parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0336/ # command:# Making conformation for sequence T0336 numbered 1 through 253 Created new target T0336 from T0336.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0336/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0336/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0336//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0336/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0336/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0336/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1un0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1un0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1un0A/merged-good-all-a2m.gz for input Trying 1un0A/merged-good-all-a2m Error: Couldn't open file 1un0A/merged-good-all-a2m or 1un0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xqsA expands to /projects/compbio/data/pdb/1xqs.pdb.gz 1xqsA:# T0336 read from 1xqsA/merged-good-all-a2m # 1xqsA read from 1xqsA/merged-good-all-a2m # adding 1xqsA to template set # found chain 1xqsA in template set T0336 4 :EEEEFDIREALAN 1xqsA 90 :VEQMKSCLRVLSQ # choosing archetypes in rotamer library T0336 17 :GEHLE 1xqsA 106 :PTAGE T0336 22 :KILIMAKYDESVLKKLIELL 1xqsA 112 :EQAADQQEREGALELLADLC T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1xqsA 155 :EAGAAGLRWRAAQLIGTCSQNVAAIQEQVLG T0336 73 :KLFSLLKKSEAIPLTQEIAKAFGQMAKE 1xqsA 191 :KLLRLLDRDACDTVRVKALFAISCLVRE T0336 102 :PE 1xqsA 219 :QE T0336 129 :YALEEIAKAN 1xqsA 221 :AGLLQFLRLD T0336 145 :IVRDFMSMLSSKNR 1xqsA 231 :GFSVLMRAMQQQVQ T0336 159 :EDKLT 1xqsA 247 :KVKSA T0336 164 :ALNFIEAMGENSFKYV 1xqsA 253 :LLQNLLVGHPEHKGTL T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1xqsA 271 :MGMVQQLVALVRTEHSPFHEHVLGALCSLVT T0336 211 :LNDKLR 1xqsA 306 :GVRECR T0336 217 :KVVIKRLEELNDT 1xqsA 319 :ELLRHRCQLLQQH T0336 230 :SSLVNKTVKEGISR 1xqsA 334 :YQEELEFCEKLLQT Number of specific fragments extracted= 14 number of extra gaps= 0 total=14 Number of alignments=1 # 1xqsA read from 1xqsA/merged-good-all-a2m # found chain 1xqsA in template set T0336 7 :EFDIREALAN 1xqsA 90 :VEQMKSCLRV T0336 17 :GEHLEKILIMAKYDESVLKKLIELL 1xqsA 107 :TAGEAEQAADQQEREGALELLADLC T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLY 1xqsA 155 :EAGAAGLRWRAAQLIGTCSQNVAAIQ T0336 68 :EPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMI 1xqsA 186 :LGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFL T0336 110 :PVLFANYRIGDEKTKINVSYALEEIAKANPMLMASI 1xqsA 233 :SVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTL T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGEN 1xqsA 274 :VQQLVALVRTEHSPFHEHVLGALCSLVTD T0336 183 :LPRIINLL 1xqsA 303 :FPQGVREC T0336 198 :RASA 1xqsA 311 :REPE T0336 209 :ATLNDKLRKVVIKRL 1xqsA 315 :LGLEELLRHRCQLLQ T0336 225 :ELNDT 1xqsA 330 :QHEEY T0336 231 :SLVNKTVKEGISRLL 1xqsA 335 :QEELEFCEKLLQTCF Number of specific fragments extracted= 11 number of extra gaps= 0 total=25 Number of alignments=2 # 1xqsA read from 1xqsA/merged-good-all-a2m # found chain 1xqsA in template set T0336 5 :EEEFDIREALANGEH 1xqsA 88 :GEVEQMKSCLRVLSQ T0336 20 :LEKILIMAKYDESVLKKLIELLDDD 1xqsA 110 :EAEQAADQQEREGALELLADLCENM T0336 65 :DLYEPMLKK 1xqsA 135 :DNAADFCQL T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1xqsA 149 :LVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLG T0336 111 :VLFANY 1xqsA 191 :KLLRLL T0336 117 :RIGDEKTKINVSYALEEIAKANPMLMASI 1xqsA 198 :RDACDTVRVKALFAISCLVREQEAGLLQF T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1xqsA 232 :FSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLC T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKV 1xqsA 275 :QQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRE T0336 219 :VIKRLEEL 1xqsA 317 :LEELLRHR T0336 227 :NDTSSLVN 1xqsA 329 :QQHEEYQE T0336 235 :KTVKEGISRL 1xqsA 339 :EFCEKLLQTC Number of specific fragments extracted= 11 number of extra gaps= 0 total=36 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xm9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xm9A expands to /projects/compbio/data/pdb/1xm9.pdb.gz 1xm9A:# T0336 read from 1xm9A/merged-good-all-a2m # 1xm9A read from 1xm9A/merged-good-all-a2m # adding 1xm9A to template set # found chain 1xm9A in template set Warning: unaligning (T0336)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xm9A)V397 T0336 4 :EEEEFDIREALANGEHLE 1xm9A 347 :QKQLTGLLWNLSSTDELK T0336 27 :AKYDESVLKKLIELL 1xm9A 365 :EELIADALPVLADRV T0336 44 :DLWTVVKNAISIIMVIAK 1xm9A 398 :VDPEVFFNATGCLRNLSS T0336 64 :EDLYEP 1xm9A 416 :ADAGRQ T0336 70 :MLKKLFSLLKKSEA 1xm9A 429 :LIDSLMAYVQNCVA T0336 84 :IPLTQEIAKAFGQMA 1xm9A 448 :DKSVENCMCVLHNLS T0336 106 :KSMIPV 1xm9A 463 :YRLDAE T0336 116 :YR 1xm9A 469 :VP T0336 124 :KIN 1xm9A 472 :RYR T0336 140 :MLMASIVRDFMSMLSSKNR 1xm9A 522 :LYHSDAIRTYLNLMGKSKK T0336 159 :EDKLT 1xm9A 543 :TLEAC T0336 164 :ALNFI 1xm9A 550 :ALQNL T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1xm9A 573 :EKGLPQIARLLQSGNSDVVRSGASLLSNMSR T0336 211 :LNDKLR 1xm9A 607 :LHRVMG T0336 217 :KVVIKRL 1xm9A 617 :PEVTRLL Number of specific fragments extracted= 15 number of extra gaps= 0 total=51 Number of alignments=4 # 1xm9A read from 1xm9A/merged-good-all-a2m # found chain 1xm9A in template set Warning: unaligning (T0336)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xm9A)V397 T0336 17 :GEHLEK 1xm9A 361 :DELKEE T0336 29 :YDESVLKKLIELL 1xm9A 367 :LIADALPVLADRV T0336 44 :DLWTVVKNAISIIMVIA 1xm9A 398 :VDPEVFFNATGCLRNLS T0336 61 :KTREDLY 1xm9A 421 :QTMRNYS T0336 69 :PMLKKLFSLLKKSEA 1xm9A 428 :GLIDSLMAYVQNCVA T0336 84 :IPLTQEIAKAFGQMA 1xm9A 448 :DKSVENCMCVLHNLS T0336 100 :EK 1xm9A 463 :YR T0336 112 :LFANYR 1xm9A 465 :LDAEVP T0336 130 :ALEE 1xm9A 547 :CAGA T0336 138 :NPMLMASIVR 1xm9A 558 :KGLMSSGMSQ T0336 148 :DFMSMLSSKNREDKLTALNFIEAMGE 1xm9A 578 :QIARLLQSGNSDVVRSGASLLSNMSR T0336 176 :FKYVNPF 1xm9A 604 :HPLLHRV T0336 183 :LPRIINLLHDGDE 1xm9A 616 :FPEVTRLLTSHTG T0336 198 :RASAVEALVHL 1xm9A 629 :NTSNSEDILSS T0336 211 :LNDKLRKVVIK 1xm9A 640 :ACYTVRNLMAS T0336 229 :TSSLVNKTV 1xm9A 651 :QPQLAKQYF T0336 238 :KEGISRLL 1xm9A 661 :SSMLNNII T0336 246 :LLEG 1xm9A 672 :RSSA Number of specific fragments extracted= 18 number of extra gaps= 0 total=69 Number of alignments=5 # 1xm9A read from 1xm9A/merged-good-all-a2m # found chain 1xm9A in template set T0336 1 :MSMEEEEFDIREALANGEHLEK 1xm9A 257 :QDEKYQAIGAYYIQHTCFQDES T0336 24 :LIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1xm9A 279 :AKQQVYQLGGICKLVDLLRSPNQNVQQAAAGALRNLVFRSTTNKLETRRQ T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1xm9A 334 :AVSLLRRTGNAEIQKQLTGLLWNLSSTDE T0336 103 :ELVKSMIP 1xm9A 366 :ELIADALP T0336 111 :VLFANY 1xm9A 530 :TYLNLM T0336 117 :RIGDEKTKINVSYALEEIAK 1xm9A 537 :KSKKDATLEACAGALQNLTA T0336 137 :ANPMLMASI 1xm9A 560 :LMSSGMSQL T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGEN 1xm9A 576 :LPQIARLLQSGNSDVVRSGASLLSNMSRH T0336 175 :SFKY 1xm9A 607 :LHRV T0336 179 :VNPFLPRIINLLH 1xm9A 612 :GNQVFPEVTRLLT T0336 192 :DGDEIVRASAVEALVHLATLNDKLRKV 1xm9A 631 :SNSEDILSSACYTVRNLMASQPQLAKQ T0336 219 :VIKRLEELNDTS 1xm9A 663 :MLNNIINLCRSS T0336 231 :SLVNKTVKEGISRLLLLEGHSS 1xm9A 677 :PKAAEAARLLLSDMWSSKELQG Number of specific fragments extracted= 13 number of extra gaps= 0 total=82 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bk6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bk6A expands to /projects/compbio/data/pdb/1bk6.pdb.gz 1bk6A:# T0336 read from 1bk6A/merged-good-all-a2m # 1bk6A read from 1bk6A/merged-good-all-a2m # adding 1bk6A to template set # found chain 1bk6A in template set T0336 5 :EEEFDIREALAN 1bk6A 102 :QEQLSATVKFRQ T0336 18 :EHLEKILIMAKYDESVLKKLIELL 1bk6A 116 :SREHRPPIDVVIQAGVVPRLVEFM T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1bk6A 141 :ENQPEMLQLEAAWALTNIASGTSAQTKVVVD T0336 73 :KLFSLLKKSE 1bk6A 177 :LFIQLLYTGS T0336 85 :PLTQEIAK 1bk6A 187 :VEVKEQAI T0336 93 :AFGQMAKEK 1bk6A 196 :ALGNVAGDS T0336 102 :PELVKSMIPVLFANYR 1bk6A 214 :CNAMEPILGLFNSNKP T0336 118 :IGDEKTKINVSYALEEIAKANPMLMASIV 1bk6A 268 :SMDTETLVDACWAISYLSDGPQEAIQAVI T0336 147 :RDFMSMLSSKNR 1bk6A 302 :KRLVELLSHEST T0336 159 :EDKLT 1bk6A 315 :VQTPA T0336 164 :ALNFI 1bk6A 322 :AVGNI T0336 176 :FKYV 1bk6A 373 :TEQI T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1bk6A 382 :ANLIPPLVKLLEVAEYKTKKEACWAISNASS T0336 211 :LNDKLR 1bk6A 420 :IIRYLV T0336 217 :KVVIKRLEELN 1bk6A 431 :KPLCDLLEIAD T0336 228 :DTSSLVNKTVK 1bk6A 443 :RIIEVTLDALE T0336 239 :EGISRLLLLEGHSS 1bk6A 457 :KMGEADKEARGLNI Number of specific fragments extracted= 17 number of extra gaps= 0 total=99 Number of alignments=7 # 1bk6A read from 1bk6A/merged-good-all-a2m # found chain 1bk6A in template set Warning: unaligning (T0336)E64 because of BadResidue code BAD_PEPTIDE in next template residue (1bk6A)P248 Warning: unaligning (T0336)D65 because of BadResidue code BAD_PEPTIDE at template residue (1bk6A)P248 T0336 23 :ILIMAKYDESVLKKLIELL 1bk6A 197 :LGNVAGDSTDYRDYVLQCN T0336 42 :DDDLWTVVKNAISIIMVIAKTR 1bk6A 225 :NSNKPSLIRTATWTLSNLCRGK T0336 66 :LY 1bk6A 249 :QP T0336 68 :EPMLKKLFSLLKKSEA 1bk6A 252 :WSVVSQALPTLAKLIY T0336 84 :IPLTQEIAKAFGQMAKEKPELVKSMIP 1bk6A 271 :TETLVDACWAISYLSDGPQEAIQAVID T0336 111 :VLFANYR 1bk6A 303 :RLVELLS T0336 120 :DEKTKIN 1bk6A 310 :HESTLVQ T0336 127 :VSYALEEIAKANPMLMASIVR 1bk6A 319 :ALRAVGNIVTGNDLQTQVVIN T0336 148 :DFMSMLSSKNREDKLTALNFIEAMGENSFKYVN 1bk6A 345 :ALRLLLSSPKENIKKEACWTISNITAGNTEQIQ T0336 181 :PFLPRIINLLHDGDE 1bk6A 383 :NLIPPLVKLLEVAEY T0336 210 :TLNDKLRKVVIKRLEELNDTSSLVNKTVK 1bk6A 398 :KTKKEACWAISNASSGGLQRPDIIRYLVS T0336 240 :GISRLL 1bk6A 429 :CIKPLC T0336 246 :LLEGHS 1bk6A 436 :LLEIAD Number of specific fragments extracted= 13 number of extra gaps= 1 total=112 Number of alignments=8 # 1bk6A read from 1bk6A/merged-good-all-a2m # found chain 1bk6A in template set Warning: unaligning (T0336)P102 because of BadResidue code BAD_PEPTIDE in next template residue (1bk6A)P248 T0336 2 :SMEEEEFDIREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1bk6A 143 :QPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQC T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEK 1bk6A 219 :PILGLFNSNKPSLIRTATWTLSNLCRGK T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKANPMLMASIV 1bk6A 253 :SVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVI T0336 147 :RDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1bk6A 302 :KRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVI T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKR 1bk6A 344 :PALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDA Number of specific fragments extracted= 5 number of extra gaps= 1 total=117 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ibrB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ibrB expands to /projects/compbio/data/pdb/1ibr.pdb.gz 1ibrB:# T0336 read from 1ibrB/merged-good-all-a2m # 1ibrB read from 1ibrB/merged-good-all-a2m # adding 1ibrB to template set # found chain 1ibrB in template set Warning: unaligning (T0336)G17 because of BadResidue code BAD_PEPTIDE in next template residue (1ibrB)Q303 Warning: unaligning (T0336)E18 because of BadResidue code BAD_PEPTIDE at template residue (1ibrB)Q303 T0336 3 :MEEEEFDIREALAN 1ibrB 286 :VCDEEMDLAIEASE T0336 19 :HLEKILIMAKYDESVLKKLIELL 1ibrB 304 :GRPPEHTSKFYAKGALQYLVPIL T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPML 1ibrB 338 :DDDDWNPCKAAGVCLMLLATCCEDDIVPHV T0336 75 :FSLLKKSEA 1ibrB 368 :LPFIKEHIK T0336 84 :IPLTQEIAK 1ibrB 379 :DWRYRDAAV T0336 93 :AFGQMA 1ibrB 389 :AFGCIL T0336 100 :EKPEL 1ibrB 395 :EGPEP T0336 106 :KSMIPVLFANYR 1ibrB 400 :SQLKPLVIQAMP T0336 118 :IGDEKTKIN 1ibrB 417 :MKDPSVVVR T0336 127 :VSYALEEIAKA 1ibrB 428 :AAWTVGRICEL T0336 138 :NPMLMASIVRDF 1ibrB 445 :NDVYLAPLLQCL Number of specific fragments extracted= 11 number of extra gaps= 1 total=128 Number of alignments=10 # 1ibrB read from 1ibrB/merged-good-all-a2m # found chain 1ibrB in template set Warning: unaligning (T0336)H19 because of BadResidue code BAD_PEPTIDE in next template residue (1ibrB)Q303 Warning: unaligning (T0336)L20 because of BadResidue code BAD_PEPTIDE at template residue (1ibrB)Q303 T0336 4 :EEEEFDIREALANGE 1ibrB 287 :CDEEMDLAIEASEAA T0336 21 :E 1ibrB 304 :G T0336 28 :KYDESVLKKLIELL 1ibrB 313 :FYAKGALQYLVPIL T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPML 1ibrB 338 :DDDDWNPCKAAGVCLMLLATCCEDDIVPHV T0336 75 :FSLLKKSEA 1ibrB 368 :LPFIKEHIK T0336 84 :IPLTQEIAK 1ibrB 379 :DWRYRDAAV T0336 93 :AFGQMA 1ibrB 389 :AFGCIL T0336 100 :EKPEL 1ibrB 395 :EGPEP T0336 106 :KSMIPVLFANYR 1ibrB 400 :SQLKPLVIQAMP T0336 118 :IGDEKTKIN 1ibrB 417 :MKDPSVVVR T0336 127 :VSYALEEIAKA 1ibrB 428 :AAWTVGRICEL T0336 138 :NPMLMASIVRDFM 1ibrB 445 :NDVYLAPLLQCLI Number of specific fragments extracted= 12 number of extra gaps= 1 total=140 Number of alignments=11 # 1ibrB read from 1ibrB/merged-good-all-a2m # found chain 1ibrB in template set T0336 3 :MEEEEFDIREALANGEHLEKI 1ibrB 14 :DRLELEAAQKFLERAAVENLP T0336 32 :SVLKKLIELLDDD 1ibrB 35 :TFLVELSRVLANP T0336 45 :LWTVVKNAISIIMV 1ibrB 50 :SQVARVAAGLQIKN T0336 59 :IAKTREDLYEPMLKK 1ibrB 65 :LTSKDPDIKAQYQQR T0336 74 :LFSLLKKSE 1ibrB 133 :LVANVTNPN T0336 83 :AIPLTQEIAKAFGQMAKEKP 1ibrB 143 :TEHMKESTLEAIGYICQDID T0336 103 :ELVKSMIPVLFANY 1ibrB 168 :DKSNEILTAIIQGM T0336 117 :RIGDEKTKINVSYALEEIAK 1ibrB 184 :EEPSNNVKLAATNALLNSLE T0336 137 :ANPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1ibrB 210 :DKESERHFIMQVVCEATQCPDTRVRVAALQNLVKIMSLYYQYMETYM T0336 184 :PRII 1ibrB 258 :PALF T0336 188 :NLLH 1ibrB 328 :QTLT T0336 192 :DGDEIVRASAVEALVHLAT 1ibrB 339 :DDDWNPCKAAGVCLMLLAT T0336 211 :LNDKLRKVVIKRLEELNDTSSLVNKTVKEGISRLLLLEGHSS 1ibrB 359 :CEDDIVPHVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPS Number of specific fragments extracted= 13 number of extra gaps= 0 total=153 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1ee5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1ee5A/merged-good-all-a2m.gz for input Trying 1ee5A/merged-good-all-a2m Error: Couldn't open file 1ee5A/merged-good-all-a2m or 1ee5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qbkB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qbkB expands to /projects/compbio/data/pdb/1qbk.pdb.gz 1qbkB:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0336 read from 1qbkB/merged-good-all-a2m # 1qbkB read from 1qbkB/merged-good-all-a2m # adding 1qbkB to template set # found chain 1qbkB in template set T0336 31 :ESVLKKLIELL 1qbkB 270 :ENVALEACEFW T0336 42 :D 1qbkB 368 :D T0336 43 :DDLWTVVKNAISIIMVIAKTREDLYEPML 1qbkB 370 :ISDWNLRKCSAAALDVLANVYRDELLPHI T0336 75 :FSLLKKSEA 1qbkB 399 :LPLLKELLF T0336 84 :IPLTQEIAK 1qbkB 410 :EWVVKESGI T0336 93 :AFGQMA 1qbkB 420 :VLGAIA T0336 100 :EKP 1qbkB 426 :EGC T0336 103 :ELVKSMIPVLFANYR 1qbkB 431 :GMIPYLPELIPHLIQ T0336 118 :IGDEKTKIN 1qbkB 447 :LSDKKALVR T0336 127 :VSYALEEIAKANP 1qbkB 462 :LSRYAHWVVSQPP T0336 140 :MLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFLPRIINLL 1qbkB 476 :TYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDTL T0336 191 :HDGDEIVRASAVEALVHLAT 1qbkB 531 :SKYQHKNLLILYDAIGTLAD T0336 211 :LNDKLRKVVIKRLEE 1qbkB 561 :YIQMLMPPLIQKWNM T0336 226 :LNDTSSLVNKTVKEGISRL 1qbkB 605 :CEPVYQRCVNLVQKTLAQA T0336 245 :LLLEGHS 1qbkB 626 :NNAQPDQ T0336 252 :S 1qbkB 634 :E Number of specific fragments extracted= 16 number of extra gaps= 0 total=169 Number of alignments=13 # 1qbkB read from 1qbkB/merged-good-all-a2m # found chain 1qbkB in template set Warning: unaligning (T0336)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qbkB)D358 T0336 11 :REALANGE 1qbkB 359 :DDDDEIDD T0336 42 :DD 1qbkB 367 :DD T0336 44 :DLWTVVKNAISIIMVIAKTREDLYEPML 1qbkB 371 :SDWNLRKCSAAALDVLANVYRDELLPHI T0336 75 :FSLLKKSEA 1qbkB 399 :LPLLKELLF T0336 84 :IPLTQEIAK 1qbkB 410 :EWVVKESGI T0336 93 :AFGQMA 1qbkB 420 :VLGAIA T0336 100 :EK 1qbkB 426 :EG T0336 102 :PELVKSMIPVLFANYR 1qbkB 433 :IPYLPELIPHLIQCLS T0336 120 :DEKTKIN 1qbkB 449 :DKKALVR T0336 127 :VSYALEEIAKA 1qbkB 462 :LSRYAHWVVSQ T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFLPRIINLLHDGDEIVR 1qbkB 474 :PDTYLKPLMTELLKRILDSNKRVQEAACSAFATLEEEACTELVPYLAYILDTLVFAFSKYQ T0336 203 :EALVHL 1qbkB 535 :HKNLLI T0336 211 :LNDKLRKVVIKRLEELND 1qbkB 541 :LYDAIGTLADSVGHHLNK T0336 230 :SSLVNKTVKEGISRLLLLEGHS 1qbkB 559 :PEYIQMLMPPLIQKWNMLKDED Number of specific fragments extracted= 14 number of extra gaps= 0 total=183 Number of alignments=14 # 1qbkB read from 1qbkB/merged-good-all-a2m # found chain 1qbkB in template set T0336 4 :EEEEFDIREALANGEHLEKILIMAKYD 1qbkB 606 :EPVYQRCVNLVQKTLAQAMLNNAQPDQ T0336 31 :ESVLK 1qbkB 660 :EQLVA T0336 36 :KLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1qbkB 671 :LMYQCMQDKMPEVRQSSFALLGDLTKACFQHVKPCIAD T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1qbkB 712 :ILGTNLNPEFISVCNNATWAIGEISIQMG T0336 103 :ELVKSMIPVLFANYRIGD 1qbkB 745 :PYIPMVLHQLVEIINRPN T0336 121 :EKTKINVSYALEEIAKANPMLM 1qbkB 765 :KTLLENTAITIGRLGYVCPQEV T0336 143 :ASIVRDFMSMLSS 1qbkB 791 :QQFIRPWCTSLRN T0336 156 :KNREDKLTALNFIEAMGENSFKYVNPFLPRIINLLH 1qbkB 805 :RDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVA T0336 192 :DGDEIVRASAVEALVHLATL 1qbkB 844 :NPKDDLRDMFCKILHGFKNQ T0336 212 :NDKLRKVVIK 1qbkB 865 :GDENWRRFSD T0336 228 :DTSSLVNKTVKEG 1qbkB 875 :QFPLPLKERLAAF Number of specific fragments extracted= 11 number of extra gaps= 0 total=194 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c1tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/2c1tA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/2c1tA/merged-good-all-a2m.gz for input Trying 2c1tA/merged-good-all-a2m Error: Couldn't open file 2c1tA/merged-good-all-a2m or 2c1tA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2awiA expands to /projects/compbio/data/pdb/2awi.pdb.gz 2awiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0336 read from 2awiA/merged-good-all-a2m # 2awiA read from 2awiA/merged-good-all-a2m # adding 2awiA to template set # found chain 2awiA in template set Warning: unaligning (T0336)E239 because last residue in template chain is (2awiA)N301 T0336 6 :E 2awiA 7 :V T0336 10 :IREALAN 2awiA 8 :LKQIRQE T0336 17 :GEHLEKILIMAKYD 2awiA 24 :SGIMSKSVYIKVEA T0336 31 :ESVLKKLIELL 2awiA 44 :VEELSKFSERL T0336 46 :WTVVKNAISI 2awiA 105 :TSLQYFSIYL T0336 56 :IMVIAKTRE 2awiA 116 :YISIAHHYN T0336 65 :DLYEPMLKKLFSLLKKSEAIPLTQEI 2awiA 128 :PTFNKTITSDLKHLYDKRTTFFGIDC T0336 92 :KAFGQMA 2awiA 154 :EIVSNLL T0336 100 :EKPE 2awiA 161 :NVLP T0336 105 :VKSMIPVLFANYRIGD 2awiA 165 :YEEVSSIIKPMYPIVD T0336 121 :EKT 2awiA 184 :KDY T0336 139 :PMLMASIV 2awiA 187 :DLTIQTVL T0336 147 :RDFMSMLSSKNR 2awiA 196 :NALTISIMNRNL T0336 161 :KLT 2awiA 208 :KEA T0336 164 :ALNFIEAMGE 2awiA 213 :YINQFEHLKT T0336 174 :NSFKYV 2awiA 224 :KNISIN T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 2awiA 236 :INYLKQIYQFLTDKNIDSYLNAVNIINIFKI T0336 211 :LNDKLRKVVIKRLEELN 2awiA 272 :IHRSLVEELTKISAKEK T0336 228 :DTSSLVNKTVK 2awiA 290 :TPPKEVTMYYE Number of specific fragments extracted= 19 number of extra gaps= 0 total=213 Number of alignments=16 # 2awiA read from 2awiA/merged-good-all-a2m # found chain 2awiA in template set T0336 11 :REALANGEHLEKILIMAKYD 2awiA 20 :IDLYSGIMSKSVYIKVEADS T0336 31 :ESVLKKLIELLDDDLWTVVKN 2awiA 44 :VEELSKFSERLGVNFFEILNR T0336 52 :AISIIMVIAKTREDL 2awiA 75 :TGKEKLLISKIFTNP T0336 69 :PMLKKLFSLLK 2awiA 90 :DLFDKNFQRIE T0336 80 :KSEAIPLTQEIAKAFGQMA 2awiA 102 :KRLTSLQYFSIYLGYISIA T0336 102 :PELVKSMIPVLFANYR 2awiA 128 :PTFNKTITSDLKHLYD T0336 118 :IGDEKTKIN 2awiA 146 :TTFFGIDCE T0336 131 :LEEIAKA 2awiA 165 :YEEVSSI T0336 138 :NPM 2awiA 183 :GKD T0336 141 :LMASIV 2awiA 189 :TIQTVL T0336 147 :RDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFLPRIINLLHDGDEIVRASAVEALV 2awiA 196 :NALTISIMNRNLKEAQYYINQFEHLKTIKNISINGYYDLEINYLKQIYQFLTDKNIDSYL T0336 210 :TLNDKLRKVVIK 2awiA 256 :NAVNIINIFKII T0336 225 :ELNDTSSLVNKTVKEGISRL 2awiA 268 :GKEDIHRSLVEELTKISAKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=226 Number of alignments=17 # 2awiA read from 2awiA/merged-good-all-a2m # found chain 2awiA in template set T0336 4 :EEEEFDIR 2awiA 29 :KSVYIKVE T0336 24 :LIMAKYDESVLKKLIELLDDDLWTVVKNA 2awiA 37 :ADSRPISVEELSKFSERLGVNFFEILNRA T0336 60 :AKTREDLYEPMLKKLFSLLKKS 2awiA 85 :IFTNPDLFDKNFQRIEPKRLTS T0336 87 :TQEIAKAFGQMAKEKP 2awiA 107 :LQYFSIYLGYISIAHH T0336 103 :ELVKSMIPVLFANYRIGDE 2awiA 128 :PTFNKTITSDLKHLYDKRT T0336 122 :K 2awiA 150 :G T0336 126 :NVSYALEEIAK 2awiA 151 :IDCEIVSNLLN T0336 137 :ANPM 2awiA 163 :LPYE T0336 141 :LMASIVRDFMSMLSSKNREDKLTALNFIEAMGE 2awiA 190 :IQTVLKNALTISIMNRNLKEAQYYINQFEHLKT T0336 174 :NSFKYVNPFLPRIINLLHDGDEIVRASAVEALVHLATL 2awiA 230 :GYYDLEINYLKQIYQFLTDKNIDSYLNAVNIINIFKII T0336 212 :NDKLRKVVIKRLEELNDTSS 2awiA 269 :KEDIHRSLVEELTKISAKEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=237 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bnxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bnxA expands to /projects/compbio/data/pdb/2bnx.pdb.gz 2bnxA:Skipped atom 676, because occupancy 0.5 <= existing 0.500 in 2bnxA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 688, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2232, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2234, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2236, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2238, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2240, because occupancy 0.500 <= existing 0.500 in 2bnxA Skipped atom 2242, because occupancy 0.500 <= existing 0.500 in 2bnxA # T0336 read from 2bnxA/merged-good-all-a2m # 2bnxA read from 2bnxA/merged-good-all-a2m # adding 2bnxA to template set # found chain 2bnxA in template set Warning: unaligning (T0336)Y29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bnxA)G175 Warning: unaligning (T0336)D30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bnxA)G175 Warning: unaligning (T0336)L104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bnxA)E264 Warning: unaligning (T0336)E121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bnxA)E264 Warning: unaligning (T0336)H250 because of BadResidue code BAD_PEPTIDE in next template residue (2bnxA)R412 Warning: unaligning (T0336)S251 because of BadResidue code BAD_PEPTIDE at template residue (2bnxA)R412 T0336 6 :EEFDIREALANGE 2bnxA 155 :CLESLRVSLNNNP T0336 23 :ILIMAK 2bnxA 168 :VSWVQT T0336 31 :ESVLKKLIELL 2bnxA 176 :AEGLASLLDIL T0336 43 :DDL 2bnxA 194 :EET T0336 46 :WTVVKNAISIIMVIAK 2bnxA 202 :SRNQHEIIRCLKAFMN T0336 64 :EDLY 2bnxA 218 :NKFG T0336 71 :LKKLF 2bnxA 222 :IKTML T0336 80 :KSEA 2bnxA 227 :ETEE T0336 84 :IPLTQEIAKAFGQMA 2bnxA 244 :PNMMIDAAKLLSALC T0336 100 :EKPE 2bnxA 259 :ILPQ T0336 122 :KTKINVSYALEEIAKANP 2bnxA 265 :DMNERVLEAMTERAEMDE T0336 147 :RDFMSMLSSKNR 2bnxA 287 :QPLLDGLKSGTS T0336 159 :EDKLTALNFIEA 2bnxA 300 :ALKVGCLQLINA T0336 171 :MGENSFKYVNPFLPR 2bnxA 314 :TPAEELDFRVHIRSE T0336 186 :IINLLHDGD 2bnxA 337 :VLQELREIE T0336 198 :RASAVEALVHLATLNDKLRKVVIKRLEE 2bnxA 346 :NEDMKVQLCVFDEQGDEDFFDLKGRLDD T0336 226 :LND 2bnxA 378 :MDD T0336 229 :TSSLVNKTVK 2bnxA 384 :VFQIILNTVK T0336 239 :EGISRLLLLEG 2bnxA 400 :HFLSILQHLLL T0336 252 :S 2bnxA 413 :N Number of specific fragments extracted= 20 number of extra gaps= 3 total=257 Number of alignments=19 # 2bnxA read from 2bnxA/merged-good-all-a2m # found chain 2bnxA in template set Warning: unaligning (T0336)N51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bnxA)G175 Warning: unaligning (T0336)A52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bnxA)G175 Warning: unaligning (T0336)N138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bnxA)E264 Warning: unaligning (T0336)P139 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bnxA)E264 T0336 10 :IREALANGEHLEK 2bnxA 139 :YIQELRSGLRDMH T0336 30 :DESVLKKLIELLDDDL 2bnxA 152 :LLSCLESLRVSLNNNP T0336 46 :WTVVK 2bnxA 169 :SWVQT T0336 53 :ISIIMVIAKT 2bnxA 176 :AEGLASLLDI T0336 75 :FSLLKKSEA 2bnxA 186 :LKRLHDEKE T0336 84 :IPLTQEIAKAFGQMA 2bnxA 202 :SRNQHEIIRCLKAFM T0336 100 :EKPELVKSMIP 2bnxA 217 :NNKFGIKTMLE T0336 111 :VLFANYRIGDEKTKINVSYALEEIAKA 2bnxA 234 :LLVRAMDPAVPNMMIDAAKLLSALCIL T0336 140 :MLMASIVR 2bnxA 265 :DMNERVLE T0336 148 :DFMSMLSSKNR 2bnxA 288 :PLLDGLKSGTS T0336 159 :EDKLTALNFIEAMGENSFKY 2bnxA 300 :ALKVGCLQLINALITPAEEL T0336 181 :PFLPRIINLLHDG 2bnxA 320 :DFRVHIRSELMRL T0336 210 :TLNDKLRKV 2bnxA 333 :GLHQVLQEL T0336 219 :VIKRLEELNDTSSLVNKTVKEGISRLLL 2bnxA 349 :MKVQLCVFDEQGDEDFFDLKGRLDDIRM Number of specific fragments extracted= 14 number of extra gaps= 2 total=271 Number of alignments=20 # 2bnxA read from 2bnxA/merged-good-all-a2m # found chain 2bnxA in template set Warning: unaligning (T0336)Y29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bnxA)G175 Warning: unaligning (T0336)D30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bnxA)G175 Warning: unaligning (T0336)N227 because of BadResidue code BAD_PEPTIDE at template residue (2bnxA)R412 T0336 2 :SMEEEEFDIREALANGEHLEKILI 2bnxA 148 :RDMHLLSCLESLRVSLNNNPVSWV T0336 27 :AK 2bnxA 172 :QT T0336 31 :ESVLKKLIELL 2bnxA 176 :AEGLASLLDIL T0336 42 :DDDLWTVVKNAISIIMVIAKTR 2bnxA 198 :GNYDSRNQHEIIRCLKAFMNNK T0336 65 :DLYEPMLK 2bnxA 220 :FGIKTMLE T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 2bnxA 234 :LLVRAMDPAVPNMMIDAAKLLSALCILPQ T0336 103 :ELVKSMIP 2bnxA 265 :DMNERVLE T0336 111 :VLFANYRIGD 2bnxA 288 :PLLDGLKSGT T0336 121 :EKTKINVSYALEEIAK 2bnxA 299 :IALKVGCLQLINALIT T0336 137 :ANPMLMASIVRDFMS 2bnxA 317 :EELDFRVHIRSELMR T0336 152 :MLSSKNREDKLTALNFIEAMGENSFKYVNPFLPRI 2bnxA 340 :ELREIENEDMKVQLCVFDEQGDEDFFDLKGRLDDI T0336 192 :DGDEIVRASAVEAL 2bnxA 379 :DDFGEVFQIILNTV T0336 211 :LNDKLRKVVIKRLEEL 2bnxA 393 :KDSKAEPHFLSILQHL T0336 228 :DTS 2bnxA 413 :NDY T0336 231 :SLVNKTVKEGISRLLLLEGHSSS 2bnxA 419 :PQYYKLIEECVSQIVLHKNGTDP Number of specific fragments extracted= 15 number of extra gaps= 2 total=286 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g3jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g3jA expands to /projects/compbio/data/pdb/1g3j.pdb.gz 1g3jA:# T0336 read from 1g3jA/merged-good-all-a2m # 1g3jA read from 1g3jA/merged-good-all-a2m # adding 1g3jA to template set # found chain 1g3jA in template set T0336 23 :ILIMAKYDESVLKKLIELL 1g3jA 142 :YQDDAELATRAIPELTKLL T0336 45 :LWTVVKNAISIIMVIAKTREDLYEPMLK 1g3jA 248 :VDSVLFYAITTLHNLLLHQEGAKMAVRL T0336 73 :KLFSLLKKSEAIPLTQEIAK 1g3jA 277 :GGLQKMVALLNKTNVKFLAI T0336 93 :AFGQMAKEKPELVKSMIP 1g3jA 300 :CLQILAYGNQESKLIILA T0336 111 :VLFANYRIGDEKTKINVSYALEEIAKA 1g3jA 324 :LVNIMRTYTYEKLLWTTSRVLKVLSVC T0336 138 :NPMLMA 1g3jA 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 1g3jA 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 1g3jA 377 :LVQNC T0336 164 :ALNFIEAM 1g3jA 384 :TLRNLSDA T0336 173 :ENSFKYVNPFLPRIINLLHDGDEIVRASAVEALVHLAT 1g3jA 392 :ATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTC T0336 211 :LNDKLR 1g3jA 434 :NKMMVC T0336 217 :KVVIKRLEELNDTSSLV 1g3jA 445 :EALVRTVLRAGDREDIT Number of specific fragments extracted= 12 number of extra gaps= 0 total=298 Number of alignments=22 # 1g3jA read from 1g3jA/merged-good-all-a2m # found chain 1g3jA in template set T0336 4 :EEEEFDIREALA 1g3jA 136 :VVNLINYQDDAE T0336 29 :YDESVLKKLIELL 1g3jA 148 :LATRAIPELTKLL T0336 42 :DDDLWTVVKNAISIIMVI 1g3jA 162 :DEDQVVVNKAAVMVHQLS T0336 62 :TREDLYEP 1g3jA 183 :ASRHAIMR T0336 70 :MLKKLFSLLKKSEAIPLTQEIAKAFGQMA 1g3jA 194 :MVSAIVRTMQNTNDVETARCTAGTLHNLS T0336 100 :EKPELVKSMI 1g3jA 223 :HHREGLLAIF T0336 110 :PVLFANYR 1g3jA 238 :PALVKMLG T0336 121 :EKTK 1g3jA 267 :EGAK T0336 127 :VSYALEEIAKA 1g3jA 340 :TSRVLKVLSVC T0336 138 :NPMLMA 1g3jA 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 1g3jA 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 1g3jA 377 :LVQNC T0336 165 :LNFIEAMGENSF 1g3jA 382 :LWTLRNLSDAAT T0336 177 :KYVNPFLPRIINLLH 1g3jA 396 :EGMEGLLGTLVQLLG T0336 199 :ASA 1g3jA 411 :SDD T0336 204 :A 1g3jA 414 :I T0336 210 :TLNDKLRKVVIKRLEELNDTSSLVNK 1g3jA 415 :NVVTCAAGILSNLTCNNYKNKMMVCQ T0336 236 :TVKEGISRLLLLEGH 1g3jA 443 :GIEALVRTVLRAGDR Number of specific fragments extracted= 18 number of extra gaps= 0 total=316 Number of alignments=23 # 1g3jA read from 1g3jA/merged-good-all-a2m # found chain 1g3jA in template set T0336 2 :SMEEEEFDIREALANGEHLEKI 1g3jA 206 :NDVETARCTAGTLHNLSHHREG T0336 25 :IMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1g3jA 228 :LLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLA T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1g3jA 281 :KMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILA T0336 111 :VLFANY 1g3jA 323 :ALVNIM T0336 117 :RIGDEKTKINVSYALEEIAK 1g3jA 330 :TYTYEKLLWTTSRVLKVLSV T0336 138 :NPMLMASIVRD 1g3jA 350 :CSSNKPAIVEA T0336 149 :FMSMLSSKNREDKLTALNFIEAMGENSFKY 1g3jA 366 :LGLHLTDPSQRLVQNCLWTLRNLSDAATKQ T0336 179 :VNPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKR 1g3jA 398 :MEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQV T0336 223 :LEELNDTSSLV 1g3jA 451 :VLRAGDREDIT Number of specific fragments extracted= 9 number of extra gaps= 0 total=325 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z2cB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z2cB expands to /projects/compbio/data/pdb/1z2c.pdb.gz 1z2cB:# T0336 read from 1z2cB/merged-good-all-a2m # 1z2cB read from 1z2cB/merged-good-all-a2m # adding 1z2cB to template set # found chain 1z2cB in template set Warning: unaligning (T0336)Y29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)G175 Warning: unaligning (T0336)D30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)G175 Warning: unaligning (T0336)A60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)N217 Warning: unaligning (T0336)K61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)N217 T0336 7 :EFDIREALAN 1z2cB 156 :LESLRVSLNN T0336 23 :ILIMAK 1z2cB 168 :VSWVQT T0336 31 :ESVLKKLIELL 1z2cB 176 :AEGLASLLDIL T0336 46 :WTVVKNAISIIMVI 1z2cB 202 :SRNQHEIIRCLKAF T0336 63 :REDLYEPMLK 1z2cB 218 :NKFGIKTMLE T0336 73 :KLFSLLKKSEA 1z2cB 230 :EGILLLVRAMD T0336 84 :IPLTQEIAKAFGQMA 1z2cB 244 :PNMMIDAAKLLSALC T0336 100 :EKPEL 1z2cB 259 :ILPQP T0336 121 :EKTKINVSYALEEIAKANP 1z2cB 264 :EDMNERVLEAMTERAEMDE T0336 140 :MLMASIV 1z2cB 284 :ERFQPLL T0336 151 :SMLSSKNR 1z2cB 291 :DGLKSGTS T0336 159 :EDKLTALNFIEA 1z2cB 300 :ALKVGCLQLINA T0336 171 :MGENSFKYVNPFLPRII 1z2cB 314 :TPAEELDFRVHIRSELM T0336 188 :NLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKRLEE 1z2cB 336 :QVLQELREIENEDMKVQLCVFDEQGDEDFFDLKGRLDD T0336 226 :L 1z2cB 378 :M T0336 228 :DTSSLVNKTVK 1z2cB 379 :DDFGEVFQIIL T0336 239 :EGISRLLLLEGHS 1z2cB 400 :HFLSILQHLLLVR Number of specific fragments extracted= 17 number of extra gaps= 2 total=342 Number of alignments=25 # 1z2cB read from 1z2cB/merged-good-all-a2m # found chain 1z2cB in template set Warning: unaligning (T0336)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)N217 Warning: unaligning (T0336)E100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)N217 Warning: unaligning (T0336)L246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)T391 Warning: unaligning (T0336)E248 because of BadResidue code BAD_PEPTIDE in next template residue (1z2cB)D394 Warning: unaligning (T0336)G249 because of BadResidue code BAD_PEPTIDE at template residue (1z2cB)D394 T0336 5 :EEE 1z2cB 99 :EKQ T0336 11 :REALA 1z2cB 102 :QPLRE T0336 18 :EHLEKILIMAKYDE 1z2cB 107 :KDIVIKREMVSQYL T0336 34 :LKKLIELLDDDLWTV 1z2cB 136 :AMMYIQELRSGLRDM T0336 51 :NAISIIMVIAKTREDLYEPMLK 1z2cB 151 :HLLSCLESLRVSLNNNPVSWVQ T0336 73 :KLFSLLKKSEA 1z2cB 181 :SLLDILKRLHD T0336 84 :IPLTQEIAKAFGQM 1z2cB 202 :SRNQHEIIRCLKAF T0336 101 :KPELVKSMI 1z2cB 218 :NKFGIKTML T0336 110 :PVLFANYRIGDEKTKIN 1z2cB 233 :LLLVRAMDPAVPNMMID T0336 130 :ALEEIAKA 1z2cB 250 :AAKLLSAL T0336 138 :NPMLMASIVRDFMSM 1z2cB 263 :PEDMNERVLEAMTER T0336 153 :LSSKNR 1z2cB 293 :LKSGTS T0336 159 :EDKLTALNFIEAMGENSFKY 1z2cB 300 :ALKVGCLQLINALITPAEEL T0336 179 :VNPFLPRII 1z2cB 322 :RVHIRSELM T0336 188 :NLLHDGDE 1z2cB 336 :QVLQELRE T0336 198 :RASA 1z2cB 344 :IENE T0336 205 :LVHL 1z2cB 348 :DMKV T0336 211 :LNDKLRKVVIKRLEELNDTSSLVNK 1z2cB 352 :QLCVFDEQGDEDFFDLKGRLDDIRM T0336 239 :E 1z2cB 383 :E T0336 241 :ISRLL 1z2cB 384 :VFQII T0336 247 :L 1z2cB 392 :V T0336 250 :HS 1z2cB 395 :SK Number of specific fragments extracted= 22 number of extra gaps= 3 total=364 Number of alignments=26 # 1z2cB read from 1z2cB/merged-good-all-a2m # found chain 1z2cB in template set Warning: unaligning (T0336)Y29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)G175 Warning: unaligning (T0336)D30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)G175 Warning: unaligning (T0336)L45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z2cB)D201 Warning: unaligning (T0336)A60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)N217 Warning: unaligning (T0336)K61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)N217 Warning: unaligning (T0336)E203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z2cB)T391 Warning: unaligning (T0336)A204 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z2cB)T391 Warning: unaligning (T0336)L211 because of BadResidue code BAD_PEPTIDE in next template residue (1z2cB)D394 Warning: unaligning (T0336)N212 because of BadResidue code BAD_PEPTIDE at template residue (1z2cB)D394 T0336 2 :SMEEEEFDIREALANGEHLEKILI 1z2cB 148 :RDMHLLSCLESLRVSLNNNPVSWV T0336 27 :AK 1z2cB 172 :QT T0336 31 :ESVLKKLIELL 1z2cB 176 :AEGLASLLDIL T0336 46 :WTVVKNAISIIMVI 1z2cB 202 :SRNQHEIIRCLKAF T0336 62 :T 1z2cB 218 :N T0336 65 :DLYEPMLKK 1z2cB 219 :KFGIKTMLE T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1z2cB 234 :LLVRAMDPAVPNMMIDAAKLLSALCILPQ T0336 103 :ELVKSMIP 1z2cB 265 :DMNERVLE T0336 111 :VLFANYRIGD 1z2cB 288 :PLLDGLKSGT T0336 121 :EKTKINVSYALEEIAK 1z2cB 299 :IALKVGCLQLINALIT T0336 137 :ANPM 1z2cB 317 :EELD T0336 141 :LMASIVRD 1z2cB 325 :IRSELMRL T0336 149 :FMSMLSS 1z2cB 334 :LHQVLQE T0336 156 :KNREDKLTALNFIEAMGE 1z2cB 344 :IENEDMKVQLCVFDEQGD T0336 181 :PFLPRIINLLH 1z2cB 362 :EDFFDLKGRLD T0336 192 :DGDEIVRASAV 1z2cB 379 :DDFGEVFQIIL T0336 210 :T 1z2cB 392 :V T0336 213 :DKLRKVVIKRLEEL 1z2cB 395 :SKAEPHFLSILQHL T0336 227 :NDTS 1z2cB 413 :NDYE T0336 231 :SLVNKTVKEGISRLLLLEGHS 1z2cB 419 :PQYYKLIEECVSQIVLHKNGT Number of specific fragments extracted= 20 number of extra gaps= 4 total=384 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q1sC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1q1sC/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1q1sC/merged-good-all-a2m.gz for input Trying 1q1sC/merged-good-all-a2m Error: Couldn't open file 1q1sC/merged-good-all-a2m or 1q1sC/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5nS/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1m5nS/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1m5nS/merged-good-all-a2m.gz for input Trying 1m5nS/merged-good-all-a2m Error: Couldn't open file 1m5nS/merged-good-all-a2m or 1m5nS/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c1mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/2c1mA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/2c1mA/merged-good-all-a2m.gz for input Trying 2c1mA/merged-good-all-a2m Error: Couldn't open file 2c1mA/merged-good-all-a2m or 2c1mA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xqrA expands to /projects/compbio/data/pdb/1xqr.pdb.gz 1xqrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0336 read from 1xqrA/merged-good-all-a2m # 1xqrA read from 1xqrA/merged-good-all-a2m # adding 1xqrA to template set # found chain 1xqrA in template set T0336 4 :EEEEFDIREALAN 1xqrA 90 :VEQMKSCLRVLSQ T0336 17 :GEHLEKILIMAKYDESVLKKLIELL 1xqrA 107 :TAGEAEQAADQQEREGALELLADLC T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1xqrA 155 :EAGAAGLRWRAAQLIGTCSQNVAAIQEQVLG T0336 73 :KLFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIPV 1xqrA 191 :KLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRL T0336 130 :ALEEIAKA 1xqrA 231 :GFSVLMRA T0336 138 :NPMLMASIVRDFMSMLSSKNR 1xqrA 243 :VQKLKVKSAFLLQNLLVGHPE T0336 159 :EDKLT 1xqrA 265 :KGTLC T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1xqrA 271 :MGMVQQLVALVRTEHSPFHEHVLGALCSLVT T0336 211 :LNDKLR 1xqrA 306 :GVRECR T0336 217 :KVVIKRLEELNDT 1xqrA 319 :ELLRHRCQLLQQH T0336 230 :SSLVNKTVKEGISR 1xqrA 334 :YQEELEFCEKLLQT Number of specific fragments extracted= 11 number of extra gaps= 0 total=395 Number of alignments=28 # 1xqrA read from 1xqrA/merged-good-all-a2m # found chain 1xqrA in template set Warning: unaligning (T0336)I118 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1xqrA)Q242 Warning: unaligning (T0336)G119 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1xqrA)Q242 T0336 4 :EEEEFDIREALAN 1xqrA 87 :RGEVEQMKSCLRV T0336 17 :GEHLEKILIMAKYDESVLKKLIELL 1xqrA 107 :TAGEAEQAADQQEREGALELLADLC T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLY 1xqrA 155 :EAGAAGLRWRAAQLIGTCSQNVAAIQ T0336 68 :EPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMI 1xqrA 186 :LGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFL T0336 110 :PVLFANYR 1xqrA 233 :SVLMRAMQ T0336 120 :DEKTKINVSYALEEIAKANPMLMASI 1xqrA 243 :VQKLKVKSAFLLQNLLVGHPEHKGTL T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGEN 1xqrA 274 :VQQLVALVRTEHSPFHEHVLGALCSLVTD T0336 183 :LPRIINLL 1xqrA 303 :FPQGVREC T0336 198 :RASA 1xqrA 311 :REPE T0336 209 :ATLNDKLRKVVIKRL 1xqrA 315 :LGLEELLRHRCQLLQ T0336 224 :EELNDT 1xqrA 332 :EEYQEE T0336 234 :NKTVKEGISRLL 1xqrA 338 :LEFCEKLLQTCF Number of specific fragments extracted= 12 number of extra gaps= 1 total=407 Number of alignments=29 # 1xqrA read from 1xqrA/merged-good-all-a2m # found chain 1xqrA in template set Warning: unaligning (T0336)S155 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1xqrA)Q242 Warning: unaligning (T0336)K156 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1xqrA)Q242 Warning: unaligning (T0336)L247 because last residue in template chain is (1xqrA)S350 T0336 3 :MEEEEFDIREALANGEH 1xqrA 86 :QRGEVEQMKSCLRVLSQ T0336 20 :LEKILIMAKYDESVLKKLIELLDDDL 1xqrA 110 :EAEQAADQQEREGALELLADLCENMD T0336 55 :IIMVIAKTR 1xqrA 136 :NAADFCQLS T0336 70 :MLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1xqrA 145 :GMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLG T0336 111 :VLFANY 1xqrA 191 :KLLRLL T0336 117 :RIGDEKTKINVSYALEEIAKANPMLMASI 1xqrA 198 :RDACDTVRVKALFAISCLVREQEAGLLQF T0336 146 :VRDFMSMLS 1xqrA 232 :FSVLMRAMQ T0336 157 :NREDKLTALNFIEAMGENSFKYVNPFL 1xqrA 243 :VQKLKVKSAFLLQNLLVGHPEHKGTLC T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKV 1xqrA 275 :QQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRE T0336 219 :VIKRLEE 1xqrA 317 :LEELLRH T0336 226 :LNDTSSLVN 1xqrA 328 :LQQHEEYQE T0336 235 :KTVKEGISRLLL 1xqrA 338 :LEFCEKLLQTCF Number of specific fragments extracted= 12 number of extra gaps= 1 total=419 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hz4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0336 read from 1hz4A/merged-good-all-a2m # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set Warning: unaligning (T0336)L245 because last residue in template chain is (1hz4A)N366 T0336 4 :EEEEFDIREALAN 1hz4A 29 :DEAERLAKLALEE T0336 17 :GEHLEKILIMAKYDE 1hz4A 43 :PPGWFYSRIVATSVL T0336 32 :SVLKKLIELL 1hz4A 72 :ALMQQTEQMA T0336 42 :DDDLWTVVKNAISIIM 1hz4A 83 :QHDVWHYALWSLIQQS T0336 58 :VIAKTREDLYEPMLKKLFSLLKKSE 1hz4A 101 :LFAQGFLQTAWETQEKAFQLINEQH T0336 83 :AIPLTQEIAK 1hz4A 127 :EQLPMHEFLV T0336 93 :AFGQMAKEKP 1hz4A 138 :IRAQLLWAWA T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKA 1hz4A 150 :DEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLA T0336 138 :NPMLMASIVRDFMSMLSSKNR 1hz4A 187 :DLDNARSQLNRLENLLGNGKY T0336 159 :EDKLTALNFI 1hz4A 209 :SDWISNANKV T0336 169 :EA 1hz4A 260 :AQ T0336 171 :MG 1hz4A 264 :LG T0336 175 :SFKYVNPFLPRIINLL 1hz4A 266 :EFEPAEIVLEELNENA T0336 191 :HDGDEIVRASAVEALV 1hz4A 304 :AGRKSDAQRVLLDALK T0336 207 :HLATLNDKLRKVVIKRLEE 1hz4A 329 :HFVIEGEAMAQQLRQLIQL T0336 227 :NDTSSLVNKTVKEGISRL 1hz4A 348 :NTLPELEQHRAQRILREI Number of specific fragments extracted= 16 number of extra gaps= 0 total=435 Number of alignments=31 # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set T0336 2 :SMEEEEFDIRE 1hz4A 4 :DIREDTMHAEF T0336 19 :HLEKILIMAK 1hz4A 15 :NALRAQVAIN T0336 29 :YDESVLKKLIELL 1hz4A 30 :EAERLAKLALEEL T0336 42 :DDDLWTVVKNAISI 1hz4A 83 :QHDVWHYALWSLIQ T0336 57 :MVIAKTREDLYEPMLKKLFSLLKKSE 1hz4A 100 :ILFAQGFLQTAWETQEKAFQLINEQH T0336 83 :AIPLTQEIAK 1hz4A 127 :EQLPMHEFLV T0336 93 :AFGQMA 1hz4A 138 :IRAQLL T0336 99 :KEKPELVKSMIPVLFANYRIGDEKTKIN 1hz4A 146 :WARLDEAEASARSGIEVLSSYQPQQQLQ T0336 127 :VSYALEEIAKANPMLMASIVRDFMSMLSSKNR 1hz4A 176 :AMLIQCSLARGDLDNARSQLNRLENLLGNGKY T0336 159 :EDKLTALN 1hz4A 209 :SDWISNAN T0336 167 :FIEAMGEN 1hz4A 221 :IYWQMTGD T0336 183 :LPRIINLLHDGD 1hz4A 229 :KAAAANWLRHTA T0336 198 :RASAVEALVHLATL 1hz4A 241 :KPEFANNHFLQGQW T0336 214 :KLRKVVIKRLEEL 1hz4A 255 :RNIARAQILLGEF T0336 231 :SLVNKTVKEGISRLLLLE 1hz4A 268 :EPAEIVLEELNENARSLR Number of specific fragments extracted= 15 number of extra gaps= 0 total=450 Number of alignments=32 # 1hz4A read from 1hz4A/merged-good-all-a2m # found chain 1hz4A in training set T0336 3 :MEEEEFDIREALANGEHLEKILIMA 1hz4A 9 :TMHAEFNALRAQVAINDGNPDEAER T0336 33 :VLKKLIELLDDDLWTVVKNAISIIMVI 1hz4A 34 :LAKLALEELPPGWFYSRIVATSVLGEV T0336 60 :AKTREDLYEPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1hz4A 63 :CKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQG T0336 103 :ELVKSMIPVLFANY 1hz4A 108 :QTAWETQEKAFQLI T0336 117 :RIGDEKTKINVSY 1hz4A 125 :HLEQLPMHEFLVR T0336 130 :ALEEIAKANPMLMASIVRDFMSMLSS 1hz4A 140 :AQLLWAWARLDEAEASARSGIEVLSS T0336 156 :KNREDKLTALNFIEAMGENSFKYVNPFLPRIINLLHDG 1hz4A 168 :PQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNG T0336 194 :DEIVRASA 1hz4A 208 :HSDWISNA T0336 202 :VEALVHLATLNDKLRK 1hz4A 218 :VRVIYWQMTGDKAAAA T0336 221 :KRLEELNDT 1hz4A 234 :NWLRHTAKP Number of specific fragments extracted= 10 number of extra gaps= 0 total=460 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qgrA expands to /projects/compbio/data/pdb/1qgr.pdb.gz 1qgrA:# T0336 read from 1qgrA/merged-good-all-a2m # 1qgrA read from 1qgrA/merged-good-all-a2m # adding 1qgrA to template set # found chain 1qgrA in template set T0336 3 :MEEEEFDIREALAN 1qgrA 286 :VCDEEMDLAIEASE T0336 17 :GEHLE 1qgrA 304 :GRPPE T0336 24 :LIMAKYDESVLKKLIELL 1qgrA 309 :HTSKFYAKGALQYLVPIL T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPML 1qgrA 338 :DDDDWNPCKAAGVCLMLLATCCEDDIVPHV T0336 75 :FSLLKKSEA 1qgrA 368 :LPFIKEHIK T0336 84 :IPLTQEIAK 1qgrA 379 :DWRYRDAAV T0336 93 :AFGQMA 1qgrA 389 :AFGCIL T0336 100 :EKPEL 1qgrA 395 :EGPEP T0336 106 :KSMIPVLFANYR 1qgrA 400 :SQLKPLVIQAMP T0336 118 :IGDEKTKIN 1qgrA 417 :MKDPSVVVR T0336 127 :VSYALEEIAKA 1qgrA 432 :VGRICELLPEA T0336 138 :NPMLMASIVRDFMSMLSSKNR 1qgrA 445 :NDVYLAPLLQCLIEGLSAEPR T0336 159 :EDKLT 1qgrA 467 :ASNVC T0336 164 :ALNFI 1qgrA 473 :AFSSL T0336 171 :MGENS 1qgrA 488 :ADDQE T0336 176 :FKYVNPFLPRIINLL 1qgrA 496 :TYCLSSSFELIVQKL T0336 191 :HDGDEIVRASAVEALVHLAT 1qgrA 518 :DGHQNNLRSSAYESLMEIVK T0336 211 :LNDKLRKVVIKRLEE 1qgrA 546 :AVQKTTLVIMERLQQ T0336 226 :LNDT 1qgrA 568 :IQST T0336 235 :KTVKEGISRLLLL 1qgrA 572 :SDRIQFNDLQSLL Number of specific fragments extracted= 20 number of extra gaps= 0 total=480 Number of alignments=34 # 1qgrA read from 1qgrA/merged-good-all-a2m # found chain 1qgrA in template set T0336 4 :EEEEFDI 1qgrA 287 :CDEEMDL T0336 11 :REALANGEHLE 1qgrA 298 :SEAAEQGRPPE T0336 28 :KYDESVLKKLIELL 1qgrA 313 :FYAKGALQYLVPIL T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPML 1qgrA 338 :DDDDWNPCKAAGVCLMLLATCCEDDIVPHV T0336 75 :FSLLKKSEA 1qgrA 368 :LPFIKEHIK T0336 84 :IPLTQEIAK 1qgrA 379 :DWRYRDAAV T0336 93 :AFGQMA 1qgrA 389 :AFGCIL T0336 100 :EKPEL 1qgrA 395 :EGPEP T0336 106 :KSMIPVLFANYR 1qgrA 400 :SQLKPLVIQAMP T0336 118 :IGDEKTKIN 1qgrA 417 :MKDPSVVVR T0336 127 :VSYALEEIAKA 1qgrA 432 :VGRICELLPEA T0336 138 :NPMLMASIVRDFMSMLSSKNR 1qgrA 445 :NDVYLAPLLQCLIEGLSAEPR T0336 159 :EDKLTAL 1qgrA 467 :ASNVCWA T0336 166 :NFIEAMGENSF 1qgrA 476 :SLAEAAYEAAD T0336 177 :KY 1qgrA 496 :TY T0336 179 :VNPFLPRIINLLHDGDE 1qgrA 499 :LSSSFELIVQKLLETTD T0336 198 :RASAVEALVHLA 1qgrA 516 :RPDGHQNNLRSS T0336 211 :LNDKLRKVVIKRLE 1qgrA 528 :AYESLMEIVKNSAK T0336 228 :DTSSLVNKTVKEGISRLL 1qgrA 542 :DCYPAVQKTTLVIMERLQ T0336 246 :LLEGHSS 1qgrA 561 :VLQMESH Number of specific fragments extracted= 20 number of extra gaps= 0 total=500 Number of alignments=35 # 1qgrA read from 1qgrA/merged-good-all-a2m # found chain 1qgrA in template set T0336 3 :MEEEEFDIREALANGEHLEKILIMAKYD 1qgrA 272 :IDEVALQGIEFWSNVCDEEMDLAIEASE T0336 33 :VLKKLIELL 1qgrA 318 :ALQYLVPIL T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1qgrA 338 :DDDDWNPCKAAGVCLMLLATCCEDDIVPHVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPE T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAK 1qgrA 404 :PLVIQAMPTLIELMKDPSVVVRDTAAWTVGRICE T0336 137 :ANPMLMASIVRDFMSMLSSK 1qgrA 444 :INDVYLAPLLQCLIEGLSAE T0336 158 :REDKLTALNFIEAMGENSFK 1qgrA 464 :PRVASNVCWAFSSLAEAAYE T0336 178 :YVNPFLPRIINLLHDGDE 1qgrA 502 :SFELIVQKLLETTDRPDG T0336 196 :IVRASAVEALVHLATLN 1qgrA 523 :NLRSSAYESLMEIVKNS T0336 213 :DKLRKVVIKRLEEL 1qgrA 548 :QKTTLVIMERLQQV T0336 227 :NDTSSLVNKTVKEGISRL 1qgrA 569 :QSTSDRIQFNDLQSLLCA Number of specific fragments extracted= 10 number of extra gaps= 0 total=510 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bk5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bk5A expands to /projects/compbio/data/pdb/1bk5.pdb.gz 1bk5A:# T0336 read from 1bk5A/merged-good-all-a2m # 1bk5A read from 1bk5A/merged-good-all-a2m # adding 1bk5A to template set # found chain 1bk5A in template set T0336 6 :EEFDIREALANGEHL 1bk5A 107 :ATVKFRQILSREHRP T0336 24 :LIMAKYDESVLKKLIELL 1bk5A 122 :PIDVVIQAGVVPRLVEFM T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1bk5A 141 :ENQPEMLQLEAAWALTNIASGTSAQTKVVVD T0336 73 :KLFSLLKKSE 1bk5A 177 :LFIQLLYTGS T0336 85 :PLTQEIAKAFGQMAKEK 1bk5A 188 :EVKEQAIWALGNVAGDS T0336 102 :PELVKSMIPVLFANYR 1bk5A 214 :CNAMEPILGLFNSNKP T0336 118 :IGDEKTKINVSYALEEIAKANPMLMASIV 1bk5A 268 :SMDTETLVDACWAISYLSDGPQEAIQAVI T0336 147 :RDFMSMLSSKNR 1bk5A 302 :KRLVELLSHEST T0336 159 :EDKLT 1bk5A 315 :VQTPA T0336 164 :ALNFI 1bk5A 322 :AVGNI T0336 178 :YV 1bk5A 378 :AV T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1bk5A 382 :ANLIPPLVKLLEVAEYKTKKEACWAISNASS T0336 211 :LNDKLR 1bk5A 420 :IIRYLV T0336 217 :KVVIKRLEELN 1bk5A 431 :KPLCDLLEIAD T0336 228 :DTSSLVNKTVK 1bk5A 443 :RIIEVTLDALE T0336 239 :EGISRLLLLEGHSS 1bk5A 457 :KMGEADKEARGLNI Number of specific fragments extracted= 16 number of extra gaps= 0 total=526 Number of alignments=37 # 1bk5A read from 1bk5A/merged-good-all-a2m # found chain 1bk5A in template set Warning: unaligning (T0336)E64 because of BadResidue code BAD_PEPTIDE in next template residue (1bk5A)P248 Warning: unaligning (T0336)D65 because of BadResidue code BAD_PEPTIDE at template residue (1bk5A)P248 T0336 23 :ILIMAKYDESVLKKLIELL 1bk5A 197 :LGNVAGDSTDYRDYVLQCN T0336 42 :DDDLWTVVKNAISIIMVIAKTR 1bk5A 225 :NSNKPSLIRTATWTLSNLCRGK T0336 66 :LY 1bk5A 249 :QP T0336 68 :EPMLKKLFSLLKKSEA 1bk5A 252 :WSVVSQALPTLAKLIY T0336 84 :IPLTQEIAKAFGQMAKEKPELVKSMIP 1bk5A 271 :TETLVDACWAISYLSDGPQEAIQAVID T0336 111 :VLFANYR 1bk5A 303 :RLVELLS T0336 120 :DEKTKIN 1bk5A 310 :HESTLVQ T0336 127 :VSYALEEIAKANPMLMASIVR 1bk5A 319 :ALRAVGNIVTGNDLQTQVVIN T0336 148 :DFMSMLSSKNREDKLTALNFIEAMGENSF 1bk5A 345 :ALRLLLSSPKENIKKEACWTISNITAGNT T0336 180 :NPFLPRIINLLHDGDEIV 1bk5A 382 :ANLIPPLVKLLEVAEYKT T0336 198 :RASAVEALVHL 1bk5A 417 :RPDIIRYLVSQ T0336 210 :TLNDKLRKVVIK 1bk5A 428 :GCIKPLCDLLEI T0336 225 :ELNDTSSLVNKTVKEGISRLL 1bk5A 440 :ADNRIIEVTLDALENILKMGE Number of specific fragments extracted= 13 number of extra gaps= 1 total=539 Number of alignments=38 # 1bk5A read from 1bk5A/merged-good-all-a2m # found chain 1bk5A in template set Warning: unaligning (T0336)P102 because of BadResidue code BAD_PEPTIDE in next template residue (1bk5A)P248 T0336 3 :MEEEEFDIREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1bk5A 144 :PEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQC T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEK 1bk5A 219 :PILGLFNSNKPSLIRTATWTLSNLCRGK T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKANPMLMASIV 1bk5A 253 :SVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVI T0336 147 :RDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1bk5A 302 :KRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVI T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIK 1bk5A 344 :PALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVID Number of specific fragments extracted= 5 number of extra gaps= 1 total=544 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wa5B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wa5B expands to /projects/compbio/data/pdb/1wa5.pdb.gz 1wa5B:# T0336 read from 1wa5B/merged-good-all-a2m # 1wa5B read from 1wa5B/merged-good-all-a2m # adding 1wa5B to template set # found chain 1wa5B in template set T0336 5 :EEEFDIREALAN 1wa5B 102 :QEQLSATVKFRQ T0336 18 :EHLEKILIMAKYDESVLKKLIELL 1wa5B 116 :SREHRPPIDVVIQAGVVPRLVEFM T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1wa5B 141 :ENQPEMLQLEAAWALTNIASGTSAQTKVVVD T0336 73 :KLFSLLKKSE 1wa5B 177 :LFIQLLYTGS T0336 85 :PLTQEIAK 1wa5B 187 :VEVKEQAI T0336 93 :AFGQMAKEKPELVKSMIPV 1wa5B 196 :ALGNVAGDSTDYRDYVLQC T0336 112 :LFAN 1wa5B 220 :ILGL T0336 118 :IGDEKTKIN 1wa5B 224 :FNSNKPSLI T0336 127 :VSYALEEIAKANPMLMASIVR 1wa5B 277 :ACWAISYLSDGPQEAIQAVID T0336 148 :DFMSMLSSKNREDKLTALNFI 1wa5B 303 :RLVELLSHESTLVQTPALRAV T0336 169 :EAMGENS 1wa5B 413 :GGLQRPD T0336 176 :FKYV 1wa5B 421 :IRYL T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLR 1wa5B 427 :QGCIKPLCDLLEIADNRIIEVTLDALENILKMGEADK T0336 217 :KVV 1wa5B 475 :DFI Number of specific fragments extracted= 14 number of extra gaps= 0 total=558 Number of alignments=40 # 1wa5B read from 1wa5B/merged-good-all-a2m # found chain 1wa5B in template set Warning: unaligning (T0336)S251 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wa5B)D514 T0336 23 :ILIMAKYDESVLKKLIELL 1wa5B 197 :LGNVAGDSTDYRDYVLQCN T0336 44 :DLWTVVKNAISIIMVIAKTREDLY 1wa5B 227 :NKPSLIRTATWTLSNLCRGKKPQP T0336 68 :EPMLKKLFSLLKKSEA 1wa5B 252 :WSVVSQALPTLAKLIY T0336 84 :IPLTQEIAKAFGQMAKEKPELVKSMIP 1wa5B 271 :TETLVDACWAISYLSDGPQEAIQAVID T0336 111 :VLFANYR 1wa5B 303 :RLVELLS T0336 121 :EKTKIN 1wa5B 311 :ESTLVQ T0336 127 :VSYA 1wa5B 357 :IKKE T0336 138 :NPMLMASIVR 1wa5B 372 :NTEQIQAVID T0336 148 :DFMSMLS 1wa5B 387 :PLVKLLE T0336 155 :SKNR 1wa5B 395 :AEYK T0336 159 :EDKLTAL 1wa5B 400 :KKEACWA T0336 166 :NFIEAMGENSF 1wa5B 409 :NASSGGLQRPD T0336 177 :KYVNPF 1wa5B 422 :RYLVSQ T0336 183 :LPRIINLLHDGDE 1wa5B 430 :IKPLCDLLEIADN T0336 203 :EALVHLATLNDKLRKVVIKRLEELN 1wa5B 443 :RIIEVTLDALENILKMGEADKEARG T0336 228 :DTSSLVNK 1wa5B 472 :ENADFIEK T0336 237 :VKEGISRLL 1wa5B 497 :IYEKAYKII T0336 247 :LEGH 1wa5B 509 :FGEE Number of specific fragments extracted= 18 number of extra gaps= 1 total=576 Number of alignments=41 # 1wa5B read from 1wa5B/merged-good-all-a2m # found chain 1wa5B in template set T0336 2 :SMEEEEFDIREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1wa5B 143 :QPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQC T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1wa5B 219 :PILGLFNSNKPSLIRTATWTLSNLCRGKK T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKANPMLMASIVRD 1wa5B 253 :SVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDV T0336 149 :FMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1wa5B 304 :LVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVI T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIK 1wa5B 344 :PALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVID Number of specific fragments extracted= 5 number of extra gaps= 0 total=581 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oyzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oyzA expands to /projects/compbio/data/pdb/1oyz.pdb.gz 1oyzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0336 read from 1oyzA/merged-good-all-a2m # 1oyzA read from 1oyzA/merged-good-all-a2m # adding 1oyzA to template set # found chain 1oyzA in template set T0336 9 :DIREALANGEHLEKILIMAKYD 1oyzA 27 :ELFRLLDDHNSLKRISSARVLQ T0336 31 :ESVLKKLIELLDDDLWTVVKNAISIIM 1oyzA 53 :QDAVRLAIEFCSDKNYIRRDIGAFILG T0336 63 :REDLYEPMLKKLFSLLKKS 1oyzA 84 :CKKCEDNVFNILNNMALND T0336 83 :AIPLTQEIAK 1oyzA 103 :KSACVRATAI T0336 93 :AFGQMAKEKPELVKSMIPVLF 1oyzA 114 :STAQRCKKNPIYSPKIVEQSQ T0336 118 :IGDEKTKIN 1oyzA 137 :AFDKSTNVR T0336 127 :VSYALEEIAKA 1oyzA 176 :RNWAAFAININ T0336 138 :N 1oyzA 190 :N T0336 143 :ASIVRDFMSMLSSKNREDKLTALNFIEAMGE 1oyzA 191 :SDIRDCFVEMLQDKNEEVRIEAIIGLSYRKD T0336 180 :NPFLPRIINLLHDGD 1oyzA 222 :KRVLSVLCDELKKNT T0336 197 :VRASAVEALVHLAT 1oyzA 237 :VYDDIIEAAGELGD T0336 213 :DKLRKVVIKRLEELNDT 1oyzA 251 :KTLLPVLDTMLYKFDDN T0336 235 :KTVKEGISRLL 1oyzA 268 :EIITSAIDKLK Number of specific fragments extracted= 13 number of extra gaps= 0 total=594 Number of alignments=43 # 1oyzA read from 1oyzA/merged-good-all-a2m # found chain 1oyzA in template set T0336 2 :SMEEEEFDIREALAN 1oyzA 8 :RKASKEYGLYNQCKK T0336 17 :GEHLEKILIMAKYD 1oyzA 34 :DHNSLKRISSARVL T0336 31 :ESVLKKLIELLDDDLWTVVKNAISIIM 1oyzA 53 :QDAVRLAIEFCSDKNYIRRDIGAFILG T0336 62 :TREDLYEPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIPVL 1oyzA 83 :ICKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNPIYSPKIVEQS T0336 117 :R 1oyzA 134 :Q T0336 118 :IGDEKTKIN 1oyzA 137 :AFDKSTNVR T0336 127 :VSYALEEIAKA 1oyzA 172 :NGDVRNWAAFA T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLTAL 1oyzA 186 :NKYDNSDIRDCFVEMLQDKNEEVRIEAI T0336 166 :NFIEA 1oyzA 215 :GLSYR T0336 175 :SF 1oyzA 220 :KD T0336 180 :NPFLPRIINLLHD 1oyzA 222 :KRVLSVLCDELKK T0336 195 :EIVRAS 1oyzA 235 :NTVYDD T0336 211 :LNDKLRKV 1oyzA 241 :IIEAAGEL T0336 224 :EELNDTSSLVNK 1oyzA 251 :KTLLPVLDTMLY T0336 236 :TVKEGISRLL 1oyzA 269 :IITSAIDKLK Number of specific fragments extracted= 15 number of extra gaps= 0 total=609 Number of alignments=44 # 1oyzA read from 1oyzA/merged-good-all-a2m # found chain 1oyzA in template set T0336 2 :SMEEEEFDIREAL 1oyzA 35 :HNSLKRISSARVL T0336 26 :MAKYDESVLKKLIELLDDDLWTVVKNAISIIMVI 1oyzA 48 :QLRGGQDAVRLAIEFCSDKNYIRRDIGAFILGQI T0336 63 :REDLYEPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1oyzA 84 :CKKCEDNVFNILNNMALNDKSACVRATAIESTAQRCKKNP T0336 103 :ELVKSMIP 1oyzA 127 :PKIVEQSQ T0336 111 :VLFANYRIGDEKTKINVSYAL 1oyzA 163 :LLINLLKDPNGDVRNWAAFAI T0336 133 :EIAKANPM 1oyzA 184 :NINKYDNS T0336 144 :SIVRDFMSMLSSKNREDKLTALNFIEAMGE 1oyzA 192 :DIRDCFVEMLQDKNEEVRIEAIIGLSYRKD T0336 180 :NPFLPRIINLLHDGD 1oyzA 222 :KRVLSVLCDELKKNT T0336 197 :VRASAVEALVHL 1oyzA 237 :VYDDIIEAAGEL T0336 211 :LNDKLRKVVIKRLEELNDTS 1oyzA 249 :GDKTLLPVLDTMLYKFDDNE T0336 232 :LVNKTVKE 1oyzA 269 :IITSAIDK Number of specific fragments extracted= 11 number of extra gaps= 0 total=620 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wa5C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wa5C expands to /projects/compbio/data/pdb/1wa5.pdb.gz 1wa5C:# T0336 read from 1wa5C/merged-good-all-a2m # 1wa5C read from 1wa5C/merged-good-all-a2m # adding 1wa5C to template set # found chain 1wa5C in template set Warning: unaligning (T0336)N157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wa5C)K196 T0336 9 :DIREALAN 1wa5C 6 :TVAKFLAE T0336 17 :GEHLEKILIMAKYD 1wa5C 17 :ASTAKTSERNLRQL T0336 31 :ESVLKKLIELL 1wa5C 34 :DGFGLTLLHVI T0336 42 :DDDLWTVVKNAISIIMVIAKT 1wa5C 47 :TNLPLSTRLAGALFFKNFIKR T0336 63 :REDLYEPMLKKLFSLLKKSEAI 1wa5C 79 :PANNVELIKKEIVPLMISLPNN T0336 86 :LTQEIAKAFGQMAK 1wa5C 101 :LQVQIGEAISSIAD T0336 100 :EKPELVKSMIPVLFANYR 1wa5C 116 :DFPDRWPTLLSDLASRLS T0336 118 :IGDEKTKINVSYALEEIA 1wa5C 158 :FRSDELFLEIKLVLDVFT T0336 140 :MLMASIVRDFMSMLSSK 1wa5C 176 :APFLNLLKTVDEQITAN T0336 159 :EDKLT 1wa5C 198 :SLNIL T0336 164 :ALNFI 1wa5C 205 :VLLVL T0336 170 :AMGENS 1wa5C 215 :DFNCQD T0336 176 :FKYVNPFLPRIINLL 1wa5C 222 :PEFFEDNIQVGMGIF T0336 191 :HDGDEIVRASAVEALVHLAT 1wa5C 256 :ASVLIKVKSSIQELVQLYTT T0336 211 :LNDKLRKVVIKRLEELN 1wa5C 284 :MINEFIQITWNLLTSIS T0336 228 :DTSSLVNKTVK 1wa5C 304 :KYDILVSKSLS Number of specific fragments extracted= 16 number of extra gaps= 0 total=636 Number of alignments=46 # 1wa5C read from 1wa5C/merged-good-all-a2m # found chain 1wa5C in template set Warning: unaligning (T0336)N157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wa5C)K196 Warning: unaligning (T0336)A199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wa5C)H255 T0336 7 :EFDIREALANGEHLEKILIMAKY 1wa5C 24 :ERNLRQLETQDGFGLTLLHVIAS T0336 42 :DDDLWTVVKNAISIIMVIAKTR 1wa5C 47 :TNLPLSTRLAGALFFKNFIKRK T0336 64 :EDLYEPMLKKLFSLLKKSEAIPLT 1wa5C 80 :ANNVELIKKEIVPLMISLPNNLQV T0336 89 :EIAKAFGQMA 1wa5C 104 :QIGEAISSIA T0336 100 :EK 1wa5C 114 :DS T0336 102 :PELVKSMIPVLFANYRIGDEKTKI 1wa5C 118 :PDRWPTLLSDLASRLSNDDMVTNK T0336 127 :VSYALEEIAKANPMLMASIVRDFMSMLSSK 1wa5C 163 :LFLEIKLVLDVFTAPFLNLLKTVDEQITAN T0336 159 :EDKLTA 1wa5C 198 :SLNILF T0336 165 :LNFIEAM 1wa5C 210 :IKLYYDF T0336 172 :GENSFKYVNPFLPRIINLLHDGDEI 1wa5C 218 :CQDIPEFFEDNIQVGMGIFHKYLSY T0336 200 :SAVEALVHLA 1wa5C 256 :ASVLIKVKSS T0336 211 :LNDKLRKVVIKRLEELNDTSSLVNKTVKEGIS 1wa5C 266 :IQELVQLYTTRYEDVFGPMINEFIQITWNLLT T0336 246 :L 1wa5C 298 :S Number of specific fragments extracted= 13 number of extra gaps= 0 total=649 Number of alignments=47 # 1wa5C read from 1wa5C/merged-good-all-a2m # found chain 1wa5C in template set T0336 4 :EEEEFDIREALANGEHLE 1wa5C 99 :NNLQVQIGEAISSIADSD T0336 26 :MAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKT 1wa5C 117 :FPDRWPTLLSDLASRLSNDDMVTNKGVLTVAHSIFKR T0336 63 :REDLYEPMLKK 1wa5C 160 :SDELFLEIKLV T0336 74 :LFSLLKKS 1wa5C 181 :LLKTVDEQ T0336 82 :EAIPLTQEIAKAFGQMAKEKP 1wa5C 197 :ASLNILFDVLLVLIKLYYDFN T0336 103 :ELVKSMIP 1wa5C 223 :EFFEDNIQ T0336 111 :VLFANYRIGDE 1wa5C 235 :IFHKYLSYSNP T0336 122 :KTKINVSYALEEIAK 1wa5C 261 :KVKSSIQELVQLYTT T0336 137 :ANPMLMASIVRDFMSMLSS 1wa5C 280 :VFGPMINEFIQITWNLLTS T0336 156 :KNREDKLTALNFIEAMGE 1wa5C 304 :KYDILVSKSLSFLTAVTR T0336 174 :NSFKYVNPFLPRII 1wa5C 330 :NNESAMNNITEQII Number of specific fragments extracted= 11 number of extra gaps= 0 total=660 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ee4A expands to /projects/compbio/data/pdb/1ee4.pdb.gz 1ee4A:# T0336 read from 1ee4A/merged-good-all-a2m # 1ee4A read from 1ee4A/merged-good-all-a2m # adding 1ee4A to template set # found chain 1ee4A in template set T0336 6 :EEFDIREALANGEHLE 1ee4A 107 :ATVKFRQILSREHRPP T0336 25 :IMAKYDESVLKKLIELL 1ee4A 123 :IDVVIQAGVVPRLVEFM T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1ee4A 141 :ENQPEMLQLEAAWALTNIASGTSAQTKVVVD T0336 73 :KLFSLLKKSE 1ee4A 177 :LFIQLLYTGS T0336 85 :PLTQEIAKAFGQMAKEKPELVKSMIPV 1ee4A 188 :EVKEQAIWALGNVAGDSTDYRDYVLQC T0336 112 :LFANYRIGDEKTKI 1ee4A 220 :ILGLFNSNKPSLIR T0336 127 :VSYALEEIAKA 1ee4A 235 :ATWTLSNLCRG T0336 138 :NP 1ee4A 247 :KP T0336 140 :MLMASIVRDFMSMLSSKNR 1ee4A 253 :SVVSQALPTLAKLIYSMDT T0336 159 :EDKLT 1ee4A 274 :LVDAC T0336 164 :ALNFI 1ee4A 280 :AISYL T0336 172 :GENSFKYV 1ee4A 285 :SDGPQEAI T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKR 1ee4A 298 :VRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINA T0336 228 :DTSSLVN 1ee4A 341 :GVLPALR Number of specific fragments extracted= 14 number of extra gaps= 0 total=674 Number of alignments=49 # 1ee4A read from 1ee4A/merged-good-all-a2m # found chain 1ee4A in template set T0336 8 :FDIREALANGEHLE 1ee4A 90 :PQMTQQLNSDDMQE T0336 22 :KILIMAKY 1ee4A 107 :ATVKFRQI T0336 30 :DESV 1ee4A 123 :IDVV T0336 34 :LKKLIELL 1ee4A 132 :VPRLVEFM T0336 43 :DDLWTVVKNAISIIMVIAKTREDLY 1ee4A 142 :NQPEMLQLEAAWALTNIASGTSAQT T0336 68 :EPMLKKLFSLLKKSE 1ee4A 172 :ADAVPLFIQLLYTGS T0336 84 :IPLTQEIAKAFGQMAKEKPELVKSMIP 1ee4A 187 :VEVKEQAIWALGNVAGDSTDYRDYVLQ T0336 111 :VLFANYR 1ee4A 219 :PILGLFN T0336 118 :IGDEKTKIN 1ee4A 268 :SMDTETLVD T0336 127 :VSYALEEIAKANPMLMASIVR 1ee4A 319 :ALRAVGNIVTGNDLQTQVVIN T0336 148 :DFMSMLSSKNREDKLTALNFIEAMGENSF 1ee4A 345 :ALRLLLSSPKENIKKEACWTISNITAGNT T0336 180 :NPFLPRIINLLHDGDE 1ee4A 382 :ANLIPPLVKLLEVAED T0336 210 :TLNDKLRKVVIKRLEELNDTSSLVNKTVK 1ee4A 398 :KTKKEACWAISNASSGGLQRPDIIRYLVS T0336 239 :EGISRLLL 1ee4A 431 :KPLCDLLE Number of specific fragments extracted= 14 number of extra gaps= 0 total=688 Number of alignments=50 # 1ee4A read from 1ee4A/merged-good-all-a2m # found chain 1ee4A in template set T0336 2 :SMEEEEFDIREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1ee4A 143 :QPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQC T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1ee4A 219 :PILGLFNSNKPSLIRTATWTLSNLCRGKK T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKANPMLMASIV 1ee4A 253 :SVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVI T0336 147 :RDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFL 1ee4A 302 :KRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVI T0336 184 :PRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIK 1ee4A 344 :PALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVID Number of specific fragments extracted= 5 number of extra gaps= 0 total=693 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ialA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ialA expands to /projects/compbio/data/pdb/1ial.pdb.gz 1ialA:# T0336 read from 1ialA/merged-good-all-a2m # 1ialA read from 1ialA/merged-good-all-a2m # adding 1ialA to template set # found chain 1ialA in template set T0336 9 :DIREALANGEHLEKILI 1ialA 80 :DIVKGINSNNLESQLQA T0336 26 :MAKYDE 1ialA 112 :IDNIIR T0336 32 :SVLKKLIELLD 1ialA 119 :GLIPKFVSFLG T0336 43 :DDLWTVVKNAISIIMVIAKTREDLYEPMLK 1ialA 131 :TDCSPIQFESAWALTNIASGTSEQTKAVVD T0336 73 :KLFSLLKKSEA 1ialA 162 :GAIPAFISLLA T0336 84 :IPLTQEIAK 1ialA 175 :HAHISEQAV T0336 93 :AFGQMAKEKP 1ialA 185 :ALGNIAGDGS T0336 103 :ELVKSMIPVLFA 1ialA 204 :GAIDPLLALLAV T0336 117 :R 1ialA 216 :P T0336 118 :IG 1ialA 221 :LA T0336 122 :KTKIN 1ialA 223 :CGYLR T0336 127 :VSYALEEIAK 1ialA 229 :LTWTLSNLCR T0336 138 :NP 1ialA 241 :NP T0336 140 :MLMASIVRDFMSMLSSKNR 1ialA 247 :DAVEQILPTLVRLLHHNDP T0336 159 :EDKLTALNFI 1ialA 269 :ADSCWAISYL T0336 173 :ENSFKYV 1ialA 283 :NERIEMV T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKR 1ialA 292 :KGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDA T0336 225 :ELNDTSSLV 1ialA 335 :GALAVFPSL Number of specific fragments extracted= 18 number of extra gaps= 0 total=711 Number of alignments=52 # 1ialA read from 1ialA/merged-good-all-a2m # found chain 1ialA in template set T0336 8 :FDIREALANGEHLE 1ialA 79 :EDIVKGINSNNLES T0336 22 :KILIMAKY 1ialA 96 :ATQAARKL T0336 30 :DESV 1ialA 112 :IDNI T0336 34 :LKKLIELLD 1ialA 121 :IPKFVSFLG T0336 43 :DDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1ialA 131 :TDCSPIQFESAWALTNIASGTSEQTKAVVDG T0336 74 :LFSLLKKSEA 1ialA 163 :AIPAFISLLA T0336 84 :IPLTQEIAK 1ialA 175 :HAHISEQAV T0336 93 :AFGQMAKEKPELVKSM 1ialA 185 :ALGNIAGDGSAFRDLV T0336 109 :IPVLFANYRIGD 1ialA 206 :IDPLLALLAVPD T0336 121 :EKTKIN 1ialA 219 :STLACG T0336 127 :VSYALEEIAKA 1ialA 249 :VEQILPTLVRL T0336 138 :NPMLMASI 1ialA 282 :PNERIEMV T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGENSF 1ialA 295 :VPQLVKLLGATELPIVTPALRAIGNIVTGTD T0336 177 :KYVNPF 1ialA 371 :QQVVNH T0336 183 :LPRIINLLHDGDEIV 1ialA 379 :VPFLVGVLSKADFKT T0336 198 :RASAVE 1ialA 430 :SAKDTK T0336 205 :LVHL 1ialA 436 :IIQV T0336 211 :LNDKLRKVVIKR 1ialA 440 :ILDAISNIFQAA T0336 225 :ELNDTSSLVNKTVKEG 1ialA 452 :EKLGETEKLSIMIEEC T0336 241 :ISRLLLLEGHS 1ialA 470 :LDKIEALQRHE Number of specific fragments extracted= 20 number of extra gaps= 0 total=731 Number of alignments=53 # 1ialA read from 1ialA/merged-good-all-a2m # found chain 1ialA in template set T0336 2 :SMEEEEFDIREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1ialA 132 :DCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKH T0336 74 :LFSLLKKSEAI 1ialA 208 :PLLALLAVPDL T0336 85 :PLTQEIAKAFGQMAKEKP 1ialA 224 :GYLRNLTWTLSNLCRNKN T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAKANPMLMASI 1ialA 247 :DAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMV T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFLP 1ialA 295 :VPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVID T0336 185 :RIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIK 1ialA 339 :VFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVN T0336 222 :RLEE 1ialA 381 :FLVG T0336 226 :LNDTSSLVNKTVKEGISRLL 1ialA 386 :LSKADFKTQKEAAWAITNYT Number of specific fragments extracted= 8 number of extra gaps= 0 total=739 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w63B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1w63B/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1w63B/merged-good-all-a2m.gz for input Trying 1w63B/merged-good-all-a2m Error: Couldn't open file 1w63B/merged-good-all-a2m or 1w63B/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uklA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1uklA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1uklA/merged-good-all-a2m.gz for input Trying 1uklA/merged-good-all-a2m Error: Couldn't open file 1uklA/merged-good-all-a2m or 1uklA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u6gC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1u6gC/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1u6gC/merged-good-all-a2m.gz for input Trying 1u6gC/merged-good-all-a2m Error: Couldn't open file 1u6gC/merged-good-all-a2m or 1u6gC/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b6cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b6cA expands to /projects/compbio/data/pdb/2b6c.pdb.gz 2b6cA:Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2b6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 120, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2b6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 329, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 344, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 348, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 350, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 352, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 354, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 356, because occupancy 0.400 <= existing 0.600 in 2b6cA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 2b6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1282, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 2b6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1699, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1796, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1800, because occupancy 0.500 <= existing 0.500 in 2b6cA Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 2b6cA # T0336 read from 2b6cA/merged-good-all-a2m # 2b6cA read from 2b6cA/merged-good-all-a2m # adding 2b6cA to template set # found chain 2b6cA in template set T0336 4 :EEEEFDIREALAN 2b6cA 10 :PETAAKMSAYMKH T0336 17 :GEHLEKILIMAKY 2b6cA 26 :FAGIPAPERQALS T0336 31 :ESVLK 2b6cA 39 :KQLLK T0336 36 :KLIELL 2b6cA 52 :KLCQEI T0336 45 :LWTVVKNAISIIMVIAKTREDLYEPMLKKLFSLLKKSE 2b6cA 62 :QKTEREYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKA T0336 84 :IPLTQEIAK 2b6cA 100 :WWDSVDAWR T0336 93 :AFGQMAKEKPEL 2b6cA 110 :FFGSWVALHLTE T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGENSFK 2b6cA 122 :LPTIFALFYGAENFWNRRVALNLQLMLKEKTN T0336 180 :NPFLPRIINLLHDGD 2b6cA 154 :QDLLKKAIIYDRTTE T0336 195 :EIVRASAVEALVHLATLN 2b6cA 170 :FFIQKAIGWSLRQYSKTN T0336 216 :RKVVIKRLEEL 2b6cA 188 :PQWVEELMKEL T0336 228 :DTSSLVNKT 2b6cA 199 :VLSPLAQRE Number of specific fragments extracted= 12 number of extra gaps= 0 total=751 Number of alignments=55 # 2b6cA read from 2b6cA/merged-good-all-a2m # found chain 2b6cA in template set T0336 1 :MSMEEEEFDIREALAN 2b6cA 7 :QKNPETAAKMSAYMKH T0336 17 :GEHLEKILIMA 2b6cA 28 :GIPAPERQALS T0336 31 :ESVLKK 2b6cA 39 :KQLLKE T0336 37 :LIELL 2b6cA 53 :LCQEI T0336 44 :D 2b6cA 64 :T T0336 49 :VKNAISIIMVIAKTREDLYEPMLKKLFSLLKKSE 2b6cA 66 :REYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKA T0336 84 :IPLTQEIAK 2b6cA 100 :WWDSVDAWR T0336 93 :AFGQMAKEKPEL 2b6cA 110 :FFGSWVALHLTE T0336 146 :VRDFMSMLSSKNREDKLT 2b6cA 122 :LPTIFALFYGAENFWNRR T0336 167 :FIEAMGE 2b6cA 140 :VALNLQL T0336 178 :YVNPF 2b6cA 147 :MLKEK T0336 183 :LPRIINLLHDGDE 2b6cA 154 :QDLLKKAIIYDRT T0336 198 :RASA 2b6cA 167 :TEEF T0336 210 :TLNDKLRKVVIKRLE 2b6cA 171 :FIQKAIGWSLRQYSK T0336 228 :DTSSLVNKTVKE 2b6cA 186 :TNPQWVEELMKE Number of specific fragments extracted= 15 number of extra gaps= 0 total=766 Number of alignments=56 # 2b6cA read from 2b6cA/merged-good-all-a2m # found chain 2b6cA in template set T0336 1 :MSMEEEEFDIREALAN 2b6cA 7 :QKNPETAAKMSAYMKH T0336 20 :LEKILIMAKYDESVLKK 2b6cA 28 :GIPAPERQALSKQLLKE T0336 63 :REDLYEPMLKKLFSLLKKSEAIPLTQEIAKAFGQMAKEKP 2b6cA 45 :SHTWPKEKLCQEIEAYYQKTEREYQYVAIDLALQNVQRFS T0336 103 :ELVKSM 2b6cA 86 :EEVVAF T0336 117 :RIGDEKTKINVSYALEEIAKANPMLMASIVR 2b6cA 97 :QKAWWDSVDAWRKFFGSWVALHLTELPTIFA T0336 152 :MLSSKNREDKLTALNFIE 2b6cA 128 :LFYGAENFWNRRVALNLQ T0336 173 :ENSFKY 2b6cA 146 :LMLKEK T0336 183 :LPRIINLL 2b6cA 154 :QDLLKKAI T0336 191 :HDGDEIVRASAVEALVHLATLNDK 2b6cA 166 :TTEEFFIQKAIGWSLRQYSKTNPQ T0336 218 :VVIKRLEELN 2b6cA 190 :WVEELMKELV Number of specific fragments extracted= 10 number of extra gaps= 0 total=776 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qsaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0336 read from 1qsaA/merged-good-all-a2m # 1qsaA read from 1qsaA/merged-good-all-a2m # found chain 1qsaA in training set T0336 6 :EEFDIREALANGEHLEKILIMAKYD 1qsaA 138 :ACDKLFSVWRASGKQDPLAYLERIR T0336 32 :SVLKKLIELLDDDLWTVVKNAIS 1qsaA 171 :GLVTVLAGQMPADYQTIASAIIS T0336 59 :IAK 1qsaA 194 :LAN T0336 64 :E 1qsaA 197 :N T0336 71 :LKKLFSLLKKSEAIPLTQEIAK 1qsaA 198 :PNTVLTFARTTGATDFTRQMAA T0336 93 :AFGQMAKEKPEL 1qsaA 221 :AFASVARQDAEN T0336 127 :VSYALEEIAKA 1qsaA 233 :ARLMIPSLAQA T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLT 1qsaA 247 :NEDQIQELRDIVAWRLMGNDVTDEQA T0336 182 :FLPRIINLLH 1qsaA 274 :WRDDAIMRSQ T0336 198 :RASAVEALVHLATLN 1qsaA 284 :STSLIERRVRMALGT T0336 217 :KVVIKRLEELND 1qsaA 302 :RGLNTWLARLPM T0336 230 :SSLVNKTVK 1qsaA 321 :WRYWQADLL T0336 239 :EGISRLLLLEG 1qsaA 337 :EAKEILHQLMQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=789 Number of alignments=58 # 1qsaA read from 1qsaA/merged-good-all-a2m # found chain 1qsaA in training set T0336 17 :GEHLEKILIMAKYD 1qsaA 115 :TGQSEEAWQGAKEL T0336 32 :SVLKKLIELL 1qsaA 137 :NACDKLFSVW T0336 42 :DDDLWTVVKNAISI 1qsaA 151 :KQDPLAYLERIRLA T0336 56 :IMVIAKTREDLYEPM 1qsaA 173 :VTVLAGQMPADYQTI T0336 71 :LKKLFSLLKKSEAIPLTQEIAK 1qsaA 198 :PNTVLTFARTTGATDFTRQMAA T0336 93 :AFGQMAKEKPELVKSMIPVLFANYR 1qsaA 221 :AFASVARQDAENARLMIPSLAQAQQ T0336 118 :IGDEKTKIN 1qsaA 265 :NDVTDEQAK T0336 127 :VSYALEEIAKA 1qsaA 288 :IERRVRMALGT T0336 138 :NPML 1qsaA 300 :DRRG T0336 146 :VRDFMSMLSSKNREDKLTA 1qsaA 304 :LNTWLARLPMEAKEKDEWR T0336 165 :LNFIEAMGENSFKY 1qsaA 324 :WQADLLLERGREAE T0336 183 :LPRIINLLHDGDEIV 1qsaA 338 :AKEILHQLMQQRGFY T0336 199 :ASAVEALVHLATLNDKLRKVVIK 1qsaA 372 :PQNVDSALTQGPEMARVRELMYW T0336 228 :DTSSLVNKTVKEGI 1qsaA 395 :NLDNTARSEWANLV Number of specific fragments extracted= 14 number of extra gaps= 0 total=803 Number of alignments=59 # 1qsaA read from 1qsaA/merged-good-all-a2m # found chain 1qsaA in training set T0336 1 :MSMEEEEFDIREALANGEHLEKILIMAKYDE 1qsaA 1 :DSLDEQRSRYAQIKQAWDNRQMDVVEQMMPG T0336 36 :KLIELLD 1qsaA 57 :TVTNFVR T0336 43 :DDL 1qsaA 65 :NPT T0336 46 :WTVVKNAISIIMVIAKT 1qsaA 69 :PPARTLQSRFVNELARR T0336 65 :DLYEPMLKK 1qsaA 86 :EDWRGLLAF T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIPVLFANYRIGDEKTKINVSY 1qsaA 108 :YYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASGKQDPLAYLERIRL T0336 130 :ALEEIAKANPMLMASIVRDFMSMLSS 1qsaA 172 :LVTVLAGQMPADYQTIASAIISLANN T0336 156 :KNREDKLTALNFIEAMGENSFKYVNPFLPRIINLLHDGDEIVRA 1qsaA 210 :ATDFTRQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQE T0336 205 :LVHLA 1qsaA 254 :LRDIV T0336 210 :TL 1qsaA 264 :GN T0336 212 :NDKLRKVVIKRLEELNDTS 1qsaA 268 :TDEQAKWRDDAIMRSQSTS T0336 232 :LVNKTVKE 1qsaA 287 :LIERRVRM Number of specific fragments extracted= 12 number of extra gaps= 0 total=815 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pjmB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1pjmB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1pjmB/merged-good-all-a2m.gz for input Trying 1pjmB/merged-good-all-a2m Error: Couldn't open file 1pjmB/merged-good-all-a2m or 1pjmB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jdhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jdhA expands to /projects/compbio/data/pdb/1jdh.pdb.gz 1jdhA:# T0336 read from 1jdhA/merged-good-all-a2m # 1jdhA read from 1jdhA/merged-good-all-a2m # adding 1jdhA to template set # found chain 1jdhA in template set T0336 3 :MEEEEFDIREALANGEHLEKILI 1jdhA 168 :VNKAAVMVHQLSKKEASRHAIMR T0336 30 :DESVLKKLIELL 1jdhA 191 :SPQMVSAIVRTM T0336 45 :LWTVVKNAISIIMVIAKTREDLYEPMLK 1jdhA 248 :VDSVLFYAITTLHNLLLHQEGAKMAVRL T0336 73 :KLFSLLKKSEAIPLTQEIAK 1jdhA 277 :GGLQKMVALLNKTNVKFLAI T0336 93 :AFGQMAKEKPE 1jdhA 300 :CLQILAYGNQE T0336 104 :LVKSMIPVLFA 1jdhA 320 :GPQALVNIMRT T0336 118 :IGDEKTKINVSYALEEIAKA 1jdhA 331 :YTYEKLLWTTSRVLKVLSVC T0336 138 :NPMLMA 1jdhA 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 1jdhA 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 1jdhA 377 :LVQNC T0336 164 :ALNFIEAMG 1jdhA 384 :TLRNLSDAA T0336 174 :NSFKYVNPFLPRIINLLHDGDEIVRASAVEALVHLAT 1jdhA 393 :TKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTC T0336 211 :LNDKLR 1jdhA 434 :NKMMVC T0336 217 :KVVIKRLEELNDTSSLV 1jdhA 445 :EALVRTVLRAGDREDIT Number of specific fragments extracted= 14 number of extra gaps= 0 total=829 Number of alignments=61 # 1jdhA read from 1jdhA/merged-good-all-a2m # found chain 1jdhA in template set T0336 31 :ESVLKKLIELL 1jdhA 192 :PQMVSAIVRTM T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLY 1jdhA 287 :NKTNVKFLAITTDCLQILAYGNQESK T0336 68 :EPMLKKLFSLLKKSEAIPLTQEIAKAFGQMA 1jdhA 318 :SGGPQALVNIMRTYTYEKLLWTTSRVLKVLS T0336 100 :E 1jdhA 349 :V T0336 105 :VKSMIPVLFAN 1jdhA 350 :CSSNKPAIVEA T0336 118 :IGDEKTKIN 1jdhA 370 :LTDPSQRLV T0336 127 :VSYALEEIAKA 1jdhA 381 :CLWTLRNLSDA T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSF 1jdhA 394 :KQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNY T0336 181 :PFLPRIINLLHDGDEIV 1jdhA 442 :GGIEALVRTVLRAGDRE T0336 211 :LNDKL 1jdhA 481 :AQNAV Number of specific fragments extracted= 10 number of extra gaps= 0 total=839 Number of alignments=62 # 1jdhA read from 1jdhA/merged-good-all-a2m # found chain 1jdhA in template set T0336 2 :SMEEEEFDIREALANGEHLEKI 1jdhA 206 :NDVETARCTAGTLHNLSHHREG T0336 25 :IMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1jdhA 228 :LLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLA T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1jdhA 281 :KMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILA T0336 111 :VLFANY 1jdhA 323 :ALVNIM T0336 117 :RIGDEKTKINVSYALEEIAK 1jdhA 330 :TYTYEKLLWTTSRVLKVLSV T0336 138 :NPMLMASIVRD 1jdhA 350 :CSSNKPAIVEA T0336 149 :FMSMLSSKNREDKLTALNFIEAMGENSFKY 1jdhA 366 :LGLHLTDPSQRLVQNCLWTLRNLSDAATKQ T0336 179 :VNPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKL 1jdhA 398 :MEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKN T0336 216 :RKVVIKRLEELNDTSSLV 1jdhA 444 :IEALVRTVLRAGDREDIT Number of specific fragments extracted= 9 number of extra gaps= 0 total=848 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bptA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bptA expands to /projects/compbio/data/pdb/2bpt.pdb.gz 2bptA:# T0336 read from 2bptA/merged-good-all-a2m # 2bptA read from 2bptA/merged-good-all-a2m # adding 2bptA to template set # found chain 2bptA in template set Warning: unaligning (T0336)D42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bptA)E341 Warning: unaligning (T0336)T47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bptA)V347 Warning: unaligning (T0336)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bptA)V347 T0336 3 :MEEEEFDIREALAN 2bptA 293 :ICEEEIDIAYELAQ T0336 17 :GEHLEKILIMAKYDESVLKKLIELL 2bptA 309 :QSPLQSYNFALSSIKDVVPNLLNLL T0336 43 :DDLW 2bptA 342 :DDDW T0336 49 :VKNAISIIMVIAKTREDLYEPML 2bptA 348 :SMSAGACLQLFAQNCGNHILEPV T0336 75 :FSLLKKSEA 2bptA 371 :LEFVEQNIT T0336 84 :IPLTQEIAK 2bptA 382 :NWRNREAAV T0336 93 :AFGQMA 2bptA 392 :AFGSIM T0336 100 :EKPEL 2bptA 398 :DGPDK T0336 106 :KSMIPVLFANYR 2bptA 403 :VQRTYYVHQALP T0336 118 :IGDEKTKIN 2bptA 420 :MNDQSLQVK T0336 127 :VSYALEEIAKA 2bptA 435 :IGRIADSVAES T0336 138 :NP 2bptA 447 :DP T0336 140 :MLMASIVRDFMSMLSSKNR 2bptA 450 :QHLPGVVQACLIGLQDHPK T0336 159 :EDKLT 2bptA 470 :ATNCS T0336 164 :ALNFIEAMGENSFKYVNPFLPRIINLL 2bptA 477 :IINLVEQLAEATPSPIYNFYPALVDGL T0336 191 :HDGDEIVRASAVEALVHLAT 2bptA 510 :IDNEFNARASAFSALTTMVE T0336 211 :LNDKLRKVVIKRLEE 2bptA 538 :TSASISTFVMDKLGQ T0336 226 :LN 2bptA 554 :MS T0336 228 :DTSSLVNKTVKEGISRLLLL 2bptA 557 :DENQLTLEDAQSLQELQSNI Number of specific fragments extracted= 19 number of extra gaps= 1 total=867 Number of alignments=64 # 2bptA read from 2bptA/merged-good-all-a2m # found chain 2bptA in template set Warning: unaligning (T0336)D42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bptA)E341 Warning: unaligning (T0336)T47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bptA)V347 Warning: unaligning (T0336)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bptA)V347 T0336 4 :EEEEFDIREALAN 2bptA 294 :CEEEIDIAYELAQ T0336 17 :GEHLEKILIMAK 2bptA 308 :PQSPLQSYNFAL T0336 29 :YDESVLKKLIELL 2bptA 321 :SIKDVVPNLLNLL T0336 43 :DDLW 2bptA 342 :DDDW T0336 49 :VKNAISIIMVIAKTREDLYEP 2bptA 348 :SMSAGACLQLFAQNCGNHILE T0336 73 :KLFSLLKKSEA 2bptA 369 :PVLEFVEQNIT T0336 84 :IPLTQEIAK 2bptA 382 :NWRNREAAV T0336 93 :AFGQMA 2bptA 392 :AFGSIM T0336 100 :EKPEL 2bptA 398 :DGPDK T0336 106 :KSMIPVLFANYR 2bptA 403 :VQRTYYVHQALP T0336 118 :IGDEKTKIN 2bptA 420 :MNDQSLQVK T0336 127 :VSYALEEIAKA 2bptA 435 :IGRIADSVAES T0336 138 :NPMLMASIVRDFMSMLSSKNR 2bptA 448 :PQQHLPGVVQACLIGLQDHPK T0336 159 :EDKLTA 2bptA 470 :ATNCSW T0336 165 :LNFIEAMGENSFKYVNPFLPRIINLLHDGDE 2bptA 478 :INLVEQLAEATPSPIYNFYPALVDGLIGAAN T0336 198 :RASA 2bptA 509 :RIDN T0336 203 :EALVHLA 2bptA 513 :EFNARAS T0336 211 :LNDKLRKVVIKRLEELNDTSSLVNKTVKEGISRLLLLEGHS 2bptA 520 :AFSALTTMVEYATDTVAETSASISTFVMDKLGQTMSVDENQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=885 Number of alignments=65 # 2bptA read from 2bptA/merged-good-all-a2m # found chain 2bptA in template set Warning: unaligning (T0336)I196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bptA)V347 Warning: unaligning (T0336)V197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bptA)V347 T0336 15 :ANGEHLEKILIMAKYD 2bptA 109 :PRIANAAAQLIAAIAD T0336 31 :ESVLKKLIELLDDD 2bptA 133 :PELMKIMVDNTGAE T0336 45 :LWTVVKNAISIIMVIAKTRED 2bptA 148 :PENVKRASLLALGYMCESADP T0336 66 :LYEPMLKKLFSLL 2bptA 176 :SSNNILIAIVQGA T0336 79 :KKSEAIPLTQEIAKAFGQMAKEKP 2bptA 190 :STETSKAVRLAALNALADSLIFIK T0336 103 :ELVKSMIPVLFANYRIGDEKTKINVSYALEEIAK 2bptA 220 :GERNYLMQVVCEATQAEDIEVQAAAFGCLCKIMS T0336 137 :ANPMLMA 2bptA 258 :FMKPYME T0336 144 :SIVRDFMSMLSSKNREDKLTALNFIEAMGEN 2bptA 266 :ALYALTIATMKSPNDKVASMTVEFWSTICEE T0336 175 :SFKYVNPFLPRIINLLH 2bptA 318 :ALSSIKDVVPNLLNLLT T0336 192 :DGDE 2bptA 342 :DDDW T0336 198 :RASAVEALVHLAT 2bptA 348 :SMSAGACLQLFAQ T0336 211 :LNDKLRKVVIKRLEELNDTSSLVNKTVKEGISRLLLLEGH 2bptA 362 :CGNHILEPVLEFVEQNITADNWRNREAAVMAFGSIMDGPD Number of specific fragments extracted= 12 number of extra gaps= 1 total=897 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gw5A expands to /projects/compbio/data/pdb/1gw5.pdb.gz 1gw5A: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 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 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 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 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 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 # T0336 read from 1gw5A/merged-good-all-a2m # 1gw5A read from 1gw5A/merged-good-all-a2m # adding 1gw5A to template set # found chain 1gw5A in template set T0336 8 :FDIREALANGEHLEKI 1gw5A 14 :AVFISDIRNCKSKEAE T0336 27 :AKYDESVLKKLIELL 1gw5A 30 :IKRINKELANIRSKF T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLY 1gw5A 158 :GDTMDSVKQSAALCLLRLYRTSPDLV T0336 69 :PMLKKLFSLL 1gw5A 187 :DWTSRVVHLL T0336 81 :SEAIPLTQEIAK 1gw5A 197 :NDQHLGVVTAAT T0336 93 :AFGQMAKEKPELVKSMIPVLFANYR 1gw5A 210 :LITTLAQKNPEEFKTSVSLAVSRLS T0336 119 :GDEKTKIN 1gw5A 270 :PPEDPAVR T0336 127 :VSYALEEIAKA 1gw5A 310 :LFEAISLIIHH T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLTALNFIEA 1gw5A 323 :EPNLLVRACNQLGQFLQHRETNLRYLALESMCT T0336 171 :MGENS 1gw5A 357 :ASSEF T0336 176 :FKYVNPFLPRIINLLHD 1gw5A 363 :HEAVKTHIETVINALKT T0336 193 :GDEIVRASAVEALVHLAT 1gw5A 381 :RDVSVRQRAVDLLYAMCD T0336 211 :LNDKLRKVVIKRLEELNDT 1gw5A 401 :NAQQIVAEMLSYLETADYS T0336 230 :SSLVNKTVKEGI 1gw5A 421 :REEIVLKVAILA Number of specific fragments extracted= 14 number of extra gaps= 0 total=911 Number of alignments=67 # 1gw5A read from 1gw5A/merged-good-all-a2m # found chain 1gw5A in template set Warning: unaligning (T0336)T163 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5A)N304 Warning: unaligning (T0336)A164 because of BadResidue code BAD_PEPTIDE at template residue (1gw5A)N304 T0336 1 :MSMEEEEFDIREALAN 1gw5A 103 :NSNSELIRLINNAIKN T0336 17 :GEHLEKILIMAKYDESV 1gw5A 122 :SRNPTFMGLALHCIANV T0336 34 :LKKLIELL 1gw5A 140 :SREMAEAF T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLY 1gw5A 158 :GDTMDSVKQSAALCLLRLYRTSPDLV T0336 68 :EPMLKKLFSLLK 1gw5A 186 :GDWTSRVVHLLN T0336 83 :AIPLTQEIAK 1gw5A 199 :QHLGVVTAAT T0336 93 :AFGQMAKEKPELVKSMIPVLFANYR 1gw5A 210 :LITTLAQKNPEEFKTSVSLAVSRLS T0336 138 :NPM 1gw5A 273 :DPA T0336 141 :LMASIVRDFMSMLSSKNR 1gw5A 279 :RLTECLETILNKAQEPPK T0336 159 :EDKL 1gw5A 299 :KVQH T0336 165 :L 1gw5A 305 :A T0336 166 :NFIEAMGE 1gw5A 312 :EAISLIIH T0336 175 :SFKY 1gw5A 320 :HDSE T0336 180 :NPFLPRIINLLHDGDE 1gw5A 324 :PNLLVRACNQLGQFLQ T0336 201 :AVEALVHLA 1gw5A 340 :HRETNLRYL T0336 211 :LNDKLRKVV 1gw5A 349 :ALESMCTLA T0336 221 :KRLEELNDTSSLVNKTVKE 1gw5A 361 :FSHEAVKTHIETVINALKT Number of specific fragments extracted= 17 number of extra gaps= 1 total=928 Number of alignments=68 # 1gw5A read from 1gw5A/merged-good-all-a2m # found chain 1gw5A in template set T0336 1 :MSMEEEEFDIREALANGEHLEKILIMAKY 1gw5A 103 :NSNSELIRLINNAIKNDLASRNPTFMGLA T0336 30 :DESVLK 1gw5A 140 :SREMAE T0336 36 :KLIELLDDDL 1gw5A 150 :EIPKILVAGD T0336 46 :WTVVKNAISIIMVIAKTREDLY 1gw5A 162 :DSVKQSAALCLLRLYRTSPDLV T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1gw5A 191 :RVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVS T0336 111 :VLFANY 1gw5A 260 :KLLRLL T0336 117 :RIGDEKTKINVSYALEEIAK 1gw5A 270 :PPEDPAVRGRLTECLETILN T0336 137 :ANPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGE 1gw5A 322 :SEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLAS T0336 174 :NSFKYVNPFLPRIINLLH 1gw5A 361 :FSHEAVKTHIETVINALK T0336 192 :DGDEIVRASAVEALVHLATLN 1gw5A 380 :ERDVSVRQRAVDLLYAMCDRS T0336 213 :DKLRKVVIKRLEELN 1gw5A 403 :QQIVAEMLSYLETAD T0336 230 :S 1gw5A 418 :Y T0336 235 :KTVKEGISRL 1gw5A 419 :SIREEIVLKV Number of specific fragments extracted= 13 number of extra gaps= 0 total=941 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1te4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1te4A/merged-good-all-a2m.gz for input Trying 1te4A/merged-good-all-a2m Error: Couldn't open file 1te4A/merged-good-all-a2m or 1te4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gw5B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gw5B expands to /projects/compbio/data/pdb/1gw5.pdb.gz 1gw5B: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 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 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 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 # T0336 read from 1gw5B/merged-good-all-a2m # 1gw5B read from 1gw5B/merged-good-all-a2m # adding 1gw5B to template set # found chain 1gw5B in template set Warning: unaligning (T0336)I84 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)N99 Warning: unaligning (T0336)P85 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)L101 Warning: unaligning (T0336)L86 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)L101 Warning: unaligning (T0336)L141 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)D158 Warning: unaligning (T0336)M142 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)D158 Warning: unaligning (T0336)N174 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)H191 Warning: unaligning (T0336)S175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gw5B)P192 Warning: unaligning (T0336)R222 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)L248 Warning: unaligning (T0336)L223 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)L248 T0336 8 :FDIREALANGEHLEKILIMAKYDE 1gw5B 16 :FELKAELNNEKKEKRKEAVKKVIA T0336 32 :SVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKKLFS 1gw5B 49 :SLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVK T0336 81 :SEA 1gw5B 94 :DCE T0336 87 :TQEIAK 1gw5B 102 :IRALAV T0336 93 :AFGQMA 1gw5B 109 :TMGCIR T0336 101 :KPELVKSMIP 1gw5B 115 :VDKITEYLCE T0336 115 :NYR 1gw5B 125 :PLR T0336 118 :IGDEKTKIN 1gw5B 130 :LKDEDPYVR T0336 127 :VSYALEEIAKANP 1gw5B 141 :AAVCVAKLHDINA T0336 140 :M 1gw5B 156 :V T0336 143 :ASIVRDFMSMLSSKNREDKLTALNFIEAMGE 1gw5B 159 :QGFLDSLRDLIADSNPMVVANAVAALSEISE T0336 176 :FKYV 1gw5B 193 :NSNL T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVH 1gw5B 201 :PQNINKLLTALNECTEWGQIFILDCLSN T0336 209 :AT 1gw5B 229 :YN T0336 211 :LNDKLRKVVIK 1gw5B 236 :EAQSICERVTP Number of specific fragments extracted= 15 number of extra gaps= 4 total=956 Number of alignments=70 # 1gw5B read from 1gw5B/merged-good-all-a2m # found chain 1gw5B in template set Warning: unaligning (T0336)I84 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)N99 Warning: unaligning (T0336)P85 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)L101 Warning: unaligning (T0336)L86 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)L101 Warning: unaligning (T0336)L141 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)D158 Warning: unaligning (T0336)M142 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)D158 Warning: unaligning (T0336)N174 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)H191 Warning: unaligning (T0336)S175 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)H191 Warning: unaligning (T0336)F176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gw5B)P192 Warning: unaligning (T0336)E224 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)K272 Warning: unaligning (T0336)E225 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)K272 T0336 5 :EEEFDIREALANGEHLEKILIMAKYDE 1gw5B 13 :GEIFELKAELNNEKKEKRKEAVKKVIA T0336 32 :SVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKKLFSLL 1gw5B 49 :SLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDC T0336 82 :E 1gw5B 96 :E T0336 87 :TQEIAK 1gw5B 102 :IRALAV T0336 93 :AFGQMAKEK 1gw5B 109 :TMGCIRVDK T0336 104 :LVKSMIPVLFANY 1gw5B 118 :ITEYLCEPLRKCL T0336 119 :GDEKTKIN 1gw5B 131 :KDEDPYVR T0336 127 :VSYALEEIAKA 1gw5B 141 :AAVCVAKLHDI T0336 138 :NPM 1gw5B 154 :QMV T0336 143 :ASIVRDFMSMLSSKNREDKLTALNFIEAMGE 1gw5B 159 :QGFLDSLRDLIADSNPMVVANAVAALSEISE T0336 177 :KYVNPF 1gw5B 194 :SNLLDL T0336 183 :LPRIINLLHDGDEIV 1gw5B 204 :INKLLTALNECTEWG T0336 210 :TLNDKL 1gw5B 239 :SICERV T0336 216 :RKVVIKRL 1gw5B 253 :SAVVLSAV T0336 226 :LNDTSSLVNKTVKEGISRL 1gw5B 273 :DSDYYNMLLKKLAPPLVTL Number of specific fragments extracted= 15 number of extra gaps= 4 total=971 Number of alignments=71 # 1gw5B read from 1gw5B/merged-good-all-a2m # found chain 1gw5B in template set Warning: unaligning (T0336)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)D158 Warning: unaligning (T0336)V105 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)D158 Warning: unaligning (T0336)L189 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)L248 Warning: unaligning (T0336)L190 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)L248 Warning: unaligning (T0336)H191 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)S249 Warning: unaligning (T0336)D192 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)H250 Warning: unaligning (T0336)A209 because of BadResidue code BAD_PEPTIDE in next template residue (1gw5B)E268 Warning: unaligning (T0336)T210 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)E268 Warning: unaligning (T0336)L211 because of BadResidue code BAD_PEPTIDE at template residue (1gw5B)K272 T0336 1 :MSMEEEEFDIREALANGEHLEK 1gw5B 25 :EKKEKRKEAVKKVIAAMTVGKD T0336 30 :DESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1gw5B 47 :VSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNS T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1gw5B 125 :PLRKCLKDEDPYVRKTAAVCVAKLHDINA T0336 106 :KSMIPVLFANYRIGDEKTKINVSYALEEIAK 1gw5B 159 :QGFLDSLRDLIADSNPMVVANAVAALSEISE T0336 137 :ANPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFKYVNPFLPRIIN 1gw5B 195 :NLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSICERVTP T0336 193 :GDEIVRASAVEALVHL 1gw5B 251 :ANSAVVLSAVKVLMKF T0336 212 :NDKLRKVVIKR 1gw5B 273 :DSDYYNMLLKK T0336 223 :LEELNDTSSLVNKTVKEGISRLLLLEGH 1gw5B 288 :LVTLLSGEPEVQYVALRNINLIVQKRPE Number of specific fragments extracted= 8 number of extra gaps= 4 total=979 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ho8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ho8A expands to /projects/compbio/data/pdb/1ho8.pdb.gz 1ho8A:# T0336 read from 1ho8A/merged-good-all-a2m # 1ho8A read from 1ho8A/merged-good-all-a2m # adding 1ho8A to template set # found chain 1ho8A in template set Warning: unaligning (T0336)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ho8A)H237 Warning: unaligning (T0336)S81 because of BadResidue code BAD_PEPTIDE in next template residue (1ho8A)I282 Warning: unaligning (T0336)E82 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)I282 Warning: unaligning (T0336)A83 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)K283 T0336 17 :GEHLEKILIMAKYDESVLKKLIELL 1ho8A 107 :DKYGDDTVKFFQEDPKQLEQLFDVS T0336 44 :DLWTVVKNAISIIMV 1ho8A 238 :LGIQLQYHSLLLIWL T0336 59 :IAKTREDLYEPMLKKLFSLLKK 1ho8A 259 :FANELVQKYLSDFLDLLKLVKI T0336 89 :EIAK 1ho8A 285 :KVSR T0336 93 :AFGQMAKEKPELVKSMIPVLFAN 1ho8A 290 :CISIILQCCSTRVKQHKKVIKQL T0336 127 :VSYALEEIAKA 1ho8A 315 :LGNALPTVQSL T0336 138 :NPMLMASIVRDFMSMLSSKNR 1ho8A 331 :SDEELRQDISNLKEILENEYQ T0336 159 :EDKLT 1ho8A 353 :LTSFD T0336 164 :ALNFI 1ho8A 359 :YVAEL T0336 169 :EAMGENS 1ho8A 385 :DEFKKDN T0336 180 :NPFLPRIINLL 1ho8A 392 :YKIFRQLIELL T0336 192 :DGD 1ho8A 412 :NAK T0336 195 :EIVRASAVEALVHLAT 1ho8A 417 :KIIIQVALNDITHVVE T0336 211 :LNDKLRKV 1ho8A 437 :SIDVLDKT T0336 219 :VIKRLEELND 1ho8A 446 :GKADIMELLN T0336 229 :TSSLVNKTVKEGISRLLLLE 1ho8A 457 :SDSRVKYEALKATQAIIGYT Number of specific fragments extracted= 16 number of extra gaps= 1 total=995 Number of alignments=73 # 1ho8A read from 1ho8A/merged-good-all-a2m # found chain 1ho8A in template set T0336 17 :GEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKKLFS 1ho8A 107 :DKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLK T0336 77 :LLKKSEA 1ho8A 173 :ILQNIEQ T0336 84 :IPLT 1ho8A 181 :DTCY T0336 88 :QEIAK 1ho8A 191 :QELAV T0336 93 :AFGQMAKE 1ho8A 198 :EYRDVIWL T0336 104 :LVKSMIPVLFANYR 1ho8A 206 :HEKKFMPTLFKILQ T0336 127 :VSYALEEIAKA 1ho8A 315 :LGNALPTVQSL T0336 138 :NPMLMASIVRDFMSML 1ho8A 331 :SDEELRQDISNLKEIL T0336 154 :SSKNREDKLTALNFI 1ho8A 350 :YQELTSFDEYVAELD T0336 173 :ENSF 1ho8A 365 :SKLL T0336 177 :KYV 1ho8A 385 :DEF T0336 180 :NPF 1ho8A 390 :DNY T0336 183 :LPRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIK 1ho8A 395 :FRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVEL T0336 226 :LNDTSSLVNKT 1ho8A 434 :LPESIDVLDKT T0336 237 :VKEGISRLLLL 1ho8A 446 :GKADIMELLNH Number of specific fragments extracted= 15 number of extra gaps= 0 total=1010 Number of alignments=74 # 1ho8A read from 1ho8A/merged-good-all-a2m # found chain 1ho8A in template set Warning: unaligning (T0336)Y29 because of BadResidue code BAD_PEPTIDE in next template residue (1ho8A)N73 Warning: unaligning (T0336)D30 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)N73 Warning: unaligning (T0336)E31 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)G74 Warning: unaligning (T0336)D120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ho8A)H237 Warning: unaligning (T0336)K156 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)I282 Warning: unaligning (T0336)N157 because of BadResidue code BAD_PEPTIDE at template residue (1ho8A)K283 T0336 4 :EEEEFDIREALANGE 1ho8A 38 :EIDASTAKALESILV T0336 32 :SVLKKLIELL 1ho8A 75 :KTLIPLIHLL T0336 42 :DDDLWTVVKNAISIIMVIAKT 1ho8A 86 :TSDNEDCKKSVQNLIAELLSS T0336 63 :REDLYEPMLKK 1ho8A 110 :GDDTVKFFQED T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1ho8A 170 :LINILQNIEQMDTCYVCIRLLQELAVIPE T0336 103 :ELV 1ho8A 201 :DVI T0336 106 :KSMIPVLFANY 1ho8A 208 :KKFMPTLFKIL T0336 121 :EKTKINVSYALEEIAK 1ho8A 240 :IQLQYHSLLLIWLLTF T0336 138 :NPMLMASIVR 1ho8A 256 :NPVFANELVQ T0336 148 :DFMSMLSS 1ho8A 273 :DLLKLVKI T0336 158 :REDKLTALNFIEAMGE 1ho8A 284 :EKVSRLCISIILQCCS T0336 174 :NSFK 1ho8A 304 :QHKK T0336 178 :YVNPFLPRIINLLHDG 1ho8A 314 :LLGNALPTVQSLSERK T0336 194 :DEIVRASA 1ho8A 332 :DEELRQDI T0336 217 :KVVIKRLEELNDTSSLVNKTVKEGISRLLLLEGHSSS 1ho8A 340 :SNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVD Number of specific fragments extracted= 15 number of extra gaps= 1 total=1025 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f59A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1f59A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1f59A/merged-good-all-a2m.gz for input Trying 1f59A/merged-good-all-a2m Error: Couldn't open file 1f59A/merged-good-all-a2m or 1f59A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gcjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1gcjA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1gcjA/merged-good-all-a2m.gz for input Trying 1gcjA/merged-good-all-a2m Error: Couldn't open file 1gcjA/merged-good-all-a2m or 1gcjA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1upkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1upkA expands to /projects/compbio/data/pdb/1upk.pdb.gz 1upkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 525, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 940, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1072, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1274, because occupancy 0.250 <= existing 0.750 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1276, because occupancy 0.250 <= existing 0.750 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1278, because occupancy 0.250 <= existing 0.750 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1280, because occupancy 0.250 <= existing 0.750 in 1upkA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1901, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1903, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1905, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1982, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1upkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2435, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2437, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2439, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2441, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2466, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2468, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2470, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2472, because occupancy 0.500 <= existing 0.500 in 1upkA Skipped atom 2474, because occupancy 0.500 <= existing 0.500 in 1upkA # T0336 read from 1upkA/merged-good-all-a2m # 1upkA read from 1upkA/merged-good-all-a2m # adding 1upkA to template set # found chain 1upkA in template set Warning: unaligning (T0336)H19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1upkA)S32 Warning: unaligning (T0336)S252 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1upkA)Q339 Warning: unaligning (T0336)S253 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1upkA)Q339 T0336 5 :EEEFDIREALAN 1upkA 14 :DIVKNLKESMAV T0336 20 :LEKILIMAKYDESVLKKLIELL 1upkA 33 :DKKAEKATEEVSKNLVAMKEIL T0336 45 :LWTVVKNAISIIMVIAKTREDLYEPMLK 1upkA 91 :DFEGKKDVAQIFNNILRRQIGTRTPTVE T0336 73 :KLFSLLKKSEAIP 1upkA 125 :NILFMLLKGYESP T0336 89 :EIAKAFGQMAKEKPEL 1upkA 138 :EIALNCGIMLRECIRH T0336 106 :KSMIPVLFANYR 1upkA 154 :EPLAKIILWSEQ T0336 118 :IGDEKTKIN 1upkA 173 :VEMSTFDIA T0336 127 :VSYALEEIAKANPMLMASIVRDFMSMLSSKNREDKLTALNFI 1upkA 192 :LTRHKLLSAEFLEQHYDRFFSEYEKLLHSENYVTKRQSLKLL T0336 169 :EAMGE 1upkA 248 :KYISK T0336 180 :NPFLPRIINLLHDGDEIVRASAVEALVHLAT 1upkA 253 :PENLKLMMNLLRDKSRNIQFEAFHVFKVFVA T0336 211 :LNDKLRKVVIKRLEELNDTSS 1upkA 287 :KTQPILDILLKNQAKLIEFLS T0336 232 :LVNKTVKEGISRLLLLEGHS 1upkA 318 :QFNDEKTYLVKQIRDLKRPA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1037 Number of alignments=76 # 1upkA read from 1upkA/merged-good-all-a2m # found chain 1upkA in template set Warning: unaligning (T0336)L226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1upkA)E315 Warning: unaligning (T0336)D228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1upkA)E315 Warning: unaligning (T0336)S252 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1upkA)Q339 Warning: unaligning (T0336)S253 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1upkA)Q339 T0336 30 :DESVLKKLIELL 1upkA 43 :VSKNLVAMKEIL T0336 42 :DDDL 1upkA 135 :ESPE T0336 48 :VVKNAISIIMVIAKTRE 1upkA 139 :IALNCGIMLRECIRHEP T0336 66 :LYEPMLKKLFSLLK 1upkA 161 :LWSEQFYDFFRYVE T0336 81 :SEAIPLTQEIAKAFGQMAKEKPEL 1upkA 175 :MSTFDIASDAFATFKDLLTRHKLL T0336 108 :MIPVLFANYR 1upkA 199 :SAEFLEQHYD T0336 118 :IGDEKTKIN 1upkA 218 :LHSENYVTK T0336 127 :VSYALEEIA 1upkA 230 :LKLLGELLL T0336 136 :KANPMLM 1upkA 240 :RHNFTIM T0336 143 :ASIVRDFMSMLSSKNREDKLTALNFIEAMGENSF 1upkA 253 :PENLKLMMNLLRDKSRNIQFEAFHVFKVFVANPN T0336 184 :PRIINLLHDGD 1upkA 289 :QPILDILLKNQ T0336 213 :DKLRKVVIKRLEE 1upkA 300 :AKLIEFLSKFQND T0336 229 :TSS 1upkA 316 :DEQ T0336 233 :VNKTVKEGISRLLLLEGHS 1upkA 319 :FNDEKTYLVKQIRDLKRPA Number of specific fragments extracted= 14 number of extra gaps= 1 total=1051 Number of alignments=77 # 1upkA read from 1upkA/merged-good-all-a2m # found chain 1upkA in template set Warning: unaligning (T0336)S252 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1upkA)Q339 T0336 2 :SMEEEEFDIREALANGEHLE 1upkA 35 :KAEKATEEVSKNLVAMKEIL T0336 22 :KILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1upkA 68 :AQLAQELYNSGLLSTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEY T0336 74 :LFSLLKKS 1upkA 126 :ILFMLLKG T0336 82 :EAIPLTQEIAKAFGQMAKEKP 1upkA 135 :ESPEIALNCGIMLRECIRHEP T0336 103 :ELVKSMI 1upkA 164 :EQFYDFF T0336 114 :ANYRIGDEKTKINVSYALEEIAKANPMLMASI 1upkA 171 :RYVEMSTFDIASDAFATFKDLLTRHKLLSAEF T0336 146 :VRDFMSMLSSKNREDKLTALNFIEAMGE 1upkA 211 :FSEYEKLLHSENYVTKRQSLKLLGELLL T0336 174 :NSFKY 1upkA 245 :IMTKY T0336 179 :VNPFLPRIINLLHDGDEIVRASAVEALVHLATLND 1upkA 252 :KPENLKLMMNLLRDKSRNIQFEAFHVFKVFVANPN T0336 214 :KLRKVV 1upkA 290 :PILDIL T0336 220 :IKRLEELNDT 1upkA 303 :IEFLSKFQND T0336 230 :SSLVNKTVKEGISRLLLLEGHS 1upkA 316 :DEQFNDEKTYLVKQIRDLKRPA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1063 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i7wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i7wA expands to /projects/compbio/data/pdb/1i7w.pdb.gz 1i7wA:Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2207, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2209, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2211, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2213, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2322, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2324, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2326, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2328, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2330, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2332, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2334, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2336, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2338, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 1i7wA Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 1i7wA # T0336 read from 1i7wA/merged-good-all-a2m # 1i7wA read from 1i7wA/merged-good-all-a2m # adding 1i7wA to template set # found chain 1i7wA in template set T0336 4 :EEEEFDIREALANGEHLEKILI 1i7wA 169 :NKAAVMVHQLSKKEASRHAIMR T0336 30 :DESVLKKLIELL 1i7wA 191 :SPQMVSAIVRTM T0336 44 :DLWTVVKNAISIIMVIAKTREDLYEPMLK 1i7wA 247 :PVDSVLFYAITTLHNLLLHQEGAKMAVRL T0336 73 :KLFSLLKKSEAIPLTQEIAK 1i7wA 277 :GGLQKMVALLNKTNVKFLAI T0336 93 :AFGQMAKEKPE 1i7wA 300 :CLQILAYGNQE T0336 104 :LVKSMIPVLFAN 1i7wA 320 :GPQALVNIMRTY T0336 119 :GDEKTKINVSYALEEIAKA 1i7wA 332 :TYEKLLWTTSRVLKVLSVC T0336 138 :NPMLMA 1i7wA 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 1i7wA 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 1i7wA 378 :VQNCL T0336 164 :ALNFIEAMG 1i7wA 384 :TLRNLSDAA T0336 174 :NSFKYVNPFLPRIINLLHDGDEIVRASAVEALVHLAT 1i7wA 393 :TKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTC T0336 212 :NDKLRKVVIKR 1i7wA 431 :NYKNKMMVCQV T0336 228 :DTSSLVNKTV 1i7wA 442 :GGIEALVRTV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1077 Number of alignments=79 # 1i7wA read from 1i7wA/merged-good-all-a2m # found chain 1i7wA in template set T0336 12 :EALANGEHLEKILI 1i7wA 177 :QLSKKEASRHAIMR T0336 30 :DESVLKKLIELL 1i7wA 191 :SPQMVSAIVRTM T0336 47 :TVVKNAISIIMVIAKTREDLYEP 1i7wA 250 :SVLFYAITTLHNLLLHQEGAKMA T0336 70 :MLKKLFSLLK 1i7wA 278 :GLQKMVALLN T0336 81 :SEAIPLTQEIAKAFGQMAKEKPELVKSMI 1i7wA 288 :KTNVKFLAITTDCLQILAYGNQESKLIIL T0336 110 :PVLFANYR 1i7wA 322 :QALVNIMR T0336 118 :IGDEKTKINVSYALEEIAKA 1i7wA 331 :YTYEKLLWTTSRVLKVLSVC T0336 138 :NPMLMA 1i7wA 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 1i7wA 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 1i7wA 377 :LVQNC T0336 165 :LNFIEAMGENSFKY 1i7wA 382 :LWTLRNLSDAATKQ T0336 179 :VNPFLPRIINLL 1i7wA 398 :MEGLLGTLVQLL T0336 195 :E 1i7wA 410 :G T0336 199 :AS 1i7wA 411 :SD T0336 203 :EA 1i7wA 413 :DI T0336 210 :TLNDKLRKVVIKRLEELNDTSSLVNK 1i7wA 415 :NVVTCAAGILSNLTCNNYKNKMMVCQ T0336 236 :TVKEGISRLLLLEGH 1i7wA 443 :GIEALVRTVLRAGDR Number of specific fragments extracted= 17 number of extra gaps= 0 total=1094 Number of alignments=80 # 1i7wA read from 1i7wA/merged-good-all-a2m # found chain 1i7wA in template set T0336 2 :SMEEEEFDIREALANGEHLEKIL 1i7wA 206 :NDVETARCTAGTLHNLSHHREGL T0336 26 :MAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 1i7wA 229 :LAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLA T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 1i7wA 281 :KMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILA T0336 111 :VLFANY 1i7wA 323 :ALVNIM T0336 117 :RIGDEKTKINVSYALEEIAK 1i7wA 330 :TYTYEKLLWTTSRVLKVLSV T0336 138 :NPMLMASIVRD 1i7wA 350 :CSSNKPAIVEA T0336 149 :FMSMLSSKNREDKLTALNFIEAMGENSFKY 1i7wA 366 :LGLHLTDPSQRLVQNCLWTLRNLSDAATKQ T0336 179 :VNPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLRKVVIKR 1i7wA 398 :MEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQV T0336 223 :LEELNDTSSLVNKTVK 1i7wA 451 :VLRAGDREDITEPAIC Number of specific fragments extracted= 9 number of extra gaps= 0 total=1103 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lrv expands to /projects/compbio/data/pdb/1lrv.pdb.gz 1lrv:Warning: there is no chain 1lrv will retry with 1lrvA # T0336 read from 1lrv/merged-good-all-a2m # 1lrv read from 1lrv/merged-good-all-a2m # adding 1lrv to template set # found chain 1lrv in template set T0336 56 :IMVIAKTREDLYEPML 1lrv 44 :IDRFFRNNPHLAVQYL T0336 81 :SEAIPLTQEIAK 1lrv 60 :ADPFWERRAIAV T0336 99 :KEKPELVKSMIP 1lrv 73 :YSPVEALTPLIR T0336 111 :VLFANYR 1lrv 93 :AVAYRLP T0336 118 :IGDEKTKIN 1lrv 107 :MFDEDREVR T0336 127 :VSYALEEIAKA 1lrv 135 :DYLVRAYVVQR T0336 138 :NPMLM 1lrv 147 :PPGRL T0336 143 :ASIVRDFMSMLSSKN 1lrv 160 :RQVRKLVAKRLPEES T0336 158 :REDKLTALNFIEAMGENSFKYV 1lrv 181 :DPEPEVRRIVASRLRGDDLLEL T0336 190 :LHDGDEIVRASAVEA 1lrv 203 :LHDPDWTVRLAAVEH T0336 209 :AT 1lrv 218 :AS T0336 221 :KRLEELNDTSSLVNKTVK 1lrv 221 :EALRELDEPDPEVRLAIA Number of specific fragments extracted= 12 number of extra gaps= 0 total=1115 Number of alignments=82 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set Warning: unaligning (T0336)R117 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 T0336 31 :ESVLKKLIELL 1lrv 41 :GRQIDRFFRNN T0336 42 :DDDLWTVVKNAI 1lrv 60 :ADPFWERRAIAV T0336 61 :KT 1lrv 72 :RY T0336 66 :LYEPMLKKLF 1lrv 74 :SPVEALTPLI T0336 83 :A 1lrv 84 :R T0336 84 :IPLTQEI 1lrv 87 :DEVVRRA T0336 91 :AK 1lrv 95 :AY T0336 99 :KEKPELV 1lrv 100 :REQLSAL T0336 106 :KSMIPVLFANY 1lrv 112 :REVRITVADRL T0336 118 :IGDEKTKIN 1lrv 131 :AADRDYLVR T0336 132 :EEIAKA 1lrv 140 :AYVVQR T0336 138 :NPMLMAS 1lrv 147 :PPGRLFR T0336 152 :MLSSKNREDKL 1lrv 154 :FMRDEDRQVRK T0336 166 :NFIEAMGENSFKYVNPF 1lrv 165 :LVAKRLPEESLGLMTQD T0336 183 :LPRIINLLHDGDE 1lrv 183 :EPEVRRIVASRLR T0336 199 :ASAVEALVH 1lrv 196 :GDDLLELLH T0336 209 :ATLNDKLRKVVIKRLEE 1lrv 205 :DPDWTVRLAAVEHASLE T0336 232 :LVNK 1lrv 222 :ALRE Number of specific fragments extracted= 18 number of extra gaps= 1 total=1133 Number of alignments=83 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set T0336 30 :DESVLKKLIEL 1lrv 40 :SGRQIDRFFRN T0336 41 :LDDDLWTVVKNA 1lrv 59 :LADPFWERRAIA T0336 59 :IAKTREDLYEP 1lrv 71 :VRYSPVEALTP T0336 78 :LKKSEAIPLTQEIA 1lrv 82 :LIRDSDEVVRRAVA T0336 99 :KEKP 1lrv 96 :YRLP T0336 103 :ELVKSM 1lrv 101 :EQLSAL T0336 116 :YRIGDEKTKINVSY 1lrv 107 :MFDEDREVRITVAD T0336 130 :ALEEIAK 1lrv 138 :VRAYVVQ T0336 137 :ANPMLM 1lrv 146 :IPPGRL T0336 143 :ASIVRDFMSMLSS 1lrv 160 :RQVRKLVAKRLPE T0336 156 :KNREDKLTALNFI 1lrv 182 :PEPEVRRIVASRL T0336 184 :PRIINLLHDGDEIVRASAVE 1lrv 197 :DDLLELLHDPDWTVRLAAVE T0336 210 :TLNDK 1lrv 217 :HASLE T0336 222 :RLEELNDTSSLVNKTVK 1lrv 222 :ALRELDEPDPEVRLAIA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1147 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b3uA expands to /projects/compbio/data/pdb/1b3u.pdb.gz 1b3uA:# T0336 read from 1b3uA/merged-good-all-a2m # 1b3uA read from 1b3uA/merged-good-all-a2m # adding 1b3uA to template set # found chain 1b3uA in template set T0336 30 :DESVLKKLIELL 1b3uA 262 :VADKFTELQKAV T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEPMLK 1b3uA 291 :KDCEAEVRAAASHKVKEFCENLSADCRENVI T0336 73 :KLFSLLKKSEA 1b3uA 324 :QILPCIKELVS T0336 84 :IPLTQEIAK 1b3uA 337 :NQHVKSALA T0336 94 :FGQMA 1b3uA 351 :LSPIL T0336 101 :KPE 1b3uA 356 :GKD T0336 104 :LVKSMIPVLFA 1b3uA 360 :TIEHLLPLFLA T0336 118 :IGDEKTKINVSYA 1b3uA 372 :LKDECPEVRLNII T0336 131 :LEEIAKA 1b3uA 387 :LDCVNEV T0336 138 :N 1b3uA 395 :G T0336 139 :PMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGEN 1b3uA 397 :RQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQ T0336 175 :SFKYVNPFLPRII 1b3uA 434 :GVEFFDEKLNSLC T0336 188 :NLLHDGDEIVRASAVEALVHLAT 1b3uA 448 :AWLVDHVYAIREAATSNLKKLVE T0336 212 :NDKLRKVVIKRLEELNDTSSLVN 1b3uA 474 :KEWAHATIIPKVLAMSGDPNYLH Number of specific fragments extracted= 14 number of extra gaps= 0 total=1161 Number of alignments=85 # 1b3uA read from 1b3uA/merged-good-all-a2m # found chain 1b3uA in template set T0336 29 :YDESVLKKLIELL 1b3uA 261 :MVADKFTELQKAV T0336 42 :DDDLWTVVKNAISIIMVIAKTREDLYEP 1b3uA 291 :KDCEAEVRAAASHKVKEFCENLSADCRE T0336 70 :MLKKLFSLLKKSEA 1b3uA 321 :IMSQILPCIKELVS T0336 84 :IPLTQEIAK 1b3uA 337 :NQHVKSALA T0336 93 :AFGQMA 1b3uA 350 :GLSPIL T0336 101 :KPELV 1b3uA 356 :GKDNT T0336 106 :KSMIPVLFANYR 1b3uA 362 :EHLLPLFLAQLK T0336 120 :DEKTKINVSYA 1b3uA 374 :DECPEVRLNII T0336 131 :LEEIAKA 1b3uA 387 :LDCVNEV T0336 138 :NPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSF 1b3uA 396 :IRQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQLG T0336 180 :NPFL 1b3uA 435 :VEFF T0336 184 :PRIINLLHDG 1b3uA 440 :EKLNSLCMAW T0336 198 :RASAVE 1b3uA 450 :LVDHVY T0336 205 :LVHLA 1b3uA 456 :AIREA T0336 211 :LNDKLRKVVIKR 1b3uA 461 :ATSNLKKLVEKF T0336 229 :TSSLVNKT 1b3uA 473 :GKEWAHAT T0336 240 :GISRLLLLEGHSS 1b3uA 481 :IIPKVLAMSGDPN Number of specific fragments extracted= 17 number of extra gaps= 0 total=1178 Number of alignments=86 # 1b3uA read from 1b3uA/merged-good-all-a2m # found chain 1b3uA in template set T0336 10 :IREALANGEHLEKILIMAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKT 1b3uA 259 :RYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVKEFCEN T0336 63 :REDLYEPMLKK 1b3uA 313 :SADCRENVIMS T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKP 1b3uA 406 :AIVELAEDAKWRVRLAIIEYMPLLAGQLG T0336 103 :ELV 1b3uA 436 :EFF T0336 106 :KSMIPVLFANYRIGDEKTKINVSYALEEIAK 1b3uA 440 :EKLNSLCMAWLVDHVYAIREAATSNLKKLVE T0336 137 :ANPMLM 1b3uA 472 :FGKEWA T0336 143 :ASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFK 1b3uA 479 :ATIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQ T0336 178 :YVNPFLPRIINLLHDGDEIVRASAVEALVHLAT 1b3uA 516 :TTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGP T0336 211 :LNDKLRK 1b3uA 550 :LDNSTLQ T0336 218 :VVIKRLEEL 1b3uA 558 :EVKPILEKL T0336 227 :NDTSSLVNKTVKEGISRLL 1b3uA 568 :QDQDVDVKYFAQEALTVLS Number of specific fragments extracted= 11 number of extra gaps= 0 total=1189 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bct/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3bct expands to /projects/compbio/data/pdb/3bct.pdb.gz 3bct:Warning: there is no chain 3bct will retry with 3bctA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 583, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1836, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1838, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1840, because occupancy 0.500 <= existing 0.500 in 3bct Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 3bct Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 3bct Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2915, because occupancy 0.500 <= existing 0.500 in 3bct Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0336 read from 3bct/merged-good-all-a2m # 3bct read from 3bct/merged-good-all-a2m # adding 3bct to template set # found chain 3bct in template set T0336 31 :ESVLKKLIELL 3bct 234 :SGGIPALVKML T0336 44 :DLWTVVKNAISIIMVIAKTREDLYEPMLK 3bct 247 :PVDSVLFYAITTLHNLLLHQEGAKMAVRL T0336 73 :KLFSLLKKSEAIPLTQEIAK 3bct 277 :GGLQKMVALLNKTNVKFLAI T0336 93 :AFGQMAKEKPELVKSMIP 3bct 300 :CLQILAYGNQESKLIILA T0336 111 :VLFANYRIGDEKTKINVSYALEEIAKA 3bct 324 :LVNIMRTYTYEKLLWTTSRVLKVLSVC T0336 138 :NPMLMA 3bct 354 :KPAIVE T0336 144 :SIVRDFMSMLSSKNR 3bct 361 :GGMQALGLHLTDPSQ T0336 159 :EDKLT 3bct 377 :LVQNC T0336 164 :ALNFI 3bct 384 :TLRNL T0336 172 :GENSFKYVNPFLPRIINLLHDGDEIVRASAVEALVHLAT 3bct 391 :AATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTC T0336 211 :LNDKLR 3bct 434 :NKMMVC T0336 217 :KVVIKRLEELNDTSSLV 3bct 445 :EALVRTVLRAGDREDIT Number of specific fragments extracted= 12 number of extra gaps= 0 total=1201 Number of alignments=88 # 3bct read from 3bct/merged-good-all-a2m # found chain 3bct in template set Warning: unaligning (T0336)S155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bct)G563 Warning: unaligning (T0336)K156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bct)G563 T0336 31 :ESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLY 3bct 399 :EGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNK T0336 68 :EPMLKKLFSLLKKSEAIPLTQEIAK 3bct 441 :VGGIEALVRTVLRAGDREDITEPAI T0336 93 :AFGQMA 3bct 467 :ALRHLT T0336 100 :EKPELVKSMI 3bct 473 :SRHQEAEMAQ T0336 110 :PVLFANYRIGDEKTKIN 3bct 492 :PVVVKLLHPPSHWPLIK T0336 127 :VSYA 3bct 511 :VGLI T0336 131 :LEEIAKA 3bct 524 :HAPLREQ T0336 138 :NPMLMASIVRDFMSMLS 3bct 532 :AIPRLVQLLVRAHQDTQ T0336 157 :NREDKLTA 3bct 564 :VRMEEIVE T0336 165 :LNFIEAMGENSF 3bct 574 :TGALHILARDVH T0336 178 :YVNPF 3bct 589 :VIRGL T0336 183 :LPRIINLLH 3bct 596 :IPLFVQLLY T0336 200 :SAVEALVHL 3bct 605 :SPIENIQRV T0336 211 :LNDKLRKVVI 3bct 614 :AAGVLCELAQ T0336 226 :LNDTSSLVNK 3bct 624 :DKEAAEAIEA T0336 237 :VKEGISRLLL 3bct 636 :ATAPLTELLH Number of specific fragments extracted= 16 number of extra gaps= 1 total=1217 Number of alignments=89 # 3bct read from 3bct/merged-good-all-a2m # found chain 3bct in template set T0336 1 :MSMEEEEFDIREALANGEHLEKI 3bct 206 :NDVETARCTAGTLHNLSHHREGL T0336 26 :MAKYDESVLKKLIELLDDDLWTVVKNAISIIMVIAKTREDLYEPMLKK 3bct 229 :LAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLA T0336 74 :LFSLLKKSEAIPLTQEIAKAFGQMAKEKPELVKSMIP 3bct 281 :KMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILA T0336 111 :VLFANY 3bct 323 :ALVNIM T0336 117 :RIGDEKTKINVSYALEEIAK 3bct 330 :TYTYEKLLWTTSRVLKVLSV T0336 138 :NPMLMASIVR 3bct 350 :CSSNKPAIVE T0336 148 :DFMSMLSSKNREDKLTALNFIEAMGENSFKY 3bct 365 :ALGLHLTDPSQRLVQNCLWTLRNLSDAATKQ T0336 179 :VNPFLPRIINLLHDGDEIVRASAVEALVHLATLNDKLR 3bct 398 :MEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNK T0336 217 :KVVIKRLEELNDTSSLVNKTV 3bct 445 :EALVRTVLRAGDREDITEPAI Number of specific fragments extracted= 9 number of extra gaps= 0 total=1226 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y2aC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0336/1y2aC/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0336/1y2aC/merged-good-all-a2m.gz for input Trying 1y2aC/merged-good-all-a2m Error: Couldn't open file 1y2aC/merged-good-all-a2m or 1y2aC/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w9cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w9cA expands to /projects/compbio/data/pdb/1w9c.pdb.gz 1w9cA:# T0336 read from 1w9cA/merged-good-all-a2m # 1w9cA read from 1w9cA/merged-good-all-a2m # adding 1w9cA to template set # found chain 1w9cA in template set T0336 4 :EEEEFDIREALANGEHL 1w9cA 753 :RETLKLISGWVSRSNDP T0336 27 :AKYDESVLKKLIELL 1w9cA 770 :QMVAENFVPPLLDAV T0336 51 :NAISIIMVIAKTREDLYEPMLK 1w9cA 799 :EVLSTMAIIVNKLGGHITAEIP T0336 73 :KLFSLLKKSEA 1w9cA 829 :CTLNMINKDFE T0336 84 :IPLTQEIAK 1w9cA 841 :YPEHRTNFF T0336 93 :AFGQMAKE 1w9cA 851 :LLQAVNSH T0336 101 :KPELVKSMIPVLF 1w9cA 867 :PPTQFKLVLDSII T0336 118 :IGDEKTKIN 1w9cA 882 :FKHTMRNVA T0336 127 :VSYALEEIAKANP 1w9cA 897 :LFTLLQNVAQEEA T0336 140 :MLMASIVRDFMSMLSSKNR 1w9cA 917 :TYFCDILQHIFSVVTDTSH T0336 159 :EDKLT 1w9cA 939 :LTMHA T0336 164 :ALNFI 1w9cA 945 :ILAYM T0336 169 :EAMGENSFKYVNPFLPRII 1w9cA 960 :TSLNPGNPVNNQIFLQEYV T0336 188 :NLL 1w9cA 980 :NLL T0336 191 :HDGDEIVRASAVEALVHLATLNDKLRKVVIKRLEELNDT 1w9cA 987 :PHLQDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEF Number of specific fragments extracted= 15 number of extra gaps= 0 total=1241 Number of alignments=91 # 1w9cA read from 1w9cA/merged-good-all-a2m # found chain 1w9cA in template set T0336 11 :REALAN 1w9cA 746 :RSMRTV T0336 17 :GEHLEKILIMA 1w9cA 753 :RETLKLISGWV T0336 28 :KYDESVLKKLIELL 1w9cA 771 :MVAENFVPPLLDAV T0336 52 :AISIIMVIAKTREDLYEP 1w9cA 800 :VLSTMAIIVNKLGGHITA T0336 70 :MLKKLFSLLKKSEA 1w9cA 826 :VFECTLNMINKDFE T0336 84 :IPLT 1w9cA 843 :EHRT T0336 88 :QEIAK 1w9cA 853 :QAVNS T0336 93 :AFGQMAKEKPELVKSMIPVLFANYRIGD 1w9cA 859 :CFPAFLAIPPTQFKLVLDSIIWAFKHTM T0336 123 :TKIN 1w9cA 887 :RNVA T0336 127 :VSYALEEIAKA 1w9cA 897 :LFTLLQNVAQE T0336 138 :NPMLMASIVRDFMSMLSSKNR 1w9cA 915 :YQTYFCDILQHIFSVVTDTSH T0336 160 :DKLT 1w9cA 940 :TMHA T0336 165 :LNFIEAMGENSF 1w9cA 947 :AYMFNLVEEGKI T0336 179 :VNPFLPRII 1w9cA 970 :NQIFLQEYV T0336 188 :NLLHDGDEIVR 1w9cA 980 :NLLKSAFPHLQ T0336 203 :EALV 1w9cA 991 :DAQV T0336 216 :RKVVIKRL 1w9cA 995 :KLFVTGLF T0336 225 :ELNDTSSLVNKTVKEGISRLLLLE 1w9cA 1003 :SLNQDIPAFKEHLRDFLVQIKEFA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1259 Number of alignments=92 # 1w9cA read from 1w9cA/merged-good-all-a2m # found chain 1w9cA in template set T0336 1 :MSMEEEEFDIREALANGEHLEKI 1w9cA 712 :RIYLDMLNVYKCLSENISAAIQA T0336 24 :LIMAKYDESVLKKLIELLD 1w9cA 746 :RSMRTVKRETLKLISGWVS T0336 43 :DDLWT 1w9cA 766 :SNDPQ T0336 65 :DLYEPMLKKLFSLLKKSE 1w9cA 771 :MVAENFVPPLLDAVLIDY T0336 83 :AIPLTQEIAKAFGQMAKEKPELVKSMIPVLFANY 1w9cA 797 :EPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECT T0336 117 :RIGDEKTKINVSYALEEIAK 1w9cA 838 :FEEYPEHRTNFFLLLQAVNS T0336 137 :ANPMLMASIVRDFMSMLSSKNREDKLTALNFIEAMGENSFK 1w9cA 866 :IPPTQFKLVLDSIIWAFKHTMRNVADTGLQILFTLLQNVAQ T0336 178 :YVNPFLPRIINLLH 1w9cA 918 :YFCDILQHIFSVVT T0336 194 :DEIVRASAVEALVHLATL 1w9cA 971 :QIFLQEYVANLLKSAFPH T0336 212 :NDKLRKVVIKRLEELNDTSSLVNKTVKEGISRLLLL 1w9cA 990 :QDAQVKLFVTGLFSLNQDIPAFKEHLRDFLVQIKEF Number of specific fragments extracted= 10 number of extra gaps= 0 total=1269 Number of alignments=93 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 93 Done printing distance constraints # command: