# 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 T0356 numbered 1 through 505 Created new target T0356 from T0356.a2m # command:CPU_time= 6.350 sec, elapsed time= 6.405 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0356-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0356 read from 1wqaA/T0356-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0356-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0356 28 :PVDPHLEIT 1wqaA 17 :KITPEFAMK # choosing archetypes in rotamer library T0356 37 :EIADRTLRAGG 1wqaA 29 :AFGTLLKREGR T0356 59 :SMPVLCNLFGT 1wqaA 41 :KPLVVVGRDTR T0356 80 :EDVSAL 1wqaA 52 :VSGEML T0356 86 :REVGKLLAFLK 1wqaA 59 :EALISGLLSVG T0356 110 :KLPQFKQVLN 1wqaA 82 :AVQWATKHFN T0356 160 :TWGLTVTRGPHK 1wqaA 92 :ADGGAVITASHN T0356 185 :GKNKLIMRWLSHRGGA 1wqaA 104 :PPEYNGIKLLEPNGMG T0356 201 :LDYQEWCAA 1wqaA 126 :AIVEELFFK T0356 212 :GE 1wqaA 135 :ED T0356 214 :RFPVSVALGAD 1wqaA 174 :KPFVVVDTSNG T0356 241 :EYAFAGLLRGTKTEVVKCIS 1wqaA 189 :TLPYLLRELGCKVITVNAQP T0356 285 :EGP 1wqaA 209 :DGY T0356 321 :YTGRPPDEPA 1wqaA 212 :FPARNPEPNE T0356 336 :LNEVFVPILQKQ 1wqaA 223 :NLKEFMEIVKAL T0356 352 :VDFYLPPEGCSYRLAV 1wqaA 238 :FGVAQDGDADRAVFID T0356 371 :KKQY 1wqaA 255 :NGRF T0356 375 :AGHAKRVMMGVWSFLRQF 1wqaA 262 :DKTFALVADAVLKEKGGG T0356 398 :VIVCDDDVN 1wqaA 280 :LLVTTVATS T0356 412 :D 1wqaA 293 :D T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVENTPIDYLDFASP 1wqaA 319 :NNGTIGGEENGGVIFPEHVLG T0356 458 :KWPGETQREWGRPIKKD 1wqaA 366 :ELPKYYQIKTKRHVEGD T0356 475 :PDVVAHIDAIWDELAI 1wqaA 384 :HAIVNKVAEMARERGY Number of specific fragments extracted= 24 number of extra gaps= 0 total=24 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 1wqaA/T0356-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1wqaA/T0356-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0356-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0356 8 :DLRDF 1wqaA 56 :MLKEA T0356 13 :LTLLEQQG 1wqaA 62 :ISGLLSVG T0356 21 :ELKRITL 1wqaA 71 :DVIDVGI T0356 33 :LEITEIADRTLRAGGPALLFENPKGYS 1wqaA 78 :APTPAVQWATKHFNADGGAVITASHNP T0356 62 :VLCNLFG 1wqaA 108 :NGIKLLE T0356 75 :MGMGQED 1wqaA 116 :NGMGLKK T0356 83 :SALREVGKLLAF 1wqaA 123 :EREAIVEELFFK T0356 96 :KEPEPPKG 1wqaA 135 :EDFDRAKW T0356 119 :NMPTKR 1wqaA 145 :IGEVRR T0356 197 :RGGALDYQEWCAA 1wqaA 151 :EDIIKPYIEAIKS T0356 214 :RFPVSVALGADPAT 1wqaA 174 :KPFVVVDTSNGAGS T0356 239 :LSEYAFAGLL 1wqaA 188 :LTLPYLLREL T0356 250 :GTKTEVVKCI 1wqaA 198 :GCKVITVNAQ T0356 261 :NDLEVPA 1wqaA 208 :PDGYFPA T0356 291 :HTG 1wqaA 215 :RNP T0356 324 :RPPDEP 1wqaA 218 :EPNEEN T0356 337 :NEVFVPILQKQ 1wqaA 224 :LKEFMEIVKAL T0356 352 :VDFYLPPEGCSYRLAV 1wqaA 238 :FGVAQDGDADRAVFID T0356 371 :KKQYAGHAKRVMMGVWSFLRQFMYTK 1wqaA 255 :NGRFIQGDKTFALVADAVLKEKGGGL T0356 399 :IVCDDDVN 1wqaA 281 :LVTTVATS T0356 410 :WND 1wqaA 291 :LDD T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVENTPIDYLDFASPVSG 1wqaA 319 :NNGTIGGEENGGVIFPEHVLGRDG T0356 458 :KWPGETQREWGRPIKKD 1wqaA 366 :ELPKYYQIKTKRHVEGD T0356 475 :PDVVAHIDAIWDELAI 1wqaA 384 :HAIVNKVAEMARERGY Number of specific fragments extracted= 25 number of extra gaps= 0 total=49 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 1wqaA/T0356-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1wqaA/T0356-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0356-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0356 22 :LKRITLPVDPHLEI 1wqaA 11 :RGIANEKITPEFAM T0356 36 :TEIADRTLRAGGPALLF 1wqaA 28 :MAFGTLLKREGRKKPLV T0356 61 :PVLCNLFGTPKRVA 1wqaA 45 :VVGRDTRVSGEMLK T0356 86 :REVGKLLAFLK 1wqaA 59 :EALISGLLSVG T0356 123 :KRLRGAPCQQK 1wqaA 73 :IDVGIAPTPAV T0356 147 :IMTCWPEDAAPLITWG 1wqaA 86 :ATKHFNADGGAVITAS T0356 169 :P 1wqaA 102 :H T0356 184 :IGKNKLIMRWLSHRGGA 1wqaA 103 :NPPEYNGIKLLEPNGMG T0356 201 :LDYQEWCA 1wqaA 126 :AIVEELFF T0356 214 :RFPVSVALGADPATILG 1wqaA 174 :KPFVVVDTSNGAGSLTL T0356 242 :YAFAGLLR 1wqaA 191 :PYLLRELG T0356 253 :TEVVKCISN 1wqaA 199 :CKVITVNAQ T0356 262 :DLEVPAS 1wqaA 209 :DGYFPAR T0356 299 :D 1wqaA 216 :N T0356 323 :GRPPDEP 1wqaA 217 :PEPNEEN T0356 337 :NEVFVPILQKQ 1wqaA 224 :LKEFMEIVKAL T0356 350 :EIVDFYLPPEGCSYRLAV 1wqaA 235 :GADFGVAQDGDADRAVFI T0356 373 :QY 1wqaA 257 :RF T0356 376 :GHAKRVMMGVWSFLRQ 1wqaA 260 :QGDKTFALVADAVLKE T0356 393 :MYTKFVIVC 1wqaA 276 :KGGGLLVTT T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVEN 1wqaA 319 :NNGTIGGEEN T0356 435 :IDYLDFASPVSG 1wqaA 329 :GGVIFPEHVLGR T0356 462 :ETQREWGRPIKKDPDVVAHIDAIWDELAIFNN 1wqaA 368 :PKYYQIKTKRHVEGDRHAIVNKVAEMARERGY Number of specific fragments extracted= 24 number of extra gaps= 0 total=73 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 1w1wA/T0356-1w1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w1wA expands to /projects/compbio/data/pdb/1w1w.pdb.gz 1w1wA:# T0356 read from 1w1wA/T0356-1w1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w1wA read from 1w1wA/T0356-1w1wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w1wA to template set # found chain 1w1wA in template set Warning: unaligning (T0356)Q79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)L62 Warning: unaligning (T0356)P101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)L62 Warning: unaligning (T0356)K123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)P89 Warning: unaligning (T0356)Q174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)P89 Warning: unaligning (T0356)F348 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)G1095 Warning: unaligning (T0356)P357 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)K1113 Warning: unaligning (T0356)T369 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)K1113 Warning: unaligning (T0356)D474 because last residue in template chain is (1w1wA)Y1223 T0356 24 :RITLPV 1w1wA 18 :VTKVGF T0356 45 :AGGPALLFENPKGY 1w1wA 24 :GESNFTSIIGPNGS T0356 69 :TPKRVAMGMG 1w1wA 42 :MMDAISFVLG T0356 102 :KGF 1w1wA 63 :KDL T0356 120 :MPT 1w1wA 66 :IYR T0356 175 :NLGIYRQQLIGKN 1w1wA 90 :QSAYVKAFYQKGN T0356 188 :KLIMRWLSHRG 1w1wA 106 :ELMRIISRNGD T0356 200 :ALDYQEWCAAHP 1w1wA 128 :YKDYSIFLENEN T0356 212 :GE 1w1wA 152 :GD T0356 333 :GVALNEVFVPILQKQ 1w1wA 1068 :FDYVSDHLDAIYREL T0356 353 :DFYL 1w1wA 1096 :NASL T0356 370 :IKK 1w1wA 1114 :YHA T0356 373 :QYAGHAKRVMMGVWSFLRQFMYTKFVIVCD 1w1wA 1128 :YLSGGEKTVAALALLFAINSYQPSPFFVLD T0356 403 :DDVNARDWNDVIWAITTRMDPARDTVLV 1w1wA 1161 :AALDITNVQRIAAYIRRHRNPDLQFIVI T0356 447 :LGSKMGLDATNKWPGETQREWGRPIKK 1w1wA 1196 :EKSDALVGVYRQQQENSSKIITLDLSN Number of specific fragments extracted= 15 number of extra gaps= 0 total=88 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 1w1wA/T0356-1w1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1w1wA/T0356-1w1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w1wA read from 1w1wA/T0356-1w1wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w1wA in template set Warning: unaligning (T0356)Q79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)L62 Warning: unaligning (T0356)P101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)L62 Warning: unaligning (T0356)K123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)P89 Warning: unaligning (T0356)R173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)P89 Warning: unaligning (T0356)F348 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)G1095 Warning: unaligning (T0356)C361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)G1095 Warning: unaligning (T0356)A366 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)K1113 Warning: unaligning (T0356)D474 because last residue in template chain is (1w1wA)Y1223 T0356 25 :ITLPV 1w1wA 19 :TKVGF T0356 45 :AGGPALLFENPKGY 1w1wA 24 :GESNFTSIIGPNGS T0356 68 :GTPKRVAMGMG 1w1wA 41 :NMMDAISFVLG T0356 102 :KGF 1w1wA 63 :KDL T0356 120 :MPT 1w1wA 66 :IYR T0356 174 :QNLGIYRQQLIGKN 1w1wA 90 :QSAYVKAFYQKGNK T0356 188 :KLIMRWLSHRG 1w1wA 106 :ELMRIISRNGD T0356 199 :GALDYQEWCAAHP 1w1wA 127 :SYKDYSIFLENEN T0356 212 :GE 1w1wA 152 :GD T0356 333 :GVALNEVFVPILQKQ 1w1wA 1068 :FDYVSDHLDAIYREL T0356 362 :SYRL 1w1wA 1096 :NASL T0356 375 :AGHAKRVMMGVWSFLRQFMYTKFVIV 1w1wA 1131 :GGEKTVAALALLFAINSYQPSPFFVL T0356 401 :CDDDVNARDWNDVIWAITTRMDPARDTVLVEN 1w1wA 1159 :VDAALDITNVQRIAAYIRRHRNPDLQFIVISL T0356 444 :V 1w1wA 1191 :K T0356 447 :LGSKMGLDATNKWPGETQREWGRPIKK 1w1wA 1196 :EKSDALVGVYRQQQENSSKIITLDLSN Number of specific fragments extracted= 15 number of extra gaps= 0 total=103 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 1w1wA/T0356-1w1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1w1wA/T0356-1w1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w1wA read from 1w1wA/T0356-1w1wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w1wA in template set T0356 375 :AGHAKRVMMGVWSFLRQFMYTKFVIV 1w1wA 1131 :GGEKTVAALALLFAINSYQPSPFFVL T0356 401 :CDDDVNARDWNDVIWAITTRMDPARDTVLVEN 1w1wA 1159 :VDAALDITNVQRIAAYIRRHRNPDLQFIVISL Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 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 2u1a/T0356-2u1a-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2u1a expands to /projects/compbio/data/pdb/2u1a.pdb.gz 2u1a:Warning: there is no chain 2u1a will retry with 2u1aA # T0356 read from 2u1a/T0356-2u1a-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2u1a read from 2u1a/T0356-2u1a-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2u1a to template set # found chain 2u1a in template set T0356 312 :REDAIYHSTYTGRPPDE 2u1a 8 :SENPPNHILFLTNLPEE T0356 337 :NEVFVPIL 2u1a 27 :ELMLSMLF T0356 346 :KQFPEIVDFYLPPEG 2u1a 35 :NQFPGFKEVRLVPGR T0356 363 :YRLAVVTI 2u1a 50 :HDIAFVEF T0356 373 :QYAGHAKRVMMG 2u1a 58 :DNEVQAGAARDA Number of specific fragments extracted= 5 number of extra gaps= 0 total=110 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 2u1a/T0356-2u1a-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 2u1a/T0356-2u1a-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2u1a read from 2u1a/T0356-2u1a-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2u1a in template set T0356 312 :REDAIYHSTYTGRPPDE 2u1a 8 :SENPPNHILFLTNLPEE T0356 337 :NEVFVPILQK 2u1a 27 :ELMLSMLFNQ T0356 348 :FPEIVDFYLPPEGC 2u1a 37 :FPGFKEVRLVPGRH T0356 364 :RLAVVTIK 2u1a 51 :DIAFVEFD T0356 374 :YAGHAKRVMM 2u1a 59 :NEVQAGAARD Number of specific fragments extracted= 5 number of extra gaps= 0 total=115 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 2u1a/T0356-2u1a-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 2u1a/T0356-2u1a-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2u1a read from 2u1a/T0356-2u1a-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2u1a in template set T0356 313 :EDAIYHSTYTGRPPDEP 2u1a 9 :ENPPNHILFLTNLPEET T0356 337 :NEVFVPILQKQFPEIVDFYLPPEGC 2u1a 26 :NELMLSMLFNQFPGFKEVRLVPGRH T0356 364 :RLAVVTIK 2u1a 51 :DIAFVEFD T0356 374 :YAGHAKRVMM 2u1a 59 :NEVQAGAARD Number of specific fragments extracted= 4 number of extra gaps= 0 total=119 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 1e9rA/T0356-1e9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e9rA expands to /projects/compbio/data/pdb/1e9r.pdb.gz 1e9rA:# T0356 read from 1e9rA/T0356-1e9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9rA read from 1e9rA/T0356-1e9rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e9rA to template set # found chain 1e9rA in template set T0356 341 :VPILQKQFPE 1e9rA 96 :GGKLKRMTRE T0356 351 :IVDFYLPPEGCSYRLAV 1e9rA 112 :VAGVPMPRDAEPRHLLV T0356 374 :YAGHAKRVMMGVWSFLRQFMYTKFVIVCDDD 1e9rA 131 :ATGTGKSVLLRELAYTGLLRGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTPIDY 1e9rA 163 :MLSKFGRDKDIILNPYDQRTK T0356 438 :LDFASPVSG 1e9rA 185 :WSFFNEIRN T0356 460 :PGETQR 1e9rA 194 :DYDWQR T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 7 number of extra gaps= 0 total=126 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 1e9rA/T0356-1e9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1e9rA/T0356-1e9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9rA read from 1e9rA/T0356-1e9rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e9rA in template set T0356 28 :PVDPHLEITEIADRTLR 1e9rA 133 :GTGKSVLLRELAYTGLL T0356 393 :MYTKFVIVCDDD 1e9rA 150 :RGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTP 1e9rA 163 :MLSKFGRDKDIILNPYDQ T0356 435 :IDYLDFASPVSG 1e9rA 185 :WSFFNEIRNDYD T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=131 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 1e9rA/T0356-1e9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1e9rA/T0356-1e9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9rA read from 1e9rA/T0356-1e9rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e9rA in template set T0356 313 :EDAIYHSTYTGRPPDEP 1e9rA 106 :KAKQVTVAGVPMPRDAE T0356 349 :PEIVDFYLPPEGC 1e9rA 123 :PRHLLVNGATGTG T0356 375 :AGHAKRVMMGVWS 1e9rA 137 :SVLLRELAYTGLL T0356 393 :MYTKFVIVCDDD 1e9rA 150 :RGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTPIDYLDFASPVSG 1e9rA 163 :MLSKFGRDKDIILNPYDQRTKGWSFFNEIR T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=137 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 1q7zA/T0356-1q7zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q7zA expands to /projects/compbio/data/pdb/1q7z.pdb.gz 1q7zA:# T0356 read from 1q7zA/T0356-1q7zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7zA read from 1q7zA/T0356-1q7zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q7zA to template set # found chain 1q7zA in template set T0356 9 :LRDFLTLLE 1q7zA 121 :FEEFYENFR T0356 37 :EIADRTLRAGGPALLFENP 1q7zA 130 :ETVEIMVEEGVDGIIFETF T0356 57 :GYSMPVLCNLFG 1q7zA 165 :SRDVFLIAHMTF T0356 69 :TPKRVAMGM 1q7zA 187 :DPANFAITF T0356 85 :LREVGKLLAF 1q7zA 211 :PEEILPIFQE T0356 114 :FKQ 1q7zA 221 :LSQ T0356 158 :LITWGLTVTRGPHKERQ 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 185 :GKNK 1q7zA 241 :ENGK T0356 194 :LSHRGGALDYQEWCAA 1q7zA 249 :LKPHDFAVHIDSYYEL T0356 212 :G 1q7zA 265 :G T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 224 :DPATI 1q7zA 276 :TPEHV T0356 242 :YAFAGLLRGTKTEVVKCIS 1q7zA 281 :KLFRKVLGNRKPLQRKKKR T0356 262 :DLEVPAS 1q7zA 300 :IFAVSSP T0356 307 :THITQREDAIYHSTYTG 1q7zA 307 :SKLVTFDHFVVIGERIN T0356 325 :PPDEPAVLGVAL 1q7zA 324 :PAGRKKLWAEMQ T0356 337 :NEVFVPILQKQ 1q7zA 339 :EEIVIKEAKTQ T0356 348 :FPEIVDFYLPPEGCSY 1q7zA 353 :GAEVLDVNFGIESQID T0356 375 :AGHAKRVMMGVWSFLRQF 1q7zA 369 :VRYVEKIVQTLPYVSNVP T0356 399 :IVCD 1q7zA 387 :LSLD T0356 407 :ARDWNDVIWAITTRM 1q7zA 391 :IQNVDLTERALRAYP T0356 426 :DTVLVENTPID 1q7zA 406 :GRSLFNSAKVD T0356 448 :GSKMGLDATN 1q7zA 431 :GGTLIVLLMG T0356 468 :GRPIKKDPDVVA 1q7zA 441 :KDVPKSFEERKE T0356 480 :HIDAIWDELAIFN 1q7zA 456 :KALKILERHDFSD Number of specific fragments extracted= 25 number of extra gaps= 0 total=162 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 1q7zA/T0356-1q7zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1q7zA/T0356-1q7zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7zA read from 1q7zA/T0356-1q7zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7zA in template set T0356 6 :YNDLRDFLTLLEQQG 1q7zA 125 :YENFRETVEIMVEEG T0356 29 :VDPHLEITEIADRTLRA 1q7zA 148 :FSDILELKAAVLAAREV T0356 46 :GGPALLFENP 1q7zA 167 :DVFLIAHMTF T0356 56 :KG 1q7zA 179 :KG T0356 58 :YSMPVLC 1q7zA 198 :LDIDALG T0356 65 :NLFGTPKRVA 1q7zA 206 :NCSLGPEEIL T0356 83 :SALREVGK 1q7zA 216 :PIFQELSQ T0356 158 :LITWGLTVTRGPHKERQ 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 185 :GKNKLI 1q7zA 241 :ENGKTV T0356 194 :LSHRGGALDYQEWCAAH 1q7zA 249 :LKPHDFAVHIDSYYELG T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 224 :DPAT 1q7zA 276 :TPEH T0356 241 :EYAFAGLLRGTKTEVVKCIS 1q7zA 280 :VKLFRKVLGNRKPLQRKKKR T0356 262 :DLEVPAS 1q7zA 300 :IFAVSSP T0356 307 :THITQREDAIYHSTYT 1q7zA 307 :SKLVTFDHFVVIGERI T0356 324 :RPPDEPAVLGVAL 1q7zA 323 :NPAGRKKLWAEMQ T0356 337 :NEVFVPILQKQFP 1q7zA 339 :EEIVIKEAKTQVE T0356 350 :EIVDFYLPPEGCS 1q7zA 355 :EVLDVNFGIESQI T0356 374 :YAGHAKRVMMGVWSFLRQF 1q7zA 368 :DVRYVEKIVQTLPYVSNVP T0356 398 :VIV 1q7zA 387 :LSL T0356 406 :NARDWNDVIWAITTRM 1q7zA 390 :DIQNVDLTERALRAYP T0356 426 :DTVLVENTPID 1q7zA 406 :GRSLFNSAKVD T0356 447 :LGSKMGLDATNK 1q7zA 430 :YGGTLIVLLMGK T0356 469 :RPIKKDP 1q7zA 442 :DVPKSFE T0356 476 :DVVAHIDAIWDELAIFN 1q7zA 452 :EYFEKALKILERHDFSD Number of specific fragments extracted= 25 number of extra gaps= 0 total=187 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 1q7zA/T0356-1q7zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1q7zA/T0356-1q7zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q7zA read from 1q7zA/T0356-1q7zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q7zA in template set T0356 7 :NDLRDFLTLLEQQG 1q7zA 126 :ENFRETVEIMVEEG T0356 28 :PVDPHLEITEIADRTLR 1q7zA 147 :TFSDILELKAAVLAARE T0356 45 :AGGPALLFENP 1q7zA 166 :RDVFLIAHMTF T0356 56 :KGY 1q7zA 179 :KGR T0356 59 :SMPVL 1q7zA 199 :DIDAL T0356 64 :CNLFGTPKRVA 1q7zA 205 :INCSLGPEEIL T0356 83 :SALREVGK 1q7zA 216 :PIFQELSQ T0356 117 :VLNMPTKRLRGAPCQQK 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 170 :HKERQNL 1q7zA 241 :ENGKTVY T0356 194 :LSHRGGALDYQEWCAAH 1q7zA 249 :LKPHDFAVHIDSYYELG T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 237 :DTLSEYAFAGLLRGTKTEVVKCISN 1q7zA 276 :TPEHVKLFRKVLGNRKPLQRKKKRI T0356 263 :LEVPASAEIV 1q7zA 301 :FAVSSPSKLV T0356 276 :YI 1q7zA 311 :TF T0356 313 :EDA 1q7zA 313 :DHF T0356 316 :IYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPE 1q7zA 318 :IGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEK T0356 351 :IVDFYLPPEGCS 1q7zA 356 :VLDVNFGIESQI T0356 374 :YAGHAKRVMMGVWSFLR 1q7zA 368 :DVRYVEKIVQTLPYVSN T0356 395 :TKFVIVC 1q7zA 385 :VPLSLDI T0356 409 :DWNDVIWAITT 1q7zA 393 :NVDLTERALRA T0356 433 :TPIDYLDFASPVSG 1q7zA 404 :YPGRSLFNSAKVDE T0356 447 :LGSKMGLDATNK 1q7zA 430 :YGGTLIVLLMGK T0356 469 :RPIKKDPDVVAHIDAIWDELAIFNNGK 1q7zA 442 :DVPKSFEERKEYFEKALKILERHDFSD Number of specific fragments extracted= 23 number of extra gaps= 0 total=210 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 1ejeA/T0356-1ejeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ejeA expands to /projects/compbio/data/pdb/1eje.pdb.gz 1ejeA:# T0356 read from 1ejeA/T0356-1ejeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejeA read from 1ejeA/T0356-1ejeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ejeA to template set # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0356)Q181 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0356 162 :GLTVTRG 1ejeA 30 :VMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 182 :QLI 1ejeA 49 :TMP T0356 185 :GKNKLIMRWLSHRGGALDYQEW 1ejeA 55 :DPPVVAFASAPDHHTARNIEST T0356 216 :PVSVALGA 1ejeA 78 :EFVINITP T0356 225 :PATILGAVTPVPDTLSEYAFA 1ejeA 89 :IERMWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPV 1ejeA 137 :RMFEVGDHNL T0356 304 :FTVTHITQREDAI 1ejeA 149 :GSVVSASVRSGAV Number of specific fragments extracted= 9 number of extra gaps= 1 total=219 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 1ejeA/T0356-1ejeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1ejeA/T0356-1ejeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejeA read from 1ejeA/T0356-1ejeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0356)Q181 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0356 162 :GLTVTRG 1ejeA 30 :VMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 182 :QLI 1ejeA 49 :TMP T0356 185 :GKNKLIMRWLSHRGGALDYQE 1ejeA 55 :DPPVVAFASAPDHHTARNIES T0356 208 :AA 1ejeA 76 :TH T0356 216 :PVSVALGAD 1ejeA 78 :EFVINITPA T0356 225 :PATILGAVTPVPDTLSEYAFA 1ejeA 89 :IERMWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPV 1ejeA 137 :RMFEVGDHNL T0356 304 :FTVTHITQREDAI 1ejeA 149 :GSVVSASVRSGAV Number of specific fragments extracted= 10 number of extra gaps= 1 total=229 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 1ejeA/T0356-1ejeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1ejeA/T0356-1ejeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejeA read from 1ejeA/T0356-1ejeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 T0356 161 :WGLTVTRG 1ejeA 29 :TVMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 181 :QQLIG 1ejeA 49 :TMPVS T0356 186 :KNKLIMRWLSHRGGALDYQEW 1ejeA 56 :PPVVAFASAPDHHTARNIEST T0356 216 :PVSVALGADPAT 1ejeA 78 :EFVINITPADII T0356 228 :ILGAVTPVPDTLSEYAFA 1ejeA 92 :MWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPVFT 1ejeA 137 :RMFEVGDHNLIT T0356 306 :VTHITQREDAI 1ejeA 151 :VVSASVRSGAV Number of specific fragments extracted= 9 number of extra gaps= 1 total=238 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 1vjeA/T0356-1vjeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjeA expands to /projects/compbio/data/pdb/1vje.pdb.gz 1vjeA:# T0356 read from 1vjeA/T0356-1vjeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjeA read from 1vjeA/T0356-1vjeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjeA to template set # found chain 1vjeA in template set Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 Warning: unaligning (T0356)L498 because last residue in template chain is (1vjeA)L156 T0356 297 :EVDSFPVFTVTHITQRED 1vjeA 15 :TKVKAPYVRLAGVKTTPK T0356 315 :AIYHSTYTGRPPDE 1vjeA 35 :QISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :CSYRLAV 1vjeA 84 :TGMYMAV T0356 371 :KKQYAGHAKRVMMGVWSFLRQFM 1vjeA 92 :GEPDEQGVMKAFEAALKDTAGHD T0356 403 :DD 1vjeA 115 :QP T0356 430 :VENTP 1vjeA 117 :IPGVS T0356 461 :GETQREWG 1vjeA 122 :ELECGNYR T0356 472 :KKD 1vjeA 130 :DHD T0356 475 :PDVVAHIDAIWDE 1vjeA 134 :AAARQHARDVLDQ T0356 489 :AIFNNGKSA 1vjeA 147 :GLKVQETIL Number of specific fragments extracted= 11 number of extra gaps= 0 total=249 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 1vjeA/T0356-1vjeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1vjeA/T0356-1vjeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjeA read from 1vjeA/T0356-1vjeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjeA in template set Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 T0356 291 :HTGYYNEVDSFPVFTVTHITQR 1vjeA 9 :SFDLDHTKVKAPYVRLAGVKTT T0356 313 :EDAIYHSTYTGRPPDE 1vjeA 33 :GDQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :C 1vjeA 84 :T T0356 365 :LAVVTIKKQY 1vjeA 85 :GMYMAVIGEP T0356 375 :AGHAKRVMMGVWSFLRQF 1vjeA 96 :EQGVMKAFEAALKDTAGH T0356 402 :DD 1vjeA 114 :DQ T0356 430 :VENTP 1vjeA 117 :IPGVS T0356 444 :VSGL 1vjeA 122 :ELEC T0356 468 :GRPIKKD 1vjeA 126 :GNYRDHD T0356 475 :PDVVAHIDAIWDE 1vjeA 134 :AAARQHARDVLDQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=260 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 1vjeA/T0356-1vjeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1vjeA/T0356-1vjeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjeA read from 1vjeA/T0356-1vjeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjeA in template set Warning: unaligning (T0356)D290 because first residue in template chain is (1vjeA)E8 Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 T0356 291 :HTGYYNEVDSFPVFTVTHITQRE 1vjeA 9 :SFDLDHTKVKAPYVRLAGVKTTP T0356 314 :DAIYHSTYTGRPPDE 1vjeA 34 :DQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :CSYRLAV 1vjeA 84 :TGMYMAV T0356 370 :IKKQYAGHAKRVMMGVWSFLRQ 1vjeA 91 :IGEPDEQGVMKAFEAALKDTAG T0356 421 :MDP 1vjeA 113 :HDQ T0356 438 :LDFASPVSGLG 1vjeA 116 :PIPGVSELECG T0356 460 :PGETQ 1vjeA 127 :NYRDH T0356 473 :KDPDVVAHIDAIWDE 1vjeA 132 :DLAAARQHARDVLDQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=269 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 1aisB/T0356-1aisB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aisB expands to /projects/compbio/data/pdb/1ais.pdb.gz 1aisB:# T0356 read from 1aisB/T0356-1aisB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisB read from 1aisB/T0356-1aisB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aisB to template set # found chain 1aisB in template set T0356 7 :NDLRDFLTLLEQQG 1aisB 1131 :EEAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 45 :AGG 1aisB 1166 :LKV T0356 67 :FGTPKRVAMGMGQEDVSALREVGKLLAFLK 1aisB 1169 :PRTLDEIADIARVDKKEIGRSYRFIARNLN T0356 98 :PEPPKGFRDLFDKLPQFKQVLNMPTK 1aisB 1199 :LTPKKLFVKPTDYVNKFADELGLSEK T0356 196 :HRGGALDYQEWCAA 1aisB 1226 :RRRAIEILDEAYKR T0356 212 :G 1aisB 1240 :G T0356 222 :GADPATILGAV 1aisB 1244 :GKSPAGLVAAA T0356 242 :YAFAGLLRGTKTE 1aisB 1255 :LYIASLLEGEKRT Number of specific fragments extracted= 9 number of extra gaps= 0 total=278 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 1aisB/T0356-1aisB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1aisB/T0356-1aisB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisB read from 1aisB/T0356-1aisB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aisB in template set T0356 7 :NDLRDFLTLLEQQG 1aisB 1131 :EEAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 45 :AG 1aisB 1166 :LK T0356 66 :LFGTPKRVAMGMGQED 1aisB 1168 :VPRTLDEIADIARVDK T0356 83 :SALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMP 1aisB 1184 :KEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS T0356 197 :RGGALDYQEWCAA 1aisB 1223 :EKVRRRAIEILDE T0356 210 :HPGE 1aisB 1238 :KRGL T0356 222 :GADPATILGAV 1aisB 1244 :GKSPAGLVAAA T0356 242 :YAFAGLLRGTKTE 1aisB 1255 :LYIASLLEGEKRT Number of specific fragments extracted= 9 number of extra gaps= 0 total=287 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 1aisB/T0356-1aisB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1aisB/T0356-1aisB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisB read from 1aisB/T0356-1aisB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aisB in template set T0356 8 :DLRDFLTLLEQQG 1aisB 1132 :EAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 46 :GG 1aisB 1167 :KV T0356 67 :FGTPKRVAMGMGQED 1aisB 1169 :PRTLDEIADIARVDK T0356 83 :SALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMP 1aisB 1184 :KEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS T0356 132 :QKIV 1aisB 1223 :EKVR T0356 197 :RGGALDYQ 1aisB 1227 :RRAIEILD T0356 207 :CAAHPGE 1aisB 1235 :EAYKRGL T0356 222 :GADPATILGA 1aisB 1244 :GKSPAGLVAA T0356 241 :EYAFAGLLRGTKTE 1aisB 1254 :ALYIASLLEGEKRT Number of specific fragments extracted= 10 number of extra gaps= 0 total=297 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 1o2dA/T0356-1o2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o2dA expands to /projects/compbio/data/pdb/1o2d.pdb.gz 1o2dA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 308, because occupancy 0.35 <= existing 0.650 in 1o2dA Skipped atom 310, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 397, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 399, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 401, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 403, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1118, because occupancy 0.500 <= existing 0.500 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1299, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1301, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1303, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1507, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1509, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1570, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1572, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1598, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1600, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1886, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1888, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1918, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1992, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1996, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 1998, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2000, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2002, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2004, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2006, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2125, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2127, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2129, because occupancy 0.350 <= existing 0.650 in 1o2dA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2736, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2738, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2740, because occupancy 0.350 <= existing 0.650 in 1o2dA Skipped atom 2742, because occupancy 0.350 <= existing 0.650 in 1o2dA # T0356 read from 1o2dA/T0356-1o2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o2dA read from 1o2dA/T0356-1o2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o2dA to template set # found chain 1o2dA in template set Warning: unaligning (T0356)G286 because of BadResidue code BAD_PEPTIDE at template residue (1o2dA)G139 T0356 55 :PKGYSMPVLCNLFGT 1o2dA 24 :IDLLGKRALVVTGKS T0356 78 :GQEDVSALREVGKLLAFLK 1o2dA 39 :SSKKNGSLDDLKKLLDETE T0356 120 :MPTKRLRG 1o2dA 58 :ISYEIFDE T0356 130 :CQ 1o2dA 66 :VE T0356 138 :D 1o2dA 68 :E T0356 197 :RGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 69 :NPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLRGTKTEV 1o2dA 103 :KAVAVLLKEKDLSV T0356 278 :EQGETAPE 1o2dA 121 :DREKVKHW T0356 287 :PYGDHTGYY 1o2dA 140 :TGSEVTPYS T0356 309 :ITQREDAIYHSTYTGRP 1o2dA 149 :ILTDPEGNKRGCTLMFP T0356 352 :VDFYLPPEGCSYR 1o2dA 166 :VYAFLDPRYTYSM T0356 374 :YAGHAKRVMMGVWSF 1o2dA 179 :SDELTLSTGVDALSH T0356 412 :DVIWAITTRM 1o2dA 194 :AVEGYLSRKS T0356 474 :DPDVVAHIDAIWDEL 1o2dA 204 :TPPSDALAIEAMKII Number of specific fragments extracted= 14 number of extra gaps= 1 total=311 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 1o2dA/T0356-1o2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1o2dA/T0356-1o2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o2dA read from 1o2dA/T0356-1o2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o2dA in template set Warning: unaligning (T0356)G323 because of BadResidue code BAD_PEPTIDE in next template residue (1o2dA)G139 Warning: unaligning (T0356)R324 because of BadResidue code BAD_PEPTIDE at template residue (1o2dA)G139 T0356 107 :LFDKLPQFKQVLNMPTKRLRG 1o2dA 45 :SLDDLKKLLDETEISYEIFDE T0356 135 :V 1o2dA 66 :V T0356 195 :SHRGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 67 :EENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLRGTKT 1o2dA 103 :KAVAVLLKEKDL T0356 264 :EV 1o2dA 115 :SV T0356 293 :GYYNEVD 1o2dA 118 :DLYDREK T0356 315 :AIYHSTYT 1o2dA 130 :PVVEIPTT T0356 325 :PPDE 1o2dA 140 :TGSE T0356 329 :PAVL 1o2dA 146 :PYSI T0356 348 :FPE 1o2dA 152 :DPE T0356 351 :IVDFYLPPEGCSYR 1o2dA 165 :PVYAFLDPRYTYSM T0356 374 :YAGHAKRVMMGVWSFL 1o2dA 179 :SDELTLSTGVDALSHA T0356 413 :VIWAITTRM 1o2dA 195 :VEGYLSRKS T0356 474 :DPDVVAHIDAIWDELAIF 1o2dA 204 :TPPSDALAIEAMKIIHRN Number of specific fragments extracted= 14 number of extra gaps= 1 total=325 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 1o2dA/T0356-1o2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1o2dA/T0356-1o2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o2dA read from 1o2dA/T0356-1o2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o2dA in template set T0356 106 :DLFDKLPQFKQVLNMPTKRLRG 1o2dA 44 :GSLDDLKKLLDETEISYEIFDE T0356 194 :LSHRGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 66 :VEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLR 1o2dA 103 :KAVAVLLK T0356 260 :SNDLEV 1o2dA 111 :EKDLSV T0356 278 :EQGETAPEGP 1o2dA 121 :DREKVKHWLP T0356 288 :YGDHTGYY 1o2dA 141 :GSEVTPYS T0356 296 :NEVDSF 1o2dA 152 :DPEGNK T0356 351 :IVDFYLPPEGC 1o2dA 165 :PVYAFLDPRYT T0356 375 :AGHAKRVMMGVWSF 1o2dA 180 :DELTLSTGVDALSH T0356 412 :DVIWAITTRM 1o2dA 194 :AVEGYLSRKS T0356 474 :DPDVVAHIDAIWDEL 1o2dA 204 :TPPSDALAIEAMKII Number of specific fragments extracted= 11 number of extra gaps= 0 total=336 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 1sviA/T0356-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sviA expands to /projects/compbio/data/pdb/1svi.pdb.gz 1sviA:# T0356 read from 1sviA/T0356-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0356-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sviA to template set # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 214 :RFPVSVALG 1sviA 22 :GLPEIALAG T0356 236 :PDTLSEYAFAGLLRG 1sviA 31 :RSNVGKSSFINSLIN T0356 303 :VFTVTHI 1sviA 61 :TLNFYII T0356 313 :EDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYL 1sviA 68 :NDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQ T0356 367 :VVTIKKQYAGHAKRVMMGVWS 1sviA 112 :IVDLRHAPSNDDVQMYEFLKY T0356 392 :FMYTKFVIVCD 1sviA 133 :YGIPVIVIATK T0356 403 :DDVNARDWNDVIWAITT 1sviA 145 :DKIPKGKWDKHAKVVRQ T0356 420 :RMDPARDTVLVEN 1sviA 164 :NIDPEDELILFSS T0356 444 :VSGLG 1sviA 177 :ETKKG T0356 450 :K 1sviA 182 :K T0356 475 :PDVVAHIDAIW 1sviA 183 :DEAWGAIKKMI Number of specific fragments extracted= 11 number of extra gaps= 0 total=347 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 1sviA/T0356-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1sviA/T0356-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0356-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 212 :GERFPVSVALG 1sviA 20 :EGGLPEIALAG T0356 236 :PDTLSEYAFAGLLRG 1sviA 31 :RSNVGKSSFINSLIN T0356 303 :VFTVTHI 1sviA 61 :TLNFYII T0356 313 :EDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYL 1sviA 68 :NDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQ T0356 367 :VVTIKKQYAGHAKRVMMGVWS 1sviA 112 :IVDLRHAPSNDDVQMYEFLKY T0356 392 :FMYTKFVIVCD 1sviA 133 :YGIPVIVIATK T0356 403 :DDVNARDWNDVIWAITT 1sviA 145 :DKIPKGKWDKHAKVVRQ T0356 420 :RMDPARDTVLVEN 1sviA 164 :NIDPEDELILFSS T0356 444 :VSGLG 1sviA 177 :ETKKG T0356 478 :VAHIDAIWDEL 1sviA 182 :KDEAWGAIKKM Number of specific fragments extracted= 10 number of extra gaps= 0 total=357 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 1sviA/T0356-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0356 read from 1sviA/T0356-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0356-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 212 :GERFPVSVALGA 1sviA 20 :EGGLPEIALAGR T0356 237 :DTLSEYAFAGLLRG 1sviA 32 :SNVGKSSFINSLIN T0356 303 :VFTV 1sviA 61 :TLNF T0356 310 :TQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLP 1sviA 65 :YIINDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQI T0356 368 :VTIKKQYAGHAKRVMMGVWSF 1sviA 113 :VDLRHAPSNDDVQMYEFLKYY T0356 393 :MYTKFVIVCDDD 1sviA 134 :GIPVIVIATKAD T0356 405 :VNARDWNDVIWAI 1sviA 147 :IPKGKWDKHAKVV T0356 418 :TTRMDPARDTVLVEN 1sviA 162 :TLNIDPEDELILFSS T0356 442 :SPV 1sviA 177 :ETK T0356 475 :PDVVAHIDAIW 1sviA 183 :DEAWGAIKKMI Number of specific fragments extracted= 10 number of extra gaps= 0 total=367 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 15.384 sec, elapsed time= 16.953 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 127260 constraints to all_contacts Done adding distance constraints # command:CPU_time= 15.669 sec, elapsed time= 17.269 sec. # command:Reading probabilities from T0356.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.683 Optimizing... Probability sum: -979.813, CN propb: -979.813 weights: 0.182 constraints: 1731 # command:CPU_time= 445.362 sec, elapsed time= 448.801 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1731 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1731 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 2637 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 2637 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 118888 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 118888 # command:CPU_time= 447.588 sec, elapsed time= 452.505 sec. # command: