch5A 15 :SEVLLVS T0628 25 :GEECLESRQSEA 2ch5A 23 :DGKILAEADGLS T0628 37 :GVTRLNGRSPAAVLAEITQHWRD 2ch5A 36 :NHWLIGTDKCVERINEMVNRAKR T0628 60 :GA 2ch5A 64 :PL T0628 62 :TPVVMAGM 2ch5A 69 :RSLGLSLS T0628 83 :PLP 2ch5A 77 :GGD T0628 88 :FSDIGQQLTAV 2ch5A 80 :QEDAGRILIEE T0628 99 :GDNIWIIP 2ch5A 99 :SESYLITT T0628 123 :ETQLLGARALAPSSVYVMPGTHCKWVLA 2ch5A 107 :DAAGSIATATPDGGVVLISGTGSNCRLI T0628 151 :DRRQIHDFR 2ch5A 136 :PDGSESGCG T0628 160 :TVLTGELHHLLLQLSLVGA 2ch5A 153 :EGSAYWIAHQAVKIVFDSI T0628 179 :GLPPQETSAAAFAAGLQRGINN 2ch5A 173 :NLEAAPHDIGYVKQAMFHYFQV T0628 203 :VLPQLFEVRASHVLGAL 2ch5A 212 :RFAGFCRKIAEGAQQGD T0628 222 :EQVSEFL 2ch5A 229 :PLSRYIF T0628 229 :SGLLIGAEVATLSDTFAGQ 2ch5A 238 :AGEMLGRHIVAVLPEIDPV T0628 248 :QAISLVAGS 2ch5A 263 :GLPILCVGS T0628 257 :SLTSRYQQAFAAI 2ch5A 278 :LLKEGFLLALTQG T0628 271 :REVSAVAGDTAFQTGIRSIAYAVAN 2ch5A 300 :SSFTLMKLRHSSALGGASLGARHIG Number of specific fragments extracted= 19 number of extra gaps= 3 total=528 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 2ch5A/T0628-2ch5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2ch5A/T0628-2ch5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ch5A read from 2ch5A/T0628-2ch5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ch5A in template set Warning: unaligning (T0628)A3 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ch5A)M1 Warning: unaligning (T0628)M4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ch5A)M1 Warning: unaligning (T0628)T16 because of BadResidue code BAD_PEPTIDE in next template residue (2ch5A)R14 Warning: unaligning (T0628)N17 because of BadResidue code BAD_PEPTIDE at template residue (2ch5A)R14 Warning: unaligning (T0628)V273 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2ch5A)F299 T0628 2 :N 2ch5A -1 :Q T0628 5 :TARYIAIDWGS 2ch5A 2 :AAIYGGVEGGG T0628 18 :LRAWLYQ 2ch5A 15 :SEVLLVS T0628 25 :GEECLESRQSEAG 2ch5A 23 :DGKILAEADGLST T0628 38 :VTRLNGRSPAAVLAEITQHWRD 2ch5A 37 :HWLIGTDKCVERINEMVNRAKR T0628 60 :GA 2ch5A 64 :PL T0628 63 :PVVMAG 2ch5A 70 :SLGLSL T0628 70 :VGSNV 2ch5A 76 :SGGDQ T0628 88 :FSDIGQQLTAV 2ch5A 84 :GRILIEELRDR T0628 99 :GDNIWIIP 2ch5A 99 :SESYLITT T0628 123 :ETQLLGARALAPSSVYVMPGTHCKWVLAD 2ch5A 107 :DAAGSIATATPDGGVVLISGTGSNCRLIN T0628 152 :RRQIHD 2ch5A 137 :DGSESG T0628 158 :FRTVLTGELHHLLLQLS 2ch5A 155 :SAYWIAHQAVKIVFDSI T0628 178 :AGLPPQETSAAAFAAGLQRGINNPAV 2ch5A 172 :DNLEAAPHDIGYVKQAMFHYFQVPDR T0628 204 :LPQLFEVRASHVLGAL 2ch5A 213 :FAGFCRKIAEGAQQGD T0628 222 :EQVSEFLS 2ch5A 229 :PLSRYIFR T0628 230 :GLLIGAEVATLSDTFAGQ 2ch5A 239 :GEMLGRHIVAVLPEIDPV T0628 248 :QAISLVAG 2ch5A 263 :GLPILCVG T0628 256 :SSLTSRYQQAFAAI 2ch5A 277 :ELLKEGFLLALTQG T0628 272 :E 2ch5A 296 :Q T0628 274 :SAV 2ch5A 300 :SSF T0628 279 :DTAFQTGIRSIAYAVA 2ch5A 309 :HSSALGGASLGARHIG Number of specific fragments extracted= 22 number of extra gaps= 3 total=550 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 2ch5A/T0628-2ch5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2ch5A/T0628-2ch5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ch5A read from 2ch5A/T0628-2ch5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ch5A in template set Warning: unaligning (T0628)A3 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ch5A)M1 Warning: unaligning (T0628)M4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ch5A)M1 Warning: unaligning (T0628)T16 because of BadResidue code BAD_PEPTIDE in next template residue (2ch5A)R14 Warning: unaligning (T0628)N17 because of BadResidue code BAD_PEPTIDE at template residue (2ch5A)R14 T0628 5 :TARYIAIDWGS 2ch5A 2 :AAIYGGVEGGG T0628 18 :LRAWLYQGEECLE 2ch5A 15 :SEVLLVSEDGKIL T0628 31 :SRQSEAGVT 2ch5A 29 :EADGLSTNH T0628 45 :SPAAVLA 2ch5A 41 :GTDKCVE T0628 52 :EITQHWRD 2ch5A 51 :EMVNRAKR T0628 60 :GATPVVMAGMVGSNV 2ch5A 66 :VPLRSLGLSLSGGDQ T0628 85 :PAAFSDIGQQLTAV 2ch5A 81 :EDAGRILIEELRDR T0628 99 :GDNIWIIP 2ch5A 99 :SESYLITT T0628 123 :ETQLLGARALAPSSVYVMPGTHCKWVLAD 2ch5A 107 :DAAGSIATATPDGGVVLISGTGSNCRLIN T0628 152 :RRQIHD 2ch5A 137 :DGSESG T0628 158 :FRTVLTGELHHLLLQL 2ch5A 155 :SAYWIAHQAVKIVFDS T0628 176 :VGAGLPPQETSAAAFAAGLQRG 2ch5A 171 :IDNLEAAPHDIGYVKQAMFHYF T0628 198 :INNPAVLPQLFEVRASHVLGAL 2ch5A 207 :DFDKCRFAGFCRKIAEGAQQGD T0628 222 :EQVSEFLSGLL 2ch5A 229 :PLSRYIFRKAG T0628 233 :IGAEVATLSDTF 2ch5A 242 :LGRHIVAVLPEI T0628 245 :AGQQAISLVAG 2ch5A 260 :GKIGLPILCVG T0628 256 :SSLTSRYQQAFAAI 2ch5A 277 :ELLKEGFLLALTQG Number of specific fragments extracted= 17 number of extra gaps= 2 total=567 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 2gtdA/T0628-2gtdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gtdA expands to /projects/compbio/data/pdb/2gtd.pdb.gz 2gtdA:# T0628 read from 2gtdA/T0628-2gtdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gtdA read from 2gtdA/T0628-2gtdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gtdA to template set # found chain 2gtdA in template set Warning: unaligning (T0628)M4 because first residue in template chain is (2gtdA)M1 Warning: unaligning (T0628)P134 because of BadResidue code BAD_PEPTIDE in next template residue (2gtdA)K122 T0628 5 :TARYIAIDWGSTNLRAWLYQ 2gtdA 2 :DPMYLLVDVGNTHSVFSITE T0628 25 :GEECL 2gtdA 23 :GKTFR T0628 37 :GVTRLNGRSPAAVLAEITQHWRDGA 2gtdA 29 :WRLSTGVFQTEDELFSHLHPLLGDA T0628 62 :TPVVMAGMV 2gtdA 58 :KGIGVASVV T0628 89 :SDIGQQLTAV 2gtdA 67 :PTQNTVIERF T0628 99 :GDNIWIIP 2gtdA 82 :HISPIWVK T0628 107 :GLCVSRDDNHNVMRGEETQLLGARALA 2gtdA 94 :CVKWNVKNPSEVGADRVANVVAFVKEY T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 2gtdA 123 :NGIIIDMGTATTVDLVVNGSYEGGA T0628 163 :TGELHHLLLQLSLVGAGLPPQETS 2gtdA 152 :FFMMVHSLFRGTAKLPLVEVKPAD T0628 201 :PAVLPQLFEVRASHV 2gtdA 180 :KDTEENIRLGVVNGS T0628 225 :SEFLSGL 2gtdA 195 :VYALEGI T0628 237 :VATLSDTFAGQQ 2gtdA 202 :IGRIKEVYGDLP T0628 250 :ISLVAG 2gtdA 214 :VVLTGG T0628 256 :SSLTSR 2gtdA 222 :KIVKDM T0628 271 :REVSAVAGD 2gtdA 228 :IKHEIFDED T0628 281 :AFQTGIRSIAY 2gtdA 237 :LTIKGVYHFCF Number of specific fragments extracted= 16 number of extra gaps= 1 total=583 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 2gtdA/T0628-2gtdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2gtdA/T0628-2gtdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gtdA read from 2gtdA/T0628-2gtdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gtdA in template set Warning: unaligning (T0628)M4 because first residue in template chain is (2gtdA)M1 Warning: unaligning (T0628)A133 because of BadResidue code BAD_PEPTIDE in next template residue (2gtdA)K122 Warning: unaligning (T0628)P134 because of BadResidue code BAD_PEPTIDE at template residue (2gtdA)K122 T0628 5 :TARYIAIDWGSTNLRAWLYQ 2gtdA 2 :DPMYLLVDVGNTHSVFSITE T0628 25 :GEECL 2gtdA 23 :GKTFR T0628 36 :AGVTRLNGRSPAAVLAEITQHW 2gtdA 28 :RWRLSTGVFQTEDELFSHLHPL T0628 58 :RDGATPVVMAGMV 2gtdA 54 :MREIKGIGVASVV T0628 87 :AFSDIGQQLTAV 2gtdA 68 :TQNTVIERFSQK T0628 99 :GDNI 2gtdA 94 :CVKW T0628 111 :S 2gtdA 98 :N T0628 113 :DDNHNVMRGE 2gtdA 99 :VKNPSEVGAD T0628 123 :ETQLLGARAL 2gtdA 111 :ANVVAFVKEY T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRTV 2gtdA 123 :NGIIIDMGTATTVDLVVNGSYEGGAIL T0628 162 :LTGELHHLLLQLSLVGAG 2gtdA 152 :FFMMVHSLFRGTAKLPLV T0628 180 :LPPQETS 2gtdA 174 :ADFVVGK T0628 187 :AAAFAAGLQRGI 2gtdA 184 :ENIRLGVVNGSV T0628 202 :AVL 2gtdA 196 :YAL T0628 234 :GAEVATLSDT 2gtdA 199 :EGIIGRIKEV T0628 245 :AGQQAISLVAG 2gtdA 209 :YGDLPVVLTGG T0628 256 :SSLTSR 2gtdA 222 :KIVKDM T0628 271 :REVSAVAG 2gtdA 228 :IKHEIFDE T0628 280 :TAFQTGIRSIA 2gtdA 236 :DLTIKGVYHFC Number of specific fragments extracted= 19 number of extra gaps= 1 total=602 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 2gtdA/T0628-2gtdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2gtdA/T0628-2gtdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gtdA read from 2gtdA/T0628-2gtdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gtdA in template set Warning: unaligning (T0628)M4 because first residue in template chain is (2gtdA)M1 Warning: unaligning (T0628)P134 because of BadResidue code BAD_PEPTIDE in next template residue (2gtdA)K122 T0628 5 :TARYIAIDWGSTNLRAWLYQGEECLESR 2gtdA 2 :DPMYLLVDVGNTHSVFSITEDGKTFRRW T0628 38 :VTRLNGRSPAAVLAEITQHWRD 2gtdA 30 :RLSTGVFQTEDELFSHLHPLLG T0628 60 :GATPVVMAGMV 2gtdA 55 :REIKGIGVASV T0628 85 :PAAFSDIGQQLTAV 2gtdA 66 :VPTQNTVIERFSQK T0628 99 :GDNIWIIPGLC 2gtdA 82 :HISPIWVKAKN T0628 110 :VSRDDNHNVMRGEETQLLGARALA 2gtdA 97 :WNVKNPSEVGADRVANVVAFVKEY T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRTV 2gtdA 123 :NGIIIDMGTATTVDLVVNGSYEGGAIL T0628 163 :TGELHHLLLQLSLVGAGLPPQETS 2gtdA 152 :FFMMVHSLFRGTAKLPLVEVKPAD T0628 187 :AAAFAAGLQR 2gtdA 183 :EENIRLGVVN T0628 223 :QVSEFLSGL 2gtdA 193 :GSVYALEGI T0628 237 :VATLSDTFA 2gtdA 202 :IGRIKEVYG T0628 247 :QQAISLVAG 2gtdA 211 :DLPVVLTGG T0628 256 :SSLTS 2gtdA 222 :KIVKD T0628 271 :REVSAVAGD 2gtdA 228 :IKHEIFDED T0628 281 :AFQTGIRSIAY 2gtdA 237 :LTIKGVYHFCF Number of specific fragments extracted= 15 number of extra gaps= 1 total=617 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 1xc3A/T0628-1xc3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xc3A expands to /projects/compbio/data/pdb/1xc3.pdb.gz 1xc3A:Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1xc3A Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1xc3A # T0628 read from 1xc3A/T0628-1xc3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xc3A read from 1xc3A/T0628-1xc3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xc3A to template set # found chain 1xc3A in template set T0628 7 :RYIAIDWGSTNLRAWLYQ 1xc3A 1 :MLGGIEAGGTKFVCAVGR T0628 25 :GEECLESRQSE 1xc3A 20 :DGTIIDRIEFP T0628 43 :GRSPAAVLAEITQHWRD 1xc3A 31 :TKMPDETIEKVIQYFSQ T0628 60 :GATPVVMA 1xc3A 49 :SLQAIGIG T0628 68 :GMVGSNV 1xc3A 59 :GPVDNDK T0628 75 :GWKIAPYLPLP 1xc3A 67 :SQTYGTITATP T0628 91 :IGQQLTAV 1xc3A 86 :FLQTVKNE T0628 99 :GDNIWIIP 1xc3A 95 :KIPVGFST T0628 122 :EETQLLGARALAP 1xc3A 104 :VNAAALGEFLFGE T0628 135 :SSVYVMPGTHCKWVLADRRQIH 1xc3A 122 :SCLYITIGTGIGAGAIVEGRLL T0628 173 :LSLVGAGLPP 1xc3A 149 :PEMGHIYIRR T0628 183 :Q 1xc3A 160 :P T0628 184 :ET 1xc3A 163 :VY T0628 199 :NNPA 1xc3A 169 :PYHG T0628 203 :VLPQLFEVRASHVLGA 1xc3A 175 :FEGLASGPAIEARWGK T0628 220 :P 1xc3A 191 :K T0628 221 :REQVSEFLSG 1xc3A 198 :IAQVWELEGY T0628 232 :LIGAEVATLSDTF 1xc3A 208 :YIAQALAQYILIL T0628 246 :GQQAISLVA 1xc3A 221 :APKKIILGG T0628 255 :GSSLTSRYQQAFAAI 1xc3A 234 :QKQVFSYIYQYVPKI T0628 273 :VSAVA 1xc3A 266 :IVPPR T0628 278 :GDTAFQTGIRSIAYAVA 1xc3A 272 :GSNAGIIGTLVLAHQAL Number of specific fragments extracted= 22 number of extra gaps= 0 total=639 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 1xc3A/T0628-1xc3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1xc3A/T0628-1xc3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xc3A read from 1xc3A/T0628-1xc3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xc3A in template set T0628 7 :RYIAIDWGSTNLRAWLYQ 1xc3A 1 :MLGGIEAGGTKFVCAVGR T0628 25 :GEECLESRQSE 1xc3A 20 :DGTIIDRIEFP T0628 43 :GRSPAAVLAEITQHWRD 1xc3A 31 :TKMPDETIEKVIQYFSQ T0628 60 :GATPVVMA 1xc3A 49 :SLQAIGIG T0628 68 :GMVGS 1xc3A 59 :GPVDN T0628 73 :NVGWKIAPYLPLPA 1xc3A 65 :KTSQTYGTITATPK T0628 87 :A 1xc3A 85 :P T0628 91 :IGQQLTAV 1xc3A 86 :FLQTVKNE T0628 99 :GDNIWIIP 1xc3A 95 :KIPVGFST T0628 122 :EETQLLGARALAP 1xc3A 104 :VNAAALGEFLFGE T0628 135 :SSVYVMPGTHCKWVLADRRQIH 1xc3A 122 :SCLYITIGTGIGAGAIVEGRLL T0628 173 :LSLVGAGLPPQE 1xc3A 149 :PEMGHIYIRRHP T0628 187 :AAAFAAGLQRGINNP 1xc3A 177 :GLASGPAIEARWGKK T0628 202 :AVL 1xc3A 196 :SDI T0628 222 :EQVSEFLSGL 1xc3A 199 :AQVWELEGYY T0628 233 :IGAEVATLSDT 1xc3A 209 :IAQALAQYILI T0628 245 :AGQQAISLVAG 1xc3A 220 :LAPKKIILGGG T0628 256 :SSLTSRYQQAFAAI 1xc3A 235 :KQVFSYIYQYVPKI T0628 270 :GREVSA 1xc3A 250 :NSYLDF T0628 276 :VAG 1xc3A 267 :VPP T0628 279 :DTAFQTGIRSIAYAVA 1xc3A 273 :SNAGIIGTLVLAHQAL Number of specific fragments extracted= 21 number of extra gaps= 0 total=660 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 1xc3A/T0628-1xc3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1xc3A/T0628-1xc3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xc3A read from 1xc3A/T0628-1xc3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xc3A in template set Warning: unaligning (T0628)A6 because first residue in template chain is (1xc3A)A0 T0628 7 :RYIAIDWGSTNLRAWLYQGEECLES 1xc3A 1 :MLGGIEAGGTKFVCAVGREDGTIID T0628 38 :VTRLNGRSPAAVLAEITQHWRD 1xc3A 26 :RIEFPTKMPDETIEKVIQYFSQ T0628 60 :GATPVVMA 1xc3A 49 :SLQAIGIG T0628 68 :GMVGSNVGW 1xc3A 59 :GPVDNDKTS T0628 77 :KIAPYLPLPA 1xc3A 69 :TYGTITATPK T0628 90 :DIGQQLTAV 1xc3A 85 :PFLQTVKNE T0628 99 :GDNIWIIP 1xc3A 95 :KIPVGFST T0628 122 :EETQLLGARALAP 1xc3A 104 :VNAAALGEFLFGE T0628 135 :SSVYVMPGTHCKWVLADRRQIH 1xc3A 122 :SCLYITIGTGIGAGAIVEGRLL T0628 173 :LSLVGAGLPP 1xc3A 149 :PEMGHIYIRR T0628 183 :QETS 1xc3A 160 :PDDV T0628 187 :AAAFAAGL 1xc3A 181 :GPAIEARW T0628 195 :QRGINNPAVLPQLFEV 1xc3A 193 :ADLSDIAQVWELEGYY T0628 233 :IGAEVATLSDTF 1xc3A 209 :IAQALAQYILIL T0628 247 :QQAISLVAGS 1xc3A 221 :APKKIILGGG T0628 257 :SLTSRYQQAFAAI 1xc3A 236 :QVFSYIYQYVPKI T0628 275 :AVA 1xc3A 266 :IVP T0628 278 :GDTAFQTGIRSIAYAVA 1xc3A 272 :GSNAGIIGTLVLAHQAL Number of specific fragments extracted= 18 number of extra gaps= 0 total=678 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 1z6rA/T0628-1z6rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z6rA expands to /projects/compbio/data/pdb/1z6r.pdb.gz 1z6rA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 1z6rA/T0628-1z6rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6rA read from 1z6rA/T0628-1z6rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z6rA to template set # found chain 1z6rA in template set Warning: unaligning (T0628)A150 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)T230 Warning: unaligning (T0628)D151 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)T230 Warning: unaligning (T0628)T243 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)F333 Warning: unaligning (T0628)F244 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)F333 Warning: unaligning (T0628)A277 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)Q381 Warning: unaligning (T0628)G278 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)T383 Warning: unaligning (T0628)D279 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)T383 T0628 5 :TARYIAIDWGSTNLRAWLYQ 1z6rA 84 :AWHYLSLRISRGEIFLALRD T0628 25 :GEECLESRQSE 1z6rA 105 :SSKLVVEESQE T0628 38 :VTRLNGRSPAAVLAEITQHWRD 1z6rA 116 :LALKDDLPLLDRIISHIDQFFI T0628 62 :TPVVMAGMVG 1z6rA 146 :LTSIAITLPG T0628 72 :SNVGWKIAPYLP 1z6rA 160 :ENGIVHRMPFYE T0628 85 :PAAFSD 1z6rA 175 :EMPLGE T0628 94 :QLTAV 1z6rA 181 :ALEQH T0628 99 :GDNIWIIP 1z6rA 187 :GVPVYIQH T0628 122 :EETQLLGARALAP 1z6rA 196 :ISAWTMAEALFGA T0628 135 :SSVYVMPGTHCKWVL 1z6rA 214 :DVIQVVIDHNVGAGV T0628 152 :RRQIHD 1z6rA 231 :DGHLLH T0628 173 :LS 1z6rA 242 :LV T0628 175 :LVGAGLPPQ 1z6rA 245 :IGHTQVDPY T0628 187 :AAAFAAGLQRGINNPA 1z6rA 271 :VDSILELAQLRLNQSM T0628 203 :VL 1z6rA 289 :ML T0628 205 :PQLFEVR 1z6rA 298 :DSLCQAA T0628 216 :LGAL 1z6rA 305 :LRGD T0628 222 :EQVSEFL 1z6rA 309 :LLAKDII T0628 229 :SGLLIGAEVATLSD 1z6rA 318 :VGAHVGRILAIMVN T0628 245 :AGQ 1z6rA 334 :NPQ T0628 250 :ISLVAGS 1z6rA 337 :KILIGSP T0628 258 :LTSRYQQAFA 1z6rA 351 :LFPVISDSIR T0628 268 :AIGREVSAV 1z6rA 368 :SQHISVEST T0628 280 :TAFQTGIRS 1z6rA 384 :MAGAALVKD Number of specific fragments extracted= 24 number of extra gaps= 3 total=702 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 1z6rA/T0628-1z6rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1z6rA/T0628-1z6rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6rA read from 1z6rA/T0628-1z6rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z6rA in template set Warning: unaligning (T0628)A150 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)T230 Warning: unaligning (T0628)D151 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)T230 Warning: unaligning (T0628)T243 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)F333 Warning: unaligning (T0628)F244 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)F333 Warning: unaligning (T0628)A277 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)Q381 Warning: unaligning (T0628)G278 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)T383 Warning: unaligning (T0628)D279 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)T383 T0628 5 :TARYIAIDWGSTNLRAWLYQ 1z6rA 84 :AWHYLSLRISRGEIFLALRD T0628 25 :GEECLESRQSE 1z6rA 105 :SSKLVVEESQE T0628 38 :VTRLNGRSPAAVLAEITQHW 1z6rA 116 :LALKDDLPLLDRIISHIDQF T0628 58 :RDGAT 1z6rA 139 :HQKKL T0628 63 :PVVMA 1z6rA 148 :SIAIT T0628 68 :GMVGSNVG 1z6rA 155 :GIIDTENG T0628 76 :WKIAPYLP 1z6rA 164 :VHRMPFYE T0628 85 :PAAFSD 1z6rA 175 :EMPLGE T0628 94 :QLTAV 1z6rA 181 :ALEQH T0628 99 :GDNIWIIP 1z6rA 187 :GVPVYIQH T0628 122 :EETQLLGARALAP 1z6rA 196 :ISAWTMAEALFGA T0628 135 :SSVYVMPGTHCKWVL 1z6rA 214 :DVIQVVIDHNVGAGV T0628 152 :RRQIHD 1z6rA 231 :DGHLLH T0628 173 :LSLVGAGLPPQ 1z6rA 243 :VEIGHTQVDPY T0628 187 :AAAFAAGLQRGINNPA 1z6rA 271 :VDSILELAQLRLNQSM T0628 204 :LPQLFEV 1z6rA 297 :VDSLCQA T0628 215 :VLGAL 1z6rA 304 :ALRGD T0628 222 :EQVSEFLSGL 1z6rA 309 :LLAKDIITGV T0628 232 :LIGAEVATLSD 1z6rA 321 :HVGRILAIMVN T0628 246 :GQQ 1z6rA 334 :NPQ T0628 250 :ISLVAG 1z6rA 337 :KILIGS T0628 256 :SSLTSRYQQAFAAI 1z6rA 349 :DILFPVISDSIRQQ T0628 270 :GREVSAV 1z6rA 370 :HISVEST T0628 280 :TA 1z6rA 384 :MA T0628 285 :GIRSIAYA 1z6rA 386 :GAALVKDA Number of specific fragments extracted= 25 number of extra gaps= 3 total=727 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 1z6rA/T0628-1z6rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1z6rA/T0628-1z6rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6rA read from 1z6rA/T0628-1z6rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z6rA in template set Warning: unaligning (T0628)A150 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)T230 Warning: unaligning (T0628)D151 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)T230 Warning: unaligning (T0628)N200 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)P294 Warning: unaligning (T0628)P201 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)P294 Warning: unaligning (T0628)T243 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1z6rA)F333 Warning: unaligning (T0628)F244 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1z6rA)F333 T0628 5 :TARYIAIDWGSTNLRAWLYQGEECLESRQS 1z6rA 84 :AWHYLSLRISRGEIFLALRDLSSKLVVEES T0628 35 :E 1z6rA 115 :E T0628 38 :VTRLNGRSPAAVLAEITQHWRD 1z6rA 116 :LALKDDLPLLDRIISHIDQFFI T0628 60 :GATPVVMA 1z6rA 145 :RLTSIAIT T0628 68 :GMVGSNVG 1z6rA 155 :GIIDTENG T0628 76 :WKIAPYLP 1z6rA 164 :VHRMPFYE T0628 84 :LPAAFS 1z6rA 174 :KEMPLG T0628 93 :QQLTAV 1z6rA 180 :EALEQH T0628 99 :GDNIWIIP 1z6rA 187 :GVPVYIQH T0628 122 :EETQLLGARALAP 1z6rA 196 :ISAWTMAEALFGA T0628 135 :SSVYVMPGTHCKWVL 1z6rA 214 :DVIQVVIDHNVGAGV T0628 152 :RRQIHD 1z6rA 231 :DGHLLH T0628 173 :LSLVGAGLPPQETS 1z6rA 243 :VEIGHTQVDPYGKR T0628 187 :AAAFAAGLQR 1z6rA 271 :VDSILELAQL T0628 199 :N 1z6rA 292 :G T0628 202 :AVLPQLFEV 1z6rA 295 :LTVDSLCQA T0628 215 :VLGAL 1z6rA 304 :ALRGD T0628 222 :EQVSEFLSGL 1z6rA 309 :LLAKDIITGV T0628 232 :LIGAEVATLSD 1z6rA 321 :HVGRILAIMVN T0628 245 :A 1z6rA 334 :N T0628 247 :QQAISLVAG 1z6rA 335 :PQKILIGSP T0628 256 :SSLTSRYQQAFAAI 1z6rA 349 :DILFPVISDSIRQQ T0628 270 :GREVSAVA 1z6rA 370 :HISVESTQ Number of specific fragments extracted= 23 number of extra gaps= 3 total=750 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 1huxA/T0628-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1huxA expands to /projects/compbio/data/pdb/1hux.pdb.gz 1huxA:# T0628 read from 1huxA/T0628-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0628-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1huxA to template set # found chain 1huxA in template set Warning: unaligning (T0628)T5 because first residue in template chain is (1huxA)S2 T0628 6 :ARYIAIDWGSTNLRAWLYQ 1huxA 3 :IYTLGIDVGSTASKCIILK T0628 25 :GEECLESR 1huxA 23 :GKEIVAKS T0628 38 :VTRLNGRS 1huxA 31 :LVAVGTGT T0628 46 :PAAVLAEITQHW 1huxA 41 :PARSISEVLENA T0628 58 :RDGATPVVMAG 1huxA 56 :KEDMAFTLATG T0628 106 :PGLCVSRDDNHNVMRGEETQLLGARALAPSS 1huxA 67 :YGRNSLEGIADKQMSELSCHAMGASFIWPNV T0628 137 :VYVMPGTHCKWVLADRRQIHDFR 1huxA 100 :VIDIGGQDVKVIHVENGTMTNFQ T0628 164 :GELHHLLLQLSLVGAG 1huxA 132 :GRFLDVMANILEVKVS T0628 180 :LPPQ 1huxA 156 :STKR T0628 184 :ETSAA 1huxA 164 :STCTV T0628 202 :AVLPQLF 1huxA 169 :FAESEVI T0628 213 :SHVLGALPREQVSEFLSGLL 1huxA 176 :SQLSKGTDKIDIIAGIHRSV T0628 234 :GAEVATLSDTFAGQQAISLVAGSSLTSRYQQAF 1huxA 196 :ASRVIGLANRVGIVKDVVMTGGVAQNYGVRGAL T0628 267 :AAIGREVSAVA 1huxA 230 :EGLGVEIKTSP T0628 279 :DTAFQTGIRSIAYAVA 1huxA 243 :QYNGALGAALYAYKKA Number of specific fragments extracted= 15 number of extra gaps= 0 total=765 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 1huxA/T0628-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1huxA/T0628-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0628-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huxA in template set Warning: unaligning (T0628)T5 because first residue in template chain is (1huxA)S2 T0628 6 :ARYIAIDWGSTNLRAWLYQ 1huxA 3 :IYTLGIDVGSTASKCIILK T0628 25 :GEECLESR 1huxA 23 :GKEIVAKS T0628 38 :VTRLNGRS 1huxA 31 :LVAVGTGT T0628 46 :PAAVLAEITQHW 1huxA 41 :PARSISEVLENA T0628 58 :RDGATPVVMAGMVGSNVG 1huxA 56 :KEDMAFTLATGYGRNSLE T0628 113 :DDNHNVMRGEETQLLGARALAP 1huxA 74 :GIADKQMSELSCHAMGASFIWP T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 1huxA 98 :HTVIDIGGQDVKVIHVENGTMTNFQ T0628 160 :TVLTGELHHLL 1huxA 132 :GRFLDVMANIL T0628 172 :QLSLVGAGLPPQ 1huxA 148 :DLAELGAKSTKR T0628 184 :ETS 1huxA 161 :AIS T0628 199 :N 1huxA 165 :T T0628 203 :VLPQLFEVRASHVLGALPREQVSEFLSGLLIGAEVATLSDTFAGQQ 1huxA 166 :CTVFAESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVKD T0628 250 :ISLVAG 1huxA 212 :VVMTGG T0628 256 :SSLTSRYQQAF 1huxA 222 :YGVRGALEEGL T0628 270 :GREVSAVAG 1huxA 233 :GVEIKTSPL T0628 279 :DTAFQTGIRSIAYAV 1huxA 243 :QYNGALGAALYAYKK Number of specific fragments extracted= 16 number of extra gaps= 0 total=781 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 1huxA/T0628-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1huxA/T0628-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0628-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huxA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQGEECLESR 1huxA 3 :IYTLGIDVGSTASKCIILKDGKEIVAK T0628 37 :GVTRLNGRSPA 1huxA 30 :SLVAVGTGTSG T0628 48 :AVLAEITQHWRD 1huxA 43 :RSISEVLENAHM T0628 60 :GATPVVMAGM 1huxA 58 :DMAFTLATGY T0628 94 :QLTAVGDNIWIIPGL 1huxA 68 :GRNSLEGIADKQMSE T0628 122 :EETQLLGARALAP 1huxA 83 :LSCHAMGASFIWP T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRT 1huxA 98 :HTVIDIGGQDVKVIHVENGTMTNFQM T0628 162 :LTGELHHLLLQL 1huxA 130 :GTGRFLDVMANI T0628 174 :SLVGAGLPPQE 1huxA 150 :AELGAKSTKRV T0628 187 :AAAFAAGLQRGINNPAVLPQLFEV 1huxA 171 :ESEVISQLSKGTDKIDIIAGIHRS T0628 232 :LIG 1huxA 195 :VAS T0628 236 :EVATLSDTFAGQQAISLVAG 1huxA 198 :RVIGLANRVGIVKDVVMTGG T0628 256 :SSLTSRYQQAF 1huxA 222 :YGVRGALEEGL T0628 270 :GREVSA 1huxA 233 :GVEIKT T0628 278 :GDTAFQTGIRSIAYAV 1huxA 239 :SPLAQYNGALGAALYA Number of specific fragments extracted= 15 number of extra gaps= 0 total=796 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 1woqA/T0628-1woqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1woqA expands to /projects/compbio/data/pdb/1woq.pdb.gz 1woqA:# T0628 read from 1woqA/T0628-1woqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woqA read from 1woqA/T0628-1woqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1woqA to template set # found chain 1woqA in template set Warning: unaligning (T0628)T5 because first residue in template chain is (1woqA)N11 Warning: unaligning (T0628)A294 because last residue in template chain is (1woqA)H263 T0628 6 :ARYIAIDWGSTNLRAWLYQ 1woqA 12 :APLIGIDIGGTGIKGGIVD T0628 25 :GEECLESR 1woqA 32 :KKGKLLGE T0628 36 :AGVTRLNG 1woqA 40 :RFRVPTPQ T0628 44 :RSPAAVLAEITQHWRDGA 1woqA 52 :ESVAEAVALVVAELSARP T0628 62 :TPVVMAGMVGS 1woqA 76 :SPVGVTFPGII T0628 73 :NVGWKIAPYLP 1woqA 88 :HGVVHSAANVD T0628 86 :A 1woqA 104 :T T0628 90 :DIGQQLTAV 1woqA 105 :DIDALLTAR T0628 99 :GDNIWIIP 1woqA 115 :GRPVEVIN T0628 122 :EETQLLGARALAP 1woqA 124 :ADAAGLAEARYGA T0628 137 :VYVMPGTHCKWVLADRRQIH 1woqA 145 :LVITLGTGIGSAFIFDGKLV T0628 172 :QLSLVGAG 1woqA 165 :PNAELGHL T0628 180 :LPPQ 1woqA 174 :IDGH T0628 189 :AFAAG 1woqA 179 :AETKA T0628 194 :LQRG 1woqA 185 :AVAR T0628 215 :VLGALPREQVSEFL 1woqA 189 :ERDGLSWDEYSVLL T0628 234 :GAEVATLSDTFA 1woqA 203 :QRYFSHVEFLFS T0628 247 :QQAISLVAG 1woqA 215 :PELFIVGGG T0628 256 :SSLTS 1woqA 229 :DEYLP T0628 269 :IGREVSAVA 1woqA 237 :LRTPIVPAV T0628 278 :GDTAFQTGIRSIAYAV 1woqA 247 :RNEAGIVGAAIEIALQ Number of specific fragments extracted= 21 number of extra gaps= 0 total=817 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 1woqA/T0628-1woqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1woqA/T0628-1woqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woqA read from 1woqA/T0628-1woqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1woqA in template set Warning: unaligning (T0628)T5 because first residue in template chain is (1woqA)N11 Warning: unaligning (T0628)A294 because last residue in template chain is (1woqA)H263 T0628 6 :ARYIAIDWGSTNLRAWLYQ 1woqA 12 :APLIGIDIGGTGIKGGIVD T0628 25 :GEECLESRQ 1woqA 33 :KGKLLGERF T0628 38 :VTRLNG 1woqA 42 :RVPTPQ T0628 44 :RSPAAVLAEITQHWRD 1woqA 52 :ESVAEAVALVVAELSA T0628 60 :GATPVVMAGMVGSNVG 1woqA 74 :AGSPVGVTFPGIIQHG T0628 76 :WKIAPYLPLP 1woqA 91 :VHSAANVDKS T0628 86 :AA 1woqA 104 :TD T0628 91 :IGQQLTAV 1woqA 106 :IDALLTAR T0628 99 :GDNIWIIP 1woqA 115 :GRPVEVIN T0628 122 :EETQLLGARALAP 1woqA 124 :ADAAGLAEARYGA T0628 135 :SS 1woqA 142 :GT T0628 137 :VYVMPGTHCKWVLADRRQIH 1woqA 145 :LVITLGTGIGSAFIFDGKLV T0628 171 :LQLSLVGAGLPPQETSAAAFAAGLQRG 1woqA 165 :PNAELGHLEIDGHDAETKASAVARERD T0628 218 :ALPREQVSEFLSGLL 1woqA 192 :GLSWDEYSVLLQRYF T0628 238 :ATLSDT 1woqA 207 :SHVEFL T0628 245 :AGQQAISLVAG 1woqA 213 :FSPELFIVGGG T0628 256 :SSLTSR 1woqA 229 :DEYLPN T0628 269 :IGREVSAVA 1woqA 237 :LRTPIVPAV T0628 278 :GDTAFQTGIRSIAYAV 1woqA 247 :RNEAGIVGAAIEIALQ Number of specific fragments extracted= 19 number of extra gaps= 0 total=836 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 1woqA/T0628-1woqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 1woqA/T0628-1woqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1woqA read from 1woqA/T0628-1woqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1woqA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQGEE 1woqA 12 :APLIGIDIGGTGIKGGIVDLKK T0628 28 :CLESRQSEAGVTRLNGRSPAAVLAEITQHWRD 1woqA 36 :LLGERFRVPTPQPATPESVAEAVALVVAELSA T0628 60 :GATPVVMAGMVGSNVG 1woqA 74 :AGSPVGVTFPGIIQHG T0628 76 :WKIAPYLPLPAAFSDIGQQLTAV 1woqA 91 :VHSAANVDKSWLNTDIDALLTAR T0628 99 :GDNIWIIP 1woqA 115 :GRPVEVIN T0628 122 :EETQLLGARALAP 1woqA 124 :ADAAGLAEARYGA T0628 135 :SSVYVMPGTHCKWVLADRRQIH 1woqA 143 :TVLVITLGTGIGSAFIFDGKLV T0628 171 :LQLSLVGAGLPPQETSAAAFAAGLQR 1woqA 165 :PNAELGHLEIDGHDAETKASAVARER T0628 217 :GALPREQVSEFLS 1woqA 191 :DGLSWDEYSVLLQ T0628 235 :AEVATLSDTFA 1woqA 204 :RYFSHVEFLFS T0628 247 :QQAISLVAG 1woqA 215 :PELFIVGGG T0628 256 :SSLTS 1woqA 229 :DEYLP T0628 270 :GREVSAVA 1woqA 238 :RTPIVPAV T0628 278 :GDTAFQTGIRSIAYAV 1woqA 247 :RNEAGIVGAAIEIALQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=850 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 3lm2A/T0628-3lm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lm2A expands to /projects/compbio/data/pdb/3lm2.pdb.gz 3lm2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 348, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 416, because occupancy 0.300 <= existing 0.700 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 420, because occupancy 0.300 <= existing 0.700 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 422, because occupancy 0.300 <= existing 0.700 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 424, because occupancy 0.220 <= existing 0.530 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 426, because occupancy 0.300 <= existing 0.700 in 3lm2A Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 778, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 782, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 784, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 786, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 788, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 790, because occupancy 0.400 <= existing 0.600 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 962, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1024, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1028, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1032, because occupancy 0.370 <= existing 0.380 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1571, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1575, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1577, because occupancy 0.500 <= existing 0.500 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1624, because occupancy 0.400 <= existing 0.600 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1628, because occupancy 0.400 <= existing 0.600 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1630, because occupancy 0.400 <= existing 0.600 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1632, because occupancy 0.300 <= existing 0.450 in 3lm2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1634, because occupancy 0.400 <= existing 0.600 in 3lm2A Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1702, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1732, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1734, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1736, because occupancy 0.500 <= existing 0.500 in 3lm2A Skipped atom 1738, because occupancy 0.500 <= existing 0.500 in 3lm2A # T0628 read from 3lm2A/T0628-3lm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lm2A read from 3lm2A/T0628-3lm2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lm2A to template set # found chain 3lm2A in template set T0628 3 :AMTARYIAIDWGSTNLRAWLYQGEECL 3lm2A 2 :AEDQTVLAIDIGGSHVKIGLSTDGEER T0628 38 :VTRLNGRSPAAVLAEITQHWRDGA 3lm2A 29 :KVESGKTMTGPEMVAAVTAMAKDM T0628 62 :TPVVMAGMVGSNV 3lm2A 55 :DVIAMGYPGPVVH T0628 75 :GWKIAPYLP 3lm2A 70 :PLREPVNLG T0628 86 :AAFSDIG 3lm2A 84 :YDYEGAF T0628 99 :GDNIWIIP 3lm2A 91 :GRPVRIVN T0628 123 :ETQLLGARALAPS 3lm2A 99 :DALMQAIGSYNGG T0628 136 :SVYVMPGTHCKWVLADRRQIHDFR 3lm2A 113 :MLFLGLGTGLGAAMIVENVAQPME T0628 176 :VGAG 3lm2A 137 :IAHL T0628 180 :LPPQ 3lm2A 142 :YRKG T0628 194 :LQ 3lm2A 149 :EH T0628 198 :INNPAVLPQL 3lm2A 151 :YVSEAYREKK T0628 220 :PREQVSEFLSGL 3lm2A 161 :GNAKWQKRVQDV T0628 237 :VATLSDTF 3lm2A 173 :VERLSAAL T0628 246 :GQQAISLVAGSSL 3lm2A 181 :EPDEVVIGGGNVE T0628 270 :GR 3lm2A 196 :EN T0628 273 :VSAVA 3lm2A 202 :CRRGD T0628 279 :DTAFQTGIRSIAY 3lm2A 207 :NAMAFEGGFRLWK Number of specific fragments extracted= 18 number of extra gaps= 0 total=868 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 3lm2A/T0628-3lm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3lm2A/T0628-3lm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lm2A read from 3lm2A/T0628-3lm2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lm2A in template set Warning: unaligning (T0628)N2 because first residue in template chain is (3lm2A)M1 T0628 3 :AMTARYIAIDWGSTNLRAWLYQGEECLESR 3lm2A 2 :AEDQTVLAIDIGGSHVKIGLSTDGEERKVE T0628 41 :LNGRSPAAVLAEITQHWRDG 3lm2A 32 :SGKTMTGPEMVAAVTAMAKD T0628 61 :ATPVVMAGMVG 3lm2A 53 :TYDVIAMGYPG T0628 73 :NVGWK 3lm2A 67 :HNKPL T0628 78 :IAPYLPLPA 3lm2A 73 :EPVNLGEGW T0628 87 :AFSDIG 3lm2A 85 :DYEGAF T0628 99 :GDNIWIIP 3lm2A 91 :GRPVRIVN T0628 123 :ETQLLGARALAPS 3lm2A 99 :DALMQAIGSYNGG T0628 136 :SVYVMPGTHCKWVLADRRQIHDFR 3lm2A 113 :MLFLGLGTGLGAAMIVENVAQPME T0628 176 :VGAG 3lm2A 137 :IAHL T0628 180 :LPPQ 3lm2A 142 :YRKG T0628 194 :LQRGINNPAVLPQ 3lm2A 148 :YEHYVSEAYREKK T0628 220 :PREQVSEFL 3lm2A 161 :GNAKWQKRV T0628 234 :GAEVATLSDTF 3lm2A 170 :QDVVERLSAAL T0628 246 :GQQAISLVAG 3lm2A 181 :EPDEVVIGGG T0628 273 :VSAVAGDTAFQTGIR 3lm2A 202 :CRRGDNAMAFEGGFR T0628 289 :IA 3lm2A 217 :LW Number of specific fragments extracted= 17 number of extra gaps= 0 total=885 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 3lm2A/T0628-3lm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3lm2A/T0628-3lm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lm2A read from 3lm2A/T0628-3lm2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lm2A in template set T0628 3 :AMTARYIAIDWGSTNLRAWLYQGEECLE 3lm2A 2 :AEDQTVLAIDIGGSHVKIGLSTDGEERK T0628 39 :TRLNGRSPAAVLAEITQHWRD 3lm2A 30 :VESGKTMTGPEMVAAVTAMAK T0628 60 :GATPVVMAGMVGS 3lm2A 53 :TYDVIAMGYPGPV T0628 73 :NVGWKIAPYLPLPA 3lm2A 68 :NKPLREPVNLGEGW T0628 87 :AFSDIG 3lm2A 85 :DYEGAF T0628 99 :GDNIWIIP 3lm2A 91 :GRPVRIVN T0628 123 :ETQLLGARALAP 3lm2A 99 :DALMQAIGSYNG T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 3lm2A 112 :RMLFLGLGTGLGAAMIVENVAQPME T0628 176 :VGAG 3lm2A 137 :IAHL T0628 180 :LPPQ 3lm2A 142 :YRKG T0628 194 :LQRGIN 3lm2A 148 :YEHYVS T0628 201 :PAVLPQ 3lm2A 154 :EAYREK T0628 219 :LPREQVSEFLSG 3lm2A 160 :KGNAKWQKRVQD T0628 236 :EVATLSDTFA 3lm2A 172 :VVERLSAALE T0628 247 :QQAISLVAG 3lm2A 182 :PDEVVIGGG T0628 273 :VSAVA 3lm2A 202 :CRRGD T0628 279 :DTAFQTGIRSIAY 3lm2A 207 :NAMAFEGGFRLWK Number of specific fragments extracted= 17 number of extra gaps= 0 total=902 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 2hoeA/T0628-2hoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hoeA expands to /projects/compbio/data/pdb/2hoe.pdb.gz 2hoeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 2hoeA/T0628-2hoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hoeA read from 2hoeA/T0628-2hoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hoeA to template set # found chain 2hoeA in template set Warning: unaligning (T0628)N199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hoeA)S267 Warning: unaligning (T0628)N200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hoeA)S267 T0628 6 :ARYIAIDWGSTNLRAWLYQ 2hoeA 75 :AYVLGIEVTRDEIAACLID T0628 25 :GEECLESRQ 2hoeA 95 :SMNILAHEA T0628 39 :TRLNG 2hoeA 104 :HPLPS T0628 44 :RSPAAVLAEITQHWRD 2hoeA 113 :EETLNVMYRIIDRAKD T0628 60 :GA 2hoeA 133 :LG T0628 62 :TPVVMA 2hoeA 138 :SALTVA T0628 68 :GMVGSNVG 2hoeA 146 :GPIDTERG T0628 77 :KIAPYLPLPAAFSDIGQQLTAV 2hoeA 154 :IIIDPRNFPLSQIPLANLLKEK T0628 99 :GDNIWIIP 2hoeA 177 :GIEVWVEN T0628 122 :EETQLLGARAL 2hoeA 188 :MGAVGEKWYTK T0628 133 :APSSVYVMPGTHCKWVLADRRQIHD 2hoeA 200 :DDSFAWILTGKGIGAGIIIDGELYR T0628 172 :QLSLVGAGLPPQE 2hoeA 230 :AGEIGYTRVFNGN T0628 185 :TSAAAFAAGLQRGI 2hoeA 251 :CNENVVLKHVLSMG T0628 202 :A 2hoeA 268 :L T0628 203 :V 2hoeA 270 :E T0628 213 :SHVLGA 2hoeA 271 :ARDSGD T0628 222 :EQVSEFL 2hoeA 277 :VRVKEYF T0628 229 :SGLLIGAEVATLSDTF 2hoeA 286 :IARYFSIGLLNLIHLF T0628 246 :GQQAISLVAG 2hoeA 302 :GISKIVIGGF T0628 256 :SSLTSRYQQAFAAI 2hoeA 317 :ENFLKKIKIEVETH T0628 270 :GREVSAVAG 2hoeA 336 :SVDMSFSKV T0628 279 :DTAFQTGIRSIAYAV 2hoeA 346 :EPVIAFGAAVHALEN Number of specific fragments extracted= 22 number of extra gaps= 1 total=924 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 2hoeA/T0628-2hoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2hoeA/T0628-2hoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hoeA read from 2hoeA/T0628-2hoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hoeA in template set T0628 6 :ARYIAIDWGSTNLRAWLYQ 2hoeA 75 :AYVLGIEVTRDEIAACLID T0628 25 :GEECLESRQ 2hoeA 95 :SMNILAHEA T0628 39 :TRLNG 2hoeA 104 :HPLPS T0628 44 :RSPAAVLAEITQHWRD 2hoeA 113 :EETLNVMYRIIDRAKD T0628 60 :GATPVVMAGMVG 2hoeA 136 :KLSALTVAAPGP T0628 72 :SNVG 2hoeA 150 :TERG T0628 77 :KIAPYLPLPAAFSDIGQQLTAV 2hoeA 154 :IIIDPRNFPLSQIPLANLLKEK T0628 99 :GDNIWIIP 2hoeA 177 :GIEVWVEN T0628 121 :GEETQLLGARALAP 2hoeA 187 :DMGAVGEKWYTKRD T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 2hoeA 202 :SFAWILTGKGIGAGIIIDGELYR T0628 173 :LSLVGAG 2hoeA 230 :AGEIGYT T0628 180 :LPPQE 2hoeA 238 :VFNGN T0628 185 :TSAAAFAAGLQRG 2hoeA 251 :CNENVVLKHVLSM T0628 213 :SHVLGA 2hoeA 271 :ARDSGD T0628 222 :EQVSEFL 2hoeA 277 :VRVKEYF T0628 229 :SGLLIGAEVATLSDT 2hoeA 286 :IARYFSIGLLNLIHL T0628 245 :AGQQAISLVAG 2hoeA 301 :FGISKIVIGGF T0628 256 :SSLTSRYQQAFAAI 2hoeA 317 :ENFLKKIKIEVETH T0628 272 :EVSAVAG 2hoeA 338 :DMSFSKV T0628 279 :DTAFQTGIRSIAYAV 2hoeA 346 :EPVIAFGAAVHALEN Number of specific fragments extracted= 20 number of extra gaps= 0 total=944 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 2hoeA/T0628-2hoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2hoeA/T0628-2hoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hoeA read from 2hoeA/T0628-2hoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hoeA in template set Warning: unaligning (T0628)I198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2hoeA)S267 Warning: unaligning (T0628)N199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2hoeA)S267 T0628 6 :ARYIAIDWGSTNLRAWLYQGEECLESRQ 2hoeA 75 :AYVLGIEVTRDEIAACLIDASMNILAHE T0628 38 :VTRLNGRSPA 2hoeA 103 :AHPLPSQSDR T0628 48 :AVLAEITQHWRD 2hoeA 117 :NVMYRIIDRAKD T0628 60 :GATPVVMA 2hoeA 136 :KLSALTVA T0628 68 :GMVGSNVGWKIAPYL 2hoeA 146 :GPIDTERGIIIDPRN T0628 84 :LPAAFSDIGQQLTAV 2hoeA 161 :FPLSQIPLANLLKEK T0628 99 :GDNIWIIPG 2hoeA 177 :GIEVWVEND T0628 122 :EETQLLGARALAP 2hoeA 186 :ADMGAVGEKWYTK T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 2hoeA 202 :SFAWILTGKGIGAGIIIDGELYR T0628 173 :LSLVGAGLPPQETS 2hoeA 231 :GEIGYTRVFNGNEY T0628 187 :AAAFAAGLQR 2hoeA 253 :ENVVLKHVLS T0628 197 :G 2hoeA 264 :G T0628 201 :PAVLPQ 2hoeA 268 :LAEARD T0628 220 :PREQVSEFLSGL 2hoeA 275 :GDVRVKEYFDDI T0628 232 :LIGAEVATLSDTFA 2hoeA 289 :YFSIGLLNLIHLFG T0628 247 :QQAISLVAG 2hoeA 303 :ISKIVIGGF T0628 256 :SSLTSRYQQAFAAI 2hoeA 317 :ENFLKKIKIEVETH T0628 270 :GREVSAVA 2hoeA 336 :SVDMSFSK T0628 278 :GDTAFQTGIRSIAYAV 2hoeA 346 :EPVIAFGAAVHALENY Number of specific fragments extracted= 19 number of extra gaps= 1 total=963 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 3mcpA/T0628-3mcpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3mcpA expands to /projects/compbio/data/pdb/3mcp.pdb.gz 3mcpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0628 read from 3mcpA/T0628-3mcpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mcpA read from 3mcpA/T0628-3mcpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3mcpA to template set # found chain 3mcpA in template set Warning: unaligning (T0628)G270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3mcpA)Q298 T0628 3 :AMTARYIAIDWGSTNLRAWLYQ 3mcpA 5 :NDNRIVMTLDAGGTNFVFSAIQ T0628 25 :GEECLESRQSE 3mcpA 28 :GKEIADPVVLP T0628 41 :LNGRSPAAV 3mcpA 39 :ACADCLDKC T0628 50 :LAEITQHWRDGA 3mcpA 51 :LVEGFKAIQAGL T0628 62 :TPVVMA 3mcpA 67 :VAISFA T0628 68 :GMVGSNVG 3mcpA 75 :GPADYQAG T0628 76 :WKIAPYLPLPAAFSDI 3mcpA 87 :LPNFPSFRGGVALGPF T0628 95 :LTAV 3mcpA 103 :LEDI T0628 99 :GDNIWIIP 3mcpA 108 :GIPVFINN T0628 122 :EETQLLGARALAP 3mcpA 117 :GSLFAYGEALTGV T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 3mcpA 148 :NLLGVTLGTGFGAGVVIDGELLRGD T0628 172 :QLSLVGAGL 3mcpA 176 :GGYVWCLRN T0628 181 :PPQ 3mcpA 187 :YPE T0628 184 :ETSAAAFAAGLQRGINNPA 3mcpA 195 :SVSIRAVMRVYAERSGDAG T0628 203 :VLPQLFE 3mcpA 219 :EIFEIAE T0628 217 :GALPREQVSEFLSGL 3mcpA 228 :RPGNREAAIAAFEEL T0628 232 :LIGAEVATLSDTF 3mcpA 245 :MAGDALASAITLI T0628 248 :QAISLVAGS 3mcpA 258 :DGLIVIGGG T0628 257 :SLTSRYQQAFAAI 3mcpA 273 :YILPVLLKEMNAQ T0628 271 :REVSAVAGDTAFQ 3mcpA 299 :KEVYDLDEEKSFA Number of specific fragments extracted= 20 number of extra gaps= 0 total=983 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 3mcpA/T0628-3mcpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3mcpA/T0628-3mcpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mcpA read from 3mcpA/T0628-3mcpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3mcpA in template set Warning: unaligning (T0628)G270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3mcpA)Q298 T0628 3 :AMTARYIAIDWGSTNLRAWLYQ 3mcpA 5 :NDNRIVMTLDAGGTNFVFSAIQ T0628 25 :GEECLESRQSE 3mcpA 28 :GKEIADPVVLP T0628 41 :LNGRSPAAV 3mcpA 39 :ACADCLDKC T0628 50 :LAEITQHWRD 3mcpA 51 :LVEGFKAIQA T0628 61 :ATPVVMAGMVG 3mcpA 65 :APVAISFAFPG T0628 72 :SNVGWK 3mcpA 79 :YQAGII T0628 78 :IAPYLPLPAAFSDIG 3mcpA 89 :NFPSFRGGVALGPFL T0628 93 :QQL 3mcpA 105 :DIF T0628 99 :GDNIWIIP 3mcpA 108 :GIPVFINN T0628 121 :GEETQLLGARALA 3mcpA 116 :DGSLFAYGEALTG T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 3mcpA 148 :NLLGVTLGTGFGAGVVIDGELLRGD T0628 172 :QLSLVGAGLP 3mcpA 175 :AGGYVWCLRN T0628 182 :PQE 3mcpA 187 :YPE T0628 185 :TSAAAFAAGLQRGINNPA 3mcpA 196 :VSIRAVMRVYAERSGDAG T0628 203 :VLPQLFEVR 3mcpA 216 :TPKEIFEIA T0628 214 :HVLGALPREQVSEFLS 3mcpA 225 :EGIRPGNREAAIAAFE T0628 230 :GLLIGAEVATLSDTF 3mcpA 243 :GEMAGDALASAITLI T0628 248 :QAISLVAG 3mcpA 258 :DGLIVIGG T0628 256 :SSLTSRYQQAFAAI 3mcpA 272 :KYILPVLLKEMNAQ T0628 271 :REVSAVAGDTAFQTG 3mcpA 299 :KEVYDLDEEKSFAGF Number of specific fragments extracted= 20 number of extra gaps= 0 total=1003 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 3mcpA/T0628-3mcpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3mcpA/T0628-3mcpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3mcpA read from 3mcpA/T0628-3mcpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3mcpA in template set Warning: unaligning (T0628)V273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3mcpA)Q298 T0628 2 :NAMTARYIAIDWGSTNLRAWLYQGEECLE 3mcpA 4 :TNDNRIVMTLDAGGTNFVFSAIQGGKEIA T0628 35 :EAGVTRLNGRSPAA 3mcpA 33 :DPVVLPACADCLDK T0628 49 :VLAEITQHWRD 3mcpA 50 :NLVEGFKAIQA T0628 60 :GATPVVMAGMVG 3mcpA 64 :EAPVAISFAFPG T0628 72 :SNVGWK 3mcpA 79 :YQAGII T0628 78 :IAPYL 3mcpA 86 :DLPNF T0628 83 :PLPAAF 3mcpA 94 :RGGVAL T0628 92 :GQQLTAV 3mcpA 100 :GPFLEDI T0628 99 :GDNIWIIP 3mcpA 108 :GIPVFINN T0628 121 :GEETQLLGARALAP 3mcpA 116 :DGSLFAYGEALTGV T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 3mcpA 148 :NLLGVTLGTGFGAGVVIDGELLR T0628 173 :LSLVGAGLP 3mcpA 177 :GYVWCLRNK T0628 182 :PQETS 3mcpA 187 :YPEYI T0628 187 :AAAFAAGLQRGINNPAVLPQ 3mcpA 198 :IRAVMRVYAERSGDAGARTP T0628 209 :EVRASHVLG 3mcpA 218 :KEIFEIAEG T0628 218 :ALPREQVSEFLSGL 3mcpA 229 :PGNREAAIAAFEEL T0628 232 :LIGAEVATLSDTF 3mcpA 245 :MAGDALASAITLI T0628 247 :QQAISLVAG 3mcpA 258 :DGLIVIGGG T0628 256 :SSLTSRYQQAFAAIGRE 3mcpA 272 :KYILPVLLKEMNAQTGM Number of specific fragments extracted= 19 number of extra gaps= 0 total=1022 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 2h3gX/T0628-2h3gX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h3gX expands to /projects/compbio/data/pdb/2h3g.pdb.gz 2h3gX:Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 2h3gX Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 2h3gX # T0628 read from 2h3gX/T0628-2h3gX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3gX read from 2h3gX/T0628-2h3gX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h3gX to template set # found chain 2h3gX in template set Warning: unaligning (T0628)R7 because first residue in template chain is (2h3gX)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2h3gX)A133 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2h3gX)A133 Warning: unaligning (T0628)Q172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2h3gX)I171 Warning: unaligning (T0628)L180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2h3gX)I171 Warning: unaligning (T0628)A294 because last residue in template chain is (2h3gX)A254 T0628 8 :YIAIDWGSTNLRAWLYQGEECLES 2h3gX 2 :IFVLDVGNTNAVLGVFEEGELRQH T0628 37 :GVTRLNG 2h3gX 26 :WRMETDR T0628 44 :RSPAAVLAEITQHW 2h3gX 37 :DEYGMLVKQLLEHE T0628 58 :RDGATPVVMAGMV 2h3gX 54 :FEDVKGIIVSSVV T0628 89 :SDIGQQLTAV 2h3gX 67 :PPIMFALERM T0628 99 :GDNIWIIP 2h3gX 82 :KIKPLVVG T0628 107 :GLCVSRDDNHNVMRGEETQLLGARALAP 2h3gX 95 :GLNIKYENPREVGADRIVNAVAGIHLYG T0628 135 :SSVYVMPG 2h3gX 124 :PLIIVDFG T0628 145 :CKWVLADRRQ 2h3gX 134 :TTYCYINEEK T0628 155 :IHDFRTVL 2h3gX 145 :YMGGVITP T0628 163 :TGELHHLLL 2h3gX 154 :IMISAEALY T0628 181 :PPQET 2h3gX 172 :EITKP T0628 199 :NNPAVLPQLFEVRASHV 2h3gX 180 :VGKNTVSAMQSGILYGY T0628 225 :SEFLSGL 2h3gX 197 :VGQVEGI T0628 237 :VATLSDTFAGQQAISLVAGS 2h3gX 204 :VKRMKEEAKQEPKVIATGGL T0628 259 :TSRYQQAF 2h3gX 224 :AKLISEES T0628 271 :REVSAVAG 2h3gX 232 :NVIDVVDP T0628 280 :TAFQTGIRSIAYAV 2h3gX 240 :FLTLKGLYMLYERN Number of specific fragments extracted= 18 number of extra gaps= 1 total=1040 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 2h3gX/T0628-2h3gX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2h3gX/T0628-2h3gX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3gX read from 2h3gX/T0628-2h3gX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h3gX in template set Warning: unaligning (T0628)R7 because first residue in template chain is (2h3gX)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2h3gX)A133 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2h3gX)A133 Warning: unaligning (T0628)Q172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2h3gX)I171 Warning: unaligning (T0628)L180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2h3gX)I171 Warning: unaligning (T0628)A294 because last residue in template chain is (2h3gX)A254 T0628 8 :YIAIDWGSTNLRAWLYQGEECLESRQ 2h3gX 2 :IFVLDVGNTNAVLGVFEEGELRQHWR T0628 39 :TRLNGRSPAAVLAEITQHW 2h3gX 28 :METDRHKTEDEYGMLVKQL T0628 58 :RDGATPVVMAGMV 2h3gX 54 :FEDVKGIIVSSVV T0628 89 :SDIGQQLTAV 2h3gX 67 :PPIMFALERM T0628 107 :GLCVSRDDNHNVMRGEETQLLGARALAP 2h3gX 95 :GLNIKYENPREVGADRIVNAVAGIHLYG T0628 135 :SSVYVMPG 2h3gX 124 :PLIIVDFG T0628 145 :CKWVLADRRQ 2h3gX 134 :TTYCYINEEK T0628 155 :IHDFRTV 2h3gX 145 :YMGGVIT T0628 163 :TGELHHLLL 2h3gX 154 :IMISAEALY T0628 181 :PPQETS 2h3gX 172 :EITKPS T0628 199 :NNPAVLPQLFEVR 2h3gX 181 :GKNTVSAMQSGIL T0628 213 :S 2h3gX 194 :Y T0628 223 :QVSEFLSGL 2h3gX 195 :GYVGQVEGI T0628 237 :VATLSDTFAGQQAISLVAGS 2h3gX 204 :VKRMKEEAKQEPKVIATGGL T0628 259 :TSRYQQA 2h3gX 224 :AKLISEE T0628 269 :IGR 2h3gX 231 :SNV T0628 273 :VSAVAG 2h3gX 234 :IDVVDP T0628 280 :TAFQTGIRSIAYAV 2h3gX 240 :FLTLKGLYMLYERN Number of specific fragments extracted= 18 number of extra gaps= 1 total=1058 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 2h3gX/T0628-2h3gX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 2h3gX/T0628-2h3gX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h3gX read from 2h3gX/T0628-2h3gX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h3gX in template set Warning: unaligning (T0628)R7 because first residue in template chain is (2h3gX)M1 Warning: unaligning (T0628)T143 because of BadResidue code BAD_PEPTIDE in next template residue (2h3gX)A133 Warning: unaligning (T0628)H144 because of BadResidue code BAD_PEPTIDE at template residue (2h3gX)A133 Warning: unaligning (T0628)Q172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2h3gX)I171 Warning: unaligning (T0628)L180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2h3gX)I171 T0628 8 :YIAIDWGSTNLRAWLYQGEECLESRQ 2h3gX 2 :IFVLDVGNTNAVLGVFEEGELRQHWR T0628 39 :TRLNGRSPAAVLAEITQHWRD 2h3gX 28 :METDRHKTEDEYGMLVKQLLE T0628 60 :GATPVVMAGMV 2h3gX 56 :DVKGIIVSSVV T0628 89 :SDIGQQLTAV 2h3gX 67 :PPIMFALERM T0628 99 :GDNIWII 2h3gX 82 :KIKPLVV T0628 106 :PGLCVSRDDNHNVMRGEETQLLGARALAP 2h3gX 94 :TGLNIKYENPREVGADRIVNAVAGIHLYG T0628 135 :SSVYVMPG 2h3gX 124 :PLIIVDFG T0628 145 :CKWVLAD 2h3gX 134 :TTYCYIN T0628 152 :RRQIHDFRTV 2h3gX 142 :EKHYMGGVIT T0628 163 :TGELHHLLL 2h3gX 154 :IMISAEALY T0628 181 :PPQETS 2h3gX 172 :EITKPS T0628 187 :AAAFAAGLQR 2h3gX 185 :VSAMQSGILY T0628 223 :QVSEFLSGL 2h3gX 195 :GYVGQVEGI T0628 237 :VATLSDTFAGQQAISLVAGS 2h3gX 204 :VKRMKEEAKQEPKVIATGGL T0628 259 :TSRYQQA 2h3gX 224 :AKLISEE T0628 269 :I 2h3gX 231 :S T0628 271 :REVSAVA 2h3gX 232 :NVIDVVD T0628 279 :DTAFQTGIRSIAYA 2h3gX 239 :PFLTLKGLYMLYER Number of specific fragments extracted= 18 number of extra gaps= 1 total=1076 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 3bexA/T0628-3bexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bexA expands to /projects/compbio/data/pdb/3bex.pdb.gz 3bexA:# T0628 read from 3bexA/T0628-3bexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bexA read from 3bexA/T0628-3bexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bexA to template set # found chain 3bexA in template set Warning: unaligning (T0628)M4 because first residue in template chain is (3bexA)M-2 T0628 5 :TARYIAIDWGSTNLRAWLYQ 3bexA -1 :DPMYLLVDVGNTHSVFSITE T0628 25 :GEECL 3bexA 20 :GKTFR T0628 31 :SR 3bexA 25 :RW T0628 38 :VTRLNG 3bexA 27 :RLSTGV T0628 44 :RSPAAVLAEITQHWRDGATPVVMAGMV 3bexA 37 :DELFSHLHPLLGDAMREIKGIGVASVV T0628 89 :SDIGQQLTAV 3bexA 64 :PTQNTVIERF T0628 99 :GDNIWIIP 3bexA 79 :HISPIWVK T0628 107 :GLCVSRDDNHNVMRGEETQLLGARALAP 3bexA 91 :CVKWNVKNPSEVGADRVANVVAFVKEYG T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFR 3bexA 120 :NGIIIDMGTATTVDLVVNGSYEGGA T0628 163 :TGELHHLLLQLS 3bexA 149 :FFMMVHSLFRGT T0628 178 :AGLPPQETS 3bexA 161 :AKLPLVEVK T0628 200 :NPAVLPQLFEVRASHV 3bexA 176 :GKDTEENIRLGVVNGS T0628 225 :SEFLSGLLIGAEVA 3bexA 192 :VYALEGIIGRIKEV T0628 244 :F 3bexA 206 :Y T0628 246 :GQQAISLVAG 3bexA 207 :GDLPVVLTGG T0628 256 :SSLTSR 3bexA 219 :KIVKDM T0628 271 :REVSAVAG 3bexA 225 :IKHEIFDE T0628 280 :TAFQTGIRSIAY 3bexA 233 :DLTIKGVYHFCF Number of specific fragments extracted= 18 number of extra gaps= 0 total=1094 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 3bexA/T0628-3bexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3bexA/T0628-3bexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bexA read from 3bexA/T0628-3bexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bexA in template set Warning: unaligning (T0628)M4 because first residue in template chain is (3bexA)M-2 T0628 5 :TARYIAIDWGSTNLRAWLYQ 3bexA -1 :DPMYLLVDVGNTHSVFSITE T0628 25 :GEECL 3bexA 20 :GKTFR T0628 36 :AGVTRLNGRSPAAVLAEITQHWRD 3bexA 25 :RWRLSTGVFQTEDELFSHLHPLLG T0628 60 :GATPVVMAGMV 3bexA 53 :EIKGIGVASVV T0628 89 :SDIGQQLTAV 3bexA 64 :PTQNTVIERF T0628 99 :GDNIWIIP 3bexA 79 :HISPIWVK T0628 107 :GLCVSRDDNHNVMRGEETQLLGARALAP 3bexA 91 :CVKWNVKNPSEVGADRVANVVAFVKEYG T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRTV 3bexA 120 :NGIIIDMGTATTVDLVVNGSYEGGAIL T0628 162 :LTGELHHL 3bexA 149 :FFMMVHSL T0628 174 :SLVGAGLPPQETS 3bexA 157 :FRGTAKLPLVEVK T0628 203 :VLPQLFEVRASH 3bexA 179 :TEENIRLGVVNG T0628 224 :VSEFLSGLLIGAEVA 3bexA 191 :SVYALEGIIGRIKEV T0628 245 :AGQQAISLVAG 3bexA 206 :YGDLPVVLTGG T0628 256 :SSLTSR 3bexA 219 :KIVKDM T0628 271 :REVSAVAG 3bexA 225 :IKHEIFDE T0628 280 :TAFQTGIRSIAY 3bexA 233 :DLTIKGVYHFCF Number of specific fragments extracted= 16 number of extra gaps= 0 total=1110 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 3bexA/T0628-3bexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3bexA/T0628-3bexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bexA read from 3bexA/T0628-3bexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bexA in template set T0628 5 :TARYIAIDWGSTNLRAWLYQGEECLESRQ 3bexA -1 :DPMYLLVDVGNTHSVFSITEDGKTFRRWR T0628 39 :TRLNGRSPAAVLAEITQHWRD 3bexA 28 :LSTGVFQTEDELFSHLHPLLG T0628 60 :GATPVVMAGMVG 3bexA 52 :REIKGIGVASVV T0628 89 :SDIGQQLTAV 3bexA 64 :PTQNTVIERF T0628 99 :GDNIWIIPGLC 3bexA 79 :HISPIWVKAKN T0628 110 :VSRDDNHNVMRGEETQLLGARALAP 3bexA 94 :WNVKNPSEVGADRVANVVAFVKEYG T0628 135 :SSVYVMPGTHCKWVLADRRQIHDFRTV 3bexA 120 :NGIIIDMGTATTVDLVVNGSYEGGAIL T0628 163 :TGELHHLLLQLS 3bexA 149 :FFMMVHSLFRGT T0628 178 :AGLPPQETS 3bexA 161 :AKLPLVEVK T0628 187 :AAAFAAGLQR 3bexA 180 :EENIRLGVVN T0628 223 :QVSEFLSGL 3bexA 190 :GSVYALEGI T0628 237 :VATLSDTFA 3bexA 199 :IGRIKEVYG T0628 247 :QQAISLVAG 3bexA 208 :DLPVVLTGG T0628 256 :SSLTSR 3bexA 219 :KIVKDM T0628 271 :REVSAVAGD 3bexA 225 :IKHEIFDED T0628 281 :AFQTGIRSIAY 3bexA 234 :LTIKGVYHFCF Number of specific fragments extracted= 16 number of extra gaps= 0 total=1126 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 3bp8A/T0628-3bp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bp8A expands to /projects/compbio/data/pdb/3bp8.pdb.gz 3bp8A:# T0628 read from 3bp8A/T0628-3bp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bp8A read from 3bp8A/T0628-3bp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bp8A to template set # found chain 3bp8A in template set Warning: unaligning (T0628)N200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3bp8A)H291 T0628 5 :TARYIAIDWGSTNLRAWLYQ 3bp8A 84 :AWHYLSLRISRGEIFLALRD T0628 25 :GEECLESRQSE 3bp8A 105 :SSKLVVEESQE T0628 38 :VTRLNGRSPAAVLAEITQHWRD 3bp8A 116 :LALKDDSPLLDRIISHIDQFFI T0628 60 :G 3bp8A 140 :Q T0628 62 :TPVVMA 3bp8A 147 :TSIAIT T0628 68 :GMVGSNVG 3bp8A 155 :GIIDTENG T0628 76 :WKIAPYLP 3bp8A 164 :VHRMPFYE T0628 86 :AA 3bp8A 176 :MP T0628 91 :IGQQLTAV 3bp8A 178 :LGEALEQH T0628 99 :GDNIWIIP 3bp8A 187 :GVPVYIQH T0628 122 :EETQLLGARALAP 3bp8A 196 :ISAWTMAEALFGA T0628 135 :SSVYVMPGTHCKWVLADRRQIH 3bp8A 214 :DVIQVVIDHNVGAGVITDGHLL T0628 173 :LSLVGAGLPPQ 3bp8A 242 :LVEIGHTQVDP T0628 187 :AAAFAAGLQRGIN 3bp8A 271 :VDSILELAQLRLN T0628 201 :PA 3bp8A 292 :GQ T0628 203 :VLPQLFEVRAS 3bp8A 296 :TVDSLCQAALR T0628 221 :REQVSEFL 3bp8A 308 :DLLAKDII T0628 229 :SGLLIGAEVATLSDTF 3bp8A 318 :VGAHVGRILAIMVNLF T0628 246 :GQQAISLVAG 3bp8A 334 :NPQKILIGSP T0628 256 :SSLTSRYQQAFA 3bp8A 349 :DILFPVISDSIR T0628 268 :AIGREVSAV 3bp8A 368 :SQHISVEST T0628 277 :AGDT 3bp8A 379 :SNQG T0628 282 :FQTGIRSIAYAVAN 3bp8A 383 :TMAGAALVKDAMYN Number of specific fragments extracted= 23 number of extra gaps= 0 total=1149 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 3bp8A/T0628-3bp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3bp8A/T0628-3bp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bp8A read from 3bp8A/T0628-3bp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bp8A in template set Warning: unaligning (T0628)N200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3bp8A)H291 T0628 5 :TARYIAIDWGSTNLRAWLYQ 3bp8A 84 :AWHYLSLRISRGEIFLALRD T0628 25 :GEECLESRQSE 3bp8A 105 :SSKLVVEESQE T0628 41 :LNGRS 3bp8A 116 :LALKD T0628 46 :PAAVLAEITQHWRD 3bp8A 124 :LLDRIISHIDQFFI T0628 60 :GAT 3bp8A 141 :KKL T0628 63 :PVVMAGMVG 3bp8A 147 :TSIAITLPG T0628 72 :SNVG 3bp8A 159 :TENG T0628 76 :WKIAPYLP 3bp8A 164 :VHRMPFYE T0628 84 :LPA 3bp8A 176 :MPL T0628 92 :GQQLTAV 3bp8A 179 :GEALEQH T0628 99 :GDNIWIIP 3bp8A 187 :GVPVYIQH T0628 122 :EETQLLGARAL 3bp8A 196 :ISAWTMAEALF T0628 134 :P 3bp8A 207 :G T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 3bp8A 214 :DVIQVVIDHNVGAGVITDGHLLH T0628 173 :LSLVGAGLPPQE 3bp8A 242 :LVEIGHTQVDPY T0628 185 :TSAAAFAAGLQRGIN 3bp8A 269 :ASVDSILELAQLRLN T0628 201 :PA 3bp8A 292 :GQ T0628 203 :VLPQLFEVRAS 3bp8A 296 :TVDSLCQAALR T0628 221 :REQVSEFLSGLL 3bp8A 308 :DLLAKDIITGVG T0628 233 :IGAEVATLSDTF 3bp8A 322 :VGRILAIMVNLF T0628 246 :GQQAISLVAG 3bp8A 334 :NPQKILIGSP T0628 256 :SSLTSRYQQAFAAI 3bp8A 349 :DILFPVISDSIRQQ T0628 270 :GREVSAVAG 3bp8A 370 :HISVESTQF T0628 279 :DTAFQTGIRSIAYAVA 3bp8A 380 :NQGTMAGAALVKDAMY Number of specific fragments extracted= 24 number of extra gaps= 0 total=1173 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 3bp8A/T0628-3bp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0628 read from 3bp8A/T0628-3bp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bp8A read from 3bp8A/T0628-3bp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bp8A in template set T0628 5 :TARYIAIDWGSTNLRAWLYQGEECLESRQS 3bp8A 84 :AWHYLSLRISRGEIFLALRDLSSKLVVEES T0628 36 :AGVTRLNGRSPAAVLAEITQHWRD 3bp8A 114 :QELALKDDSPLLDRIISHIDQFFI T0628 60 :GATPVVMAGMVGSN 3bp8A 142 :KLERLTSIAITLPG T0628 74 :VG 3bp8A 161 :NG T0628 76 :WKIAPYLP 3bp8A 164 :VHRMPFYE T0628 84 :LPA 3bp8A 176 :MPL T0628 88 :FSDIGQQL 3bp8A 179 :GEALEQHT T0628 99 :GDNIWIIPG 3bp8A 187 :GVPVYIQHD T0628 122 :EETQLLGARA 3bp8A 196 :ISAWTMAEAL T0628 133 :AP 3bp8A 206 :FG T0628 135 :SSVYVMPGTHCKWVLADRRQIHD 3bp8A 214 :DVIQVVIDHNVGAGVITDGHLLH T0628 173 :LSLVGAGLPPQETS 3bp8A 242 :LVEIGHTQVDPYGK T0628 187 :AAAFAAGLQRGI 3bp8A 271 :VDSILELAQLRL T0628 199 :NNPAVLPQLFEVRASH 3bp8A 292 :GQPLTVDSLCQAALRG T0628 221 :REQVSEFLSGLL 3bp8A 308 :DLLAKDIITGVG T0628 233 :IGAEVATLSDTFA 3bp8A 322 :VGRILAIMVNLFN T0628 247 :QQAISLVAG 3bp8A 335 :PQKILIGSP T0628 256 :SSLTSRYQQAFAAI 3bp8A 349 :DILFPVISDSIRQQ T0628 270 :GREVSAVAG 3bp8A 370 :HISVESTQF Number of specific fragments extracted= 19 number of extra gaps= 0 total=1192 Will force an alignment to be made, even if fragment is small Number of alignments=63 # command:CPU_time= 24.529 sec, elapsed time= 49.730 sec. # command:DEBUG: alignment library has 63 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 63 # Adding 3864 constraints to all_contacts Done adding distance constraints # command:CPU_time= 24.668 sec, elapsed time= 49.877 sec. # command:Reading probabilities from T0628.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 52.913 Optimizing... Probability sum: -535.616, CN propb: -535.616 weights: 0.290 constraints: 950 # command:CPU_time= 396.595 sec, elapsed time= 422.138 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 950 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 950 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 2914 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 2914 # 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= 396.659 sec, elapsed time= 423.118 sec. # command: