# 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: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # 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 T0316 numbered 1 through 373 Created new target T0316 from T0316.a2m # command:CPU_time= 6.268 sec, elapsed time= 6.320 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl2A/T0316-1vl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vl2A expands to /projects/compbio/data/pdb/1vl2.pdb.gz 1vl2A:Skipped atom 2393, because occupancy 0.5 <= existing 0.500 in 1vl2A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 1vl2A Skipped atom 2772, because occupancy 0.500 <= existing 0.500 in 1vl2A Skipped atom 2774, because occupancy 0.500 <= existing 0.500 in 1vl2A Skipped atom 2776, because occupancy 0.500 <= existing 0.500 in 1vl2A # T0316 read from 1vl2A/T0316-1vl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl2A read from 1vl2A/T0316-1vl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vl2A to template set # found chain 1vl2A in template set Warning: unaligning (T0316)K6 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0316)P97 because of BadResidue code BAD_PEPTIDE in next template residue (1vl2A)L87 Warning: unaligning (T0316)N98 because of BadResidue code BAD_PEPTIDE at template residue (1vl2A)L87 Warning: unaligning (T0316)F169 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0316)P177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 Warning: unaligning (T0316)G203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl2A)I186 Warning: unaligning (T0316)E204 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl2A)I186 Warning: unaligning (T0316)G367 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)G379 T0316 7 :TRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1vl2A 3 :EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVA # choosing archetypes in rotamer library T0316 46 :ENG 1vl2A 35 :NVG T0316 52 :ATEDYKDVVAVADQIGI 1vl2A 38 :QKDDFVAIKEKALKTGA T0316 69 :PYYSVNFEKEYWDRVFEYFL 1vl2A 56 :KVYVEDLRREFVTDYIFTAL T0316 91 :YRAGRT 1vl2A 80 :MYEGRY T0316 99 :PDVMCNKEI 1vl2A 88 :GTAIARPLI T0316 109 :FKAFLDYAITLGADYVATG 1vl2A 97 :AKRQVEIAEKEGAQYVAHG T0316 132 :VARDEDGTVHMLRGVDNGKDQTYFLSQLSQEQLQKTM 1vl2A 116 :ATGKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKF T0316 178 :EVRRLAEEAGLST 1vl2A 157 :DLINYAMEKGIPI T0316 191 :AKKKDSTGICFI 1vl2A 173 :KKRPYSEDENLM T0316 205 :KNFKNFLSNYLPAQPGRMM 1vl2A 187 :SHEAGKLEDPAHIPDEDVF T0316 248 :GIGGQHGGDNAPWFVVGKDLSKNILYVGQG 1vl2A 206 :TWTVSPKDAPDEETLLEIHFENGIPVKVVN T0316 278 :FYHDSLMSTSLEASQVHF 1vl2A 240 :TEKTDPLELFEYLNEVGA T0316 296 :T 1vl2A 261 :V T0316 304 :TLECTAKFRYRQPDSKVTVH 1vl2A 262 :GRLDMVENRFIGIKSRGVYE T0316 338 :RAIT 1vl2A 341 :ENVT T0316 343 :GQAVV 1vl2A 345 :GKVTV T0316 348 :FYDGEECLGGGLIDNAYRD 1vl2A 351 :IYKGNVMPVARYSPYSLYN Number of specific fragments extracted= 18 number of extra gaps= 2 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl2A/T0316-1vl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1vl2A/T0316-1vl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl2A read from 1vl2A/T0316-1vl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vl2A in template set Warning: unaligning (T0316)K6 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0316)P97 because of BadResidue code BAD_PEPTIDE in next template residue (1vl2A)L87 Warning: unaligning (T0316)N98 because of BadResidue code BAD_PEPTIDE at template residue (1vl2A)L87 Warning: unaligning (T0316)L174 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0316)P177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 Warning: unaligning (T0316)C200 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl2A)I186 Warning: unaligning (T0316)G343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)G379 Warning: unaligning (T0316)E352 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)G379 T0316 7 :TRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1vl2A 3 :EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVA T0316 46 :ENG 1vl2A 35 :NVG T0316 52 :ATEDYKDVVAVADQIGI 1vl2A 38 :QKDDFVAIKEKALKTGA T0316 69 :PYYSVNFEKEYWDRVFEYFL 1vl2A 56 :KVYVEDLRREFVTDYIFTAL T0316 92 :RAGRT 1vl2A 81 :YEGRY T0316 99 :PDVMCNKEI 1vl2A 88 :GTAIARPLI T0316 109 :FKAFLDYAITLGADYVATGHYA 1vl2A 97 :AKRQVEIAEKEGAQYVAHGATG T0316 134 :RDEDG 1vl2A 119 :KGNDQ T0316 139 :TVHM 1vl2A 125 :RFEL T0316 143 :LRGV 1vl2A 130 :YAAL T0316 149 :GKDQTYFLSQLSQEQLQKT 1vl2A 134 :NPNLKVISPWKDPEFLAKF T0316 178 :EVRRLAEEAGLSTAKKK 1vl2A 157 :DLINYAMEKGIPIKVSK T0316 195 :DSTGI 1vl2A 175 :RPYSE T0316 201 :FIGEKNF 1vl2A 187 :SHEAGKL T0316 208 :KNFLSNYLPAQP 1vl2A 202 :EDVFTWTVSPKD T0316 220 :GRMMTV 1vl2A 216 :DEETLL T0316 226 :DGRDMGEHAGLMYYTIGQRGGLGIG 1vl2A 251 :YLNEVGAKNGVGRLDMVENRFIGIK T0316 259 :PWFVVGK 1vl2A 276 :SRGVYET T0316 278 :FYHDSLMSTSLEASQVHFTRE 1vl2A 306 :HLRDMLAPKFAELIYNGFWFS T0316 300 :PE 1vl2A 327 :PE T0316 313 :YRQPDSKVTVHVKGEKTEVIFAEPQRAITP 1vl2A 340 :QENVTGKVTVSIYKGNVMPVARYSPYSLYN T0316 353 :EC 1vl2A 380 :GF Number of specific fragments extracted= 22 number of extra gaps= 2 total=40 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 1vl2A/T0316-1vl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1vl2A/T0316-1vl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl2A read from 1vl2A/T0316-1vl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vl2A in template set Warning: unaligning (T0316)K6 because first residue in template chain is (1vl2A)K2 Warning: unaligning (T0316)P97 because of BadResidue code BAD_PEPTIDE in next template residue (1vl2A)L87 Warning: unaligning (T0316)N98 because of BadResidue code BAD_PEPTIDE at template residue (1vl2A)L87 Warning: unaligning (T0316)L174 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl2A)T156 Warning: unaligning (T0316)P177 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl2A)T156 Warning: unaligning (T0316)L236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl2A)I186 Warning: unaligning (T0316)M237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl2A)I186 T0316 7 :TRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWD 1vl2A 3 :EKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQ T0316 53 :TEDYKDVVAVADQIGI 1vl2A 39 :KDDFVAIKEKALKTGA T0316 69 :PYYSVNFEKEYWDR 1vl2A 56 :KVYVEDLRREFVTD T0316 83 :VFEY 1vl2A 71 :IFTA T0316 92 :R 1vl2A 75 :L T0316 93 :AGRT 1vl2A 82 :EGRY T0316 99 :PDVMCN 1vl2A 88 :GTAIAR T0316 106 :EIKFKAFLDYAITLGADYVATGH 1vl2A 94 :PLIAKRQVEIAEKEGAQYVAHGA T0316 135 :DED 1vl2A 117 :TGK T0316 156 :LSQLSQEQLQKT 1vl2A 141 :SPWKDPEFLAKF T0316 178 :EVRRLAEEAGLSTAKKK 1vl2A 157 :DLINYAMEKGIPIKVSK T0316 217 :AQPGRMM 1vl2A 174 :KRPYSED T0316 232 :EHAG 1vl2A 181 :ENLM T0316 238 :YYTIGQ 1vl2A 187 :SHEAGK T0316 252 :QHGGDNA 1vl2A 193 :LEDPAHI T0316 288 :LEASQVHFTREMPE 1vl2A 200 :PDEDVFTWTVSPKD T0316 302 :EFTLECTAKFR 1vl2A 216 :DEETLLEIHFE T0316 316 :PDSKVTVHVKGEK 1vl2A 227 :NGIPVKVVNLKDG Number of specific fragments extracted= 18 number of extra gaps= 2 total=58 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 1wy5A/T0316-1wy5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wy5A expands to /projects/compbio/data/pdb/1wy5.pdb.gz 1wy5A:# T0316 read from 1wy5A/T0316-1wy5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy5A read from 1wy5A/T0316-1wy5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wy5A to template set # found chain 1wy5A in template set T0316 3 :DNSKTRVVVGMSGGVDSSVTALLLKE 1wy5A 21 :FSGERRVLIAFSGGVDSVVLTDVLLK T0316 29 :QG 1wy5A 48 :KN T0316 31 :YDVIGIFM 1wy5A 54 :KEVALAHF T0316 44 :TDENGVC 1wy5A 62 :NHMLRES T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1wy5A 69 :AERDEEFCKEFAKERNMKIFVGKED T0316 84 :FEYFLAE 1wy5A 94 :VRAFAKE T0316 94 :GR 1wy5A 101 :NR T0316 97 :PNPDVMCNKE 1wy5A 103 :MSLEEAGRFL T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 1wy5A 113 :RYKFLKEILESEGFDCIATAHHLNDLLE T0316 137 :DGTVHMLRGVDNGK 1wy5A 141 :TSLLFFTRGTGLDG T0316 164 :LQ 1wy5A 155 :LI T0316 167 :TMFPLGHLEKPEVRRLAEEAGLSTAKKKDSTGICFIGEKNFKNFLSNYLPAQP 1wy5A 165 :IRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINE T0316 220 :GRMMTVD 1wy5A 291 :EKGGEVN T0316 227 :GRDMGEHAGLM 1wy5A 299 :GKGKVLKRKER Number of specific fragments extracted= 14 number of extra gaps= 0 total=72 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 1wy5A/T0316-1wy5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wy5A/T0316-1wy5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy5A read from 1wy5A/T0316-1wy5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wy5A in template set T0316 7 :TRVVVGMSGGVDSSVTALLLKEQ 1wy5A 25 :RRVLIAFSGGVDSVVLTDVLLKL T0316 30 :G 1wy5A 49 :N T0316 31 :YDVIGIFM 1wy5A 54 :KEVALAHF T0316 46 :ENGVCT 1wy5A 62 :NHMLRE T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1wy5A 69 :AERDEEFCKEFAKERNMKIFVGKED T0316 87 :FLAEYRAGRTP 1wy5A 94 :VRAFAKENRMS T0316 100 :DVMCNKEIKFKAFLDYAITLGADYVATGHYA 1wy5A 105 :LEEAGRFLRYKFLKEILESEGFDCIATAHHL T0316 134 :RDEDGTVHM 1wy5A 136 :NDLLETSLL T0316 143 :LR 1wy5A 148 :RG T0316 145 :GVDNGKDQTYFL 1wy5A 151 :GLDGLIGFLPKE T0316 162 :E 1wy5A 163 :E T0316 166 :KTMFPLGHLEKPEVRRLAEEAGLSTAKKKDSTGICFIGEKNFKNFLSNYLPAQPG 1wy5A 164 :VIRRPLYYVKRSEIEEYAKFKGLRWVEDETNYEVSIPRNRIRHRVIPELKRINEN T0316 226 :DGRDMG 1wy5A 292 :KGGEVN Number of specific fragments extracted= 13 number of extra gaps= 0 total=85 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 1wy5A/T0316-1wy5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wy5A/T0316-1wy5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy5A read from 1wy5A/T0316-1wy5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wy5A in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQG 1wy5A 23 :GERRVLIAFSGGVDSVVLTDVLLKLK T0316 31 :YDVIGIFMKNWDDTDE 1wy5A 53 :LKEVALAHFNHMLRES T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1wy5A 69 :AERDEEFCKEFAKERNMKIFVGKED T0316 87 :FLAEYRAGRTP 1wy5A 94 :VRAFAKENRMS T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARV 1wy5A 109 :GRFLRYKFLKEILESEGFDCIATAHHLND T0316 153 :TYFLSQLSQEQ 1wy5A 144 :LFFTRGTGLDG T0316 166 :KTMF 1wy5A 155 :LIGF T0316 170 :PLGHLEKPEVRRLAEEAGLSTAKKKD 1wy5A 168 :PLYYVKRSEIEEYAKFKGLRWVEDET Number of specific fragments extracted= 8 number of extra gaps= 0 total=93 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 1k92A/T0316-1k92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k92A expands to /projects/compbio/data/pdb/1k92.pdb.gz 1k92A:Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1504, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1544, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1546, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1548, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1870, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2287, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2289, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2291, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2293, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2295, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2297, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2299, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2301, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2568, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2570, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2572, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2574, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2576, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2578, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2580, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2584, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2586, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2588, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2735, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2737, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2739, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2741, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2743, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2745, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2747, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2749, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2759, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2761, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2763, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2765, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2767, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2769, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2771, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2773, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2775, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2777, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2779, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2789, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2791, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2793, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2795, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2797, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2799, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2963, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2965, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2967, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2969, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2971, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2973, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2975, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 2977, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3347, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3349, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3351, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3353, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3355, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3357, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3359, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3361, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3363, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3365, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3367, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3447, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3449, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3451, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3453, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3455, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3457, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3459, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3461, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3471, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3473, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3475, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3477, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3479, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3481, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3483, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3485, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3487, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3489, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3491, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3493, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3495, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3497, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3499, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3501, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3503, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3505, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3507, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3509, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3511, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3513, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3515, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3517, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3519, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3521, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3523, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3525, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3527, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3529, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3531, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3533, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3535, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3537, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3539, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3541, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3543, because occupancy 0.500 <= existing 0.500 in 1k92A Skipped atom 3545, because occupancy 0.500 <= existing 0.500 in 1k92A # T0316 read from 1k92A/T0316-1k92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k92A read from 1k92A/T0316-1k92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k92A to template set # found chain 1k92A in template set T0316 3 :DNSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1k92A 7 :LPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTA T0316 46 :ENGVC 1k92A 43 :NLGQP T0316 52 :ATEDYKDVVAVADQIGI 1k92A 48 :DEEDYDAIPRRAMEYGA T0316 69 :PYYSVNFEKEYWDRV 1k92A 66 :NARLIDCRKQLVAEG T0316 88 :LAEYRAGRTPNPD 1k92A 81 :IAAIQCGAFHNTT T0316 101 :VMCNKEIKFKAFLDYAITLGADYVATG 1k92A 102 :TPLGRAVTGTMLVAAMKEDGVNIWGDG T0316 132 :VARDEDGTVHMLRGVDNGKDQTYFLSQLSQEQLQKTMF 1k92A 129 :STYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELG T0316 175 :EKPEVRRLAEEAGLST 1k92A 167 :GRHEMSEFMIACGFDY T0316 191 :AKKKDSTGICFIGEKNFKNFLSNYLPAQP 1k92A 186 :VEKAYSTDSNMLGATHEAKDLEYLNSSVK T0316 220 :GRMMTVDGRDMGEHAGLMYYTIGQRGG 1k92A 228 :SVKIPAEEVTVRFEQGHPVALNGKTFS T0316 282 :SLMSTSLEASQVHF 1k92A 255 :DDVEMMLEANRIGG T0316 305 :LECTAKFRYRQPDSKVTVH 1k92A 274 :MSDQIENRIIEAKSRGIYE Number of specific fragments extracted= 12 number of extra gaps= 0 total=105 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 1k92A/T0316-1k92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1k92A/T0316-1k92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k92A read from 1k92A/T0316-1k92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k92A in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1k92A 8 :PVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTA T0316 46 :ENGVC 1k92A 43 :NLGQP T0316 52 :ATEDYKDVVAVADQIGI 1k92A 48 :DEEDYDAIPRRAMEYGA T0316 69 :PYYSVNFEKEYWDRVFEYFL 1k92A 66 :NARLIDCRKQLVAEGIAAIQ T0316 94 :GR 1k92A 94 :GG T0316 96 :TPNPDVMCNK 1k92A 98 :YFNTTPLGRA T0316 107 :IKFKAFLDYAITLGAD 1k92A 108 :VTGTMLVAAMKEDGVN T0316 125 :ATGHYARVARDEDGTVHMLR 1k92A 124 :IWGDGSTYKGNDIERFYRYG T0316 146 :VDNGKDQTYFLSQLSQE 1k92A 144 :LLTNAELQIYKPWLDTD T0316 167 :TMFPLG 1k92A 161 :FIDELG T0316 175 :EKPEVRRLAEEAGLST 1k92A 167 :GRHEMSEFMIACGFDY T0316 191 :AKKK 1k92A 186 :VEKA T0316 195 :DSTGICFIGEKNFKNF 1k92A 194 :SNMLGATHEAKDLEYL T0316 211 :LSNY 1k92A 213 :VKIV T0316 282 :SLMSTSL 1k92A 346 :SLQRWVA T0316 314 :RQPDSKVTVHVKGEK 1k92A 353 :SQITGEVTLELRRGN T0316 329 :TEVIFAEPQRAITPG 1k92A 369 :YSILNTVSENLTYKP Number of specific fragments extracted= 17 number of extra gaps= 0 total=122 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 1k92A/T0316-1k92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1k92A/T0316-1k92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k92A read from 1k92A/T0316-1k92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k92A in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDD 1k92A 8 :PVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQP T0316 52 :ATEDYKDVVAVADQIGI 1k92A 48 :DEEDYDAIPRRAMEYGA T0316 69 :PYYSVNFEKE 1k92A 66 :NARLIDCRKQ T0316 83 :VFEYFLAEYRAGRTPN 1k92A 76 :LVAEGIAAIQCGAFHN T0316 107 :IKFKAFLDYAITLGADYVATGH 1k92A 108 :VTGTMLVAAMKEDGVNIWGDGS T0316 135 :DED 1k92A 130 :TYK T0316 149 :GKDQTYFLSQLS 1k92A 148 :AELQIYKPWLDT T0316 166 :KTMFPLG 1k92A 160 :DFIDELG T0316 175 :EKPEVRRLAEEAGLSTAKKKDS 1k92A 167 :GRHEMSEFMIACGFDYKMSVEK T0316 226 :DGRDMGEHAGLMYY 1k92A 189 :AYSTDSNMLGATHE T0316 280 :HDSLMSTSLEASQVHFTREMP 1k92A 203 :AKDLEYLNSSVKIVNPIMGVK T0316 301 :EEFTL 1k92A 227 :ESVKI T0316 316 :PDSKVTVHVKGEKTEV 1k92A 232 :PAEEVTVRFEQGHPVA Number of specific fragments extracted= 13 number of extra gaps= 0 total=135 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 1korA/T0316-1korA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1korA expands to /projects/compbio/data/pdb/1kor.pdb.gz 1korA:# T0316 read from 1korA/T0316-1korA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1korA read from 1korA/T0316-1korA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1korA to template set # found chain 1korA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1korA)M1 Warning: unaligning (T0316)K194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1korA)P171 Warning: unaligning (T0316)D366 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)G370 T0316 8 :RVVVGMSGGVDSSVTALLLKE 1korA 2 :KIVLAYSGGLDTSIILKWLKE T0316 29 :QGYDVIGIFM 1korA 24 :YRAEVIAFTA T0316 46 :ENG 1korA 34 :DIG T0316 52 :ATEDYKDVVAVADQIGI 1korA 37 :QGEEVEEAREKALRTGA T0316 69 :PYYSVNFEKEYWDRVFEYFLA 1korA 55 :KAIALDLKEEFVRDFVFPMMR T0316 90 :EYRAGRTPNPDVMCNKEI 1korA 78 :AVYEGYYLLGTSIARPLI T0316 109 :FKAFLDYAITLGADYVATG 1korA 96 :AKHLVRIAEEEGAEAIAHG T0316 132 :VARDEDGTVHMLRG 1korA 115 :ATGKGNDQVRFELT T0316 153 :TYFLSQL 1korA 129 :AYALKPD T0316 165 :QKTMFPLGHLE 1korA 136 :IKVIAPWREWS T0316 176 :KPEVRRLAEEAGLST 1korA 150 :RKEMIAYAEAHGIPV T0316 195 :DSTGICFIGEKNFKNFLSNYLPAQP 1korA 172 :YSMDANLLHISYEGGVLEDPWAEPP T0316 220 :GRMMTVDGRDMGEHAGLMYYTIGQRGG 1korA 208 :EAPDAPEYVEVEFFEGDPVAVNGERLS T0316 248 :GIGGQHGG 1korA 253 :RVDIVENR T0316 256 :DNAP 1korA 262 :VGMK T0316 260 :WFVV 1korA 267 :RGVY T0316 279 :YHDSLMSTSLEASQVHFTREMPEEFT 1korA 271 :ETPGGTILYHARRAVESLTLDREVLH T0316 338 :RAIT 1korA 331 :RSVT T0316 343 :GQAVV 1korA 335 :GVARL T0316 348 :FYDGEECLGGGLIDNAYR 1korA 341 :LYKGNVYVVGRKAPKSLY Number of specific fragments extracted= 20 number of extra gaps= 0 total=155 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 1korA/T0316-1korA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1korA/T0316-1korA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1korA read from 1korA/T0316-1korA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1korA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1korA)M1 Warning: unaligning (T0316)K194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1korA)P171 Warning: unaligning (T0316)P342 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)G370 Warning: unaligning (T0316)E353 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1korA)G370 T0316 8 :RVVVGMSGGVDSSVTALLLKEQ 1korA 2 :KIVLAYSGGLDTSIILKWLKET T0316 30 :GYDVIGIFM 1korA 25 :RAEVIAFTA T0316 46 :ENG 1korA 34 :DIG T0316 52 :ATEDYKDVVAVADQIGI 1korA 37 :QGEEVEEAREKALRTGA T0316 69 :PYYSVNFEKEYWDRVFEYFL 1korA 55 :KAIALDLKEEFVRDFVFPMM T0316 92 :RAGRTPNPDVMCNKEI 1korA 80 :YEGYYLLGTSIARPLI T0316 109 :FKAFLDYAITLGADYVATGHYARV 1korA 96 :AKHLVRIAEEEGAEAIAHGATGKG T0316 134 :RDED 1korA 120 :NDQV T0316 139 :TVHM 1korA 124 :RFEL T0316 143 :LRGV 1korA 133 :KPDI T0316 166 :KTMFPLGHL 1korA 137 :KVIAPWREW T0316 175 :EKPEVRRLAEEAGLST 1korA 149 :GRKEMIAYAEAHGIPV T0316 195 :DSTGICFIG 1korA 177 :NLLHISYEG T0316 209 :NFLSNY 1korA 186 :GVLEDP T0316 215 :LPAQPGRMMTV 1korA 193 :AEPPKGMFRMT T0316 226 :DGRDMGEHAGLMYYTIGQRGGLGIG 1korA 241 :RLNEIGGRHGVGRVDIVENRFVGMK T0316 259 :PWFVVGK 1korA 266 :SRGVYET T0316 280 :HDSL 1korA 292 :REVL T0316 284 :MSTSLEASQVHFTRE 1korA 302 :SPKYAELVYYGFWYA T0316 300 :PE 1korA 317 :PE T0316 314 :RQPDSKVTVHVKGEKTEVIFAEPQRAIT 1korA 331 :RSVTGVARLKLYKGNVYVVGRKAPKSLY Number of specific fragments extracted= 21 number of extra gaps= 0 total=176 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 1korA/T0316-1korA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1korA/T0316-1korA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1korA read from 1korA/T0316-1korA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1korA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1korA)M1 Warning: unaligning (T0316)A191 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1korA)P171 Warning: unaligning (T0316)P219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1korA)P171 T0316 8 :RVVVGMSGGVDSSVTALLLKEQ 1korA 2 :KIVLAYSGGLDTSIILKWLKET T0316 30 :GYDVIGIFMKNWDD 1korA 25 :RAEVIAFTADIGQG T0316 54 :EDYKDVVAVADQIGIP 1korA 39 :EEVEEAREKALRTGAS T0316 70 :YYSVNFEKEYWDR 1korA 56 :AIALDLKEEFVRD T0316 83 :VFEYFL 1korA 70 :VFPMMR T0316 93 :AGRTPNPDVMCNKEI 1korA 81 :EGYYLLGTSIARPLI T0316 109 :FKAFLDYAITLGADYVATGH 1korA 96 :AKHLVRIAEEEGAEAIAHGA T0316 135 :DEDG 1korA 116 :TGKG T0316 150 :KDQTYF 1korA 120 :NDQVRF T0316 156 :LSQLSQE 1korA 129 :AYALKPD T0316 166 :KTMFPLGHLE 1korA 137 :KVIAPWREWS T0316 176 :KPEVRRLAEEAGLST 1korA 150 :RKEMIAYAEAHGIPV T0316 220 :GRMMT 1korA 172 :YSMDA T0316 233 :HAGLMYYTIG 1korA 177 :NLLHISYEGG T0316 251 :GQHGGDNAP 1korA 187 :VLEDPWAEP T0316 276 :QGFYHD 1korA 196 :PKGMFR T0316 296 :TREMPEEF 1korA 202 :MTQDPEEA T0316 314 :RQPDSKVTVHVKGEKTEVIFAEP 1korA 210 :PDAPEYVEVEFFEGDPVAVNGER Number of specific fragments extracted= 18 number of extra gaps= 0 total=194 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 1gpmA/T0316-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gpmA expands to /projects/compbio/data/pdb/1gpm.pdb.gz 1gpmA:# T0316 read from 1gpmA/T0316-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0316-1gpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gpmA to template set # found chain 1gpmA in template set Warning: unaligning (T0316)Q161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gpmA)K369 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKE 1gpmA 226 :GDDKVILGLSGGVDSSVTAMLLHR T0316 29 :QGYDVIGIFM 1gpmA 251 :IGKNLTCVFV T0316 46 :ENGVC 1gpmA 261 :DNGLL T0316 52 :ATEDYKDVVAVA 1gpmA 266 :RLNEAEQVLDMF T0316 64 :DQIGIPYYSVNFEKEYWDRV 1gpmA 279 :DHFGLNIVHVPAEDRFLSAL T0316 93 :AGRTP 1gpmA 299 :AGEND T0316 100 :DVMCNKEI 1gpmA 304 :PEAKRKII T0316 109 :FKAFLDYAITL 1gpmA 312 :GRVFVEVFDEE T0316 120 :GADYVATGHYARVARDE 1gpmA 328 :DVKWLAQGTIYPDVIES T0316 165 :QKTMFPLGHLEKPEVRRLAEEAGLST 1gpmA 370 :MGLVEPLKELFKDEVRKIGLELGLPY T0316 191 :AKKKDSTGICFIG 1gpmA 399 :YRHPFPGPGLGVR T0316 216 :PAQP 1gpmA 414 :GEVK T0316 220 :GRMMTVD 1gpmA 439 :DLYDKVS T0316 235 :G 1gpmA 446 :Q T0316 240 :TIGQRGGLGIGGQHGGDNAPWFVVGKDLSKNI 1gpmA 447 :AFTVFLPVRSVGVMGDGRKYDWVVSLRAVETI T0316 272 :LYVGQGFYHDSLMSTSLEA 1gpmA 482 :TAHWAHLPYDFLGRVSNRI T0316 291 :SQVHFT 1gpmA 505 :NGISRV T0316 297 :REMPEEFTLE 1gpmA 514 :ISGKPPATIE Number of specific fragments extracted= 18 number of extra gaps= 0 total=212 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 1gpmA/T0316-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gpmA/T0316-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0316-1gpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpmA in template set Warning: unaligning (T0316)H141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gpmA)K369 Warning: unaligning (T0316)Q163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gpmA)K369 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1gpmA 226 :GDDKVILGLSGGVDSSVTAMLLHRA T0316 30 :GYDVIGIFM 1gpmA 252 :GKNLTCVFV T0316 46 :ENGVC 1gpmA 261 :DNGLL T0316 52 :ATEDYKDVVAVAD 1gpmA 266 :RLNEAEQVLDMFG T0316 65 :QIGIPYYSVNFEKEYWDRV 1gpmA 280 :HFGLNIVHVPAEDRFLSAL T0316 84 :FEYF 1gpmA 304 :PEAK T0316 104 :NKEIK 1gpmA 308 :RKIIG T0316 110 :KAFLDYAITL 1gpmA 313 :RVFVEVFDEE T0316 120 :GADYVATGHYA 1gpmA 328 :DVKWLAQGTIY T0316 134 :RDEDGTV 1gpmA 339 :PDVIESA T0316 164 :L 1gpmA 370 :M T0316 166 :KTMFPLGHLEKPEVRRLAEEAGLST 1gpmA 371 :GLVEPLKELFKDEVRKIGLELGLPY T0316 191 :AKKKDS 1gpmA 401 :HPFPGP T0316 197 :TGICFIGEKN 1gpmA 408 :LGVRVLGEVK T0316 208 :KNFLSNYLP 1gpmA 418 :KEYCDLLRR T0316 226 :DGRDMGEHAGLMYYT 1gpmA 434 :ELRKADLYDKVSQAF T0316 241 :IGQRGGLG 1gpmA 451 :FLPVRSVG T0316 249 :IGGQHGGDNAPWFVVGKDLSKNILYVGQGFY 1gpmA 460 :MGDGRKYDWVVSLRAVETIDFMTAHWAHLPY T0316 280 :HDSLMSTSLEASQVHFTREMPEEFTL 1gpmA 497 :SNRIINEVNGISRVVYDISGKPPATI Number of specific fragments extracted= 19 number of extra gaps= 0 total=231 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 1gpmA/T0316-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gpmA/T0316-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpmA read from 1gpmA/T0316-1gpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpmA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1gpmA 226 :GDDKVILGLSGGVDSSVTAMLLHRA T0316 30 :GYDVIGIFMKN 1gpmA 252 :GKNLTCVFVDN T0316 49 :VCTATEDYKDVVAVA 1gpmA 263 :GLLRLNEAEQVLDMF T0316 64 :DQIGIPYYSVNFEKEYWDRV 1gpmA 279 :DHFGLNIVHVPAEDRFLSAL T0316 93 :AGRT 1gpmA 299 :AGEN T0316 104 :NKEIKFKAFLDYAIT 1gpmA 303 :DPEAKRKIIGRVFVE T0316 120 :GADYVATGHYA 1gpmA 328 :DVKWLAQGTIY T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1gpmA 373 :VEPLKELFKDEVRKIGLELGLP T0316 208 :KNFLS 1gpmA 395 :YDMLY T0316 214 :YLPAQPG 1gpmA 400 :RHPFPGP T0316 251 :GQHGGDNAPWFVVGKD 1gpmA 439 :DLYDKVSQAFTVFLPV T0316 296 :TREMPE 1gpmA 455 :RSVGVM T0316 302 :EFTLECTAKFRY 1gpmA 463 :GRKYDWVVSLRA T0316 322 :VH 1gpmA 475 :VE T0316 324 :VKGEKTE 1gpmA 478 :IDFMTAH Number of specific fragments extracted= 15 number of extra gaps= 0 total=246 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 1xngA/T0316-1xngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xngA expands to /projects/compbio/data/pdb/1xng.pdb.gz 1xngA:# T0316 read from 1xngA/T0316-1xngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xngA read from 1xngA/T0316-1xngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xngA to template set # found chain 1xngA in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKE 1xngA 23 :RGFKKVVYGLSGGLDSAVVGVLCQK T0316 29 :QGYDVIGIFM 1xngA 49 :FKENAHALLM T0316 46 :ENGVC 1xngA 59 :PSSVS T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1xngA 64 :MPENKTDALNLCEKFSIPYTEYSIA T0316 82 :RVFEYFLAE 1xngA 89 :PYDAIFSSH T0316 92 :RAGR 1xngA 98 :FKDA T0316 98 :NPD 1xngA 102 :SLT T0316 101 :VMCNKE 1xngA 108 :NFCARL T0316 108 :KFKAFLDYAITLGADYV 1xngA 114 :RMAFLYDYSLKSDSLVI T0316 127 :GHYARVA 1xngA 131 :GTSNKSE T0316 136 :EDGTVHMLRGVDNGK 1xngA 138 :RMLGYGTLFGDLACA T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1xngA 153 :INPIGELFKTEVYELARRLNIP T0316 190 :TAKKKDSTGICF 1xngA 177 :ILNKPPSADLFV T0316 202 :IGEKNFKNFLSNYLPAQPGRMMTVD 1xngA 198 :YPYSVIDPLLKDIEALFQTKPIDTE T0316 277 :GFYHDSLMSTSLEASQVHFTREMP 1xngA 228 :GYDEILVKNITSRIQKNAFKLELP Number of specific fragments extracted= 15 number of extra gaps= 0 total=261 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 1xngA/T0316-1xngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1xngA/T0316-1xngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xngA read from 1xngA/T0316-1xngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xngA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1xngA 24 :GFKKVVYGLSGGLDSAVVGVLCQKV T0316 30 :GYDVIGIFM 1xngA 50 :KENAHALLM T0316 46 :ENGVC 1xngA 59 :PSSVS T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFEKEY 1xngA 64 :MPENKTDALNLCEKFSIPYTEYSIAPYD T0316 85 :EYFL 1xngA 92 :AIFS T0316 89 :AEYRA 1xngA 104 :TRKGN T0316 102 :MCNKE 1xngA 109 :FCARL T0316 108 :KFKAFLDYAITLGADYV 1xngA 114 :RMAFLYDYSLKSDSLVI T0316 134 :RDEDGTVHMLRGVDNGKDQTY 1xngA 131 :GTSNKSERMLGYGTLFGDLAC T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 1xngA 152 :AINPIGELFKTEVYELARRLNIPK Number of specific fragments extracted= 10 number of extra gaps= 0 total=271 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 1xngA/T0316-1xngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1xngA/T0316-1xngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xngA read from 1xngA/T0316-1xngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xngA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1xngA 24 :GFKKVVYGLSGGLDSAVVGVLCQKV T0316 31 :YDVIGIFMKNWD 1xngA 51 :ENAHALLMPSSV T0316 51 :TATEDYKDVVAVADQIGIPYYSVNFEKEYWDR 1xngA 63 :SMPENKTDALNLCEKFSIPYTEYSIAPYDAIF T0316 84 :FEYFLAEYR 1xngA 103 :LTRKGNFCA T0316 106 :EIKFKAFLDYAITLGADYVATGH 1xngA 112 :RLRMAFLYDYSLKSDSLVIGTSN T0316 151 :DQTYFLSQLSQE 1xngA 135 :KSERMLGYGTLF T0316 170 :PLGHLEKPEVRRLAEEAGLS 1xngA 155 :PIGELFKTEVYELARRLNIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=278 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 1ni5A/T0316-1ni5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ni5A expands to /projects/compbio/data/pdb/1ni5.pdb.gz 1ni5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0316 read from 1ni5A/T0316-1ni5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ni5A read from 1ni5A/T0316-1ni5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ni5A to template set # found chain 1ni5A in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQ 1ni5A 12 :SRQILVAFSGGLDSTVLLHQLVQW T0316 30 :GYDVIGIFM 1ni5A 41 :GVALRAIHV T0316 44 :TDENGVC 1ni5A 50 :HHGLSAN T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1ni5A 57 :ADAWVTHCENVCQQWQVPLVVERVQ T0316 92 :RAGRTPNPDVMCNKE 1ni5A 82 :LAQEGLGIEAQARQA T0316 108 :KFKAFLD 1ni5A 97 :RYQAFAR T0316 119 :L 1ni5A 104 :T T0316 120 :G 1ni5A 108 :G T0316 122 :DYVATGHYARVARD 1ni5A 109 :EVLVTAQHLDDQCE T0316 137 :DGTVHMLRGVDNGK 1ni5A 123 :TFLLALKRGSGPAG T0316 153 :TYFLSQLSQEQLQKTMFPLGHLEKPEVRRLAEEAGLSTAKKKDSTGICFIGEKNFKNFLSNYLPAQP 1ni5A 137 :LSAMAEVSEFAGTRLIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWP T0316 220 :GRMMTVDGRDMGEHAGLMYYTIGQRGGLGIGGQHGGDNAPWFV 1ni5A 290 :SPCLRLGAFEIRRYQSQLWWIKSVTGQSENIVPWQTWLQPLEL T0316 300 :PEEFT 1ni5A 333 :PAGLG T0316 305 :LECTAKFRYRQPDSKVTVH 1ni5A 341 :LNAGGDIRPPRADEAVSVR T0316 324 :VKGEKT 1ni5A 361 :KAPGLL T0316 342 :PGQAVVFYDGEECLGGGLI 1ni5A 392 :DTTPLLFYGETLIAAAGVF T0316 361 :DNAYRDGQVCQYI 1ni5A 414 :EGVAEGENGVSFV Number of specific fragments extracted= 17 number of extra gaps= 0 total=295 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 1ni5A/T0316-1ni5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ni5A/T0316-1ni5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ni5A read from 1ni5A/T0316-1ni5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ni5A in template set T0316 7 :TRVVVGMSGGVDSSVTALLLKE 1ni5A 13 :RQILVAFSGGLDSTVLLHQLVQ T0316 29 :Q 1ni5A 38 :E T0316 30 :GYDVIGIFM 1ni5A 41 :GVALRAIHV T0316 46 :ENGVCT 1ni5A 50 :HHGLSA T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1ni5A 57 :ADAWVTHCENVCQQWQVPLVVERVQ T0316 92 :RAGRTPNPDVMCNKE 1ni5A 82 :LAQEGLGIEAQARQA T0316 112 :FLDYAITL 1ni5A 97 :RYQAFART T0316 120 :G 1ni5A 108 :G T0316 122 :DYVATGHYA 1ni5A 109 :EVLVTAQHL T0316 134 :RDEDGTVHM 1ni5A 118 :DDQCETFLL T0316 143 :LR 1ni5A 130 :RG T0316 145 :GVDNGKDQTYFLSQLSQ 1ni5A 133 :GPAGLSAMAEVSEFAGT T0316 166 :KTMFPLGHLEKPEVRRLAEEAGLSTAKKKDSTGICFIGEKNFKNFLSNYLPAQPG 1ni5A 150 :RLIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPH T0316 231 :GE 1ni5A 289 :AS T0316 245 :GGLGIGG 1ni5A 291 :PCLRLGA T0316 261 :FVVGKDLSKNILYVGQGFYHD 1ni5A 298 :FEIRRYQSQLWWIKSVTGQSE T0316 289 :EASQVHFTREM 1ni5A 319 :NIVPWQTWLQP T0316 301 :EEFTLECTA 1ni5A 333 :PAGLGSVQL T0316 310 :KFRYRQPDSKVTVHVK 1ni5A 346 :DIRPPRADEAVSVRFK T0316 326 :GEKTEVIFAEPQRA 1ni5A 363 :PGLLHIVGRNGGRK T0316 340 :ITPGQAVVFYDGEECLGG 1ni5A 390 :LRDTTPLLFYGETLIAAA T0316 358 :GLIDNAYR 1ni5A 410 :FVTQEGVA Number of specific fragments extracted= 22 number of extra gaps= 0 total=317 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 1ni5A/T0316-1ni5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ni5A/T0316-1ni5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ni5A read from 1ni5A/T0316-1ni5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ni5A in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1ni5A 11 :TSRQILVAFSGGLDSTVLLHQLVQW T0316 30 :GYDVIGIFMKNWDDT 1ni5A 41 :GVALRAIHVHHGLSA T0316 51 :TATEDYKDVVAVADQIGIPYYSVNFE 1ni5A 56 :NADAWVTHCENVCQQWQVPLVVERVQ T0316 82 :RVFEYFLAEYRAGRTPN 1ni5A 92 :QARQARYQAFARTLLPG T0316 122 :DYVATGHYA 1ni5A 109 :EVLVTAQHL T0316 151 :DQTYFLSQLSQEQLQKT 1ni5A 218 :EQESLLDELLADDLAHC T0316 168 :MFPLGHLEKPE 1ni5A 243 :IVPMLAMSDAR T0316 179 :VRRLAEEAGLSTAK 1ni5A 258 :IRRWLAGQNAPMPS T0316 204 :EKNFKNFLSNYLP 1ni5A 272 :RDALVRIWQEVAL T0316 217 :AQPGRMMTVDGRDMGE 1ni5A 287 :EDASPCLRLGAFEIRR T0316 256 :DNAPWFVVGK 1ni5A 303 :YQSQLWWIKS T0316 280 :HDSLMSTSLEASQVHFTREMPEEFT 1ni5A 313 :VTGQSENIVPWQTWLQPLELPAGLG T0316 319 :KVTVHV 1ni5A 338 :SVQLNA T0316 325 :KGEKTEVIFAEPQRAITPGQ 1ni5A 352 :ADEAVSVRFKAPGLLHIVGR T0316 345 :AVVFYDGEECLGG 1ni5A 395 :PLLFYGETLIAAA T0316 358 :GLIDNAYRDGQVCQY 1ni5A 410 :FVTQEGVAEGENGVS Number of specific fragments extracted= 16 number of extra gaps= 0 total=333 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 2d13A/T0316-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0316 read from 2d13A/T0316-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0316-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0316)N4 because first residue in template chain is (2d13A)V2 Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0316)D55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0316)F75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0316)R92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWD 2d13A 3 :GLADVAVLYSGGKDSNYALYWALKSGLRVRYLVSMVSE T0316 56 :YKDVVAVADQIGIPYYSVN 2d13A 52 :VELTSLQARALGIPIIKGF T0316 93 :AGR 2d13A 75 :KEK T0316 108 :KFKAFLDYAITLGADYVATGHYAR 2d13A 78 :EVEDLKNVLEGLKVDGIVAGALAS T0316 162 :EQL 2d13A 102 :RYQ T0316 176 :KPEVRRLAEEAGLSTAKKKDST 2d13A 105 :KERIENVARELGLKVYTPAWEK T0316 202 :IGEKNFKNFLS 2d13A 127 :DPYQYMLEIIK T0316 234 :AGLMYYTIGQRG 2d13A 138 :LGFKVVFVAVSA T0316 246 :GLGI 2d13A 151 :GLNE T0316 254 :GGDNAP 2d13A 155 :SWLGRE T0316 278 :FYHDSLMSTSLEASQVHFTREMPEEF 2d13A 161 :LNYKNLEELKKLSEKYGIHIAGEGGE T0316 309 :AKFRYRQPD 2d13A 187 :FETFVLDMP T0316 319 :KVTVHVKGEKTEVIFAEPQR 2d13A 205 :DAEKFWDGLSGKFIIKRAHL Number of specific fragments extracted= 13 number of extra gaps= 0 total=346 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 2d13A/T0316-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2d13A/T0316-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0316-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0316)N4 because first residue in template chain is (2d13A)V2 Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0316)T53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0316)F75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWD 2d13A 3 :GLADVAVLYSGGKDSNYALYWALKSGLRVRYLVSMVSE T0316 54 :ED 2d13A 52 :VE T0316 56 :YKDV 2d13A 55 :TSLQ T0316 63 :ADQIGIPYYSVN 2d13A 59 :ARALGIPIIKGF T0316 77 :KEYW 2d13A 76 :EKEV T0316 85 :EYFLAEYRA 2d13A 80 :EDLKNVLEG T0316 95 :RTP 2d13A 89 :LKV T0316 99 :PDVMCNKE 2d13A 96 :AGALASRY T0316 108 :KFKAFLDYAITLGADYV 2d13A 104 :QKERIENVARELGLKVY T0316 129 :YARVARDEDGTVHM 2d13A 121 :TPAWEKDPYQYMLE T0316 143 :LRGV 2d13A 149 :AYGL T0316 151 :DQTYFLSQLSQEQL 2d13A 153 :NESWLGRELNYKNL T0316 177 :PEVRRLAEEAGLSTAKKKDSTGICFIG 2d13A 167 :EELKKLSEKYGIHIAGEGGEFETFVLD T0316 215 :LPAQPGRMMTVDGRDM 2d13A 194 :MPFFKAKIVIDDAEKF T0316 233 :HAGLM 2d13A 210 :WDGLS T0316 329 :TEVIFAEPQ 2d13A 215 :GKFIIKRAH Number of specific fragments extracted= 16 number of extra gaps= 0 total=362 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 2d13A/T0316-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2d13A/T0316-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0316-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0316)N4 because first residue in template chain is (2d13A)V2 Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0316)A52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)N51 Warning: unaligning (T0316)F75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0316)E78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWD 2d13A 3 :GLADVAVLYSGGKDSNYALYWALKSGLRVRYLVSMVSE T0316 53 :TEDYKD 2d13A 52 :VELTSL T0316 62 :VADQIGIPYYSVN 2d13A 58 :QARALGIPIIKGF T0316 79 :YWDRVFEYF 2d13A 78 :EVEDLKNVL T0316 92 :R 2d13A 87 :E T0316 94 :GRTPN 2d13A 88 :GLKVD T0316 100 :DVMCNKEIKFKAFLDYAITLGADYVAT 2d13A 96 :AGALASRYQKERIENVARELGLKVYTP T0316 138 :GTVHMLRGVDNGKDQTYFLSQLSQEQLQ 2d13A 140 :FKVVFVAVSAYGLNESWLGRELNYKNLE T0316 178 :EVRRLAEEAGLST 2d13A 168 :ELKKLSEKYGIHI T0316 250 :GGQH 2d13A 181 :AGEG T0316 256 :DNAPWFVVGKDL 2d13A 185 :GEFETFVLDMPF T0316 284 :MSTSLEASQVHF 2d13A 197 :FKAKIVIDDAEK T0316 323 :HVKGEKTEVIFAEPQR 2d13A 209 :FWDGLSGKFIIKRAHL Number of specific fragments extracted= 13 number of extra gaps= 0 total=375 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 1kqpA/T0316-1kqpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kqpA/T0316-1kqpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqpA read from 1kqpA/T0316-1kqpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kqpA in training set Warning: unaligning (T0316)G94 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0316)R95 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1kqpA 37 :GAKGFVLGISGGQDSTLAGRLAQLA T0316 30 :GYDVIGIFMKN 1kqpA 69 :GGDAQFIAVRL T0316 46 :ENGVCTATEDYKDVVAVA 1kqpA 80 :PHGTQQDEDDAQLALKFI T0316 67 :GI 1kqpA 98 :KP T0316 69 :PYYSVNFE 1kqpA 101 :KSWKFDIK T0316 78 :EYWDRVFEYFLAEY 1kqpA 109 :STVSAFSDQYQQET T0316 96 :TPN 1kqpA 125 :QLT T0316 100 :D 1kqpA 128 :D T0316 101 :VM 1kqpA 134 :VK T0316 104 :NKE 1kqpA 136 :ART T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 1kqpA 139 :RMIAQYAIGGQEGLLVLGTDHAAEAVTG T0316 140 :VHMLRGVDNGK 1kqpA 167 :FFTKYGDGGAD T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1kqpA 178 :LLPLTGLTKRQGRTLLKELGAP T0316 190 :TAKKKDSTGI 1kqpA 208 :TADLLDEKPQ T0316 202 :IGEKNFK 1kqpA 218 :QSDETEL T0316 209 :NFLSNYLPAQ 1kqpA 229 :DEIDDYLEGK T0316 277 :GFYHDSLMSTSLEASQVHFTREMPEE 1kqpA 239 :EVSAKVSEALEKRYSMTEHKRQVPAS Number of specific fragments extracted= 17 number of extra gaps= 1 total=392 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 1kqpA/T0316-1kqpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kqpA/T0316-1kqpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqpA read from 1kqpA/T0316-1kqpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kqpA in training set Warning: unaligning (T0316)R95 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0316)T96 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0316 5 :SKTRVVVGMSGGVDSSVTALLL 1kqpA 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQG 1kqpA 66 :REEG T0316 31 :YDVIGIFM 1kqpA 72 :AQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 1kqpA 80 :PHGTQQDEDDAQLALKF T0316 66 :IGI 1kqpA 97 :IKP T0316 69 :PYYSVNFEKEY 1kqpA 101 :KSWKFDIKSTV T0316 85 :EYFLAEYRA 1kqpA 112 :SAFSDQYQQ T0316 94 :G 1kqpA 122 :T T0316 97 :PNPD 1kqpA 125 :QLTD T0316 104 :NKE 1kqpA 136 :ART T0316 108 :KFKAFLDYAITLGADYVATGHY 1kqpA 139 :RMIAQYAIGGQEGLLVLGTDHA T0316 139 :TVHMLRGVDNGKDQTY 1kqpA 161 :AEAVTGFFTKYGDGGA T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 1kqpA 177 :DLLPLTGLTKRQGRTLLKELGAPE T0316 191 :AKKKDSTG 1kqpA 211 :LLDEKPQQ Number of specific fragments extracted= 14 number of extra gaps= 1 total=406 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 1kqpA/T0316-1kqpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kqpA/T0316-1kqpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kqpA read from 1kqpA/T0316-1kqpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kqpA in training set Warning: unaligning (T0316)G94 because of BadResidue code BAD_PEPTIDE in next template residue (1kqpA)D124 Warning: unaligning (T0316)R95 because of BadResidue code BAD_PEPTIDE at template residue (1kqpA)D124 T0316 5 :SKTRVVVGMSGGVDSSVTALLLK 1kqpA 37 :GAKGFVLGISGGQDSTLAGRLAQ T0316 28 :EQGYDVIGIFMKNWDDTD 1kqpA 67 :EEGGDAQFIAVRLPHGTQ T0316 54 :EDYKDVVAVADQIGI 1kqpA 85 :QDEDDAQLALKFIKP T0316 69 :PYYSVNFEKEYWDRVFEYFLAE 1kqpA 101 :KSWKFDIKSTVSAFSDQYQQET T0316 96 :TPN 1kqpA 125 :QLT T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVARD 1kqpA 135 :KARTRMIAQYAIGGQEGLLVLGTDHAAEAVTG T0316 145 :GVDNGKDQTY 1kqpA 167 :FFTKYGDGGA T0316 167 :TMFPLGHLEKPEVRRLAEEAGLS 1kqpA 177 :DLLPLTGLTKRQGRTLLKELGAP Number of specific fragments extracted= 8 number of extra gaps= 1 total=414 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 1wxiA/T0316-1wxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wxiA expands to /projects/compbio/data/pdb/1wxi.pdb.gz 1wxiA:# T0316 read from 1wxiA/T0316-1wxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxiA read from 1wxiA/T0316-1wxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wxiA to template set # found chain 1wxiA in template set Warning: unaligning (T0316)K194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wxiA)D223 T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQ 1wxiA 38 :PFIKSLVLGISGGQDSTLAGKLCQMA T0316 30 :GYDVIGIFM 1wxiA 75 :SLQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 1wxiA 84 :PYGVQADEQDCQDAIAF T0316 66 :IGI 1wxiA 101 :IQP T0316 69 :PYYSVNFE 1wxiA 105 :RVLTVNIK T0316 82 :RVFEYFLAEYRA 1wxiA 113 :GAVLASEQALRE T0316 94 :GRTPNPD 1wxiA 126 :GIELSDF T0316 101 :VMCNKEIKFKAFLDYAITLG 1wxiA 135 :GNEKARERMKAQYSIAGMTS T0316 123 :YVATGH 1wxiA 155 :GVVVGT T0316 129 :YARVARDE 1wxiA 162 :HAAEAITG T0316 140 :VHMLRGVDNGK 1wxiA 170 :FFTKYGDGGTD T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1wxiA 181 :INPLYRLNKRQGKQLLAALACP T0316 190 :TAKK 1wxiA 205 :LYKK T0316 209 :NFLSNYLPA 1wxiA 232 :DNIDDYLEG T0316 276 :QGFYHDSLMSTSLEASQVHFTREMPEEF 1wxiA 241 :KNVPQQVARTIENWYLKTEHKRRPPITV Number of specific fragments extracted= 15 number of extra gaps= 0 total=429 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 1wxiA/T0316-1wxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wxiA/T0316-1wxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxiA read from 1wxiA/T0316-1wxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wxiA in template set Warning: unaligning (T0316)D195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wxiA)D223 T0316 5 :SK 1wxiA 38 :PF T0316 7 :TRVVVGMSGGVDSSVTALLL 1wxiA 41 :KSLVLGISGGQDSTLAGKLC T0316 27 :KEQ 1wxiA 69 :LET T0316 30 :GYDVIGIFM 1wxiA 75 :SLQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 1wxiA 84 :PYGVQADEQDCQDAIAF T0316 66 :IGI 1wxiA 101 :IQP T0316 69 :PYYSVNFEKEYW 1wxiA 105 :RVLTVNIKGAVL T0316 85 :E 1wxiA 117 :A T0316 87 :FLAEYRA 1wxiA 118 :SEQALRE T0316 94 :GRTPN 1wxiA 126 :GIELS T0316 104 :NKEIKFKAFLDYAITLG 1wxiA 138 :KARERMKAQYSIAGMTS T0316 127 :GHYA 1wxiA 155 :GVVV T0316 134 :RDEDGTVHMLRGVDNGKDQTY 1wxiA 159 :GTDHAAEAITGFFTKYGDGGT T0316 167 :TMFPLGHLEKPEVRRLAEEAGLSTAK 1wxiA 180 :DINPLYRLNKRQGKQLLAALACPEHL T0316 193 :KK 1wxiA 207 :KK Number of specific fragments extracted= 15 number of extra gaps= 0 total=444 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 1wxiA/T0316-1wxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wxiA/T0316-1wxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxiA read from 1wxiA/T0316-1wxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wxiA in template set Warning: unaligning (T0316)K194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wxiA)D223 T0316 3 :DNSKTRVVVGMSGGVDSSVTALLLKEQ 1wxiA 37 :YPFIKSLVLGISGGQDSTLAGKLCQMA T0316 30 :GYDVIGIFMKNWDDTD 1wxiA 75 :SLQFIAVRLPYGVQAD T0316 53 :TEDYKDVVAVA 1wxiA 91 :EQDCQDAIAFI T0316 67 :GI 1wxiA 102 :QP T0316 69 :PYYSVNFEKEYWDR 1wxiA 105 :RVLTVNIKGAVLAS T0316 87 :FLAEYRAGRTPN 1wxiA 119 :EQALREAGIELS T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARV 1wxiA 138 :KARERMKAQYSIAGMTSGVVVGTDHAAEA T0316 145 :GVDNGKDQTY 1wxiA 170 :FFTKYGDGGT T0316 167 :TMFPLGHLEKPEVRRLAEEAGL 1wxiA 180 :DINPLYRLNKRQGKQLLAALAC T0316 189 :STAKK 1wxiA 204 :HLYKK Number of specific fragments extracted= 10 number of extra gaps= 0 total=454 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 1ct9A/T0316-1ct9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ct9A expands to /projects/compbio/data/pdb/1ct9.pdb.gz 1ct9A:# T0316 read from 1ct9A/T0316-1ct9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ct9A read from 1ct9A/T0316-1ct9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ct9A to template set # found chain 1ct9A in template set Warning: unaligning (T0316)V33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)L267 Warning: unaligning (T0316)S196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ct9A)K426 Warning: unaligning (T0316)C200 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)K426 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1ct9A 225 :SDVPYGVLLSGGLDSSIISAITKKY T0316 34 :IGIFM 1ct9A 268 :HSFAV T0316 46 :ENG 1ct9A 273 :GLP T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFEKEYWDRVFEYFLAEY 1ct9A 276 :GSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHI T0316 95 :RTPN 1ct9A 316 :ETYD T0316 100 :DVMCNKEIKFKAFLDYAITLGADYVATGHYARVARDEDGTVH 1ct9A 320 :VTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFH T0316 147 :DNGK 1ct9A 362 :KAPN T0316 153 :TYFLSQLSQEQLQK 1ct9A 366 :AKELHEETVRKLLA T0316 167 :TMFPLGH 1ct9A 399 :ARVPFLD T0316 178 :EVRRLAEE 1ct9A 407 :KFLDVAMR T0316 188 :LS 1ct9A 415 :IN T0316 191 :AKKKD 1ct9A 417 :PQDKM T0316 202 :IGEKNFKNFLSNYLP 1ct9A 427 :MEKHILRECFEAYLP T0316 217 :AQP 1ct9A 446 :WRQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=468 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 1ct9A/T0316-1ct9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ct9A/T0316-1ct9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ct9A read from 1ct9A/T0316-1ct9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ct9A in template set Warning: unaligning (T0316)V33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)L267 T0316 9 :VVVGMSGGVDSSVTALLLKEQ 1ct9A 229 :YGVLLSGGLDSSIISAITKKY T0316 34 :IGIFM 1ct9A 268 :HSFAV T0316 46 :ENGVC 1ct9A 273 :GLPGS T0316 54 :EDYKDVVAVADQIGIPYYSVNFE 1ct9A 278 :PDLKAAQEVANHLGTVHHEIHFT T0316 77 :KEYWDRVFEYFL 1ct9A 302 :QEGLDAIRDVIY T0316 100 :DVMCNKEIK 1ct9A 316 :ETYDVTTIR T0316 109 :FKAFLDYAITLGADYVATGHYA 1ct9A 329 :MYLMSRKIKAMGIKMVLSGEGS T0316 134 :RD 1ct9A 351 :DE T0316 142 :MLRGVDNGKDQT 1ct9A 353 :VFGGYLYFHKAP T0316 160 :SQEQL 1ct9A 365 :NAKEL T0316 176 :KPEVRRLAEE 1ct9A 370 :HEETVRKLLA Number of specific fragments extracted= 11 number of extra gaps= 0 total=479 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 1ct9A/T0316-1ct9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ct9A/T0316-1ct9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ct9A read from 1ct9A/T0316-1ct9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ct9A in template set Warning: unaligning (T0316)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ct9A)L267 T0316 7 :TRVVVGMSGGVDSSVTALLLKEQ 1ct9A 227 :VPYGVLLSGGLDSSIISAITKKY T0316 35 :GIFMKNWDD 1ct9A 268 :HSFAVGLPG T0316 53 :TEDYKDVVAVADQIGIPYYSVNF 1ct9A 277 :SPDLKAAQEVANHLGTVHHEIHF T0316 76 :EKEYWDRVFEYF 1ct9A 301 :VQEGLDAIRDVI T0316 88 :LAEYRA 1ct9A 320 :VTTIRA T0316 107 :IKFKAFLDYAITLGADYVATGHYA 1ct9A 327 :TPMYLMSRKIKAMGIKMVLSGEGS Number of specific fragments extracted= 6 number of extra gaps= 0 total=485 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 1q15A/T0316-1q15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q15A expands to /projects/compbio/data/pdb/1q15.pdb.gz 1q15A:# T0316 read from 1q15A/T0316-1q15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q15A read from 1q15A/T0316-1q15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q15A to template set # found chain 1q15A in template set Warning: unaligning (T0316)K192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q15A)S451 Warning: unaligning (T0316)I202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q15A)S451 T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1q15A 236 :PRFDTVGIPLSGGLDSSLVTALASRHFKKLNTYSI T0316 46 :ENG 1q15A 271 :GTE T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1q15A 274 :LSNEFEFSQQVADALGTHHQMKILS T0316 80 :WDRVFEYFLAEYRAGRTPNPDVMCNKE 1q15A 299 :ETEVINGIIESIYYNEIFDGLSAEIQS T0316 108 :KFKAFLDYAITL 1q15A 326 :GLFNVYRQAQGQ T0316 121 :ADYVATGHYARVARDE 1q15A 338 :VSCMLTGYGSDLLFGG T0316 137 :DGT 1q15A 356 :KPG T0316 147 :DNGK 1q15A 359 :AQYD T0316 155 :FLSQLSQEQLQK 1q15A 363 :NPNQLLAEQVYR T0316 167 :TMFPL 1q15A 393 :IRHPF T0316 174 :LEKPEV 1q15A 398 :WSHSLI T0316 180 :RRLAEEAGL 1q15A 425 :REYADSLQL T0316 189 :S 1q15A 435 :P T0316 190 :TA 1q15A 439 :VW T0316 203 :GEKNFKNFLSNYLP 1q15A 452 :VNQAFANVLGSTVD Number of specific fragments extracted= 15 number of extra gaps= 0 total=500 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 1q15A/T0316-1q15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1q15A/T0316-1q15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q15A read from 1q15A/T0316-1q15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q15A in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1q15A 236 :PRFDTVGIPLSGGLDSSLVTALASRHFKKLNTYSI T0316 46 :ENGVCT 1q15A 271 :GTELSN T0316 55 :DYKDVVAVADQIGIPYYSVNFEK 1q15A 277 :EFEFSQQVADALGTHHQMKILSE T0316 81 :DRVFEYFLAEYRAGRTP 1q15A 300 :TEVINGIIESIYYNEIF T0316 102 :MCNKEIKFKAFLDYAITL 1q15A 317 :DGLSAEIQSGLFNVYRQA T0316 120 :GADYVATG 1q15A 337 :QVSCMLTG T0316 128 :HYA 1q15A 353 :GIL T0316 134 :RDEDGT 1q15A 356 :KPGAQY Number of specific fragments extracted= 8 number of extra gaps= 0 total=508 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 1q15A/T0316-1q15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1q15A/T0316-1q15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q15A read from 1q15A/T0316-1q15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q15A in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDT 1q15A 236 :PRFDTVGIPLSGGLDSSLVTALASRHFKKLNTYSIGTELSN T0316 55 :DYKDVVAVADQIGIPYYSVNFEKE 1q15A 277 :EFEFSQQVADALGTHHQMKILSET T0316 82 :RVFEYFLAEYRAGRTPN 1q15A 301 :EVINGIIESIYYNEIFD T0316 108 :KFKAFLDYAIT 1q15A 323 :IQSGLFNVYRQ T0316 119 :LGADYVATGHY 1q15A 336 :GQVSCMLTGYG Number of specific fragments extracted= 5 number of extra gaps= 0 total=513 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 1ru8A/T0316-1ru8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ru8A expands to /projects/compbio/data/pdb/1ru8.pdb.gz 1ru8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0316 read from 1ru8A/T0316-1ru8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ru8A read from 1ru8A/T0316-1ru8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ru8A to template set # found chain 1ru8A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1ru8A)G3 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0316)T51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0316)G127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0316)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENG 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYM T0316 52 :ATEDYKDV 1ru8A 50 :INANLTDL T0316 62 :VADQIGIPYYSVNFE 1ru8A 58 :QARALGIPLVKGFTQ T0316 94 :GR 1ru8A 73 :GE T0316 104 :NKE 1ru8A 75 :KEK T0316 108 :KFKAFLDYAITLGADYVAT 1ru8A 78 :EVEDLKRVLSGLKIQGIVA T0316 135 :D 1ru8A 101 :S T0316 137 :DG 1ru8A 102 :KY T0316 175 :EKPEVRRLAEEAGLSTAKKKDSTG 1ru8A 104 :QRKRIEKVAKELGLEVYTPAWGRD T0316 207 :FKNFLSNYLP 1ru8A 128 :AKEYMRELLN T0316 234 :AGLMYYTIGQRG 1ru8A 138 :LGFKIMVVGVSA T0316 246 :GL 1ru8A 151 :GL T0316 248 :GIGGQH 1ru8A 155 :SWLGRI T0316 278 :FYHDSLMSTSLEAS 1ru8A 161 :LDESALEELITLNE T0316 292 :QVHFTREMPEEFTLEC 1ru8A 186 :EFETFVLDMPLFKYKI T0316 308 :TAKFRYRQPDSKVTVHVKGEKTE 1ru8A 205 :KAKKVWEPCTSSGKLIIEEAHLE Number of specific fragments extracted= 16 number of extra gaps= 1 total=529 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 1ru8A/T0316-1ru8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ru8A/T0316-1ru8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ru8A read from 1ru8A/T0316-1ru8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ru8A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1ru8A)G3 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0316)T51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0316)G127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0316)H128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENG 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYM T0316 52 :ATEDYKDV 1ru8A 50 :INANLTDL T0316 62 :VADQIGIPYYSVNFE 1ru8A 58 :QARALGIPLVKGFTQ T0316 77 :K 1ru8A 77 :K T0316 108 :KFKAFLDYAITLGADYVAT 1ru8A 78 :EVEDLKRVLSGLKIQGIVA T0316 172 :GHLEKPEVRRLAEEAGLSTAK 1ru8A 101 :SKYQRKRIEKVAKELGLEVYT T0316 196 :STG 1ru8A 122 :PAW T0316 204 :EKNFKNFLSNYLPA 1ru8A 125 :GRDAKEYMRELLNL T0316 220 :GRMMTV 1ru8A 139 :GFKIMV T0316 226 :DGRDMGEHAGLMY 1ru8A 177 :KVHVAGEGGEFET T0316 245 :GGLGIGGQH 1ru8A 190 :FVLDMPLFK T0316 286 :TSLEASQVHFTRE 1ru8A 199 :YKIVVDKAKKVWE T0316 300 :PEEFTLECTAKFRY 1ru8A 212 :PCTSSGKLIIEEAH Number of specific fragments extracted= 13 number of extra gaps= 1 total=542 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 1ru8A/T0316-1ru8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ru8A/T0316-1ru8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ru8A read from 1ru8A/T0316-1ru8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ru8A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1ru8A)G3 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)T49 Warning: unaligning (T0316)T51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)T49 Warning: unaligning (T0316)G127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ru8A)A100 Warning: unaligning (T0316)H128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ru8A)A100 T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENG 1ru8A 4 :LADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYM T0316 52 :ATEDYKDV 1ru8A 50 :INANLTDL T0316 62 :VADQIGIPYYSVNFEK 1ru8A 58 :QARALGIPLVKGFTQG T0316 104 :NKEIKFKAFLDYAITLGADYVAT 1ru8A 74 :EKEKEVEDLKRVLSGLKIQGIVA T0316 172 :GHLEKPEVRRLAEEAGLSTAKK 1ru8A 101 :SKYQRKRIEKVAKELGLEVYTP T0316 202 :IGEKNFKNFLSNYLP 1ru8A 123 :AWGRDAKEYMRELLN T0316 219 :PGRMMTV 1ru8A 139 :GFKIMVV T0316 246 :GLGIGG 1ru8A 177 :KVHVAG T0316 254 :GGDNAPWFVVGKDL 1ru8A 183 :EGGEFETFVLDMPL T0316 284 :MSTSLEASQVHFTRE 1ru8A 197 :FKYKIVVDKAKKVWE T0316 300 :PEEFTLECTAK 1ru8A 212 :PCTSSGKLIIE T0316 319 :KVTVHVK 1ru8A 223 :EAHLESK Number of specific fragments extracted= 12 number of extra gaps= 1 total=554 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 1m1zA/T0316-1m1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m1zA expands to /projects/compbio/data/pdb/1m1z.pdb.gz 1m1zA:# T0316 read from 1m1zA/T0316-1m1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1zA read from 1m1zA/T0316-1m1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m1zA to template set # found chain 1m1zA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKN 1m1zA 240 :PGDTPLVVLSGGIDSSGVAACAHRAAGELDTVSMGT T0316 46 :E 1m1zA 276 :D T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1m1zA 277 :TSNEFREARAVVDHLRTRHREITIP T0316 77 :KEYWDRVFEYFL 1m1zA 303 :TELLAQLPYAVW T0316 101 :VMCNKEI 1m1zA 317 :ESVDPDI T0316 109 :FKAFLDYAITL 1m1zA 324 :IEYLLPLTALY T0316 120 :GADYVATGHYARVARDE 1m1zA 340 :PERRILTGYGADIPLGG T0316 147 :DNGKDQTYFLSQLSQEQLQK 1m1zA 357 :MHREDRLPALDTVLAHDMAT Number of specific fragments extracted= 8 number of extra gaps= 0 total=562 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 1m1zA/T0316-1m1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1m1zA/T0316-1m1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1zA read from 1m1zA/T0316-1m1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m1zA in template set Warning: unaligning (T0316)G149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m1zA)A473 Warning: unaligning (T0316)F155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m1zA)A473 T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQ 1m1zA 239 :TPGDTPLVVLSGGIDSSGVAACAHRA T0316 31 :YDVIGIFM 1m1zA 266 :GELDTVSM T0316 46 :ENGVCTATEDYKDV 1m1zA 274 :GTDTSNEFREARAV T0316 63 :ADQIGIPYYSVNFE 1m1zA 288 :VDHLRTRHREITIP T0316 88 :LAEYRA 1m1zA 302 :TTELLA T0316 100 :D 1m1zA 308 :Q T0316 101 :VMCNKE 1m1zA 317 :ESVDPD T0316 108 :KFKAFLDYAITL 1m1zA 323 :IIEYLLPLTALY T0316 120 :GADYVATG 1m1zA 340 :PERRILTG T0316 128 :H 1m1zA 358 :H T0316 130 :A 1m1zA 359 :R T0316 134 :RDEDGT 1m1zA 360 :EDRLPA T0316 140 :VHMLRGVDN 1m1zA 458 :RLLLDHGVA T0316 156 :LSQLSQEQLQKTM 1m1zA 474 :KRQVVRELFDLTV T0316 169 :FPLGHLEKPEVR 1m1zA 490 :RHPSEVDTDDVV Number of specific fragments extracted= 15 number of extra gaps= 0 total=577 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 1m1zA/T0316-1m1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1m1zA/T0316-1m1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m1zA read from 1m1zA/T0316-1m1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m1zA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDD 1m1zA 240 :PGDTPLVVLSGGIDSSGVAACAHRAAGELDTVSMGTDTS T0316 54 :EDYKDVVAVADQIGIPYYSVNF 1m1zA 279 :NEFREARAVVDHLRTRHREITI T0316 76 :EKEYWDRVFEYF 1m1zA 302 :TTELLAQLPYAV T0316 92 :RAGRTPNP 1m1zA 314 :WASESVDP T0316 106 :EI 1m1zA 322 :DI T0316 109 :FKAFLDYAIT 1m1zA 324 :IEYLLPLTAL T0316 119 :LGADYVATGHYARV 1m1zA 339 :GPERRILTGYGADI T0316 166 :KTMFPLGHLEKPEVRRLAEEA 1m1zA 353 :PLGGMHREDRLPALDTVLAHD Number of specific fragments extracted= 8 number of extra gaps= 0 total=585 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 1ih8A/T0316-1ih8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ih8A expands to /projects/compbio/data/pdb/1ih8.pdb.gz 1ih8A:# T0316 read from 1ih8A/T0316-1ih8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ih8A read from 1ih8A/T0316-1ih8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ih8A to template set # found chain 1ih8A in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1ih8A 37 :GAKGFVLGISGGQDSTLAGRLAQLA T0316 30 :GYD 1ih8A 69 :GGD T0316 33 :VIGIFM 1ih8A 74 :FIAVRL T0316 46 :ENGVCTATEDYKDVVAVA 1ih8A 80 :PHGTQQDEDDAQLALKFI T0316 67 :GI 1ih8A 98 :KP T0316 69 :PYYSVNFE 1ih8A 101 :KSWKFDIK T0316 78 :EYWDRVFEYFLAEY 1ih8A 109 :STVSAFSDQYQQET T0316 94 :GRTPN 1ih8A 123 :GDQLT T0316 100 :D 1ih8A 128 :D T0316 101 :VMCNK 1ih8A 134 :VKART T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 1ih8A 139 :RMIAQYAIGGQEGLLVLGTDHAAEAVTG T0316 140 :VHMLRGVDNGK 1ih8A 167 :FFTKYGDGGAD T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1ih8A 178 :LLPLTGLTKRQGRTLLKELGAP T0316 190 :TAKKKDSTGI 1ih8A 202 :LYLKEPTADL T0316 202 :IGEKN 1ih8A 212 :LDEKP T0316 207 :FK 1ih8A 220 :DE T0316 209 :NFLSNYLPA 1ih8A 229 :DEIDDYLEG T0316 276 :QGFYHDSLMSTSLEASQVHFTREMP 1ih8A 238 :KEVSAKVSEALEKRYSMTEHKRQVP Number of specific fragments extracted= 18 number of extra gaps= 0 total=603 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 1ih8A/T0316-1ih8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ih8A/T0316-1ih8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ih8A read from 1ih8A/T0316-1ih8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ih8A in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLL 1ih8A 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQG 1ih8A 66 :REEG T0316 31 :YDVIGIFM 1ih8A 72 :AQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 1ih8A 80 :PHGTQQDEDDAQLALKF T0316 66 :IGI 1ih8A 97 :IKP T0316 69 :PYYSVNFEKEY 1ih8A 101 :KSWKFDIKSTV T0316 85 :EYFLAEYRA 1ih8A 112 :SAFSDQYQQ T0316 94 :GRTPNPD 1ih8A 122 :TGDQLTD T0316 103 :C 1ih8A 136 :A T0316 105 :KE 1ih8A 137 :RT T0316 108 :KFKAFLDYAITLGADY 1ih8A 139 :RMIAQYAIGGQEGLLV T0316 126 :TGH 1ih8A 155 :LGT T0316 134 :RDE 1ih8A 158 :DHA T0316 139 :TVHMLRGVDNGKDQTY 1ih8A 161 :AEAVTGFFTKYGDGGA T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 1ih8A 177 :DLLPLTGLTKRQGRTLLKELGAPE T0316 191 :AKKKDSTG 1ih8A 211 :LLDEKPQQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=619 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 1ih8A/T0316-1ih8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ih8A/T0316-1ih8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ih8A read from 1ih8A/T0316-1ih8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ih8A in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLK 1ih8A 37 :GAKGFVLGISGGQDSTLAGRLAQ T0316 28 :EQGYDVIGIFMKNWDDTD 1ih8A 67 :EEGGDAQFIAVRLPHGTQ T0316 54 :EDYKDVVAVADQIGI 1ih8A 85 :QDEDDAQLALKFIKP T0316 69 :PYYSVNFEKEYWDRVFEYFLAE 1ih8A 101 :KSWKFDIKSTVSAFSDQYQQET T0316 94 :GRTPN 1ih8A 123 :GDQLT T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVA 1ih8A 135 :KARTRMIAQYAIGGQEGLLVLGTDHAAEAV T0316 145 :GVDNGKDQT 1ih8A 167 :FFTKYGDGG T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 1ih8A 177 :DLLPLTGLTKRQGRTLLKELGAPE T0316 209 :NFL 1ih8A 201 :RLY Number of specific fragments extracted= 9 number of extra gaps= 0 total=628 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 1sur/T0316-1sur-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sur expands to /projects/compbio/data/pdb/1sur.pdb.gz 1sur:Warning: there is no chain 1sur will retry with 1surA # T0316 read from 1sur/T0316-1sur-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sur read from 1sur/T0316-1sur-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sur to template set # found chain 1sur in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKE 1sur 44 :PGEYVLSSSFGIQAAVSLHLVNQ T0316 29 :QGYD 1sur 69 :PDIP T0316 35 :GIFM 1sur 73 :VILT T0316 46 :ENGVC 1sur 77 :DTGYL T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1sur 82 :FPETYRFIDELTDKLKLNLKVYRAT T0316 77 :KEYWDRV 1sur 110 :AWQEARY T0316 84 :FEYFLAEY 1sur 123 :GVEGIEKY T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVARDEDGTVHMLRGVDNGK 1sur 131 :NDINKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVLAIQRGVFK T0316 168 :MFPLGHLEKPEVRRLAEEAGLSTA 1sur 178 :VLPIIDWDNRTIYQYLQKHGLKYH T0316 209 :NFLSNYLPAQP 1sur 202 :PLWDEGYLSVG Number of specific fragments extracted= 10 number of extra gaps= 0 total=638 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 1sur/T0316-1sur-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1sur/T0316-1sur-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sur read from 1sur/T0316-1sur-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sur in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQ 1sur 44 :PGEYVLSSSFGIQAAVSLHLVNQI T0316 30 :GYDVIG 1sur 70 :DIPVIL T0316 38 :M 1sur 76 :T T0316 46 :ENGVC 1sur 77 :DTGYL T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1sur 82 :FPETYRFIDELTDKLKLNLKVYRAT T0316 77 :KEYWDRV 1sur 110 :AWQEARY T0316 89 :AEYRA 1sur 128 :EKYND T0316 106 :EIKFKAFLDYAITLGADYVATGHYARVARDEDGTVHM 1sur 133 :INKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVL T0316 143 :LR 1sur 173 :RG T0316 166 :KTMFPLGHLEKPEVRRLAEEAGLSTAKKK 1sur 176 :FKVLPIIDWDNRTIYQYLQKHGLKYHPLW Number of specific fragments extracted= 10 number of extra gaps= 0 total=648 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 1sur/T0316-1sur-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1sur/T0316-1sur-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sur read from 1sur/T0316-1sur-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sur in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKN 1sur 44 :PGEYVLSSSFGIQAAVSLHLVNQIRPDIPVILTDT T0316 49 :VCTATEDYKDVVAVADQIGIPYYSVNF 1sur 79 :GYLFPETYRFIDELTDKLKLNLKVYRA T0316 76 :EKEYWDR 1sur 109 :AAWQEAR T0316 88 :LAEYRA 1sur 127 :IEKYND T0316 106 :EIKFKAFLDYAITLGADYVATGHYARVARDEDGTVHMLRGVD 1sur 133 :INKVEPMNRALKELNAQTWFAGLRREQSGSRANLPVLAIQRG T0316 168 :MFPLGHLEKPEVRRLAEEAGLSTA 1sur 178 :VLPIIDWDNRTIYQYLQKHGLKYH T0316 209 :NFLSNYLPAQP 1sur 202 :PLWDEGYLSVG Number of specific fragments extracted= 7 number of extra gaps= 0 total=655 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 2blnA/T0316-2blnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2blnA/T0316-2blnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2blnA read from 2blnA/T0316-2blnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2blnA in training set Warning: unaligning (T0316)T7 because first residue in template chain is (2blnA)M1 Warning: unaligning (T0316)E46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2blnA)F41 Warning: unaligning (T0316)D55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2blnA)F41 Warning: unaligning (T0316)E204 because of BadResidue code BAD_PEPTIDE in next template residue (2blnA)T202 Warning: unaligning (T0316)K205 because of BadResidue code BAD_PEPTIDE at template residue (2blnA)T202 T0316 8 :RVVVGM 2blnA 2 :KTVVFA T0316 19 :SSVTALLLKEQGYDVIGIFM 2blnA 12 :GCLGIEALLAAGYEISAIFT T0316 44 :TD 2blnA 32 :HT T0316 56 :YKDVVAVADQIGIPYY 2blnA 42 :YGSVARLAAERGIPVY T0316 75 :FE 2blnA 58 :AP T0316 94 :GRTP 2blnA 60 :DNVN T0316 104 :NKEI 2blnA 64 :HPLW T0316 113 :LDYAITLGADYVATGHYAR 2blnA 68 :VERIAQLSPDVIFSFYYRH T0316 137 :DG 2blnA 87 :LI T0316 139 :TVHMLRGVDNGKDQTYFLSQLSQEQLQKTM 2blnA 144 :IVAQLRIAIAPDDIAITLHHKLCHAARQLL T0316 177 :PEVRRLAEEAGLSTAKKKDSTGICFIG 2blnA 174 :EQTLPAIKHGNILEIAQRENEATCFGR T0316 206 :NFKNFLSNYLP 2blnA 203 :PDDSFLEWHKP T0316 220 :GR 2blnA 227 :PW T0316 227 :GRDMGEHAGLMYYTIGQ 2blnA 229 :PGAFSYVGNQKFTVWSS T0316 248 :GI 2blnA 246 :RV T0316 251 :GQHGGDNAPWFVVGKD 2blnA 248 :HPHASKAQPGSVISVA T0316 270 :NILY 2blnA 264 :PLLI T0316 339 :AITPGQAVV 2blnA 268 :ACGDGALEI T0316 348 :FYD 2blnA 278 :TGQ T0316 351 :GE 2blnA 282 :GD Number of specific fragments extracted= 20 number of extra gaps= 1 total=675 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 2blnA/T0316-2blnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2blnA/T0316-2blnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2blnA read from 2blnA/T0316-2blnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2blnA in training set Warning: unaligning (T0316)T7 because first residue in template chain is (2blnA)M1 Warning: unaligning (T0316)D42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2blnA)F41 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2blnA)F41 T0316 8 :RVVVGM 2blnA 2 :KTVVFA T0316 19 :SSVTALLLKEQGYDVIGIFM 2blnA 12 :GCLGIEALLAAGYEISAIFT T0316 40 :NW 2blnA 32 :HT T0316 50 :CTA 2blnA 42 :YGS T0316 59 :VVAVADQIGIPYYSVN 2blnA 45 :VARLAAERGIPVYAPD T0316 75 :F 2blnA 62 :V T0316 103 :CNKEI 2blnA 63 :NHPLW T0316 113 :LDYAITLGADYVATGHYA 2blnA 68 :VERIAQLSPDVIFSFYYR T0316 134 :RDEDGT 2blnA 86 :HLIYDE T0316 149 :GKDQTYFLSQLSQEQLQKTM 2blnA 154 :PDDIAITLHHKLCHAARQLL T0316 177 :PEVRRLAEEAGLSTAKKKDSTGICFIG 2blnA 174 :EQTLPAIKHGNILEIAQRENEATCFGR T0316 204 :EKNF 2blnA 203 :PDDS T0316 208 :KNFLSNYLPAQPGRMMTVDGRD 2blnA 218 :HNMVRAVADPWPGAFSYVGNQK T0316 239 :YTIGQRGGLGIGGQHGGDNA 2blnA 240 :FTVWSSRVHPHASKAQPGSV T0316 259 :PWFVVGKDL 2blnA 264 :PLLIACGDG T0316 308 :TAKFR 2blnA 273 :ALEIV T0316 321 :TVHVKG 2blnA 278 :TGQAGD Number of specific fragments extracted= 17 number of extra gaps= 0 total=692 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 2blnA/T0316-2blnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2blnA/T0316-2blnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2blnA read from 2blnA/T0316-2blnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2blnA in training set Warning: unaligning (T0316)T7 because first residue in template chain is (2blnA)M1 Warning: unaligning (T0316)W41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2blnA)F41 Warning: unaligning (T0316)G48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2blnA)F41 Warning: unaligning (T0316)E204 because of BadResidue code BAD_PEPTIDE in next template residue (2blnA)T202 Warning: unaligning (T0316)K205 because of BadResidue code BAD_PEPTIDE at template residue (2blnA)T202 T0316 8 :RVVVGM 2blnA 2 :KTVVFA T0316 18 :DSSVTALLLKEQGYDVIGIFMKN 2blnA 11 :MGCLGIEALLAAGYEISAIFTHT T0316 49 :VC 2blnA 42 :YG T0316 58 :DVVAVADQIGIPYYS 2blnA 44 :SVARLAAERGIPVYA T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYAR 2blnA 59 :PDNVNHPLWVERIAQLSPDVIFSFYYRH T0316 138 :GTVHMLRGVDNGKDQTYFLSQLSQEQLQKTM 2blnA 143 :AIVAQLRIAIAPDDIAITLHHKLCHAARQLL T0316 177 :PEVRRLAEEAGLSTAKKKDSTGICFIG 2blnA 174 :EQTLPAIKHGNILEIAQRENEATCFGR T0316 206 :N 2blnA 203 :P T0316 207 :FKNFLSNYLPAQPGRMMTVDGRD 2blnA 217 :LHNMVRAVADPWPGAFSYVGNQK T0316 239 :YTIGQRGGLGIGG 2blnA 240 :FTVWSSRVHPHAS T0316 256 :DNAPWFVVGK 2blnA 253 :KAQPGSVISV T0316 269 :KNILYVGQGF 2blnA 263 :APLLIACGDG T0316 308 :TAKFR 2blnA 273 :ALEIV T0316 321 :TVHVKGEKT 2blnA 278 :TGQAGDGIT Number of specific fragments extracted= 14 number of extra gaps= 1 total=706 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 1jmvA/T0316-1jmvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jmvA expands to /projects/compbio/data/pdb/1jmv.pdb.gz 1jmvA:# T0316 read from 1jmvA/T0316-1jmvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jmvA read from 1jmvA/T0316-1jmvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jmvA to template set # found chain 1jmvA in template set T0316 7 :TRVVVGM 1jmvA 3 :KHILVAV T0316 19 :SSVTAL 1jmvA 15 :SPILLK T0316 25 :LLKEQGYDVIGIFMKNWDDTDENGV 1jmvA 25 :IAKRHDAKLSIIHVDVNFSDLYTGL T0316 50 :CTATEDYKDVVAVADQIGIPY 1jmvA 60 :RISTETQKALLDLAESVDYPI T0316 71 :YSVNFE 1jmvA 84 :LSGSGD T0316 108 :KFKAFLDYAITLGADYVATGHYAR 1jmvA 90 :LGQVLSDAIEQYDVDLLVTGHHQD Number of specific fragments extracted= 6 number of extra gaps= 0 total=712 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 1jmvA/T0316-1jmvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1jmvA/T0316-1jmvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jmvA read from 1jmvA/T0316-1jmvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jmvA in template set T0316 7 :TRVVVGM 1jmvA 3 :KHILVAV T0316 19 :SSVTALLL 1jmvA 15 :SPILLKKA T0316 27 :KEQGYDVIGIFMKNWDDTDENGV 1jmvA 27 :KRHDAKLSIIHVDVNFSDLYTGL T0316 50 :CTATEDYKDVVAVADQIGIPY 1jmvA 60 :RISTETQKALLDLAESVDYPI T0316 71 :YSVNFE 1jmvA 84 :LSGSGD T0316 108 :KFKAFLDYAITLGADYVATGHYA 1jmvA 90 :LGQVLSDAIEQYDVDLLVTGHHQ T0316 134 :RDEDGTVHM 1jmvA 113 :DFWSKLMSS T0316 143 :LRGV 1jmvA 126 :MNTI Number of specific fragments extracted= 8 number of extra gaps= 0 total=720 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 1jmvA/T0316-1jmvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1jmvA/T0316-1jmvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jmvA read from 1jmvA/T0316-1jmvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jmvA in template set T0316 7 :TRVVVGM 1jmvA 3 :KHILVAV T0316 19 :SS 1jmvA 15 :SP T0316 21 :VTALLLKEQGYDVIGIFMKNWDDT 1jmvA 21 :KAVGIAKRHDAKLSIIHVDVNFSD T0316 47 :NG 1jmvA 58 :QD T0316 50 :CTATEDYKDVVAVADQIGIP 1jmvA 60 :RISTETQKALLDLAESVDYP T0316 70 :YYSVNFE 1jmvA 83 :KLSGSGD T0316 108 :KFKAFLDYAITLGADYVATGHY 1jmvA 90 :LGQVLSDAIEQYDVDLLVTGHH Number of specific fragments extracted= 7 number of extra gaps= 0 total=727 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 2nsyA/T0316-2nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2nsyA expands to /projects/compbio/data/pdb/2nsy.pdb.gz 2nsyA:Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 2nsyA Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 2nsyA # T0316 read from 2nsyA/T0316-2nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsyA read from 2nsyA/T0316-2nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nsyA to template set # found chain 2nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLL 2nsyA 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQGYD 2nsyA 66 :REEGGD T0316 33 :VIGIFM 2nsyA 74 :FIAVRL T0316 46 :ENGVCTATEDYKDVVAVA 2nsyA 80 :PHGTQQDEDDAQLALKFI T0316 67 :GI 2nsyA 98 :KP T0316 69 :PYYSVNFE 2nsyA 101 :KSWKFDIK T0316 82 :RVFEYFLAEYRAGRTPNPD 2nsyA 109 :STVSAFSDQYQQETGDQLT T0316 105 :KE 2nsyA 137 :RT T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 2nsyA 139 :RMIAQYAIGGQEGLLVLGTDHAAEAVTG T0316 140 :VHMLRGVDNGK 2nsyA 167 :FFTKYGDGGAD T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 2nsyA 178 :LLPLTGLTKRQGRTLLKELGAP T0316 193 :KKDS 2nsyA 205 :KEPT T0316 212 :SNYLPAQP 2nsyA 209 :ADLLDEKP T0316 220 :GR 2nsyA 237 :GK T0316 277 :GFYHDSLMSTSLEASQVHFTREMPEEF 2nsyA 239 :EVSAKVSEALEKRYSMTEHKRQVPASM Number of specific fragments extracted= 15 number of extra gaps= 0 total=742 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 2nsyA/T0316-2nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2nsyA/T0316-2nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsyA read from 2nsyA/T0316-2nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLL 2nsyA 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQG 2nsyA 66 :REEG T0316 31 :YDVIGIFM 2nsyA 72 :AQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 2nsyA 80 :PHGTQQDEDDAQLALKF T0316 66 :IGI 2nsyA 97 :IKP T0316 69 :PYYSVNFEKEY 2nsyA 101 :KSWKFDIKSTV T0316 85 :EYFLAEYRA 2nsyA 112 :SAFSDQYQQ T0316 94 :GRTPNPD 2nsyA 122 :TGDQLTD T0316 104 :NKE 2nsyA 136 :ART T0316 108 :KFKAFLDYAITLGADYVATGHY 2nsyA 139 :RMIAQYAIGGQEGLLVLGTDHA T0316 139 :TVHMLRGVDNGKDQTY 2nsyA 161 :AEAVTGFFTKYGDGGA T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 2nsyA 177 :DLLPLTGLTKRQGRTLLKELGAPE T0316 191 :AKKKDSTG 2nsyA 211 :LLDEKPQQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=755 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 2nsyA/T0316-2nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2nsyA/T0316-2nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsyA read from 2nsyA/T0316-2nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLL 2nsyA 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQGYDVIGIFMKNWDDTD 2nsyA 66 :REEGGDAQFIAVRLPHGTQ T0316 54 :EDYKDVVAVADQIGI 2nsyA 85 :QDEDDAQLALKFIKP T0316 69 :PYYSVNFEKEYWDRVFEYFLAE 2nsyA 101 :KSWKFDIKSTVSAFSDQYQQET T0316 94 :GRTPN 2nsyA 123 :GDQLT T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVA 2nsyA 135 :KARTRMIAQYAIGGQEGLLVLGTDHAAEAV T0316 145 :GVDNGKDQT 2nsyA 167 :FFTKYGDGG T0316 167 :TMFPLGHLEKPEVRRLAEEAGLS 2nsyA 177 :DLLPLTGLTKRQGRTLLKELGAP Number of specific fragments extracted= 8 number of extra gaps= 0 total=763 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 1nsyA/T0316-1nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nsyA expands to /projects/compbio/data/pdb/1nsy.pdb.gz 1nsyA:# T0316 read from 1nsyA/T0316-1nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nsyA read from 1nsyA/T0316-1nsyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nsyA to template set # found chain 1nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQ 1nsyA 37 :GAKGFVLGISGGQDSTLAGRLAQLA T0316 30 :GYDVIGIFM 1nsyA 71 :DAQFIAVRL T0316 46 :ENGVCTATEDYKDVVAVA 1nsyA 80 :PHGTQQDEDDAQLALKFI T0316 67 :GI 1nsyA 98 :KP T0316 69 :PYYSVNFE 1nsyA 101 :KSWKFDIK T0316 82 :RVFEYFLAEYRAGRTPNPD 1nsyA 109 :STVSAFSDQYQQETGDQLT T0316 105 :KE 1nsyA 137 :RT T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 1nsyA 139 :RMIAQYAIGGQEGLLVLGTDHAAEAVTG T0316 140 :VHMLRGVDNGK 1nsyA 167 :FFTKYGDGGAD T0316 168 :MFPLGHLEKPEVRRLAEEAGLS 1nsyA 178 :LLPLTGLTKRQGRTLLKELGAP T0316 193 :KKDSTGI 1nsyA 205 :KEPTADL T0316 215 :LPAQP 1nsyA 212 :LDEKP T0316 220 :GR 1nsyA 237 :GK T0316 277 :GFYHDSLMSTSLEASQVHFTREMPEEFT 1nsyA 239 :EVSAKVSEALEKRYSMTEHKRQVPASMF Number of specific fragments extracted= 14 number of extra gaps= 0 total=777 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 1nsyA/T0316-1nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1nsyA/T0316-1nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nsyA read from 1nsyA/T0316-1nsyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLL 1nsyA 37 :GAKGFVLGISGGQDSTLAGRLA T0316 27 :KEQG 1nsyA 66 :REEG T0316 31 :YDVIGIFM 1nsyA 72 :AQFIAVRL T0316 46 :ENGVCTATEDYKDVVAV 1nsyA 80 :PHGTQQDEDDAQLALKF T0316 66 :IGI 1nsyA 97 :IKP T0316 69 :PYYSVNFEKEY 1nsyA 101 :KSWKFDIKSTV T0316 85 :EYFLAEYRA 1nsyA 112 :SAFSDQYQQ T0316 94 :GRTPNPD 1nsyA 122 :TGDQLTD T0316 104 :NKE 1nsyA 136 :ART T0316 108 :KFKAFLDYAITLGADYVATGHY 1nsyA 139 :RMIAQYAIGGQEGLLVLGTDHA T0316 139 :TVHMLRGVDNGKDQTY 1nsyA 161 :AEAVTGFFTKYGDGGA T0316 167 :TMFPLGHLEKPEVRRLAEEAGLST 1nsyA 177 :DLLPLTGLTKRQGRTLLKELGAPE T0316 191 :AKKKDSTG 1nsyA 211 :LLDEKPQQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=790 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 1nsyA/T0316-1nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1nsyA/T0316-1nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nsyA read from 1nsyA/T0316-1nsyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nsyA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLK 1nsyA 37 :GAKGFVLGISGGQDSTLAGRLAQ T0316 28 :EQGYDVIGIFMKNWDDTD 1nsyA 67 :EEGGDAQFIAVRLPHGTQ T0316 54 :EDYKDVVAVADQIGI 1nsyA 85 :QDEDDAQLALKFIKP T0316 69 :PYYSVNFEKEYWDRVFEYFLAE 1nsyA 101 :KSWKFDIKSTVSAFSDQYQQET T0316 94 :GRTPN 1nsyA 123 :GDQLT T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVA 1nsyA 135 :KARTRMIAQYAIGGQEGLLVLGTDHAAEAV T0316 145 :GVDNGKDQT 1nsyA 167 :FFTKYGDGG T0316 167 :TMFPLGHLEKPEVRRLAEEAGLS 1nsyA 177 :DLLPLTGLTKRQGRTLLKELGAP Number of specific fragments extracted= 8 number of extra gaps= 0 total=798 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 1dv1A/T0316-1dv1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dv1A expands to /projects/compbio/data/pdb/1dv1.pdb.gz 1dv1A:Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3132, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3134, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3136, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3138, because occupancy 0.500 <= existing 0.500 in 1dv1A # T0316 read from 1dv1A/T0316-1dv1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dv1A read from 1dv1A/T0316-1dv1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dv1A to template set # found chain 1dv1A in template set Warning: unaligning (T0316)K194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dv1A)M169 Warning: unaligning (T0316)Q218 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dv1A)N195 T0316 7 :TRVVVG 1dv1A 3 :DKIVIA T0316 19 :SSVTALLLKEQGYDVIGIFM 1dv1A 14 :ALRILRACKELGIKTVAVHS T0316 44 :TDENGV 1dv1A 34 :SADRDL T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1dv1A 59 :SYLNIPAIISAAEITGAVAIHPGYG T0316 77 :KEYWDRV 1dv1A 89 :ANFAEQV T0316 92 :RAGRT 1dv1A 96 :ERSGF T0316 99 :PDVMCNKEI 1dv1A 101 :IFIGPKAET T0316 109 :FKAF 1dv1A 110 :IRLM T0316 113 :LDYAITLGAD 1dv1A 120 :IAAMKKAGVP T0316 132 :V 1dv1A 130 :C T0316 137 :DGTV 1dv1A 131 :VPGS T0316 146 :VDNGK 1dv1A 135 :DGPLG T0316 174 :LEKPEVRRLAEEAGLS 1dv1A 140 :DDMDKNRAIAKRIGYP T0316 190 :TAKK 1dv1A 157 :IIKA T0316 201 :FIGEKNFKNFLSNYLPA 1dv1A 172 :VRGDAELAQSISMTRAE T0316 220 :GRMMTVDGRDMG 1dv1A 220 :GNAIYLAERDCS T0316 232 :EHAGLMYYTIGQRGGL 1dv1A 233 :QRRHQKVVEEAPAPGI T0316 279 :YHDSLMSTSLE 1dv1A 249 :TPELRRYIGER T0316 290 :ASQVHFTR 1dv1A 261 :AKACVDIG T0316 337 :QRAI 1dv1A 269 :YRGA T0316 343 :GQAVVFYDGEECLGGGLI 1dv1A 273 :GTFEFLFENGEFYFIEMN Number of specific fragments extracted= 21 number of extra gaps= 0 total=819 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 1dv1A/T0316-1dv1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1dv1A/T0316-1dv1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dv1A read from 1dv1A/T0316-1dv1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dv1A in template set Warning: unaligning (T0316)V225 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dv1A)M169 T0316 7 :TRVVVG 1dv1A 3 :DKIVIA T0316 19 :SSVTALLLKEQGYDVIGIFM 1dv1A 14 :ALRILRACKELGIKTVAVHS T0316 46 :E 1dv1A 34 :S T0316 52 :ATEDYKDVVA 1dv1A 35 :ADRDLKHVLL T0316 71 :YSVNFE 1dv1A 47 :ETVCIG T0316 97 :PNPDVMCNKEI 1dv1A 53 :PAPSVKSYLNI T0316 110 :KAFLDYAITLGADYVATGH 1dv1A 64 :PAIISAAEITGAVAIHPGY T0316 134 :RDEDGTVHM 1dv1A 83 :GFLSENANF T0316 143 :L 1dv1A 97 :R T0316 152 :QTYFLSQLSQEQLQKTM 1dv1A 98 :SGFIFIGPKAETIRLMG T0316 175 :EKPEVRRLAEEAGLSTAKKKDS 1dv1A 115 :DKVSAIAAMKKAGVPCVPGSDG T0316 199 :I 1dv1A 137 :P T0316 202 :IGE 1dv1A 138 :LGD T0316 205 :KNFKNFLSNY 1dv1A 143 :DKNRAIAKRI T0316 215 :LPA 1dv1A 154 :YPV T0316 221 :RMMT 1dv1A 157 :IIKA T0316 226 :DGRDMGEHAGLMYYTIG 1dv1A 197 :MVYMEKYLENPRHVEIQ T0316 322 :VHVK 1dv1A 214 :VLAD T0316 326 :GEKTEVIFAEPQRAITPGQAVVFYD 1dv1A 219 :QGNAIYLAERDCSMQRRHQKVVEEA Number of specific fragments extracted= 19 number of extra gaps= 0 total=838 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 1dv1A/T0316-1dv1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1dv1A/T0316-1dv1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dv1A read from 1dv1A/T0316-1dv1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dv1A in template set Warning: unaligning (T0316)D135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dv1A)M169 T0316 8 :RVVVG 1dv1A 4 :KIVIA T0316 14 :SGGVDSSVTALLLKEQGYDVIGIFMKNWDD 1dv1A 9 :NRGEIALRILRACKELGIKTVAVHSSADRD T0316 44 :TDEN 1dv1A 55 :PSVK T0316 52 :ATEDYKDVVAVADQIGIPYYSVNF 1dv1A 59 :SYLNIPAIISAAEITGAVAIHPGY T0316 76 :EKEYWDRVFE 1dv1A 88 :NANFAEQVER T0316 86 :YFLAEYRAGRTP 1dv1A 118 :SAIAAMKKAGVP T0316 98 :NPDVMCNKEIKFKAFLDYAITLGAD 1dv1A 131 :VPGSDGPLGDDMDKNRAIAKRIGYP T0316 130 :ARVAR 1dv1A 156 :VIIKA T0316 138 :GTVHMLRGV 1dv1A 220 :GNAIYLAER T0316 147 :DNGKDQTYF 1dv1A 234 :RRHQKVVEE T0316 156 :LSQLSQEQLQKTM 1dv1A 245 :APGITPELRRYIG T0316 177 :PEVRRLAEEAGL 1dv1A 258 :ERCAKACVDIGY T0316 195 :DSTGICFI 1dv1A 280 :ENGEFYFI T0316 221 :RMMTV 1dv1A 288 :EMNTR T0316 245 :GGLGIGG 1dv1A 319 :QPLSIKQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=853 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0316-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v4vA expands to /projects/compbio/data/pdb/1v4v.pdb.gz 1v4vA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1535, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 1686, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2254, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 2256, because occupancy 0.500 <= existing 0.500 in 1v4vA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2836, because occupancy 0.500 <= existing 0.500 in 1v4vA Skipped atom 2838, because occupancy 0.500 <= existing 0.500 in 1v4vA # T0316 read from 1v4vA/T0316-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0316-1v4vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v4vA to template set # found chain 1v4vA in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1v4vA)G4 T0316 6 :KTRVVVGM 1v4vA 5 :MKRVVLAF T0316 19 :SSVTALLLKE 1v4vA 21 :MAPVYLALRG T0316 29 :QGYDVIGIFM 1v4vA 32 :PGLKPLVLLT T0316 46 :ENG 1v4vA 42 :GQH T0316 56 :YKDVVAVADQIGIPY 1v4vA 45 :REQLRQALSLFGIQE T0316 71 :YSVNFE 1v4vA 61 :RNLDVM T0316 77 :KEYW 1v4vA 73 :PDLA T0316 105 :KEI 1v4vA 77 :ARI T0316 109 :FKAFLDYAITLGADYVATG 1v4vA 80 :LPQAARALKEMGADYVLVH T0316 137 :DG 1v4vA 99 :GD T0316 139 :TVHMLRGVDNGK 1v4vA 199 :PYVTVTMHRREN T0316 153 :TYFLSQLSQ 1v4vA 211 :WPLLSDLAQ T0316 163 :QLQKTMFPLGHL 1v4vA 220 :ALKRVAEAFPHL T0316 175 :EKPEVRRLAEEA 1v4vA 239 :LNPVVREAVFPV T0316 187 :GLS 1v4vA 253 :GVR T0316 220 :GRM 1v4vA 293 :GVP T0316 272 :LYVGQG 1v4vA 296 :VVVLRN T0316 278 :FYHDSLMST 1v4vA 303 :TERPEGLKA Number of specific fragments extracted= 18 number of extra gaps= 0 total=871 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0316-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1v4vA/T0316-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0316-1v4vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4vA in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1v4vA)G4 T0316 6 :KTRVVVGM 1v4vA 5 :MKRVVLAF T0316 19 :SSVTALLLKEQ 1v4vA 21 :MAPVYLALRGI T0316 30 :GYDVIGIFM 1v4vA 33 :GLKPLVLLT T0316 48 :GV 1v4vA 42 :GQ T0316 52 :A 1v4vA 44 :H T0316 56 :YKDVVAVADQIGIPY 1v4vA 45 :REQLRQALSLFGIQE T0316 71 :YSVNFE 1v4vA 61 :RNLDVM T0316 88 :LAEYRA 1v4vA 72 :LPDLAA T0316 106 :EIK 1v4vA 78 :RIL T0316 110 :KAFLDYAITLGADYVATG 1v4vA 81 :PQAARALKEMGADYVLVH T0316 129 :YARV 1v4vA 120 :HVEA T0316 133 :ARDEDGT 1v4vA 127 :SGNLKEP T0316 140 :VHMLRGV 1v4vA 289 :GAALGVP T0316 154 :YFLSQLSQEQLQKT 1v4vA 298 :VLRNVTERPEGLKA T0316 168 :MFPLGHLEKPEVRRLAEEA 1v4vA 313 :ILKLAGTDPEGVYRVVKGL Number of specific fragments extracted= 15 number of extra gaps= 0 total=886 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4vA/T0316-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1v4vA/T0316-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4vA read from 1v4vA/T0316-1v4vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4vA in template set T0316 6 :KTRVVVGMSGG 1v4vA 5 :MKRVVLAFGTR T0316 17 :VDSSVTALLLKE 1v4vA 19 :TKMAPVYLALRG T0316 29 :QGYDVIGIFM 1v4vA 32 :PGLKPLVLLT T0316 53 :TEDYKDVVAVADQIGIPY 1v4vA 42 :GQHREQLRQALSLFGIQE T0316 71 :YSVNF 1v4vA 61 :RNLDV T0316 76 :EKEYWDRVFEYFLAEYRAGRTPNPDVM 1v4vA 72 :LPDLAARILPQAARALKEMGADYVLVH T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARV 1v4vA 99 :GDTLTTFAVAWAAFLEGIPVGHVEAGLRS T0316 134 :RDEDGT 1v4vA 128 :GNLKEP T0316 158 :QLSQEQLQKTMF 1v4vA 134 :FPEEANRRLTDV T0316 175 :EKPEVRRLAEEAGLST 1v4vA 153 :PTPLAKANLLKEGKRE T0316 197 :TGICFIGE 1v4vA 169 :EGILVTGQ T0316 207 :FKNFLSNYLPAQPG 1v4vA 181 :AVLLAAKLGRLPEG T0316 255 :GDNAP 1v4vA 195 :LPEGP T0316 271 :ILYVG 1v4vA 200 :YVTVT T0316 276 :QGFYHDSLM 1v4vA 206 :HRRENWPLL Number of specific fragments extracted= 15 number of extra gaps= 0 total=901 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gsoA/T0316-1gsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gsoA expands to /projects/compbio/data/pdb/1gso.pdb.gz 1gsoA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2180, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2513, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2515, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2517, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2519, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2521, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2523, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2900, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2902, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2904, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2906, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2908, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2910, because occupancy 0.500 <= existing 0.500 in 1gsoA Skipped atom 2912, because occupancy 0.500 <= existing 0.500 in 1gsoA # T0316 read from 1gsoA/T0316-1gsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gsoA read from 1gsoA/T0316-1gsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gsoA to template set # found chain 1gsoA in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1gsoA)E-2 Warning: unaligning (T0316)T240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gsoA)K153 Warning: unaligning (T0316)L247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gsoA)K153 T0316 6 :KTRVVVGMSGGVD 1gsoA -1 :FMKVLVIGNGGRE T0316 20 :SVTALLL 1gsoA 13 :HALAWKA T0316 29 :QGYD 1gsoA 20 :AQSP T0316 33 :VIGIFMKNWDDTDENGVC 1gsoA 25 :VETVFVAPGNAGTALEPA T0316 70 :YYSVNFE 1gsoA 43 :LQNVAIG T0316 94 :GR 1gsoA 50 :VT T0316 108 :KFKAFLDYAITLGADYVATGHYARV 1gsoA 52 :DIPALLDFAQNEKIDLTIVGPEAPL T0316 134 :RDE 1gsoA 77 :VKG T0316 139 :TVHMLRGVDNGK 1gsoA 88 :GLKIFGPTAGAA T0316 161 :QEQL 1gsoA 100 :QLEG T0316 175 :EKPEVRRLAEEAGLSTAKKK 1gsoA 104 :SKAFTKDFLARHKIPTAEYQ T0316 200 :CFIGEKNFKNFLSNYL 1gsoA 124 :NFTEVEPALAYLREKG T0316 234 :AGLMYY 1gsoA 140 :APIVIK T0316 248 :GIGGQHG 1gsoA 154 :GVIVAMT T0316 286 :TSLEASQVHFTREM 1gsoA 161 :LEEAEAAVHDMLAG T0316 300 :PEEFTLECTAKFRYRQPD 1gsoA 177 :FGDAGHRIVIEEFLDGEE T0316 343 :GQAVVFYDGEECLGGGLI 1gsoA 195 :ASFIVMVDGEHVLPMATS T0316 361 :DNAYRDGQVCQY 1gsoA 216 :KRVGDKDTGPNT Number of specific fragments extracted= 18 number of extra gaps= 0 total=919 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gsoA/T0316-1gsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gsoA/T0316-1gsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gsoA read from 1gsoA/T0316-1gsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gsoA in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1gsoA)E-2 Warning: unaligning (T0316)K265 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gsoA)K153 Warning: unaligning (T0316)L272 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gsoA)K153 T0316 6 :KTRVVVGMSGGVDSSVTALL 1gsoA -1 :FMKVLVIGNGGREHALAWKA T0316 29 :QGYD 1gsoA 20 :AQSP T0316 33 :VIGIFMKNWD 1gsoA 25 :VETVFVAPGN T0316 50 :CT 1gsoA 46 :VA T0316 52 :ATEDYKDVVAVADQIGIPYYSV 1gsoA 49 :GVTDIPALLDFAQNEKIDLTIV T0316 103 :CNKEIKFKAFLDYAITLGADY 1gsoA 71 :GPEAPLVKGVVDTFRAAGLKI T0316 126 :T 1gsoA 92 :F T0316 134 :RDEDGTVHML 1gsoA 93 :GPTAGAAQLE T0316 161 :Q 1gsoA 103 :G T0316 175 :EKPEVRRLAEEAGLSTAK 1gsoA 104 :SKAFTKDFLARHKIPTAE T0316 198 :GICFIGEKNFKNFLSNYL 1gsoA 122 :YQNFTEVEPALAYLREKG T0316 257 :NA 1gsoA 140 :AP T0316 261 :FVVG 1gsoA 142 :IVIK T0316 273 :YVGQGFYHDSLMSTS 1gsoA 154 :GVIVAMTLEEAEAAV T0316 293 :VHFTREMPE 1gsoA 169 :HDMLAGNAF T0316 302 :EFTLECTAKFRYRQPDSKVTVHVKGEKTEVIFA 1gsoA 179 :DAGHRIVIEEFLDGEEASFIVMVDGEHVLPMAT T0316 335 :EPQRAITPGQ 1gsoA 213 :QDHKRVGDKD T0316 350 :DGEECLGG 1gsoA 223 :TGPNTGGM T0316 358 :GLIDNAYRDGQVC 1gsoA 232 :AYSPAPVVTDDVH Number of specific fragments extracted= 19 number of extra gaps= 0 total=938 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gsoA/T0316-1gsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gsoA/T0316-1gsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gsoA read from 1gsoA/T0316-1gsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gsoA in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1gsoA)E-2 Warning: unaligning (T0316)G264 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gsoA)K153 Warning: unaligning (T0316)S285 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gsoA)K153 T0316 6 :KTRVVVGMSGGVDSSVTALL 1gsoA -1 :FMKVLVIGNGGREHALAWKA T0316 28 :EQGYDVIGIFMKNWDD 1gsoA 20 :AQSPLVETVFVAPGNA T0316 49 :VCTATEDYKDVVAVADQIGIPYYSVNFEKEY 1gsoA 46 :VAIGVTDIPALLDFAQNEKIDLTIVGPEAPL T0316 109 :FKAFLDYAITLGADYVAT 1gsoA 77 :VKGVVDTFRAAGLKIFGP T0316 147 :DNGKDQTY 1gsoA 95 :TAGAAQLE T0316 175 :EKPEVRRLAEEAGLSTAKKKD 1gsoA 104 :SKAFTKDFLARHKIPTAEYQN T0316 201 :FIGEKNFKNFLSNY 1gsoA 125 :FTEVEPALAYLREK T0316 257 :NAPWFVV 1gsoA 139 :GAPIVIK T0316 286 :TSLEASQ 1gsoA 154 :GVIVAMT T0316 294 :HFTREMPEE 1gsoA 170 :DMLAGNAFG T0316 315 :QPDSKVTVH 1gsoA 179 :DAGHRIVIE T0316 333 :FAEPQRA 1gsoA 189 :FLDGEEA T0316 344 :QAVVFYDGEECLGGGLID 1gsoA 196 :SFIVMVDGEHVLPMATSQ T0316 362 :NAYRDGQVCQY 1gsoA 216 :KRVGDKDTGPN Number of specific fragments extracted= 14 number of extra gaps= 0 total=952 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c78A/T0316-2c78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c78A expands to /projects/compbio/data/pdb/2c78.pdb.gz 2c78A:# T0316 read from 2c78A/T0316-2c78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c78A read from 2c78A/T0316-2c78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c78A to template set # found chain 2c78A in template set Warning: unaligning (T0316)R365 because last residue in template chain is (2c78A)E405 T0316 5 :SKTRVVVGMS 2c78A 98 :QMDGAILVVS T0316 19 :SSVTALLLKEQGYD 2c78A 116 :TREHILLARQVGVP T0316 33 :VIGIFM 2c78A 131 :IVVFMN T0316 46 :ENGVCTATEDY 2c78A 137 :KVDMVDDPELL T0316 57 :KDVVAVADQIGIP 2c78A 152 :MEVRDLLNQYEFP T0316 70 :YYSVNFE 2c78A 168 :VPVIRGS T0316 84 :FEYFLAEYRA 2c78A 175 :ALLALEQMHR T0316 94 :GRTPNP 2c78A 186 :PKTRRG T0316 104 :NKEI 2c78A 192 :ENEW T0316 109 :FKAFLDYAITL 2c78A 196 :VDKIWELLDAI T0316 131 :RVARD 2c78A 207 :DEYIP T0316 137 :DG 2c78A 212 :TP T0316 139 :TVHMLRG 2c78A 239 :TGRIERG T0316 192 :KKKDSTGICFIGE 2c78A 246 :KVKVGDEVEIVGL T0316 218 :QPGRMMTV 2c78A 259 :APETRKTV T0316 226 :DGRDMGEH 2c78A 273 :HRKTLQEG T0316 234 :AG 2c78A 282 :AG T0316 236 :LMYYTIGQRG 2c78A 286 :VGVLLRGVSR T0316 246 :GL 2c78A 297 :EV T0316 248 :GIGGQHGGD 2c78A 302 :QVLAKPGSI T0316 263 :VGKDLSKNILYVGQG 2c78A 311 :TPHTKFEASVYVLKK T0316 298 :EMPEEFTLECTAKFRYRQPDSKVTVHVKGE 2c78A 329 :GRHTGFFSGYRPQFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAEPQR 2c78A 369 :TFTVELIKPVA T0316 340 :ITPGQAVVFYDGEECLGGGLIDNAY 2c78A 380 :LEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 24 number of extra gaps= 0 total=976 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c78A/T0316-2c78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2c78A/T0316-2c78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c78A read from 2c78A/T0316-2c78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c78A in template set T0316 6 :KTRVVVGMS 2c78A 99 :MDGAILVVS T0316 19 :SSVTALLLKEQGYD 2c78A 116 :TREHILLARQVGVP T0316 33 :VIGIFM 2c78A 131 :IVVFMN T0316 46 :ENGVCTATEDYKD 2c78A 137 :KVDMVDDPELLDL T0316 59 :VVAVADQIGIP 2c78A 154 :VRDLLNQYEFP T0316 70 :YYSVNFE 2c78A 168 :VPVIRGS T0316 109 :FKAFLDYAIT 2c78A 175 :ALLALEQMHR T0316 134 :R 2c78A 185 :N T0316 154 :YFLSQLSQEQL 2c78A 186 :PKTRRGENEWV T0316 177 :PEVRRLAEEAG 2c78A 197 :DKIWELLDAID T0316 188 :LSTAKKK 2c78A 210 :IPTPVRD T0316 195 :DSTGICFIG 2c78A 218 :DKPFLMPVE T0316 221 :RMMTV 2c78A 227 :DVFTI T0316 226 :DGRDMGEHAGLMYYTIGQR 2c78A 252 :EVEIVGLAPETRKTVVTGV T0316 245 :GGL 2c78A 275 :KTL T0316 255 :GDNA 2c78A 278 :QEGI T0316 259 :PWFVVGK 2c78A 286 :VGVLLRG T0316 266 :DLSKNILYVGQGFY 2c78A 297 :EVERGQVLAKPGSI T0316 300 :PEEFTLECTA 2c78A 311 :TPHTKFEASV T0316 310 :KFRYRQPDSKVTVHVKGE 2c78A 341 :QFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAE 2c78A 369 :TFTVELIK T0316 337 :QRAITPGQAVVFYDGEECLGGGLID 2c78A 377 :PVALEEGLRFAIREGGRTVGAGVVT Number of specific fragments extracted= 22 number of extra gaps= 0 total=998 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c78A/T0316-2c78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2c78A/T0316-2c78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c78A read from 2c78A/T0316-2c78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c78A in template set T0316 7 :TRVVVGMSG 2c78A 100 :DGAILVVSA T0316 17 :VDSSVTALLLKEQGYDVIGIFMKNWDD 2c78A 114 :PQTREHILLARQVGVPYIVVFMNKVDM T0316 44 :TDE 2c78A 142 :DDP T0316 52 :ATEDYKDVVAVADQIGIP 2c78A 147 :LDLVEMEVRDLLNQYEFP T0316 71 :YSVNFEKEYWDRVFE 2c78A 170 :VIRGSALLALEQMHR T0316 98 :NPDVMCNKEI 2c78A 185 :NPKTRRGENE T0316 108 :KFKAFLDYAIT 2c78A 198 :KIWELLDAIDE T0316 121 :AD 2c78A 217 :VD T0316 130 :AR 2c78A 222 :LM T0316 132 :VARDEDGTVHMLRGVDNG 2c78A 228 :VFTITGRGTVATGRIERG T0316 192 :KKKDSTGICFIGE 2c78A 246 :KVKVGDEVEIVGL T0316 214 :YLPAQPGRMMT 2c78A 259 :APETRKTVVTG T0316 225 :VDGRDMGEHAGLMYYTI 2c78A 272 :MHRKTLQEGIAGDNVGV T0316 243 :QRGGLGIGG 2c78A 289 :LLRGVSREE T0316 267 :LSKNILYVGQGF 2c78A 298 :VERGQVLAKPGS T0316 285 :STS 2c78A 313 :HTK T0316 288 :LEASQVHFTREMPEEFTL 2c78A 323 :LKKEEGGRHTGFFSGYRP T0316 310 :KFRYRQPDSKVTVHVKGEK 2c78A 341 :QFYFRTTDVTGVVQLPPGV T0316 329 :TEVIFAEPQ 2c78A 370 :FTVELIKPV T0316 339 :AITPGQAVVFYDGEECLGGGLIDNAY 2c78A 379 :ALEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 20 number of extra gaps= 0 total=1018 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc8A/T0316-1uc8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uc8A expands to /projects/compbio/data/pdb/1uc8.pdb.gz 1uc8A:Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X # T0316 read from 1uc8A/T0316-1uc8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc8A read from 1uc8A/T0316-1uc8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uc8A to template set # found chain 1uc8A in template set Warning: unaligning (T0316)V124 because of BadResidue code BAD_PEPTIDE in next template residue (1uc8A)N78 Warning: unaligning (T0316)Y129 because of BadResidue code BAD_PEPTIDE at template residue (1uc8A)N78 Warning: unaligning (T0316)K192 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X145 Warning: unaligning (T0316)K193 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X146 Warning: unaligning (T0316)K194 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X147 Warning: unaligning (T0316)D195 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X148 Warning: unaligning (T0316)S196 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X149 Warning: unaligning (T0316)T197 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X150 Warning: unaligning (T0316)G198 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X151 Warning: unaligning (T0316)I199 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X152 Warning: unaligning (T0316)C200 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X153 Warning: unaligning (T0316)F201 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X154 Warning: unaligning (T0316)Q218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uc8A)G160 Warning: unaligning (T0316)G275 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uc8A)A209 T0316 34 :IGIFM 1uc8A 2 :LAILY T0316 46 :E 1uc8A 7 :D T0316 48 :G 1uc8A 8 :R T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFEK 1uc8A 9 :IRPDERMLFERAEALGLPYKKVYVPA T0316 93 :AGRTPNPD 1uc8A 39 :LGERPKEL T0316 101 :VMCNKEIKFKAFLDYAITLGADY 1uc8A 54 :ERCVSQSRGLAAARYLTALGIPV T0316 130 :ARVARD 1uc8A 79 :RPEVIE T0316 148 :NGKDQTYFLSQLSQEQL 1uc8A 85 :ACGDKWATSVALAKAGL T0316 174 :LEKPEVRRLAEEAGLS 1uc8A 110 :TDREEALRLMEAFGYP T0316 190 :T 1uc8A 131 :V T0316 232 :EHAGLMY 1uc8A 161 :FQHQLFY T0316 249 :IGGQHGGDNAPWFVVGKDLSKNILYV 1uc8A 168 :IQEYVEKPGRDIRVFVVGERAIAAIY T0316 278 :FYHDSLMSTSLEASQV 1uc8A 213 :PLTEEVARLSVKAAEA T0316 296 :TR 1uc8A 229 :VG T0316 342 :PGQAVV 1uc8A 231 :GGVVAV T0316 348 :FY 1uc8A 238 :LF T0316 350 :DGEECLGG 1uc8A 242 :ERGLLVNE Number of specific fragments extracted= 17 number of extra gaps= 2 total=1035 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc8A/T0316-1uc8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1uc8A/T0316-1uc8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc8A read from 1uc8A/T0316-1uc8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uc8A in template set Warning: unaligning (T0316)V124 because of BadResidue code BAD_PEPTIDE in next template residue (1uc8A)N78 Warning: unaligning (T0316)D135 because of BadResidue code BAD_PEPTIDE at template residue (1uc8A)N78 Warning: unaligning (T0316)K193 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X141 Warning: unaligning (T0316)K194 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X142 Warning: unaligning (T0316)D195 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X143 Warning: unaligning (T0316)S196 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X144 Warning: unaligning (T0316)T197 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X146 Warning: unaligning (T0316)G198 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X147 Warning: unaligning (T0316)I199 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X148 Warning: unaligning (T0316)C200 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X149 Warning: unaligning (T0316)F201 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X150 Warning: unaligning (T0316)I202 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X151 Warning: unaligning (T0316)G203 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X152 Warning: unaligning (T0316)Q276 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X153 Warning: unaligning (T0316)G277 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X154 Warning: unaligning (T0316)E301 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uc8A)G160 Warning: unaligning (T0316)A334 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uc8A)A209 T0316 34 :IGIFM 1uc8A 2 :LAILY T0316 46 :EN 1uc8A 7 :DR T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFEK 1uc8A 9 :IRPDERMLFERAEALGLPYKKVYVPA T0316 92 :RAGRTPNPD 1uc8A 38 :VLGERPKEL T0316 101 :VMCNKEIKFKAFLDYAITLGADY 1uc8A 54 :ERCVSQSRGLAAARYLTALGIPV T0316 136 :EDGTVHMLR 1uc8A 79 :RPEVIEACG T0316 156 :LSQLSQEQLQKTMFPLGH 1uc8A 88 :DKWATSVALAKAGLPQPK T0316 174 :LEKPEVRRLAEEAGL 1uc8A 110 :TDREEALRLMEAFGY T0316 189 :STAK 1uc8A 130 :PVIG Warning: shrinking fragment to make legal peptide bond T0316 302 :EFTLECTAKFRYRQPDSKVTVHVKGEK 1uc8A 161 :FQHQLFYIQEYVEKPGRDIRVFVVGER T0316 329 :TEVIF 1uc8A 189 :IAAIY Number of specific fragments extracted= 11 number of extra gaps= 3 total=1046 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc8A/T0316-1uc8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1uc8A/T0316-1uc8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc8A read from 1uc8A/T0316-1uc8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uc8A in template set Warning: unaligning (T0316)V124 because of BadResidue code BAD_PEPTIDE in next template residue (1uc8A)N78 Warning: unaligning (T0316)L159 because of BadResidue code BAD_PEPTIDE at template residue (1uc8A)N78 Warning: unaligning (T0316)T286 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X141 Warning: unaligning (T0316)S287 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X142 Warning: unaligning (T0316)L288 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X143 Warning: unaligning (T0316)E289 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X144 Warning: unaligning (T0316)A290 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X145 Warning: unaligning (T0316)S291 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X146 Warning: unaligning (T0316)Q292 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X147 Warning: unaligning (T0316)V293 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X148 Warning: unaligning (T0316)H294 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X149 Warning: unaligning (T0316)F295 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X150 Warning: unaligning (T0316)T296 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X151 Warning: unaligning (T0316)R297 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X152 Warning: unaligning (T0316)E298 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X153 Warning: unaligning (T0316)M299 because of BadResidue code NON_STANDARD_RESIDUE at template residue (1uc8A)X154 Warning: unaligning (T0316)E335 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uc8A)A209 T0316 9 :VVVGMS 1uc8A 2 :LAILYD T0316 51 :TATEDYKDVVAVADQIGIPYYSVNFEK 1uc8A 8 :RIRPDERMLFERAEALGLPYKKVYVPA T0316 93 :AGRTPNPD 1uc8A 39 :LGERPKEL T0316 101 :VMCNKEIKFKAFLDYAITLGADY 1uc8A 54 :ERCVSQSRGLAAARYLTALGIPV T0316 160 :SQEQLQKTM 1uc8A 79 :RPEVIEACG T0316 175 :EKPEVRRLAEEAGLSTAK 1uc8A 88 :DKWATSVALAKAGLPQPK T0316 199 :ICFIGE 1uc8A 106 :TALATD T0316 205 :KNFKNFLSNYL 1uc8A 113 :EEALRLMEAFG T0316 258 :APWFV 1uc8A 124 :YPVVL T0316 265 :KDL 1uc8A 129 :KPV T0316 284 :MS 1uc8A 132 :IG Warning: shrinking fragment to make legal peptide bond T0316 302 :EFTLECTAKFRYRQPDSKVTVHVKGEKTEVIFA 1uc8A 161 :FQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIY Number of specific fragments extracted= 12 number of extra gaps= 2 total=1058 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0316-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xg5A expands to /projects/compbio/data/pdb/1xg5.pdb.gz 1xg5A:Skipped atom 494, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 496, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 498, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 500, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 728, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 730, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 732, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 734, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 736, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 738, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1241, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 1xg5A Skipped atom 1769, because occupancy 0.350 <= existing 0.650 in 1xg5A Skipped atom 1771, because occupancy 0.350 <= existing 0.650 in 1xg5A # T0316 read from 1xg5A/T0316-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0316-1xg5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xg5A to template set # found chain 1xg5A in template set Warning: unaligning (T0316)V59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0316)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0316)Y71 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0316)S72 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0316)K193 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)C195 Warning: unaligning (T0316)C200 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)C195 Warning: unaligning (T0316)G203 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)G199 Warning: unaligning (T0316)E204 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)G199 T0316 5 :SKTRVVVG 1xg5A 10 :RDRLALVT T0316 14 :SGGV 1xg5A 20 :SGGI T0316 19 :SSVTALLLKEQGYDVIGIFM 1xg5A 24 :GAAVARALVQQGLKVVGCAR T0316 52 :ATEDYKD 1xg5A 44 :TVGNIEE T0316 61 :AVADQIGI 1xg5A 53 :AECKSAGY T0316 69 :PY 1xg5A 63 :TL T0316 73 :VNFE 1xg5A 67 :YRCD T0316 77 :KEYWDRVFEYFLAEY 1xg5A 74 :EEDILSMFSAIRSQH T0316 94 :GRT 1xg5A 89 :SGV T0316 105 :KEI 1xg5A 126 :SIC T0316 109 :FKAFLDYAITLGAD 1xg5A 129 :TREAYQSMKERNVD T0316 123 :YVATGHYARVARD 1xg5A 145 :HIININSMSGHRV T0316 137 :DG 1xg5A 158 :LP T0316 176 :KPEVRRLAEEAGLSTAK 1xg5A 177 :TEGLRQELREAQTHIRA T0316 201 :FI 1xg5A 196 :IS T0316 205 :KNFKNFLSNYLPAQP 1xg5A 200 :VVETQFAFKLHDKDP T0316 220 :G 1xg5A 245 :H Number of specific fragments extracted= 17 number of extra gaps= 4 total=1075 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0316-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1xg5A/T0316-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0316-1xg5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xg5A in template set Warning: unaligning (T0316)V59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0316)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0316)Y71 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0316)S72 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0316)F169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xg5A)C226 Warning: unaligning (T0316)H173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xg5A)C226 T0316 1 :MSDNSKTRVVVG 1xg5A 6 :MERWRDRLALVT T0316 14 :SGGV 1xg5A 20 :SGGI T0316 19 :SSVTALLLKEQGYDVIGIFM 1xg5A 24 :GAAVARALVQQGLKVVGCAR T0316 52 :ATEDYKD 1xg5A 44 :TVGNIEE T0316 61 :AVADQIGI 1xg5A 53 :AECKSAGY T0316 69 :PY 1xg5A 63 :TL T0316 73 :VNFE 1xg5A 67 :YRCD T0316 77 :KEYWDRVFEYFLAEY 1xg5A 74 :EEDILSMFSAIRSQH T0316 95 :RT 1xg5A 90 :GV T0316 103 :CNKE 1xg5A 124 :ALSI T0316 108 :KFKAFLDYAITLGAD 1xg5A 128 :CTREAYQSMKERNVD T0316 123 :YVATGHYARVARDEDGT 1xg5A 145 :HIININSMSGHRVLPLS T0316 151 :DQTYFLSQLSQEQLQKTM 1xg5A 204 :QFAFKLHDKDPEKAAATY T0316 174 :LEKPEVRRLAEEA 1xg5A 227 :LKPEDVAEAVIYV T0316 195 :DSTGICF 1xg5A 242 :TPAHIQI Number of specific fragments extracted= 15 number of extra gaps= 2 total=1090 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg5A/T0316-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1xg5A/T0316-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xg5A read from 1xg5A/T0316-1xg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xg5A in template set Warning: unaligning (T0316)V59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xg5A)A52 Warning: unaligning (T0316)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xg5A)A52 Warning: unaligning (T0316)Y71 because of BadResidue code BAD_PEPTIDE in next template residue (1xg5A)P66 Warning: unaligning (T0316)S72 because of BadResidue code BAD_PEPTIDE at template residue (1xg5A)P66 Warning: unaligning (T0316)F169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xg5A)C226 Warning: unaligning (T0316)H173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xg5A)C226 T0316 3 :DNSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIF 1xg5A 8 :RWRDRLALVTGASGGIGAAVARALVQQGLKVVGCA T0316 51 :TATEDYKD 1xg5A 43 :RTVGNIEE T0316 61 :AVADQIGIP 1xg5A 53 :AECKSAGYP T0316 70 :Y 1xg5A 64 :L T0316 73 :VNF 1xg5A 67 :YRC T0316 76 :EKEYWDRVFEYFLAEY 1xg5A 73 :NEEDILSMFSAIRSQH T0316 96 :TPNPDVM 1xg5A 100 :LARPDTL T0316 107 :IKFKAFLDYAITLGAD 1xg5A 127 :ICTREAYQSMKERNVD T0316 123 :YVATGHYARVARDE 1xg5A 146 :IININSMSGHRVLP T0316 150 :KDQTYFLSQLSQEQLQKTM 1xg5A 203 :TQFAFKLHDKDPEKAAATY T0316 174 :LEKPEVRRLAEEA 1xg5A 227 :LKPEDVAEAVIYV Number of specific fragments extracted= 11 number of extra gaps= 2 total=1101 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czcA/T0316-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2czcA expands to /projects/compbio/data/pdb/2czc.pdb.gz 2czcA:# T0316 read from 2czcA/T0316-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0316-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2czcA to template set # found chain 2czcA in template set T0316 6 :KTRVVVG 2czcA 2 :KVKVGVN T0316 19 :SSVTALLLKE 2czcA 14 :GKRVAYAVTK T0316 29 :QGYDVIGIFM 2czcA 25 :DDMELIGITK T0316 47 :NG 2czcA 35 :TK T0316 52 :ATEDYKDVV 2czcA 37 :PDFEAYRAK T0316 65 :QIGIPYYS 2czcA 46 :ELGIPVYA T0316 75 :FEKEYWDRVFEY 2czcA 54 :ASEEFIPRFEKE T0316 87 :FLAEYRA 2czcA 72 :TLNDLLE T0316 94 :GR 2czcA 89 :GG T0316 108 :KFKAFLDYAITLGADYVATGHYARVARD 2czcA 91 :IGAKNKPLYEKAGVKAIFQGGEKADVAE T0316 139 :TVHMLRGVDNGK 2czcA 243 :RVLLFEKEKGFD T0316 175 :EKPEVRRLAEEAGLSTAKK 2czcA 255 :STAQIIEFARDLHREWNNL T0316 197 :TGICFIGEK 2czcA 274 :YEIAVWKES T0316 322 :VHVKGEKTEVIF 2czcA 283 :INIKGNRLFYIQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1115 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czcA/T0316-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2czcA/T0316-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0316-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (2czcA)M1 T0316 8 :RVVVGMSG 2czcA 2 :KVKVGVNG T0316 16 :GVDSSVTALLLKEQ 2czcA 11 :GTIGKRVAYAVTKQ T0316 30 :GYDVIGIFM 2czcA 26 :DMELIGITK T0316 46 :EN 2czcA 35 :TK T0316 52 :ATEDYKDVV 2czcA 37 :PDFEAYRAK T0316 65 :QIGIPYYSV 2czcA 46 :ELGIPVYAA T0316 76 :EKEYWDRVFEYFL 2czcA 55 :SEEFIPRFEKEGF T0316 89 :AEYRAGR 2czcA 74 :NDLLEKV T0316 96 :TP 2czcA 87 :TP T0316 104 :NK 2czcA 89 :GG T0316 108 :KFKAFLDYAITLGADYVATGHYA 2czcA 91 :IGAKNKPLYEKAGVKAIFQGGEK T0316 134 :RDEDGT 2czcA 114 :ADVAEV T0316 167 :TMFPLGHL 2czcA 246 :LFEKEKGF T0316 175 :EKPEVRRLAEEAGLST 2czcA 255 :STAQIIEFARDLHREW T0316 195 :DS 2czcA 271 :NN T0316 197 :TGICFI 2czcA 274 :YEIAVW T0316 208 :KNFL 2czcA 280 :KESI T0316 323 :HVKGEKTEVIFA 2czcA 284 :NIKGNRLFYIQA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1133 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czcA/T0316-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2czcA/T0316-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0316-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set T0316 8 :RVVVGMSG 2czcA 2 :KVKVGVNG T0316 16 :GVDSSVTALLLKEQG 2czcA 11 :GTIGKRVAYAVTKQD T0316 31 :YDVIGIFMKNWD 2czcA 27 :MELIGITKTKPD T0316 57 :KDVVA 2czcA 39 :FEAYR T0316 63 :ADQIGIPYYSVN 2czcA 44 :AKELGIPVYAAS T0316 75 :FEKEYWDR 2czcA 58 :FIPRFEKE T0316 88 :LAEYRAGR 2czcA 73 :LNDLLEKV T0316 101 :VMCNKEIKFKAFLDYAITLGADYVATGH 2czcA 84 :VDATPGGIGAKNKPLYEKAGVKAIFQGG T0316 138 :GTVHMLRGVDN 2czcA 217 :HVHSVMVELKK T0316 158 :QLSQEQLQKTM 2czcA 228 :PLTKDDVIDIF T0316 169 :FPLGHLEKPEVRRLAEEAGLSTAKK 2czcA 249 :KEKGFDSTAQIIEFARDLHREWNNL T0316 197 :TGICFI 2czcA 274 :YEIAVW T0316 212 :SNYLP 2czcA 280 :KESIN T0316 324 :VKGEKTEVIF 2czcA 285 :IKGNRLFYIQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1147 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uluA/T0316-1uluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uluA expands to /projects/compbio/data/pdb/1ulu.pdb.gz 1uluA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0316 read from 1uluA/T0316-1uluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uluA read from 1uluA/T0316-1uluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uluA to template set # found chain 1uluA in template set Warning: unaligning (T0316)V146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uluA)F204 Warning: unaligning (T0316)S157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uluA)F204 T0316 5 :SKTRVVVG 1uluA 7 :SGKKALVM T0316 19 :SSVTALLLKEQGYD 1uluA 23 :GFAIAAKLKEAGAE T0316 34 :IGIFM 1uluA 37 :VALSY T0316 46 :E 1uluA 42 :Q T0316 52 :ATEDYKDVVAVADQIG 1uluA 43 :AERLRPEAEKLAEALG T0316 69 :PYYSVNFE 1uluA 59 :GALLFRAD T0316 77 :KEYWDRVFEYFLAEY 1uluA 70 :DEELDALFAGVKEAF T0316 94 :GR 1uluA 85 :GG T0316 139 :TVHMLRG 1uluA 184 :RVNAISA T0316 158 :QLSQEQLQK 1uluA 205 :TKMYDRVAQ T0316 168 :MFPL 1uluA 214 :TAPL T0316 172 :GHLEKPEVRRLAEEA 1uluA 219 :RNITQEEVGNLGLFL T0316 188 :LSTAK 1uluA 235 :SPLAS T0316 194 :KDSTGICFI 1uluA 240 :GITGEVVYV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1161 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uluA/T0316-1uluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1uluA/T0316-1uluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uluA read from 1uluA/T0316-1uluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uluA in template set Warning: unaligning (T0316)V146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uluA)F204 Warning: unaligning (T0316)S157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uluA)F204 T0316 3 :DNSKTRVVVG 1uluA 5 :DLSGKKALVM T0316 19 :SSVTALLLKEQGYDVIGIFM 1uluA 23 :GFAIAAKLKEAGAEVALSYQ T0316 52 :ATEDYKDVVAVADQIG 1uluA 43 :AERLRPEAEKLAEALG T0316 68 :IPYYSVNF 1uluA 60 :ALLFRADV T0316 77 :KEYWDRVFEYFL 1uluA 70 :DEELDALFAGVK T0316 89 :AEYRAGR 1uluA 99 :REAMEGR T0316 100 :DVMCNKE 1uluA 106 :YIDTRRQ T0316 108 :KFKAFLDYAITL 1uluA 113 :DWLLALEVSAYS T0316 123 :YVATGHYARVARDEDGT 1uluA 141 :GIVTLTYYASEKVVPKY T0316 144 :RG 1uluA 191 :GP T0316 158 :QLSQEQLQKTMFPLGHLEKPEVRRLAEEA 1uluA 205 :TKMYDRVAQTAPLRRNITQEEVGNLGLFL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1172 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uluA/T0316-1uluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1uluA/T0316-1uluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uluA read from 1uluA/T0316-1uluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uluA in template set T0316 5 :SKTRVVVG 1uluA 7 :SGKKALVM T0316 18 :DSSVTALLLKEQGYDVIGIF 1uluA 22 :LGFAIAAKLKEAGAEVALSY T0316 51 :TATEDYKDVVAVADQIG 1uluA 42 :QAERLRPEAEKLAEALG T0316 68 :IPYYSVNF 1uluA 60 :ALLFRADV T0316 76 :EKEYWDRVFEYFLAEY 1uluA 69 :QDEELDALFAGVKEAF T0316 97 :PNP 1uluA 96 :FAP T0316 104 :NKEIKFKAFLDYAIT 1uluA 109 :TRRQDWLLALEVSAY T0316 120 :GADYVATGHYARVARDED 1uluA 139 :GGGIVTLTYYASEKVVPK T0316 160 :SQEQLQKTMFPLGHLEKPEVRRLAEEAGLSTAK 1uluA 207 :MYDRVAQTAPLRRNITQEEVGNLGLFLLSPLAS T0316 194 :KDSTGICFIGE 1uluA 240 :GITGEVVYVDA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1182 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0316-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wyuA expands to /projects/compbio/data/pdb/1wyu.pdb.gz 1wyuA:# T0316 read from 1wyuA/T0316-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0316-1wyuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wyuA to template set # found chain 1wyuA in template set T0316 21 :VTALLLKEQGYD 1wyuA 140 :GVLLALRETGRM T0316 34 :IGIFM 1wyuA 152 :GVLVS T0316 47 :NGV 1wyuA 157 :QGV T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1wyuA 160 :HPEYRAVLRAYLEAVGAKLLTLPLE T0316 93 :AGRTPNPD 1wyuA 185 :GGRTPLPE T0316 101 :VMCNKEIKFKAFLDYAITLGADYVATGHYARVARD 1wyuA 206 :NFLGALEDLGPFAEAAHGAGALFVAVADPLSLGVL T0316 137 :DG 1wyuA 241 :KP T0316 139 :TVHMLRGVDNGKDQ 1wyuA 296 :RRGFILTLQAREQY T0316 153 :TYFLSQLSQEQLQKTM 1wyuA 331 :AMYLAALGPEGLREVA T0316 177 :PEVRRLAEEA 1wyuA 347 :LKSVEMAHKL T0316 187 :GLS 1wyuA 365 :GVR T0316 190 :TAKKKDSTGICFIGEKNFKNFLSNYLPA 1wyuA 369 :FTPKPFFNEFALALPKDPEAVRRALAER T0316 220 :GRM 1wyuA 397 :GFH T0316 248 :GIGGQHGGDNAPWFVVGKDL 1wyuA 400 :GATPVPREYGENLALFAATE T0316 278 :FYHDSLMSTSLEASQV 1wyuA 421 :HEEEDLLALREALKEV Number of specific fragments extracted= 15 number of extra gaps= 0 total=1197 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0316-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wyuA/T0316-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0316-1wyuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuA in template set T0316 21 :VTALLLKEQGYD 1wyuA 140 :GVLLALRETGRM T0316 35 :GIFM 1wyuA 152 :GVLV T0316 46 :ENGV 1wyuA 156 :SQGV T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1wyuA 160 :HPEYRAVLRAYLEAVGAKLLTLPLE T0316 93 :AGRTPNPD 1wyuA 185 :GGRTPLPE T0316 104 :N 1wyuA 210 :A T0316 106 :EIKFKAFLDYAITLGADYVATGHYARV 1wyuA 211 :LEDLGPFAEAAHGAGALFVAVADPLSL T0316 153 :TYFLSQLSQEQLQKTM 1wyuA 331 :AMYLAALGPEGLREVA T0316 177 :PEVRRLAEEA 1wyuA 347 :LKSVEMAHKL T0316 187 :GL 1wyuA 365 :GV T0316 189 :STAKKKDSTGICFIGEKNFKNFLSNYLPA 1wyuA 368 :PFTPKPFFNEFALALPKDPEAVRRALAER T0316 220 :GRMMTVDG 1wyuA 397 :GFHGATPV T0316 252 :QHGGDNAPWFVVGKD 1wyuA 405 :PREYGENLALFAATE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1210 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wyuA/T0316-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1wyuA/T0316-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wyuA read from 1wyuA/T0316-1wyuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wyuA in template set T0316 20 :SVTALLLKEQGYD 1wyuA 139 :EGVLLALRETGRM T0316 35 :GIFMKNW 1wyuA 152 :GVLVSQG T0316 51 :TATEDYKDVVAVADQIGIPYYSVNFE 1wyuA 159 :VHPEYRAVLRAYLEAVGAKLLTLPLE T0316 93 :AGRTPNPDV 1wyuA 185 :GGRTPLPEV T0316 102 :MCNKEIKFKAFLDYAITLGADYVATGHYARVA 1wyuA 207 :FLGALEDLGPFAEAAHGAGALFVAVADPLSLG T0316 152 :QTYFLSQLSQEQLQKTM 1wyuA 330 :GAMYLAALGPEGLREVA T0316 177 :PEVRRLAEEA 1wyuA 347 :LKSVEMAHKL T0316 187 :GLS 1wyuA 365 :GVR T0316 190 :TAKKKDSTGICFIGEKNFKNFLSNY 1wyuA 369 :FTPKPFFNEFALALPKDPEAVRRAL T0316 245 :GGLGIG 1wyuA 396 :RGFHGA T0316 251 :GQHGGDNAPWFVVG 1wyuA 403 :PVPREYGENLALFA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1221 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bw0A/T0316-2bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bw0A expands to /projects/compbio/data/pdb/2bw0.pdb.gz 2bw0A:# T0316 read from 2bw0A/T0316-2bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bw0A read from 2bw0A/T0316-2bw0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bw0A to template set # found chain 2bw0A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (2bw0A)Q-2 Warning: unaligning (T0316)K6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2bw0A)M1 Warning: unaligning (T0316)T7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2bw0A)M1 Warning: unaligning (T0316)N47 because of BadResidue code BAD_PEPTIDE in next template residue (2bw0A)D36 Warning: unaligning (T0316)G48 because of BadResidue code BAD_PEPTIDE at template residue (2bw0A)D36 T0316 8 :RVVVG 2bw0A 2 :KIAVI T0316 19 :SSVTALLLKEQGYDVIGIFM 2bw0A 12 :GQEVYCHLRKEGHEVVGVFT T0316 44 :TDE 2bw0A 32 :VPD T0316 49 :VC 2bw0A 37 :GK T0316 56 :YKDVVAVADQIGIPYYSVN 2bw0A 39 :ADPLGLEAEKDGVPVFKYS T0316 94 :GR 2bw0A 62 :KG T0316 102 :MCNKEI 2bw0A 64 :QALPDV T0316 113 :LDYAITLGADYVATGHYAR 2bw0A 70 :VAKYQALGAELNVLPFCSQ T0316 137 :D 2bw0A 89 :F T0316 139 :TVHM 2bw0A 148 :LQKE T0316 144 :RGVDNGK 2bw0A 152 :CEVLPDD T0316 155 :FLSQLSQEQL 2bw0A 159 :TVSTLYNRFL T0316 176 :KPEVRRLAEEA 2bw0A 169 :FPEGIKGMVQA T0316 187 :G 2bw0A 186 :G T0316 188 :LSTAKKKDSTGI 2bw0A 188 :APRLPQPEEGAT T0316 202 :IGEKNFKNFLSNYLPA 2bw0A 200 :YEGIQKKETAKINWDQ T0316 220 :GRMMTVDGRDMGEHA 2bw0A 232 :GAWTEACEQKLTFFN T0316 240 :TIGQRGGLGIGGQHGG 2bw0A 251 :TSGLVPEGDALPIPGA T0316 335 :EPQRAITPGQAVVFYDGEECLGGGLID 2bw0A 267 :HRPGVVTKAGLILFGNDDKMLLVKNIQ T0316 364 :YRDGQVCQ 2bw0A 294 :LEDGKMIL Number of specific fragments extracted= 20 number of extra gaps= 1 total=1241 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bw0A/T0316-2bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2bw0A/T0316-2bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bw0A read from 2bw0A/T0316-2bw0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bw0A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (2bw0A)Q-2 Warning: unaligning (T0316)K6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2bw0A)M1 Warning: unaligning (T0316)T7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2bw0A)M1 Warning: unaligning (T0316)D42 because of BadResidue code BAD_PEPTIDE in next template residue (2bw0A)D36 Warning: unaligning (T0316)D43 because of BadResidue code BAD_PEPTIDE at template residue (2bw0A)D36 Warning: unaligning (T0316)G187 because of BadResidue code BAD_PEPTIDE in next template residue (2bw0A)K229 Warning: unaligning (T0316)A217 because of BadResidue code BAD_PEPTIDE at template residue (2bw0A)K229 T0316 8 :RVVVG 2bw0A 2 :KIAVI T0316 19 :SSVTALLLKEQGYDVIGIFMKNW 2bw0A 12 :GQEVYCHLRKEGHEVVGVFTVPD T0316 44 :TD 2bw0A 37 :GK T0316 54 :E 2bw0A 40 :D T0316 58 :DVVAVADQIGIPYYSVN 2bw0A 41 :PLGLEAEKDGVPVFKYS T0316 75 :FE 2bw0A 59 :WR T0316 92 :RAGR 2bw0A 61 :AKGQ T0316 103 :CNKEI 2bw0A 65 :ALPDV T0316 113 :LDYAITLGADYVATGHYA 2bw0A 70 :VAKYQALGAELNVLPFCS T0316 134 :RDEDGT 2bw0A 88 :QFIPME T0316 140 :VHM 2bw0A 181 :RLI T0316 143 :LR 2bw0A 188 :AP T0316 145 :GVDNGKDQT 2bw0A 191 :LPQPEEGAT T0316 155 :FLSQLSQEQLQ 2bw0A 200 :YEGIQKKETAK T0316 172 :GHLEKPEVRRLAEEA 2bw0A 213 :WDQPAEAIHNWIRGN T0316 218 :QPGRMMTVDGR 2bw0A 230 :VPGAWTEACEQ T0316 235 :GLMYYTIG 2bw0A 241 :KLTFFNST T0316 243 :QRGGLGIGGQH 2bw0A 257 :EGDALPIPGAH T0316 336 :PQRAITPGQAVVFYDGEECLGG 2bw0A 268 :RPGVVTKAGLILFGNDDKMLLV Number of specific fragments extracted= 19 number of extra gaps= 2 total=1260 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bw0A/T0316-2bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2bw0A/T0316-2bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bw0A read from 2bw0A/T0316-2bw0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bw0A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (2bw0A)Q-2 Warning: unaligning (T0316)K6 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2bw0A)M1 Warning: unaligning (T0316)T7 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2bw0A)M1 Warning: unaligning (T0316)D42 because of BadResidue code BAD_PEPTIDE in next template residue (2bw0A)D36 Warning: unaligning (T0316)D43 because of BadResidue code BAD_PEPTIDE at template residue (2bw0A)D36 Warning: unaligning (T0316)A217 because of BadResidue code BAD_PEPTIDE at template residue (2bw0A)K229 T0316 8 :RVVVG 2bw0A 2 :KIAVI T0316 18 :DSSVTALLLKEQGYDVIGIFMKNW 2bw0A 11 :FGQEVYCHLRKEGHEVVGVFTVPD T0316 44 :TDEN 2bw0A 37 :GKAD T0316 58 :DVVAVADQIGIPYYSVNF 2bw0A 41 :PLGLEAEKDGVPVFKYSR T0316 104 :NKEIKFKAFLDYAITLGADYVATGHY 2bw0A 61 :AKGQALPDVVAKYQALGAELNVLPFC T0316 138 :GTVHMLRGVDNGKDQTYFLSQ 2bw0A 145 :DLLLQKECEVLPDDTVSTLYN T0316 166 :KTMF 2bw0A 166 :RFLF T0316 177 :PEVRRLAEEA 2bw0A 170 :PEGIKGMVQA T0316 188 :LSTAKKKDST 2bw0A 201 :EGIQKKETAK T0316 202 :I 2bw0A 211 :I T0316 203 :GEKNFKNFLSNYLP 2bw0A 213 :WDQPAEAIHNWIRG T0316 218 :QPGRMMTVDGRDMGEHAG 2bw0A 230 :VPGAWTEACEQKLTFFNS T0316 240 :TI 2bw0A 248 :TL T0316 243 :QRGGLGIGGQH 2bw0A 250 :NTSGLVPEGDA T0316 254 :GGDNAPWFVV 2bw0A 264 :PGAHRPGVVT T0316 269 :KNILYVGQGFYH 2bw0A 274 :KAGLILFGNDDK T0316 306 :ECTAKF 2bw0A 286 :MLLVKN T0316 322 :VHVKGEKTE 2bw0A 292 :IQLEDGKMI Number of specific fragments extracted= 18 number of extra gaps= 2 total=1278 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kjqA/T0316-1kjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kjqA/T0316-1kjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kjqA read from 1kjqA/T0316-1kjqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kjqA in training set Warning: unaligning (T0316)K193 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kjqA)K163 Warning: unaligning (T0316)T197 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kjqA)K163 T0316 4 :NSKTRVVVGMSG 1kjqA 10 :PAATRVMLLGSG T0316 19 :SSVTALLLKEQGYDVIGIF 1kjqA 24 :GKEVAIECQRLGVEVIAVD T0316 38 :MKNWDDTDENGVC 1kjqA 47 :APAMHVAHRSHVI T0316 52 :ATEDYKDVVAVADQIGIPYYSV 1kjqA 60 :NMLDGDALRRVVELEKPHYIVP T0316 74 :NFE 1kjqA 85 :AIA T0316 84 :FEYFLAEYRAGRTPNPDVMCNKE 1kjqA 88 :TDMLIQLEEEGLNVVPCARATKL T0316 107 :IKFKAFLDYAITL 1kjqA 112 :MNREGIRRLAAEE T0316 132 :VARD 1kjqA 125 :LQLP T0316 137 :DGTVHMLR 1kjqA 129 :TSTYRFAD T0316 175 :EKPEVRRLAEEAGLS 1kjqA 137 :SESLFREAVADIGYP T0316 190 :TAK 1kjqA 156 :PVM T0316 198 :GICFIGEKNFK 1kjqA 164 :GQTFIRSAEQL T0316 209 :NFLSN 1kjqA 176 :QAWKY T0316 214 :YLP 1kjqA 186 :RAG T0316 220 :GRMMTVDGRDMGEHAGLMYYT 1kjqA 213 :DGVHFCAPVGHRQEDGDYRES T0316 273 :YVGQGFYHDSLMSTSLEASQVHFTREM 1kjqA 234 :WQPQQMSPLALERAQEIARKVVLALGG T0316 342 :PGQAVV 1kjqA 261 :YGLFGV T0316 348 :FYDGEECLGGGLIDNA 1kjqA 269 :FVCGDEVIFSEVSPRP Number of specific fragments extracted= 18 number of extra gaps= 0 total=1296 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kjqA/T0316-1kjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kjqA/T0316-1kjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kjqA read from 1kjqA/T0316-1kjqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kjqA in training set Warning: unaligning (T0316)K193 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kjqA)K163 Warning: unaligning (T0316)T197 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kjqA)K163 T0316 4 :NSKTRVVVGMSG 1kjqA 10 :PAATRVMLLGSG T0316 19 :SSVTALLLKEQGYDVIGIFM 1kjqA 24 :GKEVAIECQRLGVEVIAVDR T0316 46 :ENGVCTATE 1kjqA 44 :YADAPAMHV T0316 68 :I 1kjqA 53 :A T0316 69 :PYYSVNFE 1kjqA 55 :RSHVINML T0316 108 :KFKAFLDYAITLGADYVATGHYA 1kjqA 63 :DGDALRRVVELEKPHYIVPEIEA T0316 134 :RDEDGTVHM 1kjqA 86 :IATDMLIQL T0316 143 :LRGVDNGKDQTYFLSQLSQEQLQ 1kjqA 96 :EEGLNVVPCARATKLTMNREGIR T0316 166 :KTMFPLGH 1kjqA 124 :ELQLPTST T0316 175 :EKPEVRRLAEEAGLS 1kjqA 137 :SESLFREAVADIGYP T0316 191 :AK 1kjqA 157 :VM T0316 198 :GICFIGE 1kjqA 164 :GQTFIRS T0316 226 :DGRD 1kjqA 199 :KFDF T0316 235 :GLMYYTIGQRGGLGI 1kjqA 203 :EITLLTVSAVDGVHF T0316 258 :APWFVVGKDLSKNILYVGQGFYHDSLMST 1kjqA 218 :CAPVGHRQEDGDYRESWQPQQMSPLALER T0316 290 :ASQVHF 1kjqA 258 :LGGYGL T0316 320 :VTVHVKGEKTEVIFAEP 1kjqA 266 :VELFVCGDEVIFSEVSP Number of specific fragments extracted= 17 number of extra gaps= 0 total=1313 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kjqA/T0316-1kjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kjqA/T0316-1kjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kjqA read from 1kjqA/T0316-1kjqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kjqA in training set Warning: unaligning (T0316)D147 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kjqA)K163 Warning: unaligning (T0316)K150 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kjqA)K163 T0316 2 :SDNSKTRVVVGMSG 1kjqA 8 :LRPAATRVMLLGSG T0316 17 :VDSSVTALLLKEQGYDVIGIF 1kjqA 22 :ELGKEVAIECQRLGVEVIAVD T0316 42 :DDT 1kjqA 44 :YAD T0316 48 :GVCTATEDYKDVVAVADQIGIPYYSV 1kjqA 56 :SHVINMLDGDALRRVVELEKPHYIVP T0316 84 :FEYFLAEYRAGRTPNPDVMCNKE 1kjqA 88 :TDMLIQLEEEGLNVVPCARATKL T0316 107 :IKFKAFLDYAIT 1kjqA 112 :MNREGIRRLAAE T0316 119 :LGAD 1kjqA 125 :LQLP T0316 129 :YARVA 1kjqA 131 :TYRFA T0316 136 :ED 1kjqA 136 :DS T0316 138 :GTVHMLRGV 1kjqA 150 :YPCIVKPVM T0316 151 :DQTYF 1kjqA 164 :GQTFI T0316 171 :LGHLEKPEVRRLAEEAGLSTA 1kjqA 169 :RSAEQLAQAWKYAQQGGRAGA T0316 197 :TGICFIGEKNFK 1kjqA 190 :GRVIVEGVVKFD T0316 234 :AGLMYYTIGQRGGLGIG 1kjqA 202 :FEITLLTVSAVDGVHFC T0316 258 :APWFVVGKDLSKNILYVGQGFYHDSLMS 1kjqA 219 :APVGHRQEDGDYRESWQPQQMSPLALER T0316 303 :FTLE 1kjqA 260 :GYGL T0316 318 :SKVTVHVKGEKTEVIFAE 1kjqA 264 :FGVELFVCGDEVIFSEVS Number of specific fragments extracted= 17 number of extra gaps= 0 total=1330 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek6A/T0316-1ek6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ek6A expands to /projects/compbio/data/pdb/1ek6.pdb.gz 1ek6A:Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1318, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1393, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1395, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 1ek6A Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 1ek6A # T0316 read from 1ek6A/T0316-1ek6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek6A read from 1ek6A/T0316-1ek6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ek6A to template set # found chain 1ek6A in template set T0316 6 :KTRVVVG 1ek6A 2 :AEKVLVT T0316 19 :SSVTALLLKEQGYDVIGIFMKNWDDTDENG 1ek6A 15 :GSHTVLELLEAGYLPVVIDNFHNAFRGGGS T0316 56 :Y 1ek6A 45 :L T0316 57 :KDVVAVADQIGIPYYSVNFE 1ek6A 47 :ESLRRVQELTGRSVEFEEMD T0316 77 :KEYWDRVFEY 1ek6A 70 :QGALQRLFKK T0316 105 :KEI 1ek6A 109 :LTG T0316 109 :FKAFLDYAITLGADYVATGHYARVARDEDG 1ek6A 112 :TIQLLEIMKAHGVKNLVFSSSATVYGNPQY T0316 139 :TVHMLRGVDNGK 1ek6A 263 :GCRIYNLGTGTG T0316 174 :LEKPEVRRLAEEA 1ek6A 275 :YSVLQMVQAMEKA T0316 187 :GLSTAKKKDSTG 1ek6A 291 :KIPYKVVARREG T0316 199 :ICFIGEKNFKNFLSNYLPA 1ek6A 306 :ACYANPSLAQEELGWTAAL T0316 279 :YHDSLMSTSLEAS 1ek6A 325 :GLDRMCEDLWRWQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=1342 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek6A/T0316-1ek6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ek6A/T0316-1ek6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek6A read from 1ek6A/T0316-1ek6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek6A in template set T0316 6 :KTRVVVG 1ek6A 2 :AEKVLVT T0316 16 :GVDSSVTALLLKEQGYDVIGIFM 1ek6A 12 :GYIGSHTVLELLEAGYLPVVIDN T0316 46 :ENGVCTATEDY 1ek6A 35 :FHNAFRGGGSL T0316 57 :KDVVAVADQIGIPYYSVN 1ek6A 47 :ESLRRVQELTGRSVEFEE T0316 75 :FEKEYWDRVFEYFL 1ek6A 68 :LDQGALQRLFKKYS T0316 89 :AEYRA 1ek6A 102 :LDYYR T0316 103 :CNKE 1ek6A 107 :VNLT T0316 108 :KFKAFLDYAITLGADYVATGHYARVARDEDGTV 1ek6A 111 :GTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLP T0316 143 :LRGVDNGKDQTYFLSQLSQEQL 1ek6A 144 :LDEAHPTGGCTNPYGKSKFFIE T0316 177 :PEVRRLAEE 1ek6A 166 :EMIRDLCQA T0316 187 :G 1ek6A 176 :K T0316 192 :K 1ek6A 192 :H T0316 195 :DSTGICFIGEKNFKNFLSNY 1ek6A 193 :ASGCIGEDPQGIPNNLMPYV T0316 215 :LPAQPG 1ek6A 217 :IGRREA T0316 223 :MTVDGRDMGEHAGLMYYTIG 1ek6A 223 :LNVFGNDYDTEDGTGVRDYI Number of specific fragments extracted= 15 number of extra gaps= 0 total=1357 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek6A/T0316-1ek6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ek6A/T0316-1ek6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek6A read from 1ek6A/T0316-1ek6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek6A in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENGVC 1ek6A 2 :AEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLP T0316 57 :KDVVAVADQIGIPYYSVNF 1ek6A 47 :ESLRRVQELTGRSVEFEEM T0316 76 :EKEYWDRVFEY 1ek6A 69 :DQGALQRLFKK T0316 87 :FLAEYRAG 1ek6A 104 :YYRVNLTG T0316 109 :FKAFLDYAITLGADYVATGHYARVARDE 1ek6A 112 :TIQLLEIMKAHGVKNLVFSSSATVYGNP T0316 145 :GVDNG 1ek6A 143 :PLDEA T0316 169 :FPLGHLE 1ek6A 148 :HPTGGCT T0316 176 :KPEVRRLAEE 1ek6A 165 :EEMIRDLCQA Number of specific fragments extracted= 8 number of extra gaps= 0 total=1365 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpnA/T0316-1rpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rpnA expands to /projects/compbio/data/pdb/1rpn.pdb.gz 1rpnA:# T0316 read from 1rpnA/T0316-1rpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpnA read from 1rpnA/T0316-1rpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rpnA to template set # found chain 1rpnA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1rpnA)R3 T0316 8 :RVVVG 1rpnA 4 :SALVT T0316 15 :GGVDSSVTALLLKEQGYDVIGIFM 1rpnA 11 :TGQDGAYLAKLLLEKGYRVHGLVA T0316 44 :TDENGVC 1rpnA 35 :RRSSDTR T0316 61 :AVADQIGI 1rpnA 42 :WRLRELGI T0316 69 :PYYSVNFE 1rpnA 52 :DIQYEDGD T0316 77 :KEYWDRVFEYF 1rpnA 63 :ACSVQRAVIKA T0316 98 :NPD 1rpnA 74 :QPQ T0316 106 :EI 1rpnA 103 :LG T0316 109 :FKAFLDYAITL 1rpnA 105 :VTHLLEAIRQF T0316 120 :GADYVATGHY 1rpnA 118 :ETRFYQASTS T0316 132 :VARDE 1rpnA 128 :EMFGL T0316 141 :HMLRGVDNGK 1rpnA 134 :QAERQDENTP T0316 153 :TYFLSQLSQEQLQ 1rpnA 144 :FYPRSPYGVAKLY T0316 167 :T 1rpnA 157 :G T0316 176 :KPEVRRLAEEAGLST 1rpnA 158 :HWITVNYRESFGLHA T0316 191 :AKKKDS 1rpnA 180 :HESPLR T0316 198 :GICFIGEKNFKNFLSNYLPAQP 1rpnA 186 :GIEFVTRKVTDAVARIKLGKQQ T0316 286 :TSLEASQVHFTREMPE 1rpnA 253 :RDMCQIAFEHVGLDYR Number of specific fragments extracted= 18 number of extra gaps= 0 total=1383 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpnA/T0316-1rpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1rpnA/T0316-1rpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpnA read from 1rpnA/T0316-1rpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rpnA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1rpnA)R3 T0316 8 :RVVVG 1rpnA 4 :SALVT T0316 15 :GGVDSSVTALLLKEQGYDVIGIFM 1rpnA 11 :TGQDGAYLAKLLLEKGYRVHGLVA T0316 42 :DDTDENG 1rpnA 35 :RRSSDTR T0316 61 :AVADQIGI 1rpnA 42 :WRLRELGI T0316 69 :PYYSVNFE 1rpnA 52 :DIQYEDGD T0316 77 :KEYWDRVFEYFL 1rpnA 63 :ACSVQRAVIKAQ T0316 89 :AEYRA 1rpnA 88 :GASWN T0316 102 :MCNKEI 1rpnA 100 :VDGLGV T0316 110 :KAFLDYAITL 1rpnA 106 :THLLEAIRQF T0316 120 :GADYVATGHYARVARDEDGT 1rpnA 118 :ETRFYQASTSEMFGLIQAER T0316 178 :EVRRLAEEAGLST 1rpnA 160 :ITVNYRESFGLHA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1394 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpnA/T0316-1rpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1rpnA/T0316-1rpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rpnA read from 1rpnA/T0316-1rpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rpnA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1rpnA)R3 T0316 8 :RVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDD 1rpnA 4 :SALVTGITGQDGAYLAKLLLEKGYRVHGLVARRSSD T0316 51 :TATEDYKDVVAVADQIGIPYYSV 1rpnA 58 :GDMADACSVQRAVIKAQPQEVYN T0316 74 :NFEKEYWDRVFEY 1rpnA 92 :NQPVTTGVVDGLG T0316 109 :FKAFLDYAIT 1rpnA 105 :VTHLLEAIRQ T0316 119 :LGADYVATGHYARVARDEDGTV 1rpnA 117 :PETRFYQASTSEMFGLIQAERQ T0316 147 :DNGK 1rpnA 139 :DENT T0316 151 :DQTYFLSQLS 1rpnA 146 :PRSPYGVAKL T0316 176 :KPEVRRLAEEAGLSTAK 1rpnA 158 :HWITVNYRESFGLHASS Number of specific fragments extracted= 8 number of extra gaps= 0 total=1402 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtA/T0316-1fmtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fmtA expands to /projects/compbio/data/pdb/1fmt.pdb.gz 1fmtA:# T0316 read from 1fmtA/T0316-1fmtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtA read from 1fmtA/T0316-1fmtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fmtA to template set # found chain 1fmtA in template set Warning: unaligning (T0316)C50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtA)L46 T0316 6 :KTRVVVGM 1fmtA 3 :SLRIIFAG T0316 20 :SVTALLLKEQGYDVIGIFM 1fmtA 16 :ARHLDALLSSGHNVVGVFT T0316 46 :ENGV 1fmtA 35 :QPDR T0316 58 :DVVAVADQIGIPYYS 1fmtA 50 :PVKVLAEEKGLPVFQ T0316 100 :DVMCNKEI 1fmtA 65 :PVSLRPQE T0316 112 :FLDYAITLGADYVATGHY 1fmtA 73 :NQQLVAELQADVMVVVAY T0316 135 :D 1fmtA 91 :G T0316 137 :DG 1fmtA 92 :LI T0316 139 :TVHMLRGVDNGKDQTYFLSQLSQEQLQK 1fmtA 154 :LSCPITAEDTSGTLYDKLAELGPQGLIT T0316 172 :GHLEKPEVRRLAEEAG 1fmtA 216 :WSLSAAQLERCIRAFN T0316 197 :TGICFI 1fmtA 233 :WPMSWL T0316 232 :EHAGLMYYTI 1fmtA 239 :EIEGQPVKVW T0316 246 :GLGIGGQHGGDNAP 1fmtA 249 :KASVIDTATNAAPG T0316 321 :TVH 1fmtA 263 :TIL T0316 324 :VKGEKTEVIFAE 1fmtA 267 :ANKQGIQVATGD T0316 343 :GQAVV 1fmtA 279 :GILNL T0316 348 :FYD 1fmtA 285 :SLQ Number of specific fragments extracted= 17 number of extra gaps= 0 total=1419 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtA/T0316-1fmtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1fmtA/T0316-1fmtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtA read from 1fmtA/T0316-1fmtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmtA in template set Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtA)L46 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmtA)L46 T0316 6 :KTRVVVGM 1fmtA 3 :SLRIIFAG T0316 19 :SSVTALLLKEQGYDVIGIFMKNWD 1fmtA 15 :AARHLDALLSSGHNVVGVFTQPDR T0316 50 :CTA 1fmtA 47 :MPS T0316 58 :DVVAVADQIGIPYYS 1fmtA 50 :PVKVLAEEKGLPVFQ T0316 100 :DVMCNKE 1fmtA 65 :PVSLRPQ T0316 110 :KA 1fmtA 72 :EN T0316 113 :LDYAITLGADYVATGHYARVA 1fmtA 74 :QQLVAELQADVMVVVAYGLIL T0316 140 :VHM 1fmtA 184 :KQL T0316 143 :LRGVDN 1fmtA 188 :DGTAKP T0316 149 :GKDQTYFLSQLSQE 1fmtA 197 :DETLVTYAEKLSKE T0316 166 :KTMFP 1fmtA 211 :EARID T0316 172 :GHLEKPEVRRLAEEAG 1fmtA 216 :WSLSAAQLERCIRAFN T0316 195 :DSTGICFIG 1fmtA 232 :PWPMSWLEI T0316 219 :PGRM 1fmtA 241 :EGQP T0316 239 :YTIGQRGGLGIGGQH 1fmtA 245 :VKVWKASVIDTATNA T0316 300 :PEEFTL 1fmtA 260 :APGTIL T0316 323 :HVKGEKTEVIFAEP 1fmtA 266 :EANKQGIQVATGDG T0316 345 :AVVF 1fmtA 280 :ILNL Number of specific fragments extracted= 18 number of extra gaps= 0 total=1437 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtA/T0316-1fmtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1fmtA/T0316-1fmtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtA read from 1fmtA/T0316-1fmtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmtA in template set Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtA)L46 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmtA)L46 T0316 5 :SKTRVVVGMS 1fmtA 2 :ESLRIIFAGT T0316 19 :SSVTALLLKEQGYDVIGIFMKNWD 1fmtA 15 :AARHLDALLSSGHNVVGVFTQPDR T0316 50 :CTA 1fmtA 47 :MPS T0316 58 :DVVAVADQIGIPYYS 1fmtA 50 :PVKVLAEEKGLPVFQ T0316 104 :NKEIKFKAFLDYAITLGADYVATGHY 1fmtA 65 :PVSLRPQENQQLVAELQADVMVVVAY T0316 138 :GTVHMLRGVDNGKDQTYFLS 1fmtA 149 :DMLYKLSCPITAEDTSGTLY T0316 162 :EQLQKTM 1fmtA 169 :DKLAELG T0316 176 :KPEVRRLAEEA 1fmtA 176 :PQGLITTLKQL T0316 188 :LSTAKK 1fmtA 201 :VTYAEK T0316 226 :DGRDMGEH 1fmtA 233 :WPMSWLEI T0316 256 :DNAPWFVVGKDLSK 1fmtA 241 :EGQPVKVWKASVID T0316 286 :TS 1fmtA 255 :TA T0316 297 :REMPEEFTLE 1fmtA 257 :TNAAPGTILE T0316 324 :VKGEKTEVIFAEPQRAI 1fmtA 267 :ANKQGIQVATGDGILNL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1451 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gy8A/T0316-1gy8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gy8A expands to /projects/compbio/data/pdb/1gy8.pdb.gz 1gy8A:# T0316 read from 1gy8A/T0316-1gy8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gy8A read from 1gy8A/T0316-1gy8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gy8A to template set # found chain 1gy8A in template set Warning: unaligning (T0316)G138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gy8A)N157 T0316 6 :KTRVVVG 1gy8A 0 :HMRVLVC T0316 19 :SSVTALLLKEQGYDVIGIFM 1gy8A 14 :SHFVRALLRDTNHSVVIVDS T0316 44 :TDENGVC 1gy8A 34 :LVGTHGK T0316 52 :ATEDY 1gy8A 41 :SDHVE T0316 57 :KDVVAVADQIG 1gy8A 48 :ENVARKLQQSD T0316 68 :IPYYSVNFE 1gy8A 69 :AALEVGDVR T0316 77 :KEYWDRVFEY 1gy8A 79 :EDFLNGVFTR T0316 95 :RTPN 1gy8A 89 :HGPI T0316 100 :D 1gy8A 93 :D T0316 106 :EI 1gy8A 120 :VG T0316 109 :FKAFLDYAITLGADYVATGHYARVARDED 1gy8A 122 :ILRLLQAMLLHKCDKIIFSSSAAIFGNPT T0316 139 :TVHMLRGVDNGK 1gy8A 298 :YFSVFNLGTSRG T0316 174 :LEKPEVRRLAEEA 1gy8A 310 :YSVREVIEVARKT T0316 187 :GLSTAKKKDSTGIC 1gy8A 326 :PIPVRECGRREGDP Number of specific fragments extracted= 14 number of extra gaps= 0 total=1465 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gy8A/T0316-1gy8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gy8A/T0316-1gy8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gy8A read from 1gy8A/T0316-1gy8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gy8A in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1gy8A)S-1 Warning: unaligning (T0316)G138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gy8A)N157 T0316 6 :KTRVVVG 1gy8A 0 :HMRVLVC T0316 19 :SSVTALLLKEQGYDVIGIFMKNW 1gy8A 14 :SHFVRALLRDTNHSVVIVDSLVG T0316 46 :ENGVCT 1gy8A 37 :THGKSD T0316 52 :ATEDYK 1gy8A 46 :TRENVA T0316 61 :AVADQI 1gy8A 52 :RKLQQS T0316 68 :IPYYSVNFE 1gy8A 69 :AALEVGDVR T0316 77 :KEYWDRVFEYFL 1gy8A 79 :EDFLNGVFTRHG T0316 89 :AEYRA 1gy8A 105 :GESVR T0316 104 :NKE 1gy8A 110 :DPL T0316 108 :KF 1gy8A 113 :KY T0316 110 :KAFLDYAITLGADYVATGHYARVARDED 1gy8A 123 :LRLLQAMLLHKCDKIIFSSSAAIFGNPT T0316 140 :V 1gy8A 284 :L T0316 143 :LRGVDNGKDQTYFLS 1gy8A 287 :VEKLGPNDKSKYFSV T0316 166 :KTMFPLGHLEKPEVRRLAEEA 1gy8A 302 :FNLGTSRGYSVREVIEVARKT T0316 187 :GLSTAKKKDS 1gy8A 326 :PIPVRECGRR Number of specific fragments extracted= 15 number of extra gaps= 0 total=1480 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gy8A/T0316-1gy8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1gy8A/T0316-1gy8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gy8A read from 1gy8A/T0316-1gy8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gy8A in template set T0316 6 :KTRVVVGMSGGVDSSVTALLLKEQ 1gy8A 0 :HMRVLVCGGAGYIGSHFVRALLRD T0316 30 :GYDVIGIFMKNWDD 1gy8A 25 :NHSVVIVDSLVGTH T0316 45 :DENGVCT 1gy8A 63 :PWADRYA T0316 52 :ATEDYKDVVAVADQI 1gy8A 75 :DVRNEDFLNGVFTRH T0316 67 :GIPYYSV 1gy8A 91 :PIDAVVH T0316 76 :EKEYWDRVFEY 1gy8A 111 :PLKYYDNNVVG T0316 109 :FKAFLDYAITLGADYVATGHYARVARDE 1gy8A 122 :ILRLLQAMLLHKCDKIIFSSSAAIFGNP T0316 145 :GVDNGKDQT 1gy8A 160 :PIDINAKKS T0316 162 :EQLQKTM 1gy8A 172 :PYGESKL T0316 176 :KPEVRRLAEEAGL 1gy8A 181 :ERMIRDCAEAYGI T0316 199 :ICF 1gy8A 196 :ICL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1491 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5aA/T0316-2c5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c5aA expands to /projects/compbio/data/pdb/2c5a.pdb.gz 2c5aA:Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2066, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2068, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2070, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2189, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2191, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2193, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2220, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2224, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2226, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2228, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2534, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2538, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2540, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2542, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2544, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2807, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2811, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2813, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2856, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2860, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2862, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2864, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2866, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2868, because occupancy 0.500 <= existing 0.500 in 2c5aA Skipped atom 2890, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2894, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2896, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2898, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2900, because occupancy 0.300 <= existing 0.700 in 2c5aA Skipped atom 2902, because occupancy 0.300 <= existing 0.700 in 2c5aA # T0316 read from 2c5aA/T0316-2c5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c5aA read from 2c5aA/T0316-2c5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c5aA to template set # found chain 2c5aA in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 2c5aA 25 :SENLKISITGAGGFIASHIARRLKHEGHYVIASDW T0316 46 :ENGVCTATEDY 2c5aA 60 :KKNEHMTEDMF T0316 68 :I 2c5aA 71 :C T0316 69 :PYYSVNFE 2c5aA 73 :EFHLVDLR T0316 84 :FEYFLAEYRAGR 2c5aA 81 :VMENCLKVTEGV T0316 100 :D 2c5aA 93 :D T0316 101 :VMCNKEI 2c5aA 116 :MYNNTMI T0316 109 :FKAFLDYAITLGADYVATGHYARVARDE 2c5aA 123 :SFNMIEAARINGIKRFFYASSACIYPEF T0316 137 :DGTVHMLRGVDNGK 2c5aA 155 :TTNVSLKESDAWPA T0316 151 :DQ 2c5aA 170 :PQ T0316 153 :TYFL 2c5aA 178 :KLAT T0316 176 :KPEVRRLAEEAG 2c5aA 277 :MNEMAEMVLSFE T0316 188 :LSTAKKKDST 2c5aA 292 :LPIHHIPGPE T0316 198 :GICFIGEKNFKNFLSNYLPAQ 2c5aA 304 :RGRNSDNNLIKEKLGWAPNMR T0316 280 :HDSLMSTSLEA 2c5aA 326 :KEGLRITYFWI T0316 291 :SQVHFTREMPEEF 2c5aA 341 :EKEKAKGSDVSLY Number of specific fragments extracted= 16 number of extra gaps= 0 total=1507 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5aA/T0316-2c5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2c5aA/T0316-2c5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c5aA read from 2c5aA/T0316-2c5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c5aA in template set T0316 4 :NSKT 2c5aA 23 :WPSE T0316 8 :RVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENGVC 2c5aA 29 :KISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFC T0316 69 :PYYSVNFE 2c5aA 73 :EFHLVDLR T0316 77 :KEYWDRVF 2c5aA 82 :MENCLKVT T0316 88 :L 2c5aA 90 :E T0316 89 :AEYRA 2c5aA 113 :SVIMY T0316 103 :CNKEI 2c5aA 118 :NNTMI T0316 109 :FKAFLDYAITLGADYVATGHYARVARDE 2c5aA 123 :SFNMIEAARINGIKRFFYASSACIYPEF T0316 137 :DGT 2c5aA 153 :LET T0316 177 :PEVRRLAEEAG 2c5aA 278 :NEMAEMVLSFE T0316 188 :LSTAKKKDSTGICF 2c5aA 292 :LPIHHIPGPEGVRG T0316 202 :IGEKNFKNFL 2c5aA 308 :SDNNLIKEKL T0316 220 :GRMMTV 2c5aA 318 :GWAPNM T0316 226 :DGRDMG 2c5aA 349 :DVSLYG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1521 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5aA/T0316-2c5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 2c5aA/T0316-2c5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c5aA read from 2c5aA/T0316-2c5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c5aA in template set T0316 2 :SDNSKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDDTDENGVC 2c5aA 23 :WPSENLKISITGAGGFIASHIARRLKHEGHYVIASDWKKNEHMTEDMFC T0316 51 :TATEDYKDVVAVAD 2c5aA 77 :VDLRVMENCLKVTE T0316 67 :GIPYYSV 2c5aA 91 :GVDHVFN T0316 80 :WDRVFEYF 2c5aA 112 :HSVIMYNN T0316 106 :EIKFKAFLDYAITLGADYVATGHYARVAR 2c5aA 120 :TMISFNMIEAARINGIKRFFYASSACIYP T0316 152 :QTYFLS 2c5aA 171 :QDAFGL T0316 162 :EQLQK 2c5aA 177 :EKLAT T0316 176 :KPEVRRLAEEAGLSTA 2c5aA 182 :EELCKHYNKDFGIECR Number of specific fragments extracted= 8 number of extra gaps= 0 total=1529 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgtA/T0316-1jgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jgtA expands to /projects/compbio/data/pdb/1jgt.pdb.gz 1jgtA:# T0316 read from 1jgtA/T0316-1jgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgtA read from 1jgtA/T0316-1jgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jgtA to template set # found chain 1jgtA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 1jgtA 240 :PGDTPLVVLSGGIDSSGVAACAHRAAGELDTVSM T0316 46 :ENG 1jgtA 274 :GTD T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1jgtA 277 :TSNEFREARAVVDHLRTRHREITIP T0316 89 :AEYRA 1jgtA 303 :TELLA T0316 102 :MCNKEI 1jgtA 318 :SVDPDI T0316 109 :FKAFLDYAITL 1jgtA 324 :IEYLLPLTALY T0316 120 :GADYVATGHYARVARDED 1jgtA 340 :PERRILTGYGADIPLGGM T0316 146 :VDN 1jgtA 358 :HRE T0316 151 :DQTYFLSQLSQEQLQK 1jgtA 361 :DRLPALDTVLAHDMAT T0316 167 :TMFPLGHLEKPEV 1jgtA 426 :LRAAMADALPAET T0316 180 :RRLAEEAGLST 1jgtA 457 :SRLLLDHGVAE T0316 279 :YHDSLMSTSLEASQVHFTREM 1jgtA 468 :DRVHEAKRQVVRELFDLTVGG T0316 300 :PEEFT 1jgtA 490 :RHPSE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1542 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgtA/T0316-1jgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1jgtA/T0316-1jgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgtA read from 1jgtA/T0316-1jgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgtA in template set T0316 4 :NSKTRVVVGMSGGVDSSVTALLLKEQ 1jgtA 239 :TPGDTPLVVLSGGIDSSGVAACAHRA T0316 31 :YDVIGIFM 1jgtA 266 :GELDTVSM T0316 46 :ENG 1jgtA 274 :GTD T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 1jgtA 277 :TSNEFREARAVVDHLRTRHREITIP T0316 88 :LAEYRA 1jgtA 302 :TTELLA T0316 100 :D 1jgtA 308 :Q T0316 101 :VMCNKEI 1jgtA 318 :SVDPDII T0316 110 :KAFLDYAITL 1jgtA 325 :EYLLPLTALY T0316 120 :GADYVATG 1jgtA 340 :PERRILTG T0316 128 :HYA 1jgtA 358 :HRE T0316 134 :RDEDGT 1jgtA 361 :DRLPAL T0316 140 :VHMLR 1jgtA 458 :RLLLD T0316 145 :GVDNGK 1jgtA 464 :GVAEDR T0316 152 :QTYFLSQLSQEQLQKT 1jgtA 470 :VHEAKRQVVRELFDLT T0316 168 :MFPLGHLEKPEVRR 1jgtA 489 :GRHPSEVDTDDVVR Number of specific fragments extracted= 15 number of extra gaps= 0 total=1557 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgtA/T0316-1jgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1jgtA/T0316-1jgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgtA read from 1jgtA/T0316-1jgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgtA in template set T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFMKNWDD 1jgtA 240 :PGDTPLVVLSGGIDSSGVAACAHRAAGELDTVSMGTDTS T0316 54 :EDYKDVVAVADQIGIPYYSVNF 1jgtA 279 :NEFREARAVVDHLRTRHREITI T0316 76 :EKEYWDRVFEYF 1jgtA 302 :TTELLAQLPYAV T0316 92 :RAGRTPNPD 1jgtA 314 :WASESVDPD T0316 107 :I 1jgtA 323 :I T0316 109 :FKAFLDYAIT 1jgtA 324 :IEYLLPLTAL T0316 119 :LGADYVATGHYARV 1jgtA 339 :GPERRILTGYGADI T0316 166 :KTMFPLGHLEKPEVRRLAEEA 1jgtA 353 :PLGGMHREDRLPALDTVLAHD Number of specific fragments extracted= 8 number of extra gaps= 0 total=1565 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5sA/T0316-2c5sA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c5sA expands to /projects/compbio/data/pdb/2c5s.pdb.gz 2c5sA:# T0316 read from 2c5sA/T0316-2c5sA-t06-local-adpstyle5.a2m # 2c5sA read from 2c5sA/T0316-2c5sA-t06-local-adpstyle5.a2m # adding 2c5sA to template set # found chain 2c5sA in template set Warning: unaligning (T0316)N47 because of BadResidue code BAD_PEPTIDE in next template residue (2c5sA)P212 Warning: unaligning (T0316)G48 because of BadResidue code BAD_PEPTIDE at template residue (2c5sA)P212 Warning: unaligning (T0316)C50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c5sA)T215 Warning: unaligning (T0316)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c5sA)T215 Warning: unaligning (T0316)A130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c5sA)G291 Warning: unaligning (T0316)R131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c5sA)G291 Warning: unaligning (T0316)K194 because of BadResidue code BAD_PEPTIDE in next template residue (2c5sA)P340 Warning: unaligning (T0316)D195 because of BadResidue code BAD_PEPTIDE at template residue (2c5sA)P340 Warning: unaligning (T0316)S196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c5sA)K356 T0316 5 :SKTRVVVGMSGGVDSSVTALLLKEQGYDVIGIFM 2c5sA 176 :VGGKVMVLLSGGIDSPVAAYLTMKRGVSVEAVHF T0316 46 :E 2c5sA 210 :H T0316 49 :V 2c5sA 213 :P T0316 52 :ATEDYKDVVAVADQIGIPYYSVNFE 2c5sA 216 :SERAKQKVIDLAQELTKYCKRVTLH T0316 82 :RVFEYFLAEYRAGRTPNPDVMC 2c5sA 241 :LVPFTEVQKTINKEIPSSYSMT T0316 104 :NKEI 2c5sA 265 :RRMM T0316 109 :FKAFLDYAITLGADYVATGHY 2c5sA 269 :MRITERIAEERNALAITTGES T0316 132 :VARDEDG 2c5sA 292 :QVASQTL T0316 140 :VHMLRGVDNGK 2c5sA 299 :DSMHTINEVTN T0316 165 :QKTMFPLGHLEKPEVRRLAEEAGLSTAKK 2c5sA 310 :YPVIRPLITMDKLEIIKIAEEIGTYDISI Number of specific fragments extracted= 10 number of extra gaps= 4 total=1575 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iirA/T0316-1iirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iirA expands to /projects/compbio/data/pdb/1iir.pdb.gz 1iirA:# T0316 read from 1iirA/T0316-1iirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iirA read from 1iirA/T0316-1iirA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iirA to template set # found chain 1iirA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1iirA)M1 Warning: unaligning (T0316)F75 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)R63 Warning: unaligning (T0316)H141 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)I149 Warning: unaligning (T0316)G149 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)I149 Warning: unaligning (T0316)Q276 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)G249 Warning: unaligning (T0316)G277 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)G249 T0316 8 :RVVVG 1iirA 2 :RVLLA T0316 18 :DS 1iirA 13 :DT T0316 20 :SVTALLLKEQGYDVI 1iirA 18 :VALAVRVRDLGADVR T0316 36 :IFM 1iirA 33 :MCA T0316 52 :ATEDYK 1iirA 36 :PPDCAE T0316 62 :VADQIGIPYYSVN 1iirA 42 :RLAEVGVPHVPVG T0316 80 :WDRVFEYFLAEYRA 1iirA 76 :TTEAIATQFDEIPA T0316 94 :GR 1iirA 92 :EG T0316 100 :D 1iirA 94 :C T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVARDE 1iirA 101 :GLLAAAIGVRSVAEKLGIPYFYAFHCPSYVPSP T0316 137 :DGTV 1iirA 135 :YPPP T0316 150 :K 1iirA 150 :D T0316 153 :TYFLSQLSQEQLQKT 1iirA 151 :IPAQWERNNQSAYQR T0316 175 :EKPEVRRLAEEAGLSTAKK 1iirA 166 :YGGLLNSHRDAIGLPPVED T0316 197 :TGICFIGE 1iirA 191 :TDHPWVAA T0316 211 :LSNYLPAQP 1iirA 199 :DPVLAPLQP T0316 220 :GR 1iirA 237 :GP T0316 270 :NILYVG 1iirA 239 :PPVYLG T0316 278 :FYHDSLMSTSLEASQ 1iirA 250 :APADAVRVAIDAIRA T0316 350 :DGEECLGGGLIDNAYRDGQV 1iirA 265 :HGRRVILSRGWADLVLPDDG Number of specific fragments extracted= 20 number of extra gaps= 1 total=1595 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iirA/T0316-1iirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1iirA/T0316-1iirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iirA read from 1iirA/T0316-1iirA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iirA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1iirA)M1 Warning: unaligning (T0316)N148 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)I149 Warning: unaligning (T0316)Q158 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)I149 Warning: unaligning (T0316)Q276 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1iirA)G249 Warning: unaligning (T0316)G277 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)G249 T0316 8 :RVVVG 1iirA 2 :RVLLA T0316 18 :DS 1iirA 13 :DT T0316 20 :SVTALLLKEQGYDVIGIF 1iirA 18 :VALAVRVRDLGADVRMCA T0316 52 :ATEDYKD 1iirA 36 :PPDCAER T0316 63 :ADQIGIPYYSVN 1iirA 43 :LAEVGVPHVPVG T0316 77 :K 1iirA 69 :A T0316 85 :EYFLAEYRA 1iirA 70 :EDVRRFTTE T0316 108 :KFKAFLDYAITL 1iirA 79 :AIATQFDEIPAA T0316 120 :GADYVATG 1iirA 93 :GCAAVVTT T0316 128 :HYARVA 1iirA 121 :FYAFHC T0316 140 :VHM 1iirA 127 :PSY T0316 143 :LRGVD 1iirA 134 :YYPPP T0316 159 :LSQEQLQKTMF 1iirA 150 :DIPAQWERNNQ T0316 177 :PEVRRLAEEAGLST 1iirA 168 :GLLNSHRDAIGLPP T0316 191 :AKKKD 1iirA 218 :WILPD T0316 204 :EKNFKNFLSNYLPAQP 1iirA 223 :ERPLSPELAAFLDAGP T0316 258 :APWF 1iirA 239 :PPVY T0316 274 :VG 1iirA 243 :LG T0316 281 :DSLMSTSLEASQVHFTREMP 1iirA 260 :DAIRAHGRRVILSRGWADLV Number of specific fragments extracted= 19 number of extra gaps= 1 total=1614 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iirA/T0316-1iirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1iirA/T0316-1iirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iirA read from 1iirA/T0316-1iirA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iirA in template set Warning: unaligning (T0316)T7 because first residue in template chain is (1iirA)M1 Warning: unaligning (T0316)K150 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1iirA)I149 T0316 8 :RVVVGMSGG 1iirA 2 :RVLLATCGS T0316 18 :DS 1iirA 13 :DT T0316 20 :SVTALLLKEQGYDVIGIF 1iirA 18 :VALAVRVRDLGADVRMCA T0316 52 :ATEDYKDV 1iirA 36 :PPDCAERL T0316 64 :DQIGIPYYSV 1iirA 44 :AEVGVPHVPV T0316 76 :EKEYWDRVFEYFLAEYR 1iirA 72 :VRRFTTEAIATQFDEIP T0316 93 :AGR 1iirA 92 :EGC T0316 99 :PDVMC 1iirA 95 :AAVVT T0316 104 :NKEIKFKAFLDYAITLGADYVATGHYARVARDED 1iirA 101 :GLLAAAIGVRSVAEKLGIPYFYAFHCPSYVPSPY T0316 151 :DQ 1iirA 150 :DI T0316 161 :QEQLQKTMFPLGHLEKPEVRRLAEEAGLSTAKK 1iirA 152 :PAQWERNNQSAYQRYGGLLNSHRDAIGLPPVED Number of specific fragments extracted= 11 number of extra gaps= 0 total=1625 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2eA/T0316-1d2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d2eA expands to /projects/compbio/data/pdb/1d2e.pdb.gz 1d2eA:# T0316 read from 1d2eA/T0316-1d2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2eA read from 1d2eA/T0316-1d2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d2eA to template set # found chain 1d2eA in template set T0316 7 :TRVVVGM 1d2eA 145 :DGCILVV T0316 19 :SSVTALLLKEQGYD 1d2eA 161 :TREHLLLARQIGVE T0316 33 :VIGIFM 1d2eA 176 :VVVYVN T0316 46 :ENGVCTATEDYKDVVAVADQI 1d2eA 182 :KADAVQDSEMVELVELEIREL T0316 67 :GIPYYSVNFE 1d2eA 212 :ETPIIVGSAL T0316 90 :EYRAGRTP 1d2eA 222 :CALEQRDP T0316 102 :MCNKEI 1d2eA 230 :ELGLKS T0316 109 :FKAFLDYAITL 1d2eA 236 :VQKLLDAVDTY T0316 133 :ARD 1d2eA 248 :PVP T0316 137 :DG 1d2eA 251 :TR T0316 140 :VHMLRG 1d2eA 277 :GTLERG T0316 192 :KKKDSTGICFIGE 1d2eA 283 :ILKKGDECEFLGH T0316 220 :GRMMTV 1d2eA 296 :SKNIRT T0316 226 :DGRDMGEHA 1d2eA 309 :FHKSLDRAE T0316 235 :GLMYYTIGQRG 1d2eA 321 :NLGALVRGLKR T0316 246 :GLG 1d2eA 333 :DLR T0316 249 :IGGQHGGDN 1d2eA 339 :VMAKPGSIQ T0316 264 :GKDLSKNILYVGQG 1d2eA 348 :PHQKVEAQVYILTK T0316 296 :TREMPEEFTLECTAKFRYRQPDSKVTVHVKGE 1d2eA 363 :EGGRHKPFVSHFMPVMFSLTWDMACRIILPPG T0316 328 :KTEVIFAEPQRAI 1d2eA 405 :KLTLILRQPMILE T0316 342 :PGQAVVFYDGEECLGGGLIDNAY 1d2eA 418 :KGQRFTLRDGNRTIGTGLVTDTP Number of specific fragments extracted= 21 number of extra gaps= 0 total=1646 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2eA/T0316-1d2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1d2eA/T0316-1d2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2eA read from 1d2eA/T0316-1d2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d2eA in template set T0316 7 :TRVVVGM 1d2eA 145 :DGCILVV T0316 19 :SSVTALLLKEQGYD 1d2eA 161 :TREHLLLARQIGVE T0316 33 :VIGIFM 1d2eA 176 :VVVYVN T0316 46 :ENGVCTATEDYKDVVAVADQI 1d2eA 182 :KADAVQDSEMVELVELEIREL T0316 67 :GIPYYSVNFE 1d2eA 212 :ETPIIVGSAL T0316 90 :EYRAGRTPN 1d2eA 222 :CALEQRDPE T0316 103 :CNKE 1d2eA 231 :LGLK T0316 108 :KFKAFLDYAITL 1d2eA 235 :SVQKLLDAVDTY T0316 133 :ARDEDGT 1d2eA 251 :TRDLEKP T0316 167 :TMFP 1d2eA 258 :FLLP T0316 188 :LST 1d2eA 262 :VES T0316 191 :AKK 1d2eA 266 :YSI T0316 195 :DSTGICFIGEKNF 1d2eA 269 :PGRGTVVTGTLER T0316 219 :PGRMMTV 1d2eA 286 :KGDECEF T0316 226 :DGRDMGEHAGLMYY 1d2eA 328 :GLKREDLRRGLVMA T0316 250 :GGQHGGDNA 1d2eA 342 :KPGSIQPHQ T0316 259 :PWFVVGKDLSKN 1d2eA 352 :VEAQVYILTKEE T0316 276 :QGFYHDSLMSTSLEASQVHF 1d2eA 364 :GGRHKPFVSHFMPVMFSLTW T0316 317 :DSKVTVHVKGE 1d2eA 384 :DMACRIILPPG T0316 328 :KTEVIFAE 1d2eA 405 :KLTLILRQ T0316 337 :QRAITPGQAVVFYDGEECLGGGLIDNAYRDGQVC 1d2eA 413 :PMILEKGQRFTLRDGNRTIGTGLVTDTPAMTEED Number of specific fragments extracted= 21 number of extra gaps= 0 total=1667 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2eA/T0316-1d2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1d2eA/T0316-1d2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2eA read from 1d2eA/T0316-1d2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d2eA in template set T0316 7 :TRVVVGMSG 1d2eA 145 :DGCILVVAA T0316 19 :SSVTALLLKEQGYD 1d2eA 161 :TREHLLLARQIGVE T0316 33 :VIGIFMKNWDDTDE 1d2eA 176 :VVVYVNKADAVQDS T0316 52 :ATEDYKDVVAVADQIGIP 1d2eA 192 :VELVELEIRELLTEFGYK T0316 70 :YYSVNFE 1d2eA 215 :IIVGSAL T0316 90 :EYRAGRTPNP 1d2eA 222 :CALEQRDPEL T0316 105 :KEIKFKAFLDYAIT 1d2eA 232 :GLKSVQKLLDAVDT T0316 119 :LGAD 1d2eA 254 :LEKP T0316 132 :VARDEDGTVHMLRGVDN 1d2eA 265 :VYSIPGRGTVVTGTLER T0316 189 :STAKKKD 1d2eA 282 :GILKKGD T0316 198 :GICFIGE 1d2eA 289 :ECEFLGH T0316 218 :QPGRMMT 1d2eA 299 :IRTVVTG T0316 225 :VDGRDMGEHA 1d2eA 308 :MFHKSLDRAE T0316 236 :LMY 1d2eA 322 :LGA T0316 243 :QRGGLGIGGQHG 1d2eA 325 :LVRGLKREDLRR T0316 255 :GDNAPWFVVG 1d2eA 344 :GSIQPHQKVE T0316 270 :NILYVGQGFYH 1d2eA 354 :AQVYILTKEEG T0316 294 :HFTREMPEEFTLECTA 1d2eA 365 :GRHKPFVSHFMPVMFS T0316 316 :PDSKVTVHVKGEK 1d2eA 383 :WDMACRIILPPGK T0316 329 :TEVIFAEPQ 1d2eA 406 :LTLILRQPM T0316 339 :AITPGQAVVFYDGEECLGGGLIDNA 1d2eA 415 :ILEKGQRFTLRDGNRTIGTGLVTDT Number of specific fragments extracted= 21 number of extra gaps= 0 total=1688 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kk1A/T0316-1kk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kk1A expands to /projects/compbio/data/pdb/1kk1.pdb.gz 1kk1A:# T0316 read from 1kk1A/T0316-1kk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kk1A read from 1kk1A/T0316-1kk1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kk1A to template set # found chain 1kk1A in template set Warning: unaligning (T0316)K193 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)K228 Warning: unaligning (T0316)Y279 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)E339 T0316 7 :TRVVVGM 1kk1A 108 :DGAILVI T0316 19 :SSVTALLLKEQGYD 1kk1A 125 :TREHLMALQIIGQK T0316 33 :VIGIFM 1kk1A 140 :IIIAQN T0316 46 :ENGVC 1kk1A 146 :KIELV T0316 52 :ATEDYKDVVAVADQI 1kk1A 151 :DKEKALENYRQIKEF T0316 67 :GIPYYSVNFE 1kk1A 173 :NAPIIPISAL T0316 93 :AGR 1kk1A 183 :HGA T0316 108 :KFKAFLDYAITL 1kk1A 186 :NIDVLVKAIEDF T0316 120 :GA 1kk1A 202 :KR T0316 132 :VARD 1kk1A 204 :DPNK T0316 137 :DGTVHMLRGVDNGK 1kk1A 208 :PPKMLVLRSFDVNK T0316 189 :S 1kk1A 222 :P T0316 194 :K 1kk1A 229 :L T0316 197 :TG 1kk1A 230 :VG T0316 226 :DGRDMGEHAGLMYYTIGQRG 1kk1A 245 :VGDEIEIRPGVPYEEHGRIK T0316 246 :GLGIGG 1kk1A 269 :TTEIVS T0316 252 :QHGG 1kk1A 281 :FVEE T0316 256 :DNAPWFVVGK 1kk1A 287 :PGGLVGVGTK T0316 266 :DLSKNILYVGQG 1kk1A 305 :DLMAGNVVGKPG T0316 280 :H 1kk1A 340 :Q T0316 297 :REMPEEFTLECTAKFRYRQPDSKVTVH 1kk1A 341 :ELKVEPIKRKEVLLLNVGTARTMGLVT T0316 324 :VKGEKTEVIFAEPQRAI 1kk1A 369 :LGKDEIEVKLQIPVCAE T0316 342 :PGQAVVFYD 1kk1A 386 :PGDRVAISR T0316 351 :GE 1kk1A 397 :GS T0316 353 :ECLGGGLID 1kk1A 401 :RLIGYGIIK Number of specific fragments extracted= 25 number of extra gaps= 0 total=1713 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kk1A/T0316-1kk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kk1A/T0316-1kk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kk1A read from 1kk1A/T0316-1kk1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kk1A in template set Warning: unaligning (T0316)G220 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kk1A)K228 Warning: unaligning (T0316)V225 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)K228 Warning: unaligning (T0316)R297 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kk1A)E339 Warning: unaligning (T0316)P300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)E339 T0316 7 :TRVVVGM 1kk1A 108 :DGAILVI T0316 19 :SSVTALLLKEQGYD 1kk1A 125 :TREHLMALQIIGQK T0316 33 :VIGIFM 1kk1A 140 :IIIAQN T0316 46 :ENGVC 1kk1A 146 :KIELV T0316 52 :ATEDYKDVVAVADQI 1kk1A 151 :DKEKALENYRQIKEF T0316 67 :GIPYYSVNF 1kk1A 173 :NAPIIPISA T0316 92 :RAGR 1kk1A 182 :LHGA T0316 108 :KFKAFLDYAITL 1kk1A 186 :NIDVLVKAIEDF T0316 188 :LSTAKKKDSTGICFIGEKNFK 1kk1A 200 :TPKRDPNKPPKMLVLRSFDVN T0316 218 :QP 1kk1A 221 :KP T0316 226 :DGRDMGEHAGLMYYTIG 1kk1A 253 :PGVPYEEHGRIKYEPIT T0316 243 :QRGGLGIGGQHGGDNA 1kk1A 271 :EIVSLQAGGQFVEEAY T0316 259 :PWFVVGKDLSKN 1kk1A 289 :GLVGVGTKLDPY T0316 271 :ILYVGQGFYHDSLMSTSLEASQVHFT 1kk1A 310 :NVVGKPGKLPPVWDSLRLEVHLLERV T0316 301 :E 1kk1A 340 :Q T0316 302 :EFTLECTAKFRY 1kk1A 348 :KRKEVLLLNVGT T0316 316 :PDSKVTVHVK 1kk1A 360 :ARTMGLVTGL T0316 326 :GEKTEVIFAEP 1kk1A 371 :KDEIEVKLQIP T0316 338 :RAITPGQAVVFY 1kk1A 382 :VCAEPGDRVAIS T0316 350 :DGEEC 1kk1A 397 :GSRWR T0316 355 :LGGGLID 1kk1A 403 :IGYGIIK Number of specific fragments extracted= 21 number of extra gaps= 0 total=1734 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kk1A/T0316-1kk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kk1A/T0316-1kk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kk1A read from 1kk1A/T0316-1kk1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kk1A in template set Warning: unaligning (T0316)Q152 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kk1A)K228 Warning: unaligning (T0316)H173 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)K228 Warning: unaligning (T0316)R297 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kk1A)E339 Warning: unaligning (T0316)P300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kk1A)E339 T0316 7 :TRVVVGMS 1kk1A 108 :DGAILVIA T0316 16 :GVDSSVTALLLKEQGYD 1kk1A 122 :RPQTREHLMALQIIGQK T0316 33 :VIGIFMKNWDDT 1kk1A 140 :IIIAQNKIELVD T0316 53 :TEDYKDVVAVADQI 1kk1A 152 :KEKALENYRQIKEF T0316 67 :GIPYYS 1kk1A 173 :NAPIIP T0316 101 :VMCNKEIKFKAFLDYAIT 1kk1A 179 :ISALHGANIDVLVKAIED T0316 122 :D 1kk1A 201 :P T0316 133 :ARDEDGTVHM 1kk1A 202 :KRDPNKPPKM T0316 143 :LRGVDNGKD 1kk1A 214 :LRSFDVNKP T0316 174 :LE 1kk1A 229 :LV T0316 189 :STAKKKDSTGIC 1kk1A 241 :GKLKVGDEIEIR T0316 219 :PGRMMTVDGRDMGEHAGLMYYTIGQRGGLGIGG 1kk1A 253 :PGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEA T0316 256 :DNAPWFVVGKDLSK 1kk1A 286 :YPGGLVGVGTKLDP T0316 270 :NILYVGQGFYHDSLMSTSLEASQVHFT 1kk1A 309 :GNVVGKPGKLPPVWDSLRLEVHLLERV T0316 301 :E 1kk1A 340 :Q T0316 303 :FTLECTAKF 1kk1A 349 :RKEVLLLNV T0316 314 :RQPDSKVTVH 1kk1A 358 :GTARTMGLVT T0316 324 :VKGEKTEVIFAEPQ 1kk1A 369 :LGKDEIEVKLQIPV T0316 339 :AITPGQAVVFYD 1kk1A 383 :CAEPGDRVAISR T0316 351 :GE 1kk1A 397 :GS T0316 353 :ECLGGGLID 1kk1A 401 :RLIGYGIIK Number of specific fragments extracted= 21 number of extra gaps= 0 total=1755 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ha3A/T0316-1ha3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ha3A expands to /projects/compbio/data/pdb/1ha3.pdb.gz 1ha3A:Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 646, because occupancy 0.300 <= existing 0.700 in 1ha3A Skipped atom 648, because occupancy 0.300 <= existing 0.700 in 1ha3A Skipped atom 650, because occupancy 0.300 <= existing 0.700 in 1ha3A Skipped atom 652, because occupancy 0.300 <= existing 0.700 in 1ha3A Skipped atom 654, because occupancy 0.300 <= existing 0.700 in 1ha3A Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 3013, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 3015, because occupancy 0.500 <= existing 0.500 in 1ha3A Skipped atom 3017, because occupancy 0.500 <= existing 0.500 in 1ha3A # T0316 read from 1ha3A/T0316-1ha3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ha3A read from 1ha3A/T0316-1ha3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ha3A to template set # found chain 1ha3A in template set T0316 6 :KTRVVVGMS 1ha3A 99 :MDGAILVVS T0316 19 :SSVTALLLKEQGYD 1ha3A 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1ha3A 131 :IVVFMN T0316 46 :ENGVCTATEDY 1ha3A 137 :KVDMVDDPELL T0316 57 :KDVVAVADQIGIP 1ha3A 152 :MEVRDLLNQYEFP T0316 70 :YYSVNFE 1ha3A 168 :VPVIRGS T0316 84 :FEYFLAEYRA 1ha3A 175 :ALLALEQMHR T0316 94 :GRTPNPD 1ha3A 186 :PKTRRGE T0316 104 :NKEI 1ha3A 193 :NEWV T0316 108 :KFKAFLDYAITL 1ha3A 198 :KIWELLDAIDEY T0316 135 :D 1ha3A 211 :P T0316 137 :DG 1ha3A 212 :TP T0316 234 :AGLMYYTIGQRGGLGIGGQ 1ha3A 249 :VGDEVEIVGLAPETRKTVV T0316 253 :HGG 1ha3A 277 :LQE T0316 256 :DNAPWFVVGK 1ha3A 282 :AGDNVGVLLR T0316 266 :DLSKNILYVGQG 1ha3A 297 :EVERGQVLAKPG T0316 298 :EMPEEF 1ha3A 323 :LKKEEG T0316 304 :TLECTAKFRYRQPDSKVTVHVKGE 1ha3A 335 :FSGYRPQFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAEPQR 1ha3A 369 :TFTVELIKPVA T0316 340 :ITPGQAVVFYDGEECLGGGLIDNAY 1ha3A 380 :LEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 20 number of extra gaps= 0 total=1775 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ha3A/T0316-1ha3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ha3A/T0316-1ha3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ha3A read from 1ha3A/T0316-1ha3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ha3A in template set T0316 7 :TRVVVGMS 1ha3A 100 :DGAILVVS T0316 19 :SSVTALLLKEQGYD 1ha3A 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1ha3A 131 :IVVFMN T0316 46 :ENGVCTATEDYK 1ha3A 137 :KVDMVDDPELLD T0316 58 :DVVAVADQIGIP 1ha3A 153 :EVRDLLNQYEFP T0316 70 :YYSVNFE 1ha3A 168 :VPVIRGS T0316 84 :FEYFLAEYRA 1ha3A 175 :ALLALEQMHR T0316 94 :GRTPNPD 1ha3A 186 :PKTRRGE T0316 104 :NKEI 1ha3A 193 :NEWV T0316 108 :KFKAFLDYAITL 1ha3A 198 :KIWELLDAIDEY T0316 131 :RVARDEDGT 1ha3A 212 :TPVRDVDKP T0316 167 :T 1ha3A 221 :F T0316 191 :AKKKDSTGICFIGEKN 1ha3A 228 :VFTITGRGTVATGRIE T0316 208 :KNFL 1ha3A 244 :RGKV T0316 218 :QPGRMMTV 1ha3A 248 :KVGDEVEI T0316 230 :MGEHAGLMYYTIGQRGG 1ha3A 256 :VGLAPETRKTVVTGVEM T0316 247 :LG 1ha3A 286 :VG T0316 249 :IGGQHGGDNAPWFVVGKD 1ha3A 290 :LRGVSREEVERGQVLAKP T0316 267 :L 1ha3A 309 :S T0316 268 :SKNILYVGQGFYHDSLMSTSLEASQV 1ha3A 314 :TKFEASVYVLKKEEGGRHTGFFSGYR T0316 309 :AKFRYRQPDSKVTVHVKGE 1ha3A 340 :PQFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAE 1ha3A 369 :TFTVELIK T0316 337 :QRAITPGQAVVFYDGEECLGGGLID 1ha3A 377 :PVALEEGLRFAIREGGRTVGAGVVT Number of specific fragments extracted= 23 number of extra gaps= 0 total=1798 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ha3A/T0316-1ha3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1ha3A/T0316-1ha3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ha3A read from 1ha3A/T0316-1ha3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ha3A in template set T0316 7 :TRVVVGMSG 1ha3A 100 :DGAILVVSA T0316 18 :DSSVTALLLKEQGYDVIGIFMKNWDDTDENG 1ha3A 115 :QTREHILLARQVGVPYIVVFMNKVDMVDDPE T0316 51 :TATEDYKDVVAVADQIGIP 1ha3A 146 :LLDLVEMEVRDLLNQYEFP T0316 70 :YYSVNFE 1ha3A 170 :VIRGSAL T0316 82 :RVFEYFLA 1ha3A 177 :LALEQMHR T0316 98 :NPDVMCNKEI 1ha3A 185 :NPKTRRGENE T0316 108 :KFKAFLDYAIT 1ha3A 198 :KIWELLDAIDE T0316 119 :LGAD 1ha3A 217 :VDKP T0316 128 :HYARVARDEDGTVHMLRGVDNGK 1ha3A 224 :PVEDVFTITGRGTVATGRIERGK T0316 191 :AKKKD 1ha3A 247 :VKVGD T0316 198 :GICFIGE 1ha3A 252 :EVEIVGL T0316 217 :A 1ha3A 259 :A T0316 226 :DGRDMGEHAGLMY 1ha3A 260 :PETRKTVVTGVEM T0316 243 :QRGGLGIGG 1ha3A 273 :HRKTLQEGI T0316 256 :DNAPWFVVGKDLSK 1ha3A 282 :AGDNVGVLLRGVSR T0316 270 :NILYVGQGF 1ha3A 301 :GQVLAKPGS T0316 285 :STS 1ha3A 313 :HTK T0316 288 :LEASQVHFTREMPEEFTL 1ha3A 323 :LKKEEGGRHTGFFSGYRP T0316 310 :KFRYRQPDSKVTVHVKGEK 1ha3A 341 :QFYFRTTDVTGVVQLPPGV T0316 329 :TEVIFAEPQ 1ha3A 370 :FTVELIKPV T0316 339 :AITPGQAVVFYDGEECLGGGLIDNAY 1ha3A 379 :ALEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 21 number of extra gaps= 0 total=1819 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exmA/T0316-1exmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1exmA expands to /projects/compbio/data/pdb/1exm.pdb.gz 1exmA:Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1702, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1704, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1706, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1710, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1712, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1716, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2100, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2102, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2104, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2106, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 1exmA Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 1exmA # T0316 read from 1exmA/T0316-1exmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exmA read from 1exmA/T0316-1exmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1exmA to template set # found chain 1exmA in template set T0316 7 :TRVVVGMS 1exmA 100 :DGAILVVS T0316 19 :SSVTALLLKEQGYD 1exmA 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1exmA 131 :IVVFMN T0316 46 :ENGVCTATEDY 1exmA 137 :KVDMVDDPELL T0316 57 :KDVVAVADQIGIP 1exmA 152 :MEVRDLLNQYEFP T0316 70 :YYSVNFE 1exmA 168 :VPVIRGS T0316 84 :FEYFLAEYRA 1exmA 175 :ALLALEQMHR T0316 94 :GRTPNPD 1exmA 186 :PKTRRGE T0316 104 :NKEI 1exmA 193 :NEWV T0316 108 :KFKAFLDYAITL 1exmA 198 :KIWELLDAIDEY T0316 137 :DG 1exmA 212 :TP T0316 198 :GICFIGEKNFK 1exmA 235 :GTVATGRIERG T0316 229 :DM 1exmA 246 :KV T0316 233 :HAGLMYYTIGQRGGL 1exmA 248 :KVGDEVEIVGLAPET T0316 248 :GIGGQHGG 1exmA 268 :TGVEMHRK T0316 256 :DNAPWFVVGKDLSK 1exmA 282 :AGDNVGVLLRGVSR T0316 270 :NILYVGQG 1exmA 301 :GQVLAKPG T0316 278 :FYHDS 1exmA 323 :LKKEE T0316 297 :REMPEEFTLECTAKFRYRQPDSKVTVHVKGE 1exmA 328 :GGRHTGFFSGYRPQFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAEPQR 1exmA 369 :TFTVELIKPVA T0316 340 :ITPGQAVVFYDGEECLGGGLIDNAY 1exmA 380 :LEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 21 number of extra gaps= 0 total=1840 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exmA/T0316-1exmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1exmA/T0316-1exmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exmA read from 1exmA/T0316-1exmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1exmA in template set T0316 7 :TRVVVGMS 1exmA 100 :DGAILVVS T0316 19 :SSVTALLLKEQGYD 1exmA 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1exmA 131 :IVVFMN T0316 46 :ENGVCTATEDYK 1exmA 137 :KVDMVDDPELLD T0316 58 :DVVAVADQI 1exmA 153 :EVRDLLNQY T0316 67 :GIPYYSVNF 1exmA 167 :EVPVIRGSA T0316 85 :EYFLAEYRA 1exmA 176 :LLALEQMHR T0316 94 :GRTPNPD 1exmA 186 :PKTRRGE T0316 104 :NKEI 1exmA 193 :NEWV T0316 108 :KFKAFLDYAITL 1exmA 198 :KIWELLDAIDEY T0316 131 :RVARDEDGTV 1exmA 212 :TPVRDVDKPF T0316 191 :AKKKDSTGICFIGEKN 1exmA 228 :VFTITGRGTVATGRIE T0316 226 :DGRDMGEHAGLMYYTIGQRGGLGIGGQHGGDNAPWFVVGK 1exmA 252 :EVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLR T0316 266 :DLSKNILYVGQGFY 1exmA 297 :EVERGQVLAKPGSI T0316 300 :PEEFTLECTA 1exmA 311 :TPHTKFEASV T0316 310 :KFRYRQPDSKVTVHVKGE 1exmA 341 :QFYFRTTDVTGVVQLPPG T0316 328 :KTEVIFAE 1exmA 369 :TFTVELIK T0316 337 :QRAITPGQAVVFYDGEECLGGGLID 1exmA 377 :PVALEEGLRFAIREGGRTVGAGVVT Number of specific fragments extracted= 18 number of extra gaps= 0 total=1858 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exmA/T0316-1exmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1exmA/T0316-1exmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1exmA read from 1exmA/T0316-1exmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1exmA in template set T0316 7 :TRVVVGMS 1exmA 100 :DGAILVVS T0316 18 :DSSVTALLLKEQGYDVIGIFMKNWDDTDEN 1exmA 115 :QTREHILLARQVGVPYIVVFMNKVDMVDDP T0316 54 :EDY 1exmA 145 :ELL T0316 57 :KDVVAVADQIGIP 1exmA 152 :MEVRDLLNQYEFP T0316 70 :YYSVNF 1exmA 170 :VIRGSA T0316 77 :K 1exmA 176 :L T0316 82 :RVFEYFLA 1exmA 177 :LALEQMHR T0316 98 :NPDVMCNKEI 1exmA 185 :NPKTRRGENE T0316 108 :KFKAFLDYAIT 1exmA 198 :KIWELLDAIDE T0316 119 :LGAD 1exmA 217 :VDKP T0316 129 :YARVARDEDGTVHMLRGVDNGK 1exmA 225 :VEDVFTITGRGTVATGRIERGK T0316 193 :KKDSTGICFIGE 1exmA 247 :VKVGDEVEIVGL T0316 214 :YLPAQPGRMMT 1exmA 259 :APETRKTVVTG T0316 236 :LMY 1exmA 270 :VEM T0316 243 :QRGGLGIGG 1exmA 273 :HRKTLQEGI T0316 256 :DNAPWFVV 1exmA 282 :AGDNVGVL T0316 264 :GKDLSKNILYVGQGFYHD 1exmA 295 :REEVERGQVLAKPGSITP T0316 285 :STS 1exmA 313 :HTK T0316 288 :LEASQVHFTREMPEEFTLE 1exmA 323 :LKKEEGGRHTGFFSGYRPQ T0316 311 :FRYRQPDSKVTVHVKGEK 1exmA 342 :FYFRTTDVTGVVQLPPGV T0316 329 :TEVIFAEPQ 1exmA 370 :FTVELIKPV T0316 339 :AITPGQAVVFYDGEECLGGGLIDNAY 1exmA 379 :ALEEGLRFAIREGGRTVGAGVVTKIL Number of specific fragments extracted= 22 number of extra gaps= 0 total=1880 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s0uA/T0316-1s0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s0uA expands to /projects/compbio/data/pdb/1s0u.pdb.gz 1s0uA:# T0316 read from 1s0uA/T0316-1s0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s0uA read from 1s0uA/T0316-1s0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s0uA to template set # found chain 1s0uA in template set Warning: unaligning (T0316)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s0uA)N213 Warning: unaligning (T0316)K108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s0uA)N213 Warning: unaligning (T0316)K150 because of BadResidue code BAD_PEPTIDE in next template residue (1s0uA)P249 Warning: unaligning (T0316)Q158 because of BadResidue code BAD_PEPTIDE at template residue (1s0uA)P249 T0316 7 :TRVVVGM 1s0uA 135 :DGAILVI T0316 19 :SSVTALLLKEQGYD 1s0uA 152 :TKEHLMALEILGID T0316 33 :VIGIFM 1s0uA 167 :IIIVQN T0316 46 :ENGVC 1s0uA 173 :KIDLV T0316 52 :ATEDYKDVVAVADQI 1s0uA 178 :DEKQAEENYEQIKEF T0316 67 :GIPYYS 1s0uA 200 :NAPIIP T0316 109 :FKAFLDYAITL 1s0uA 214 :IDVLLKAIQDF T0316 120 :GA 1s0uA 229 :KR T0316 132 :V 1s0uA 231 :D T0316 134 :RDEDGTVHMLRGVDNG 1s0uA 232 :PDATPRMYVARSFDIN T0316 159 :LSQEQLQK 1s0uA 250 :GTEIKDLK T0316 191 :AKKKDSTGICFIGEKNFKNFLSNYLPA 1s0uA 309 :LRKAHPGGLIGVGTTLDPYLTKSDALT T0316 218 :QPGRMMTV 1s0uA 341 :LPGTLPPI T0316 226 :DGRDM 1s0uA 350 :EKITI T0316 239 :YTI 1s0uA 355 :RAN T0316 249 :IGGQH 1s0uA 358 :LLDRV T0316 297 :REMPEEFTLEC 1s0uA 363 :VGTKEELKIEP T0316 308 :TAKFRYRQPDSKVTVH 1s0uA 379 :VLMLNIGTATTAGVIT T0316 324 :VKGEKTEVIFAEPQRAITPGQAVVFYD 1s0uA 396 :ARGDIADIKLKLPICAEIGDRVAISRR T0316 351 :GE 1s0uA 425 :SR T0316 353 :ECLGGGLID 1s0uA 428 :RLIGYGTIE Number of specific fragments extracted= 21 number of extra gaps= 1 total=1901 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s0uA/T0316-1s0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1s0uA/T0316-1s0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s0uA read from 1s0uA/T0316-1s0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s0uA in template set Warning: unaligning (T0316)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s0uA)N213 Warning: unaligning (T0316)K108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s0uA)N213 Warning: unaligning (T0316)R144 because of BadResidue code BAD_PEPTIDE in next template residue (1s0uA)P249 Warning: unaligning (T0316)G145 because of BadResidue code BAD_PEPTIDE at template residue (1s0uA)P249 T0316 7 :TRVVVGM 1s0uA 135 :DGAILVI T0316 19 :SSVTALLLKEQGYD 1s0uA 152 :TKEHLMALEILGID T0316 33 :VIGIFM 1s0uA 167 :IIIVQN T0316 46 :ENGVC 1s0uA 173 :KIDLV T0316 52 :ATEDYKDVVAVADQI 1s0uA 178 :DEKQAEENYEQIKEF T0316 67 :GIPYYS 1s0uA 200 :NAPIIP T0316 109 :FKAFLDYAITL 1s0uA 214 :IDVLLKAIQDF T0316 131 :RVARDEDGTVHM 1s0uA 227 :TPKRDPDATPRM T0316 143 :L 1s0uA 247 :N T0316 146 :VDNGKDQTY 1s0uA 250 :GTEIKDLKG T0316 196 :S 1s0uA 259 :G T0316 197 :TGICFIGEKN 1s0uA 261 :LGGAIIQGVF T0316 218 :QPGRMMTV 1s0uA 271 :KVGDEIEI T0316 226 :DGRDMGEHAGLMYYTIGQRGGLGIGGQH 1s0uA 289 :KTFWKPLTTKIVSLAAGNTILRKAHPGG T0316 260 :WFVVGKDLS 1s0uA 317 :LIGVGTTLD T0316 271 :ILYVGQGFYHDSLMSTSLEASQVHFTREMPE 1s0uA 337 :SVVGLPGTLPPIREKITIRANLLDRVVGTKE T0316 302 :EFTLECTAKF 1s0uA 375 :RTGEVLMLNI T0316 314 :RQPDSKVTVH 1s0uA 385 :GTATTAGVIT T0316 324 :VKGEKTEVIFAEP 1s0uA 396 :ARGDIADIKLKLP T0316 338 :RAITPGQAVVFY 1s0uA 409 :ICAEIGDRVAIS T0316 350 :DGEECLGGGLID 1s0uA 425 :SRWRLIGYGTIE Number of specific fragments extracted= 21 number of extra gaps= 1 total=1922 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s0uA/T0316-1s0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1s0uA/T0316-1s0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s0uA read from 1s0uA/T0316-1s0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s0uA in template set Warning: unaligning (T0316)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s0uA)N213 Warning: unaligning (T0316)K108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s0uA)N213 Warning: unaligning (T0316)K150 because of BadResidue code BAD_PEPTIDE in next template residue (1s0uA)P249 Warning: unaligning (T0316)D151 because of BadResidue code BAD_PEPTIDE at template residue (1s0uA)P249 Warning: unaligning (T0316)R244 because of BadResidue code BAD_PEPTIDE in next template residue (1s0uA)P280 Warning: unaligning (T0316)G245 because of BadResidue code BAD_PEPTIDE at template residue (1s0uA)P280 T0316 7 :TRVVVGMSG 1s0uA 135 :DGAILVIAA T0316 16 :GVDSSVTALLLKEQGYD 1s0uA 149 :QPQTKEHLMALEILGID T0316 33 :VIGIFMKNWDDTDEN 1s0uA 167 :IIIVQNKIDLVDEKQ T0316 52 :ATEDYKDVVAVADQI 1s0uA 182 :AEENYEQIKEFVKGT T0316 67 :GIPYYS 1s0uA 200 :NAPIIP T0316 109 :FKAFLDYAIT 1s0uA 214 :IDVLLKAIQD T0316 119 :LGAD 1s0uA 225 :IPTP T0316 134 :RDEDGTVHMLRGV 1s0uA 230 :RDPDATPRMYVAR T0316 147 :DNG 1s0uA 245 :DIN T0316 168 :MFPLGHLE 1s0uA 250 :GTEIKDLK T0316 197 :TGICFIGE 1s0uA 261 :LGGAIIQG T0316 223 :MTVDGR 1s0uA 270 :FKVGDE T0316 241 :IGQ 1s0uA 276 :IEI T0316 246 :GLGIGGQHGGDNAPWFV 1s0uA 281 :GIKVTEGNKTFWKPLTT T0316 263 :VGKDLSKNILYVGQGFYHDSLMSTSLEASQVHFTREMPE 1s0uA 309 :LRKAHPGGLIGVGTTLDPYLTKSDALTGSVVGLPGTLPP T0316 303 :FTLECTAKFRYRQPD 1s0uA 348 :IREKITIRANLLDRV T0316 318 :SKVTVH 1s0uA 389 :TAGVIT T0316 324 :VKGEKTEVIFAEPQ 1s0uA 396 :ARGDIADIKLKLPI T0316 339 :AITPGQAVVFYD 1s0uA 410 :CAEIGDRVAISR T0316 351 :GEECLGGGLID 1s0uA 426 :RWRLIGYGTIE Number of specific fragments extracted= 20 number of extra gaps= 2 total=1942 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efcA/T0316-1efcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1efcA expands to /projects/compbio/data/pdb/1efc.pdb.gz 1efcA:# T0316 read from 1efcA/T0316-1efcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efcA read from 1efcA/T0316-1efcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1efcA to template set # found chain 1efcA in template set T0316 6 :KTRVVVGM 1efcA 98 :MDGAILVV T0316 19 :SSVTALLLKEQGYD 1efcA 115 :TREHILLGRQVGVP T0316 33 :VIGIFM 1efcA 130 :IIVFLN T0316 46 :ENGVCTATEDY 1efcA 136 :KCDMVDDEELL T0316 57 :KDVVAVADQIGIP 1efcA 151 :MEVRELLSQYDFP T0316 71 :YSVNFE 1efcA 168 :PIVRGS T0316 88 :LAEYRAGR 1efcA 174 :ALKALEGD T0316 105 :KEI 1efcA 182 :AEW T0316 108 :KFKAFLDYAITL 1efcA 187 :KILELAGFLDSY T0316 122 :D 1efcA 203 :E T0316 132 :VARD 1efcA 204 :RAID T0316 137 :DGTVHM 1efcA 208 :KPFLLP T0316 143 :LRGVDNGK 1efcA 217 :VFSISGRG T0316 188 :LSTAKKKDSTGICFIGEK 1efcA 231 :VERGIIKVGEEVEIVGIK T0316 220 :GRMMT 1efcA 249 :ETQKS T0316 226 :DGRDMGEHA 1efcA 261 :FRKLLDEGR T0316 235 :GLMYYTIGQRG 1efcA 273 :NVGVLLRGIKR T0316 246 :GLGIGGQHGGD 1efcA 288 :RGQVLAKPGTI T0316 263 :VGKDLSKNILYVGQG 1efcA 299 :KPHTKFESEVYILSK T0316 298 :EMPEEFTLECTAKFRYRQPDSKVTVHVKGE 1efcA 317 :GRHTPFFKGYRPQFYFRTTDVTGTIELPEG T0316 328 :KTEVIFAEPQ 1efcA 357 :KMVVTLIHPI T0316 339 :AITPGQAVVFYDGEECLGGGLIDNAY 1efcA 367 :AMDDGLRFAIREGGRTVGAGVVAKVL Number of specific fragments extracted= 22 number of extra gaps= 0 total=1964 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efcA/T0316-1efcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1efcA/T0316-1efcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efcA read from 1efcA/T0316-1efcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1efcA in template set T0316 5 :SKTRVVVGM 1efcA 97 :QMDGAILVV T0316 19 :SSVTALLLKEQGYD 1efcA 115 :TREHILLGRQVGVP T0316 33 :VIGIFM 1efcA 130 :IIVFLN T0316 46 :ENGVCTATEDYK 1efcA 136 :KCDMVDDEELLE T0316 58 :DVVAVADQIGIP 1efcA 152 :EVRELLSQYDFP T0316 72 :SVNFE 1efcA 169 :IVRGS T0316 84 :FEYFL 1efcA 174 :ALKAL T0316 89 :AEYRA 1efcA 182 :AEWEA T0316 108 :KFKAFLDYAITL 1efcA 187 :KILELAGFLDSY T0316 143 :LRGVDNGKDQTYFLS 1efcA 199 :IPEPERAIDKPFLLP T0316 188 :LSTAKKKDSTGICFIGEKNF 1efcA 214 :IEDVFSISGRGTVVTGRVER T0316 220 :GRMMTV 1efcA 239 :GEEVEI T0316 226 :DGRDMGEHAGLMYYTIGQRGGLGI 1efcA 288 :RGQVLAKPGTIKPHTKFESEVYIL T0316 250 :GGQHGGDNA 1efcA 313 :KDEGGRHTP T0316 259 :PWFVVGKD 1efcA 328 :PQFYFRTT T0316 317 :DSKVTVHVKGE 1efcA 336 :DVTGTIELPEG T0316 328 :KTEVIFAE 1efcA 357 :KMVVTLIH T0316 337 :QRAITPGQAVVFYDGEECLGGGLID 1efcA 365 :PIAMDDGLRFAIREGGRTVGAGVVA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1982 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1efcA/T0316-1efcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1efcA/T0316-1efcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1efcA read from 1efcA/T0316-1efcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1efcA in template set T0316 7 :TRVVVGMS 1efcA 99 :DGAILVVA T0316 18 :DSSVTALLLKEQGYD 1efcA 114 :QTREHILLGRQVGVP T0316 33 :VIGIFMKNWDDTDEN 1efcA 130 :IIVFLNKCDMVDDEE T0316 51 :TATEDYKDVVAVADQIGIP 1efcA 145 :LLELVEMEVRELLSQYDFP T0316 70 :YYSVNFE 1efcA 169 :IVRGSAL T0316 77 :KEYWDRVFE 1efcA 182 :AEWEAKILE T0316 87 :FLAEYRA 1efcA 191 :LAGFLDS T0316 95 :RTPNPDVMCNKEI 1efcA 198 :YIPEPERAIDKPF T0316 132 :VARDEDGTVHMLRGVDNG 1efcA 217 :VFSISGRGTVVTGRVERG T0316 190 :TAKKK 1efcA 235 :IIKVG T0316 197 :TGICFIGEK 1efcA 240 :EEVEIVGIK T0316 216 :PAQPGRMMT 1efcA 249 :ETQKSTCTG T0316 225 :VDGRDM 1efcA 260 :MFRKLL T0316 231 :GEHAGLMYYT 1efcA 268 :GRAGENVGVL T0316 244 :RGGLGIGGQHGG 1efcA 278 :LRGIKREEIERG T0316 260 :WFVVGKDL 1efcA 290 :QVLAKPGT T0316 270 :NILYVGQGFYH 1efcA 306 :SEVYILSKDEG T0316 294 :HFTREMPEEFTL 1efcA 317 :GRHTPFFKGYRP T0316 310 :KFRYRQPDSKVTVHVKGEK 1efcA 329 :QFYFRTTDVTGTIELPEGV T0316 329 :TEVIFAEPQ 1efcA 358 :MVVTLIHPI T0316 339 :AITPGQAVVFYDGEECLGGGLIDNA 1efcA 367 :AMDDGLRFAIREGGRTVGAGVVAKV Number of specific fragments extracted= 21 number of extra gaps= 0 total=2003 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0316-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kssA expands to /projects/compbio/data/pdb/1kss.pdb.gz 1kssA:# T0316 read from 1kssA/T0316-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0316-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kssA to template set # found chain 1kssA in template set T0316 6 :KTRVVVGMSGGV 1kssA 126 :TVDVVVVGSGGA T0316 19 :SSVTALLLKEQGYDVIGIFM 1kssA 138 :GFSAAISATDSGAKVILIEK T0316 39 :KNWDDTD 1kssA 159 :PVIGGNA T0316 50 :C 1kssA 184 :K T0316 52 :ATEDYKDVVAVADQI 1kssA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1kssA 202 :NI T0316 75 :FEKEYWDRVFEYFLA 1kssA 204 :NDPALVKVLSSHSKD T0316 90 :EYRAGRTPNPD 1kssA 222 :WMTAMGADLTD T0316 101 :VMCNKEI 1kssA 251 :AGVGAHV T0316 109 :FKAFLDYAITLGADY 1kssA 258 :VQVLYDNAVKRNIDL T0316 220 :GR 1kssA 455 :GI T0316 279 :YHDSLMSTSLEASQVHFTREMPEEF 1kssA 457 :DGKALTETVARYNSLVSSGKDTDFE T0316 333 :FAEPQRAITPGQAVV 1kssA 482 :RPNLPRALNEGNYYA T0316 348 :FYDGEEC 1kssA 498 :EVTPGVH T0316 355 :LGGGLIDN 1kssA 507 :MGGVMIDT T0316 363 :AYRDGQVCQY 1kssA 519 :MNAKKQVIPG Number of specific fragments extracted= 16 number of extra gaps= 0 total=2019 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0316-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kssA/T0316-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0316-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kssA in template set T0316 7 :TR 1kssA 125 :DT T0316 9 :VVVGMSGGV 1kssA 129 :VVVVGSGGA T0316 19 :SSVTALLLKEQGYDVIGIFMKN 1kssA 138 :GFSAAISATDSGAKVILIEKEP T0316 48 :GV 1kssA 160 :VI T0316 52 :ATEDYKDVVAVADQI 1kssA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1kssA 202 :NI T0316 76 :EKEYWDRVFEYFL 1kssA 205 :DPALVKVLSSHSK T0316 89 :AEYRAGRTPNPD 1kssA 221 :DWMTAMGADLTD T0316 101 :VMCNKEI 1kssA 251 :AGVGAHV T0316 109 :FKAFLDYAITLGAD 1kssA 258 :VQVLYDNAVKRNID T0316 135 :DEDGT 1kssA 284 :DDKGT T0316 143 :LRGV 1kssA 438 :LGVA T0316 147 :DNGKDQTY 1kssA 445 :DSLVKLGK T0316 156 :LSQLSQEQLQKTM 1kssA 453 :MEGIDGKALTETV T0316 177 :PEVRRLAEEAGLSTAKKKD 1kssA 466 :ARYNSLVSSGKDTDFERPN T0316 227 :GRDMGEHAGLMYYTIGQRGGLGIGG 1kssA 485 :LPRALNEGNYYAIEVTPGVHATMGG T0316 272 :LYVGQ 1kssA 510 :VMIDT T0316 344 :QAVVFYDGEECLG 1kssA 515 :KAEVMNAKKQVIP Number of specific fragments extracted= 18 number of extra gaps= 0 total=2037 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0316-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1kssA/T0316-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0316-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kssA in template set T0316 2 :SDNSKTRVVVGMSGGV 1kssA 122 :APHDTVDVVVVGSGGA T0316 19 :SSVTALLLKEQGYDVIGIFMKNWD 1kssA 138 :GFSAAISATDSGAKVILIEKEPVI T0316 46 :ENGVCTATEDYKDVVAVADQ 1kssA 183 :KKITDSPELMFEDTMKGGQN T0316 74 :NFEKEYWDRVFEYFLAEYR 1kssA 203 :INDPALVKVLSSHSKDSVD T0316 93 :AGRTPNPDVM 1kssA 225 :AMGADLTDVG T0316 106 :EIKFKAFLDYAITLGADYVATGHYARVARDEDGTVHMLRGVDNGKDQTYF 1kssA 255 :AHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWV T0316 156 :LSQLSQEQLQKTMFPLGHLE 1kssA 315 :GFAKNNERVAKLDPSLKGFI T0316 178 :EVRRLAEEAGLS 1kssA 344 :DGLDVAENAGGA T0316 222 :M 1kssA 356 :L Number of specific fragments extracted= 9 number of extra gaps= 0 total=2046 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eft/T0316-1eft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eft expands to /projects/compbio/data/pdb/1eft.pdb.gz 1eft:Warning: there is no chain 1eft will retry with 1eftA # T0316 read from 1eft/T0316-1eft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eft read from 1eft/T0316-1eft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eft to template set # found chain 1eft in template set Warning: unaligning (T0316)T139 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)G287 Warning: unaligning (T0316)V140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)G287 Warning: unaligning (T0316)I360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)T401 Warning: unaligning (T0316)D361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)T401 T0316 6 :KTRVVVGMS 1eft 99 :MDGAILVVS T0316 19 :SSVTALLLKEQGYD 1eft 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1eft 131 :IVVFMN T0316 46 :ENGVCTATEDY 1eft 137 :KVDMVDDPELL T0316 57 :KDVVAVADQIGIP 1eft 152 :MEVRDLLNQYEFP T0316 70 :YYSVNFE 1eft 168 :VPVIRGS T0316 84 :FEYFLAEYRA 1eft 175 :ALLALEEMHK T0316 94 :GRTPNPD 1eft 186 :PKTKRGE T0316 104 :NKEI 1eft 193 :NEWV T0316 108 :KFKAFLDYAITL 1eft 198 :KIWELLDAIDEY T0316 132 :VARD 1eft 213 :PVRD T0316 141 :HMLRGVDNGK 1eft 288 :LLLRGVSREE T0316 168 :MF 1eft 298 :VE T0316 234 :AGLMYYTIGQRGGL 1eft 300 :RGQVLAKPGSITPH T0316 266 :DLSKNILYVGQG 1eft 314 :TKFEASVYVLKK T0316 297 :REMPEEFTLECTAKFRYRQPDSKVTVHVKGE 1eft 328 :GGRHTGFFSGYRPQFYFRTTDVTGVVRLPQG T0316 328 :KTEVIFAEPQR 1eft 369 :TFTVELIKPVA T0316 340 :ITPGQAVVFYDGEECLGGGL 1eft 380 :LEEGLRFAIREGGRTVGAGV T0316 362 :NAY 1eft 402 :KIL Number of specific fragments extracted= 19 number of extra gaps= 2 total=2065 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eft/T0316-1eft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1eft/T0316-1eft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eft read from 1eft/T0316-1eft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eft in template set Warning: unaligning (T0316)V225 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)T232 Warning: unaligning (T0316)D229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)V256 Warning: unaligning (T0316)M230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)V256 Warning: unaligning (T0316)G248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)K275 Warning: unaligning (T0316)P259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)G287 Warning: unaligning (T0316)W260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)G287 Warning: unaligning (T0316)I360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)T401 Warning: unaligning (T0316)D361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)T401 T0316 7 :TRVVVGMS 1eft 100 :DGAILVVS T0316 19 :SSVTALLLKEQGYD 1eft 116 :TREHILLARQVGVP T0316 33 :VIGIFM 1eft 131 :IVVFMN T0316 46 :ENGVCTATEDYKD 1eft 137 :KVDMVDDPELLDL T0316 59 :VVAVADQIGIP 1eft 154 :VRDLLNQYEFP T0316 70 :YYSVNFE 1eft 168 :VPVIRGS T0316 84 :FEYF 1eft 175 :ALLA T0316 113 :LDYAIT 1eft 179 :LEEMHK T0316 134 :R 1eft 185 :N T0316 154 :YFLSQLSQEQLQ 1eft 186 :PKTKRGENEWVD T0316 178 :EVRRLAEEAG 1eft 198 :KIWELLDAID T0316 188 :LSTAKKK 1eft 210 :IPTPVRD T0316 195 :DSTGICFIG 1eft 218 :DKPFLMPVE T0316 221 :RMMT 1eft 227 :DVFT T0316 226 :DGR 1eft 252 :EVE T0316 231 :GEHAGLMYYTIGQRGGL 1eft 257 :GLAPETRKTVVTGVEMH T0316 249 :I 1eft 277 :L T0316 252 :QHGGDNA 1eft 278 :QEGIAGD T0316 261 :FVV 1eft 288 :LLL T0316 264 :GKDLSKNILYVGQGFY 1eft 295 :REEVERGQVLAKPGSI T0316 300 :PEEFTLECTA 1eft 311 :TPHTKFEASV T0316 310 :KFRYRQPDSKVTVHVKGE 1eft 341 :QFYFRTTDVTGVVRLPQG T0316 328 :KTEVIFAE 1eft 369 :TFTVELIK T0316 337 :QRAITPGQAVVFYDGEECLGGGL 1eft 377 :PVALEEGLRFAIREGGRTVGAGV T0316 362 :N 1eft 402 :K Number of specific fragments extracted= 25 number of extra gaps= 5 total=2090 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eft/T0316-1eft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1eft/T0316-1eft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eft read from 1eft/T0316-1eft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eft in template set Warning: unaligning (T0316)D135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)T232 Warning: unaligning (T0316)E136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)T232 Warning: unaligning (T0316)F201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)V256 Warning: unaligning (T0316)I202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)V256 Warning: unaligning (T0316)R244 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)K275 Warning: unaligning (T0316)G245 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)K275 Warning: unaligning (T0316)W260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)G287 Warning: unaligning (T0316)F261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)G287 Warning: unaligning (T0316)I360 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eft)T401 Warning: unaligning (T0316)D361 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eft)T401 T0316 7 :TRVVVGMS 1eft 100 :DGAILVVS T0316 18 :DSSVTALLLKEQGYDVIGIFMKNWDDTDENGV 1eft 115 :QTREHILLARQVGVPYIVVFMNKVDMVDDPEL T0316 52 :ATEDYKDVVAVADQIGIP 1eft 147 :LDLVEMEVRDLLNQYEFP T0316 70 :YYSVN 1eft 170 :VIRGS T0316 84 :FEYFLAEYRA 1eft 175 :ALLALEEMHK T0316 94 :GRTP 1eft 186 :PKTK T0316 104 :N 1eft 193 :N T0316 108 :KFKAFLDYAIT 1eft 198 :KIWELLDAIDE T0316 129 :YARVAR 1eft 225 :VEDVFT T0316 137 :DGTVHMLRGVDNGK 1eft 233 :GRGTVATGRIERGK T0316 193 :KKDSTGIC 1eft 247 :VKVGDEVE T0316 203 :GE 1eft 257 :GL T0316 225 :VDGRDMGEHAGLMY 1eft 259 :APETRKTVVTGVEM T0316 246 :GLGIGG 1eft 276 :TLQEGI T0316 256 :DNAP 1eft 282 :AGDN T0316 262 :VV 1eft 288 :LL T0316 264 :GKDLSKNILYVGQGFYHD 1eft 295 :REEVERGQVLAKPGSITP T0316 285 :STS 1eft 313 :HTK T0316 288 :LEASQVHFTREMPEEFTL 1eft 323 :LKKEEGGRHTGFFSGYRP T0316 310 :KFRYRQPDSKVTVHVKGEK 1eft 341 :QFYFRTTDVTGVVRLPQGV T0316 329 :TEVIFAEPQ 1eft 370 :FTVELIKPV T0316 339 :AITPGQAVVFYDGEECLGGGL 1eft 379 :ALEEGLRFAIREGGRTVGAGV T0316 362 :NAY 1eft 402 :KIL Number of specific fragments extracted= 23 number of extra gaps= 5 total=2113 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0316-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y0pA expands to /projects/compbio/data/pdb/1y0p.pdb.gz 1y0pA:# T0316 read from 1y0pA/T0316-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0316-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y0pA to template set # found chain 1y0pA in template set Warning: unaligning (T0316)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0316)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0316)W41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 Warning: unaligning (T0316)D42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)G162 T0316 6 :KTR 1y0pA 124 :HDT T0316 9 :VVVGMSGGV 1y0pA 129 :VVVVGSGGA T0316 19 :SSVTALLLKEQGYD 1y0pA 138 :GFSAAISATDSGAK T0316 35 :GIFM 1y0pA 154 :LIEK T0316 39 :KN 1y0pA 159 :PV T0316 43 :DTD 1y0pA 163 :GNA T0316 50 :C 1y0pA 184 :K T0316 52 :ATEDYKDVVAVADQI 1y0pA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1y0pA 202 :NI T0316 75 :FEKEYWDRVFEYFLA 1y0pA 204 :NDPALVKVLSSHSKD T0316 90 :EYRAGRTPNPD 1y0pA 222 :WMTAMGADLTD T0316 101 :VMCNKEI 1y0pA 251 :AGVGAHV T0316 109 :FKAFLDYAITLGADY 1y0pA 258 :VQVLYDNAVKRNIDL T0316 139 :TVH 1y0pA 442 :PTA T0316 146 :VDNGK 1y0pA 445 :DSLVK T0316 153 :TYFLS 1y0pA 450 :LGKME T0316 173 :HLEKPEVRRLAEEA 1y0pA 455 :GIDGKALTETVARY T0316 291 :SQVHFTREMPEEF 1y0pA 469 :NSLVSSGKDTDFE T0316 333 :FAEPQRAITPGQAVV 1y0pA 482 :RPNLPRALNEGNYYA T0316 348 :FYDGEEC 1y0pA 498 :EVTPGVH T0316 355 :LGGGLIDN 1y0pA 507 :MGGVMIDT T0316 363 :AYRDGQVCQY 1y0pA 519 :MNAKKQVIPG Number of specific fragments extracted= 22 number of extra gaps= 2 total=2135 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0316-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1y0pA/T0316-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0316-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0pA in template set Warning: unaligning (T0316)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0316)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0316)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 T0316 7 :TR 1y0pA 125 :DT T0316 9 :VVVGMSGGV 1y0pA 129 :VVVVGSGGA T0316 19 :SSVTALLLKEQGYD 1y0pA 138 :GFSAAISATDSGAK T0316 35 :GIFMKNW 1y0pA 154 :LIEKEPV T0316 52 :ATEDYKDVVAVADQI 1y0pA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1y0pA 202 :NI T0316 76 :EKEYWDRVFEYFL 1y0pA 205 :DPALVKVLSSHSK T0316 89 :AEYRAGRTPNPD 1y0pA 221 :DWMTAMGADLTD T0316 101 :VMCNKEI 1y0pA 251 :AGVGAHV T0316 109 :FKAFLDYAITLGAD 1y0pA 258 :VQVLYDNAVKRNID T0316 123 :YVATGH 1y0pA 308 :AVILAT T0316 143 :LRGV 1y0pA 438 :LGVA T0316 147 :DNGKDQTY 1y0pA 445 :DSLVKLGK T0316 156 :LSQLSQEQLQKTM 1y0pA 453 :MEGIDGKALTETV T0316 177 :PEVRRLAEEAGLSTAKKKD 1y0pA 466 :ARYNSLVSSGKDTDFERPN T0316 227 :GRDMGEHAGLMYYTIGQRGGLGIGG 1y0pA 485 :LPRALNEGNYYAIEVTPGVHHTMGG T0316 272 :LYVG 1y0pA 510 :VMID T0316 343 :GQAVVFYDGEECL 1y0pA 514 :TKAEVMNAKKQVI Number of specific fragments extracted= 18 number of extra gaps= 2 total=2153 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0316-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1y0pA/T0316-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0316-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0pA in template set Warning: unaligning (T0316)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0316)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0316)D42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 T0316 3 :DNSKTRVVVGMSGGVD 1y0pA 123 :PHDTVDVVVVGSGGAG T0316 20 :SVTALLLKEQGYD 1y0pA 139 :FSAAISATDSGAK T0316 35 :GIFMKNW 1y0pA 154 :LIEKEPV T0316 47 :NGVCTATEDYKDVVAVADQ 1y0pA 184 :KITDSPELMFEDTMKGGQN T0316 74 :NFEKEYWDRVFEYFL 1y0pA 203 :INDPALVKVLSSHSK T0316 89 :AEYRAGRTPNPDVM 1y0pA 221 :DWMTAMGADLTDVG T0316 109 :FKAFLDYAITLGADYVATGHYARVARDEDGTVHMLRGVDNGKDQTYF 1y0pA 258 :VQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWV T0316 156 :LSQLSQEQLQKTMFPLGHLE 1y0pA 315 :GFAKNNERVAKLDPSLKGFI T0316 178 :EVRRLAEEAGL 1y0pA 344 :DGLDVAENAGG T0316 221 :RMMTVD 1y0pA 355 :ALKDMQ T0316 230 :MGEHA 1y0pA 362 :IQAHP Number of specific fragments extracted= 11 number of extra gaps= 2 total=2164 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0316-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q9iA expands to /projects/compbio/data/pdb/1q9i.pdb.gz 1q9iA:# T0316 read from 1q9iA/T0316-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0316-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q9iA to template set # found chain 1q9iA in template set Warning: unaligning (T0316)N47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0316)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0316 6 :KTR 1q9iA 124 :HDT T0316 9 :VVVGMSGGV 1q9iA 129 :VVVVGSGGA T0316 19 :SSVTALLLKEQGYDVIGIFMKN 1q9iA 138 :GFSAAISATDSGAKVILIEKEP T0316 46 :E 1q9iA 160 :V T0316 49 :V 1q9iA 163 :G T0316 50 :C 1q9iA 184 :K T0316 52 :ATEDYKDVVAVADQI 1q9iA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1q9iA 202 :NI T0316 75 :FEKEYWDRVFEYFLA 1q9iA 204 :NDPALVKVLSSHSKD T0316 90 :EYRAGRTPNPD 1q9iA 222 :WMTAMGADLTD T0316 103 :CNKEI 1q9iA 253 :VGAHV T0316 109 :FKAFLDYAITLGADY 1q9iA 258 :VQVLYDNAVKRNIDL T0316 139 :TVH 1q9iA 442 :PTA T0316 146 :VDNGK 1q9iA 445 :DSLVK T0316 153 :TYFLSQLSQEQLQKTM 1q9iA 450 :LGKMEGIDGKALTETV T0316 177 :PEVRRLAEEAGLSTAKKK 1q9iA 466 :ARYNSLVSSGKDTDFERP T0316 335 :EPQRAITPGQAVV 1q9iA 484 :NLPRALNEGNYYA T0316 348 :FYDGEEC 1q9iA 498 :EVTPGVH T0316 355 :LGGGLIDN 1q9iA 507 :MGGVMIDT T0316 363 :AYRDGQVCQY 1q9iA 519 :MNAKKQVIPG Number of specific fragments extracted= 20 number of extra gaps= 1 total=2184 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0316-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1q9iA/T0316-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0316-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q9iA in template set Warning: unaligning (T0316)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 T0316 7 :TR 1q9iA 125 :DT T0316 9 :VVVGMSGGV 1q9iA 129 :VVVVGSGGA T0316 19 :SSVTALLLKEQGYDVIGIFM 1q9iA 138 :GFSAAISATDSGAKVILIEK T0316 46 :ENG 1q9iA 158 :EPV T0316 52 :ATEDYKDVVAVADQI 1q9iA 185 :ITDSPELMFEDTMKG T0316 67 :GI 1q9iA 202 :NI T0316 76 :EKEYWDRVFEYFL 1q9iA 205 :DPALVKVLSSHSK T0316 89 :AEYRAGRTPNPD 1q9iA 221 :DWMTAMGADLTD T0316 103 :CNKEI 1q9iA 253 :VGAHV T0316 109 :FKAFLDYAITLGAD 1q9iA 258 :VQVLYDNAVKRNID T0316 133 :ARDEDGT 1q9iA 282 :LKDDKGT T0316 143 :LRGV 1q9iA 438 :LGVA T0316 147 :DNGKDQTY 1q9iA 445 :DSLVKLGK T0316 156 :LSQLSQEQLQKTM 1q9iA 453 :MEGIDGKALTETV T0316 177 :PEVRRLAEEAGLSTAKKKDS 1q9iA 466 :ARYNSLVSSGKDTDFERPNL T0316 228 :RDMGEHAGLMYYTIGQRGGLGIGG 1q9iA 486 :PRALNEGNYYAIEVTPGVHHTMGG T0316 272 :LY 1q9iA 510 :VM T0316 341 :TPGQAVVFYDGEECLGG 1q9iA 512 :IDTKAEVMNAKKQVIPG Number of specific fragments extracted= 18 number of extra gaps= 1 total=2202 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0316-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1q9iA/T0316-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0316-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q9iA in template set Warning: unaligning (T0316)D42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0316)D43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0316 3 :DNSKTRVVVGMSGGVD 1q9iA 123 :PHDTVDVVVVGSGGAG T0316 20 :SVTALLLKEQGYDVIGIFMKNW 1q9iA 139 :FSAAISATDSGAKVILIEKEPV T0316 52 :ATEDYKDVVAVADQI 1q9iA 185 :ITDSPELMFEDTMKG T0316 75 :FEKEYWDRVFEYFL 1q9iA 204 :NDPALVKVLSSHSK T0316 89 :AEYRAGRTPNPDVM 1q9iA 221 :DWMTAMGADLTDVG T0316 106 :EIKFKAFLDYAITLGADYVATGHYARVARDEDGTVHMLRGVDNGKDQTYF 1q9iA 255 :AHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILVKGMYKGYYWV T0316 156 :LSQLSQEQLQKTMFPLGHLE 1q9iA 315 :GFAKNNERVAKLDPSLKGFI T0316 178 :EVRRLAEEAGL 1q9iA 344 :DGLDVAENAGG T0316 221 :RMMTVD 1q9iA 355 :ALKDMQ T0316 230 :MGEH 1q9iA 362 :IQAH Number of specific fragments extracted= 10 number of extra gaps= 1 total=2212 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtB/T0316-1fmtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fmtB expands to /projects/compbio/data/pdb/1fmt.pdb.gz 1fmtB:# T0316 read from 1fmtB/T0316-1fmtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtB read from 1fmtB/T0316-1fmtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fmtB to template set # found chain 1fmtB in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1fmtB)E2 Warning: unaligning (T0316)C50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtB)L46 T0316 6 :KTRVVVGM 1fmtB 3 :SLRIIFAG T0316 20 :SVTALLLKEQGYDVIGIFM 1fmtB 16 :ARHLDALLSSGHNVVGVFT T0316 46 :ENGV 1fmtB 35 :QPDR T0316 58 :DVVAVADQIGIPYYS 1fmtB 50 :PVKVLAEEKGLPVFQ T0316 100 :DVMCNKEI 1fmtB 65 :PVSLRPQE T0316 112 :FLDYAITLGADYVATGHY 1fmtB 73 :NQQLVAELQADVMVVVAY T0316 137 :DG 1fmtB 91 :GL T0316 153 :TYFLSQLSQEQLQK 1fmtB 168 :YDKLAELGPQGLIT T0316 172 :GHLEKPEVRRLAEEAG 1fmtB 216 :WSLSAAQLERCIRAFN T0316 197 :TGICFI 1fmtB 233 :WPMSWL T0316 232 :EHAGLMYYTI 1fmtB 239 :EIEGQPVKVW T0316 246 :GLGIGGQHGGDNAPW 1fmtB 249 :KASVIDTATNAAPGT T0316 322 :VH 1fmtB 264 :IL T0316 324 :VKGEKTEVIFAE 1fmtB 267 :ANKQGIQVATGD T0316 343 :GQAVV 1fmtB 279 :GILNL T0316 348 :FYD 1fmtB 285 :SLQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=2228 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtB/T0316-1fmtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1fmtB/T0316-1fmtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtB read from 1fmtB/T0316-1fmtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmtB in template set Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtB)L46 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmtB)L46 T0316 6 :KTRVVVGM 1fmtB 3 :SLRIIFAG T0316 19 :SSVTALLLKEQGYDVIGIFMKNWD 1fmtB 15 :AARHLDALLSSGHNVVGVFTQPDR T0316 50 :CTA 1fmtB 47 :MPS T0316 58 :DVVAVADQIGIPYYS 1fmtB 50 :PVKVLAEEKGLPVFQ T0316 100 :DVMCNKE 1fmtB 65 :PVSLRPQ T0316 110 :KA 1fmtB 72 :EN T0316 113 :LDYAITLGADYVATGHYARVAR 1fmtB 74 :QQLVAELQADVMVVVAYGLILP T0316 140 :VHM 1fmtB 184 :KQL T0316 143 :LRGVDN 1fmtB 188 :DGTAKP T0316 149 :GKDQTYFLSQLSQE 1fmtB 197 :DETLVTYAEKLSKE T0316 166 :KTMFPL 1fmtB 211 :EARIDW T0316 173 :HLEKPEVRRLAEEAG 1fmtB 217 :SLSAAQLERCIRAFN T0316 188 :LSTAKKKD 1fmtB 235 :MSWLEIEG T0316 197 :TGICFIG 1fmtB 243 :QPVKVWK T0316 204 :EKN 1fmtB 254 :DTA T0316 215 :LPAQPGRMMTVD 1fmtB 257 :TNAAPGTILEAN T0316 326 :GEKTEVIFAE 1fmtB 269 :KQGIQVATGD T0316 344 :QAVVFY 1fmtB 279 :GILNLL Number of specific fragments extracted= 18 number of extra gaps= 0 total=2246 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmtB/T0316-1fmtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0316 read from 1fmtB/T0316-1fmtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fmtB read from 1fmtB/T0316-1fmtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fmtB in template set Warning: unaligning (T0316)S5 because first residue in template chain is (1fmtB)E2 Warning: unaligning (T0316)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fmtB)L46 Warning: unaligning (T0316)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1fmtB)L46 T0316 6 :KTRVVVGMS 1fmtB 3 :SLRIIFAGT T0316 19 :SSVTALLLKEQGYDVIGIFMKNWD 1fmtB 15 :AARHLDALLSSGHNVVGVFTQPDR T0316 50 :CTA 1fmtB 47 :MPS T0316 58 :DVVAVADQIGIPYYS 1fmtB 50 :PVKVLAEEKGLPVFQ T0316 104 :NKEIKFKAFLDYAITLGADYVATGHY 1fmtB 65 :PVSLRPQENQQLVAELQADVMVVVAY T0316 138 :GTVHMLRGVDNGKDQTYFLS 1fmtB 149 :DMLYKLSCPITAEDTSGTLY T0316 162 :EQLQKTM 1fmtB 169 :DKLAELG T0316 176 :KPEVRRLAEEAG 1fmtB 176 :PQGLITTLKQLA T0316 202 :IGE 1fmtB 204 :AEK T0316 205 :KNFKNFLS 1fmtB 218 :LSAAQLER T0316 213 :NYLPAQPGRMMTVDGR 1fmtB 228 :RAFNPWPMSWLEIEGQ T0316 259 :PWFVVGKDLSKN 1fmtB 244 :PVKVWKASVIDT T0316 296 :TREMPEEFTLE 1fmtB 256 :ATNAAPGTILE T0316 324 :VKGEKTEVIFAEPQRAI 1fmtB 267 :ANKQGIQVATGDGILNL T0316 361 :DNAYRDGQVCQ 1fmtB 284 :LSLQPAGKKAM Number of specific fragments extracted= 15 number of extra gaps= 0 total=2261 Will force an alignment to be made, even if fragment is small Number of alignments=148 # command:CPU_time= 46.981 sec, elapsed time= 51.191 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 148 Adding 69378 constraints to all_contacts Done adding distance constraints # command:CPU_time= 47.289 sec, elapsed time= 51.539 sec. # command:Reading probabilities from T0316.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 35.817 Optimizing... Probability sum: -692.523, CN propb: -692.523 weights: 0.131 constraints: 1257 # command:CPU_time= 51.945 sec, elapsed time= 56.266 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1257 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1257 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 10706 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 10706 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 54467 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 54467 # command:CPU_time= 53.112 sec, elapsed time= 58.250 sec. # command: