# 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/T0293/ # command:# Making conformation for sequence T0293 numbered 1 through 250 Created new target T0293 from T0293.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0293/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0293//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0293/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0293//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0293/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0293/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0293/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1i1nA/merged-good-all-a2m # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0293 13 :ALTCTLL 1i1nA 35 :DRSHYAK # choosing archetypes in rotamer library T0293 20 :REDFGLSIDIPLERLIP 1i1nA 43 :NPYMDSPQSIGFQATIS T0293 41 :RL 1i1nA 60 :AP T0293 46 :HWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATL 1i1nA 62 :HMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNN 1i1nA 101 :CTGKVIGIDHIKELVDDSVNNVRKDD T0293 112 :DLIKVVKVP 1i1nA 133 :GRVQLVVGD T0293 125 :LMDALKEE 1i1nA 142 :GRMGYAEE T0293 135 :IIYDFCMCNPP 1i1nA 150 :APYDAIHVGAA T0293 147 :FANQL 1i1nA 161 :APVVP T0293 192 :HDSLQLGKRLRWYSCMLGK 1i1nA 166 :QALIDQLKPGGRLILPVGP T0293 235 :CQGRTMRWALAWSFY 1i1nA 185 :AGGNQMLEQYDKLQD Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 Number of alignments=1 # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1i1nA 75 :LHEGAKALDVGSGSGILTACFARMVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQ 1i1nA 102 :TGKVIGIDHIKELVDDSVNNVRK T0293 112 :DLIKVVKVPQATLLMD 1i1nA 133 :GRVQLVVGDGRMGYAE T0293 134 :EIIYDFCMC 1i1nA 149 :EAPYDAIHV T0293 158 :SRNPRRPP 1i1nA 158 :GAAAPVVP T0293 172 :GGITEIMAEGGELEF 1i1nA 166 :QALIDQLKPGGRLIL T0293 187 :VKR 1i1nA 182 :VGP T0293 235 :CQGRTMRWALAWSFYD 1i1nA 185 :AGGNQMLEQYDKLQDG Number of specific fragments extracted= 8 number of extra gaps= 0 total=19 Number of alignments=2 # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0293 46 :HWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATL 1i1nA 62 :HMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1i1nA 101 :CTGKVIGIDHIKELVDDSVNNVRKDDPT T0293 112 :DLIKVVKVPQATLL 1i1nA 133 :GRVQLVVGDGRMGY T0293 132 :ESEIIYDFCMCNP 1i1nA 147 :AEEAPYDAIHVGA T0293 155 :GVNSRN 1i1nA 160 :AAPVVP T0293 192 :HDSLQLGKRLRWYSCMLGK 1i1nA 166 :QALIDQLKPGGRLILPVGP T0293 235 :CQGRTMRWAL 1i1nA 185 :AGGNQMLEQY Number of specific fragments extracted= 7 number of extra gaps= 0 total=26 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f3lA expands to /projects/compbio/data/pdb/1f3l.pdb.gz 1f3lA:# T0293 read from 1f3lA/merged-good-all-a2m # 1f3lA read from 1f3lA/merged-good-all-a2m # adding 1f3lA to template set # found chain 1f3lA in template set T0293 41 :RLNYIHWVEDLIG 1f3lA 233 :DKVRTESYRDFIY T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGAT 1f3lA 246 :QNPHIFKDKVVLDVGCGTGILSMFAAKA T0293 84 :NGWYFLATEVDDM 1f3lA 274 :GAKKVIAVDQSEI T0293 98 :FNYAKKNVEQNNLSDLIKVVKVP 1f3lA 287 :LYQAMDIIRLNKLEDTIVLIKGK T0293 125 :LMD 1f3lA 310 :IEE T0293 130 :KEESEIIYDFCMCNP 1f3lA 313 :VSLPVEKVDVIISEW T0293 146 :FFAN 1f3lA 328 :MGYF T0293 169 :VNTGG 1f3lA 332 :LLFES T0293 183 :ELEFVKRIIHDS 1f3lA 337 :MLDSVLYAKSKY T0293 198 :GKRLRWYS 1f3lA 349 :LAKGGSVY T0293 206 :CMLGKACSLAPLKEE 1f3lA 362 :ISLVAVSDVSKHADR T0293 229 :VTYTEFCQGRT 1f3lA 377 :IAFWDDVYGFN Number of specific fragments extracted= 12 number of extra gaps= 0 total=38 Number of alignments=4 # 1f3lA read from 1f3lA/merged-good-all-a2m # found chain 1f3lA in template set T0293 42 :LNYIHWVEDLIGH 1f3lA 234 :KVRTESYRDFIYQ T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGAT 1f3lA 247 :NPHIFKDKVVLDVGCGTGILSMFAAKA T0293 84 :NGWYFLATEVD 1f3lA 274 :GAKKVIAVDQS T0293 96 :MCFNYAKKNVEQNNLSDLIKVVKVPQATLLMD 1f3lA 285 :EILYQAMDIIRLNKLEDTIVLIKGKIEEVSLP T0293 134 :EIIYDFCMC 1f3lA 317 :VEKVDVIIS T0293 155 :GVNSRNPRRPPPSSVNTGGITEIMAEGGELEF 1f3lA 326 :EWMGYFLLFESMLDSVLYAKSKYLAKGGSVYP T0293 187 :VKRIIHDSLQLGKRLR 1f3lA 366 :AVSDVSKHADRIAFWD T0293 206 :CMLGKACS 1f3lA 382 :DVYGFNMS T0293 229 :VTYTEFCQGRTMRWALAWSF 1f3lA 485 :EKPFPVKAGEALKGKITVHK Number of specific fragments extracted= 9 number of extra gaps= 0 total=47 Number of alignments=5 # 1f3lA read from 1f3lA/merged-good-all-a2m # found chain 1f3lA in template set T0293 43 :NYIHWVEDLIGHQ 1f3lA 235 :VRTESYRDFIYQN T0293 57 :SDKSTLRRGIDIGTGASCIYPLLGAT 1f3lA 248 :PHIFKDKVVLDVGCGTGILSMFAAKA T0293 84 :NGWYFLATEVDDMC 1f3lA 274 :GAKKVIAVDQSEIL T0293 99 :NYAKKNVEQNNLSDLIKVVKVPQATLL 1f3lA 288 :YQAMDIIRLNKLEDTIVLIKGKIEEVS T0293 132 :ESEIIYDFCMCN 1f3lA 315 :LPVEKVDVIISE T0293 163 :RPPPSS 1f3lA 327 :WMGYFL T0293 179 :AEGGELEFVKRI 1f3lA 333 :LFESMLDSVLYA T0293 194 :SLQLGKRLRWYS 1f3lA 345 :KSKYLAKGGSVY T0293 238 :RTMRWALAWSFY 1f3lA 357 :PDICTISLVAVS Number of specific fragments extracted= 9 number of extra gaps= 0 total=56 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b25A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b25A expands to /projects/compbio/data/pdb/2b25.pdb.gz 2b25A:# T0293 read from 2b25A/merged-good-all-a2m # 2b25A read from 2b25A/merged-good-all-a2m # adding 2b25A to template set # found chain 2b25A in template set Warning: unaligning (T0293)K6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)V44 Warning: unaligning (T0293)R12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)V44 Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0293)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0293)L113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0293)I114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0293)A128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0293)L129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)T185 Warning: unaligning (T0293)C235 because of BadResidue code BAD_PEPTIDE in next template residue (2b25A)E244 Warning: unaligning (T0293)Q236 because of BadResidue code BAD_PEPTIDE at template residue (2b25A)E244 T0293 5 :F 2b25A 37 :L T0293 13 :ALTCTLL 2b25A 45 :PFGKIVG T0293 21 :EDFGLSIDIPLE 2b25A 52 :KFPGQILRSSFG T0293 34 :LI 2b25A 68 :LR T0293 41 :RLNYIHW 2b25A 70 :RPALEDY T0293 48 :VEDLI 2b25A 92 :INMIL T0293 55 :QDSDKSTLRRGID 2b25A 97 :SMMDINPGDTVLE T0293 70 :TGASCIYPLLGATL 2b25A 112 :SGSGGMSLFLSKAV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQN 2b25A 127 :SQGRVISFEVRKDHHDLAKKNYKHW T0293 109 :NLS 2b25A 162 :EWP T0293 115 :KVVKVP 2b25A 168 :DFIHKD T0293 125 :LMD 2b25A 174 :ISG T0293 137 :YDFCMCNP 2b25A 186 :FDAVALDM T0293 151 :LEAKGVNSRNPRRPPPSS 2b25A 194 :LNPHVTLPVFYPHLKHGG T0293 203 :WYSCMLGKACSLAPLKEELRIQGVP 2b25A 212 :VCAVYVVNITQVIELLDGIRTCELA T0293 229 :VTYTEF 2b25A 237 :LSCEKI Number of specific fragments extracted= 16 number of extra gaps= 4 total=72 Number of alignments=7 # 2b25A read from 2b25A/merged-good-all-a2m # found chain 2b25A in template set Warning: unaligning (T0293)K6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)V44 Warning: unaligning (T0293)R12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)V44 Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0293)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0293)L113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0293)I114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0293)L124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0293)M126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)T185 Warning: unaligning (T0293)T232 because of BadResidue code BAD_PEPTIDE in next template residue (2b25A)E244 Warning: unaligning (T0293)E233 because of BadResidue code BAD_PEPTIDE at template residue (2b25A)E244 T0293 5 :F 2b25A 37 :L T0293 13 :ALTCTLLR 2b25A 45 :PFGKIVGK T0293 30 :PLERLIPT 2b25A 53 :FPGQILRS T0293 38 :VPLRLNYIHWVEDLIG 2b25A 85 :AITFPKDINMILSMMD T0293 59 :KSTLRRGID 2b25A 101 :INPGDTVLE T0293 70 :TGASCIYPLLGATLN 2b25A 112 :SGSGGMSLFLSKAVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQ 2b25A 128 :QGRVISFEVRKDHHDLAKKNYKH T0293 110 :LS 2b25A 163 :WP T0293 115 :KVVKVPQAT 2b25A 168 :DFIHKDISG T0293 137 :YDFCMC 2b25A 186 :FDAVAL T0293 163 :RPPPSSVNTGGITEIMAEGGELEFVKRIIHDS 2b25A 192 :DMLNPHVTLPVFYPHLKHGGVCAVYVVNITQV T0293 215 :APLKEELRIQGVPK 2b25A 224 :IELLDGIRTCELAL T0293 229 :VTY 2b25A 240 :EKI T0293 234 :FCQGRTMR 2b25A 245 :VIVRDWLV Number of specific fragments extracted= 14 number of extra gaps= 4 total=86 Number of alignments=8 # 2b25A read from 2b25A/merged-good-all-a2m # found chain 2b25A in template set Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0293)D112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0293)L113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0293)I114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0293)L124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0293)L125 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)T185 Warning: unaligning (T0293)E233 because of BadResidue code BAD_PEPTIDE in next template residue (2b25A)E244 Warning: unaligning (T0293)F234 because of BadResidue code BAD_PEPTIDE at template residue (2b25A)E244 T0293 41 :RLNYIHWVEDL 2b25A 89 :PKDINMILSMM T0293 58 :DKSTLRRGID 2b25A 100 :DINPGDTVLE T0293 70 :TGASCIYPLLGATL 2b25A 112 :SGSGGMSLFLSKAV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQN 2b25A 127 :SQGRVISFEVRKDHHDLAKKNYKHW T0293 109 :NLS 2b25A 162 :EWP T0293 115 :KVVKVPQAT 2b25A 168 :DFIHKDISG T0293 137 :YDFCMCN 2b25A 186 :FDAVALD T0293 163 :RPPPS 2b25A 193 :MLNPH T0293 189 :RIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVP 2b25A 198 :VTLPVFYPHLKHGGVCAVYVVNITQVIELLDGIRTCELA T0293 228 :KVTYT 2b25A 238 :SCEKI T0293 235 :C 2b25A 245 :V Number of specific fragments extracted= 11 number of extra gaps= 4 total=97 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ixkA expands to /projects/compbio/data/pdb/1ixk.pdb.gz 1ixkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1ixkA/merged-good-all-a2m # 1ixkA read from 1ixkA/merged-good-all-a2m # adding 1ixkA to template set # found chain 1ixkA in template set Warning: unaligning (T0293)K154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ixkA)R213 Warning: unaligning (T0293)G172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ixkA)R213 T0293 43 :NYIHWVEDLI 1ixkA 105 :ASSMYPPVAL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATLNG 1ixkA 115 :DPKPGEIVADMAAAPGGKTSYLAQLMRN T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSD 1ixkA 144 :GVIYAFDVDENRLRETRLNLSRLGVLN T0293 114 :IKVVKVPQAT 1ixkA 171 :VILFHSSSLH T0293 125 :LMD 1ixkA 181 :IGE T0293 130 :KEE 1ixkA 184 :LNV T0293 136 :IYDFCMCNPPF 1ixkA 187 :EFDKILLDAPC T0293 148 :ANQLEA 1ixkA 198 :TGSGTI T0293 173 :GITEIMA 1ixkA 214 :TMDDIKF T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCMLG 1ixkA 221 :CQGLQMRLLEKGLEVLKPGGILVYSTC T0293 210 :KACSLAPLKEELRIQ 1ixkA 251 :PEENEFVIQWALDNF T0293 228 :KVTYTEFCQGR 1ixkA 266 :DVELLPLKYGE Number of specific fragments extracted= 12 number of extra gaps= 0 total=109 Number of alignments=10 # 1ixkA read from 1ixkA/merged-good-all-a2m # found chain 1ixkA in template set Warning: unaligning (T0293)R162 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ixkA)R213 T0293 44 :YIHWVEDLIGHQDSD 1ixkA 16 :YSKLFADRYFQLWGE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1ixkA 116 :PKPGEIVADMAAAPGGKTSYLAQLMR T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1ixkA 143 :DGVIYAFDVDENRLRETRLNLSRLGVLN T0293 114 :IKVVKVPQATL 1ixkA 171 :VILFHSSSLHI T0293 126 :MDA 1ixkA 182 :GEL T0293 134 :EIIYDFCMCNPPFFA 1ixkA 185 :NVEFDKILLDAPCTG T0293 158 :SRNP 1ixkA 200 :SGTI T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDS 1ixkA 226 :MRLLEKGLEVLKPGGILVYSTCSLEPE T0293 195 :LQLGKRLRWYSCMLG 1ixkA 259 :QWALDNFDVELLPLK Number of specific fragments extracted= 9 number of extra gaps= 0 total=118 Number of alignments=11 # 1ixkA read from 1ixkA/merged-good-all-a2m # found chain 1ixkA in template set Warning: unaligning (T0293)R163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ixkA)R213 T0293 32 :ERLIPTVPLRLNYIHWV 1ixkA 98 :GLIYIQEASSMYPPVAL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1ixkA 115 :DPKPGEIVADMAAAPGGKTSYLAQLM T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1ixkA 142 :NDGVIYAFDVDENRLRETRLNLSRLGVL T0293 113 :LIKVVKVPQATLL 1ixkA 170 :NVILFHSSSLHIG T0293 132 :ESEIIYDFCMCNPPF 1ixkA 183 :ELNVEFDKILLDAPC T0293 164 :P 1ixkA 214 :T T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCML 1ixkA 221 :CQGLQMRLLEKGLEVLKPGGILVYST T0293 209 :GKACSLAPLKEELRI 1ixkA 250 :EPEENEFVIQWALDN Number of specific fragments extracted= 8 number of extra gaps= 0 total=126 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8cA expands to /projects/compbio/data/pdb/1y8c.pdb.gz 1y8cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1y8cA/merged-good-all-a2m # 1y8cA read from 1y8cA/merged-good-all-a2m # adding 1y8cA to template set # found chain 1y8cA in template set T0293 41 :RLNYIHWVEDLIGH 1y8cA 18 :DVDYKKWSDFIIEK T0293 55 :QDSDKS 1y8cA 33 :VENNLV T0293 62 :LRRGIDIGTGASCIYPLLGATLN 1y8cA 39 :FDDYLDLACGTGNLTENLCPKFK T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1y8cA 62 :NTWAVDLSQEMLSEAENKFRSQGLK T0293 114 :IKVVKVP 1y8cA 87 :PRLACQD T0293 125 :LMD 1y8cA 94 :ISN T0293 130 :KEESE 1y8cA 97 :LNINR T0293 136 :IYDFCMCNP 1y8cA 102 :KFDLITCCL T0293 146 :FFANQLEAKGVNSRNPRRPPPSSVN 1y8cA 115 :YIIDSDDLKKYFKAVSNHLKEGGVF T0293 171 :TGG 1y8cA 187 :RDG T0293 199 :KRLRWYSCMLG 1y8cA 190 :EFYKRFDEEHE T0293 210 :KACSLAPLKEELRIQG 1y8cA 202 :RAYKEEDIEKYLKHGQ T0293 229 :VTYT 1y8cA 218 :LNIL T0293 233 :EFCQGRTMRWALAWS 1y8cA 231 :KVEKFTERITYLVKL Number of specific fragments extracted= 14 number of extra gaps= 0 total=140 Number of alignments=13 # 1y8cA read from 1y8cA/merged-good-all-a2m # found chain 1y8cA in template set T0293 40 :LRLNYIHWVEDLIGHQ 1y8cA 20 :DYKKWSDFIIEKCVEN T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1y8cA 36 :NLVFDDYLDLACGTGNLTENLCPKFK T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1y8cA 62 :NTWAVDLSQEMLSEAENKFRSQGLK T0293 114 :IKVVKVPQATLLM 1y8cA 87 :PRLACQDISNLNI T0293 134 :EIIYDFCMCNPP 1y8cA 100 :NRKFDLITCCLD T0293 146 :FFANQLE 1y8cA 115 :YIIDSDD T0293 167 :SSVNTGGITEIMAEGGELEF 1y8cA 122 :LKKYFKAVSNHLKEGGVFIF T0293 187 :VKRIIH 1y8cA 186 :VRDGEF T0293 201 :LRWYSCMLG 1y8cA 192 :YKRFDEEHE T0293 210 :KACSLAPLKEELRIQGVPKVTYTEFCQGRT 1y8cA 202 :RAYKEEDIEKYLKHGQLNILDKVDCYSNKK T0293 240 :MRWALAWS 1y8cA 238 :RITYLVKL Number of specific fragments extracted= 11 number of extra gaps= 0 total=151 Number of alignments=14 # 1y8cA read from 1y8cA/merged-good-all-a2m # found chain 1y8cA in template set T0293 11 :VRALTCTLLREDFGLS 1y8cA 5 :NKFAHIYDKLIRADVD T0293 40 :LRLNYIHWVEDLIGH 1y8cA 21 :YKKWSDFIIEKCVEN T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1y8cA 36 :NLVFDDYLDLACGTGNLTENLCPKFK T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1y8cA 62 :NTWAVDLSQEMLSEAENKFRSQGLK T0293 114 :IKVVKVPQATLL 1y8cA 87 :PRLACQDISNLN T0293 133 :SEIIYDFCMCNP 1y8cA 99 :INRKFDLITCCL T0293 166 :PSSVNT 1y8cA 111 :DSTNYI T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCMLGK 1y8cA 117 :IDSDDLKKYFKAVSNHLKEGGVFIFDINS T0293 218 :KEELRIQGVPKVTYTEF 1y8cA 146 :YYKLSQVLGNNDFNYDD T0293 235 :CQGRTMRWALAWSF 1y8cA 173 :FEDDLVSMYISFFV Number of specific fragments extracted= 10 number of extra gaps= 0 total=161 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uwvA expands to /projects/compbio/data/pdb/1uwv.pdb.gz 1uwvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1uwvA/merged-good-all-a2m # 1uwvA read from 1uwvA/merged-good-all-a2m # adding 1uwvA to template set # found chain 1uwvA in template set Warning: unaligning (T0293)W246 because of BadResidue code BAD_PEPTIDE in next template residue (1uwvA)R431 Warning: unaligning (T0293)S247 because of BadResidue code BAD_PEPTIDE at template residue (1uwvA)R431 Warning: unaligning (T0293)F248 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1uwvA)V432 T0293 8 :PEAVRALTCTLL 1uwvA 236 :SEILETVSGEMP T0293 20 :REDFGLSIDIPLERLI 1uwvA 249 :YDSNGLRLTFSPRDFI T0293 38 :VPLRLNYIHWVEDLI 1uwvA 265 :QVNAGVNQKMVARAL T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGAT 1uwvA 280 :EWLDVQPEDRVLDLFCGMGNFTLPLATQ T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1uwvA 308 :AASVVGVEGVPALVEKGQQNARLNGLQN T0293 114 :IKVVKVPQATLLMD 1uwvA 336 :VTFYHENLEEDVTK T0293 130 :KEESEIIYDFCMCNPP 1uwvA 350 :QPWAKNGFDKVLLDPA T0293 180 :EGG 1uwvA 366 :RAG T0293 184 :LEFVKRIIHDS 1uwvA 369 :AAGVMQQIIKL T0293 200 :RLRWYSCMLG 1uwvA 380 :EPIRIVYVSC T0293 213 :SLAPLKE 1uwvA 390 :NPATLAR T0293 220 :ELRIQGV 1uwvA 400 :ALLKAGY T0293 230 :TYTE 1uwvA 407 :TIAR T0293 234 :FCQGRTMRWALA 1uwvA 418 :PHTGHLESMVLF Number of specific fragments extracted= 14 number of extra gaps= 1 total=175 Number of alignments=16 # 1uwvA read from 1uwvA/merged-good-all-a2m # found chain 1uwvA in template set Warning: unaligning (T0293)A245 because of BadResidue code BAD_PEPTIDE in next template residue (1uwvA)R431 Warning: unaligning (T0293)W246 because of BadResidue code BAD_PEPTIDE at template residue (1uwvA)R431 T0293 6 :KDPEAVRALTCTLL 1uwvA 234 :PDSEILETVSGEMP T0293 20 :REDFGLSIDIPLERLIPT 1uwvA 249 :YDSNGLRLTFSPRDFIQV T0293 41 :RLNYIHWVEDLIGHQDS 1uwvA 267 :NAGVNQKMVARALEWLD T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1uwvA 284 :VQPEDRVLDLFCGMGNFTLPLATQ T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1uwvA 308 :AASVVGVEGVPALVEKGQQNARLNGLQN T0293 114 :IKVVKVPQATL 1uwvA 336 :VTFYHENLEED T0293 125 :LMDAL 1uwvA 349 :KQPWA T0293 134 :EIIYDFCMCNP 1uwvA 354 :KNGFDKVLLDP T0293 163 :RPPPSSVNTGGITEI 1uwvA 365 :ARAGAAGVMQQIIKL T0293 183 :ELEFVKRIIHDSLQLG 1uwvA 383 :RIVYVSCNPATLARDS T0293 219 :EELRIQGVPKVTY 1uwvA 399 :EALLKAGYTIARL T0293 232 :TEFCQGRTMRWAL 1uwvA 417 :FPHTGHLESMVLF Number of specific fragments extracted= 12 number of extra gaps= 1 total=187 Number of alignments=17 # 1uwvA read from 1uwvA/merged-good-all-a2m # found chain 1uwvA in template set Warning: unaligning (T0293)S247 because of BadResidue code BAD_PEPTIDE in next template residue (1uwvA)R431 T0293 23 :FGLSIDIPLERLIPT 1uwvA 252 :NGLRLTFSPRDFIQV T0293 40 :LRLNYIHWVEDLIGHQ 1uwvA 267 :NAGVNQKMVARALEWL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGAT 1uwvA 283 :DVQPEDRVLDLFCGMGNFTLPLATQ T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1uwvA 308 :AASVVGVEGVPALVEKGQQNARLNGLQ T0293 113 :LIKVVKVPQATLL 1uwvA 335 :NVTFYHENLEEDV T0293 128 :ALKEESEIIYDFCMCNPP 1uwvA 348 :TKQPWAKNGFDKVLLDPA T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCMLGK 1uwvA 389 :CNPATLARDSEALLKAGYTIARLAMLDMF T0293 235 :CQGRTMRWALAW 1uwvA 418 :PHTGHLESMVLF Number of specific fragments extracted= 8 number of extra gaps= 1 total=195 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o54A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1o54A/merged-good-all-a2m # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0293)P39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o54A)R80 Warning: unaligning (T0293)L40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o54A)R80 Warning: unaligning (T0293)Y44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o54A)V84 Warning: unaligning (T0293)I68 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 T0293 20 :REDFGLSIDIPLE 1o54A 48 :EKGPGEIIRTSAG T0293 33 :RLIP 1o54A 65 :ILIP T0293 37 :TV 1o54A 76 :NM T0293 42 :LN 1o54A 81 :TQ T0293 45 :IHWVEDLI 1o54A 86 :PKDSSFIA T0293 55 :QDSDKSTLRRGID 1o54A 94 :MMLDVKEGDRIID T0293 70 :TGASCIYPLLGATLNG 1o54A 109 :VGSGAMCAVLARAVGS T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 1o54A 126 :GKVFAYEKREEFAKLAESNLTKWGLIERVTIKVRD T0293 125 :L 1o54A 161 :I T0293 127 :D 1o54A 162 :S T0293 130 :KEESEIIYDFCMCNP 1o54A 163 :EGFDEKDVDALFLDV T0293 151 :LEAKGVNSRNPRRPPPSSVN 1o54A 178 :PDPWNYIDKCWEALKGGGRF T0293 171 :TGG 1o54A 201 :CPT T0293 188 :KRIIHDSLQLGKRLRWYSCMLGKACSLA 1o54A 204 :TNQVQETLKKLQELPFIRIEVWESLFRP T0293 225 :GVPKVTYTEFCQGRTMRWALAWSFY 1o54A 236 :PERLRPVDRMVAHTAYMIFATKVCR Number of specific fragments extracted= 15 number of extra gaps= 3 total=210 Number of alignments=19 # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0293)I35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o54A)R80 Warning: unaligning (T0293)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o54A)R80 Warning: unaligning (T0293)L40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o54A)V84 Warning: unaligning (T0293)I68 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 T0293 3 :LNFKDPE 1o54A 26 :VDLEKDK T0293 10 :AVRALTCTLL 1o54A 37 :HLGIIDLNEV T0293 20 :REDFGLSIDIPLERL 1o54A 48 :EKGPGEIIRTSAGKK T0293 38 :VP 1o54A 81 :TQ T0293 41 :RLNYIHWVEDLIG 1o54A 85 :YPKDSSFIAMMLD T0293 59 :KSTLRRGID 1o54A 98 :VKEGDRIID T0293 70 :TGASCIYPLLGATLN 1o54A 109 :VGSGAMCAVLARAVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 1o54A 125 :SGKVFAYEKREEFAKLAESNLTKWGLIERVTIKVRDISEG T0293 126 :MD 1o54A 165 :FD T0293 134 :EIIYDFCMC 1o54A 167 :EKDVDALFL T0293 163 :RPPPSSVNTGGITEIMAEGGELEFVKRIIHDS 1o54A 176 :DVPDPWNYIDKCWEALKGGGRFATVCPTTNQV T0293 215 :APLKEELRIQGVPKVTYTEFCQGRTM 1o54A 208 :QETLKKLQELPFIRIEVWESLFRPYK T0293 241 :RWALAWS 1o54A 252 :MIFATKV Number of specific fragments extracted= 13 number of extra gaps= 3 total=223 Number of alignments=20 # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0293)I68 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 T0293 43 :NYIHWVEDLI 1o54A 87 :KDSSFIAMML T0293 58 :DKSTLRRGID 1o54A 97 :DVKEGDRIID T0293 70 :TGASCIYPLLGATL 1o54A 109 :VGSGAMCAVLARAV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1o54A 124 :SSGKVFAYEKREEFAKLAESNLTKWGLIERVTIKVRDISEGF T0293 133 :SEIIYDFCMCN 1o54A 166 :DEKDVDALFLD T0293 163 :RPPPSS 1o54A 177 :VPDPWN T0293 190 :IIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTEFC 1o54A 183 :YIDKCWEALKGGGRFATVCPTTNQVQETLKKLQELPFIRIEVWESL Number of specific fragments extracted= 7 number of extra gaps= 1 total=230 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i9gA expands to /projects/compbio/data/pdb/1i9g.pdb.gz 1i9gA:# T0293 read from 1i9gA/merged-good-all-a2m # 1i9gA read from 1i9gA/merged-good-all-a2m # adding 1i9gA to template set # found chain 1i9gA in template set Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 T0293 37 :TVPLRLNY 1i9gA 75 :SMPRGPQV T0293 45 :IHWVEDLI 1i9gA 85 :PKDAAQIV T0293 55 :QDSDKSTLRRGID 1i9gA 93 :HEGDIFPGARVLE T0293 70 :TGASCIYPLLGATL 1i9gA 108 :AGSGALTLSLLRAV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQN 1i9gA 123 :PAGQVISYEQRADHAEHARRNVSGC T0293 109 :NLSDLIKVVKVP 1i9gA 150 :QPPDNWRLVVSD T0293 125 :LMD 1i9gA 162 :LAD T0293 130 :KEESEIIYDFCMCNP 1i9gA 165 :SELPDGSVDRAVLDM T0293 151 :LEAKGVN 1i9gA 180 :LAPWEVL T0293 192 :HDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQG 1i9gA 187 :DAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQ T0293 226 :VPKVTYTEFCQGRTMR 1i9gA 222 :WTEPRAWETLQRGWNV Number of specific fragments extracted= 11 number of extra gaps= 1 total=241 Number of alignments=22 # 1i9gA read from 1i9gA/merged-good-all-a2m # found chain 1i9gA in template set Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 T0293 23 :FGLSIDIPLERL 1i9gA 50 :QGSVVKSSNGAL T0293 35 :IPTVPL 1i9gA 76 :MPRGPQ T0293 41 :RLNYIHWVEDL 1i9gA 84 :YPKDAAQIVHE T0293 57 :SDKSTLRRGID 1i9gA 95 :GDIFPGARVLE T0293 70 :TGASCIYPLLGATLN 1i9gA 108 :AGSGALTLSLLRAVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQN 1i9gA 124 :AGQVISYEQRADHAEHARRNVSGC T0293 109 :N 1i9gA 149 :G T0293 110 :LSD 1i9gA 152 :PDN T0293 114 :IKVVKVPQATLLMD 1i9gA 155 :WRLVVSDLADSELP T0293 134 :EIIYDFCMC 1i9gA 169 :DGSVDRAVL T0293 163 :RPPPSSVNTGGITEIMAEGGELEFVKRIIHDS 1i9gA 178 :DMLAPWEVLDAVSRLLVAGGVLMVYVATVTQL T0293 215 :APLKEELRIQG 1i9gA 210 :SRIVEALRAKQ T0293 226 :VPKVTYTEFCQGRTMR 1i9gA 222 :WTEPRAWETLQRGWNV Number of specific fragments extracted= 13 number of extra gaps= 1 total=254 Number of alignments=23 # 1i9gA read from 1i9gA/merged-good-all-a2m # found chain 1i9gA in template set Warning: unaligning (T0293)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 T0293 45 :IHWVEDLIGHQ 1i9gA 85 :PKDAAQIVHEG T0293 58 :DKSTLRRGID 1i9gA 96 :DIFPGARVLE T0293 70 :TGASCIYPLLGATL 1i9gA 108 :AGSGALTLSLLRAV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQN 1i9gA 123 :PAGQVISYEQRADHAEHARRNVSGC T0293 109 :NLSDLIKVVKVPQATL 1i9gA 150 :QPPDNWRLVVSDLADS T0293 131 :EESEIIYDFCMCN 1i9gA 166 :ELPDGSVDRAVLD T0293 171 :TGGITEI 1i9gA 179 :MLAPWEV T0293 191 :IHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGV 1i9gA 186 :LDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQC T0293 227 :PKVTYTEFCQGRT 1i9gA 223 :TEPRAWETLQRGW Number of specific fragments extracted= 9 number of extra gaps= 1 total=263 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1inlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1inlA/merged-good-all-a2m # 1inlA read from 1inlA/merged-good-all-a2m # found chain 1inlA in training set Warning: unaligning (T0293)P144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1inlA)L182 Warning: unaligning (T0293)N170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1inlA)L182 T0293 33 :RLIP 1inlA 66 :TMTT T0293 41 :RLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1inlA 70 :EKDEFMYHEMLAHVPMFLHPNPKKVLIIGGGDGGTLREVLKH T0293 84 :NG 1inlA 112 :DS T0293 86 :WYFLATEVDDMCFNYAKKNVEQN 1inlA 115 :EKAILCEVDGLVIEAARKYLKQT T0293 110 :LS 1inlA 141 :FD T0293 112 :DLIKVVKVP 1inlA 144 :PRAEIVIAN T0293 125 :LMDALKEESE 1inlA 153 :GAEYVRKFKN T0293 136 :IYDFCMCN 1inlA 163 :EFDVIIID T0293 171 :TGG 1inlA 183 :FTE T0293 189 :RIIHDSLQLGKRLRWYSCMLG 1inlA 186 :EFYQACYDALKEDGVFSAETE T0293 210 :KACSLAPLKEELRIQG 1inlA 208 :PFYDIGWFKLAYRRIS T0293 226 :VPKVTYT 1inlA 226 :FPITRVY T0293 233 :EFCQGRTMRWALAWSFYD 1inlA 237 :TTYPSGMWSYTFASKGID Number of specific fragments extracted= 13 number of extra gaps= 0 total=276 Number of alignments=25 # 1inlA read from 1inlA/merged-good-all-a2m # found chain 1inlA in training set Warning: unaligning (T0293)R163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1inlA)L182 T0293 42 :LNYIHWVEDLIGHQD 1inlA 73 :EFMYHEMLAHVPMFL T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1inlA 88 :HPNPKKVLIIGGGDGGTLREVLKH T0293 84 :N 1inlA 112 :D T0293 85 :GWYFLATEVDDMCFNYAKKNVEQN 1inlA 114 :VEKAILCEVDGLVIEAARKYLKQT T0293 112 :DLIKVVKVPQATLLMDA 1inlA 144 :PRAEIVIANGAEYVRKF T0293 134 :EIIYDFCMCN 1inlA 161 :KNEFDVIIID T0293 168 :SVNTGGITEIMAEGGELEFVKRIIH 1inlA 185 :EEFYQACYDALKEDGVFSAETEDPF T0293 212 :CSLAPLKEELRIQG 1inlA 210 :YDIGWFKLAYRRIS T0293 226 :VPKVTY 1inlA 226 :FPITRV T0293 232 :TEFCQGRTMRWALAWSFYD 1inlA 236 :MTTYPSGMWSYTFASKGID Number of specific fragments extracted= 10 number of extra gaps= 0 total=286 Number of alignments=26 # 1inlA read from 1inlA/merged-good-all-a2m # found chain 1inlA in training set Warning: unaligning (T0293)A148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1inlA)L182 Warning: unaligning (T0293)R159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1inlA)L182 T0293 41 :RLNYIHWVEDLIGHQ 1inlA 73 :EFMYHEMLAHVPMFL T0293 59 :KSTLRRGIDIGTGASCIYPLLG 1inlA 88 :HPNPKKVLIIGGGDGGTLREVL T0293 82 :TLNGW 1inlA 110 :KHDSV T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1inlA 116 :KAILCEVDGLVIEAARKYLKQTSCG T0293 112 :DLIKVVKVPQATLL 1inlA 144 :PRAEIVIANGAEYV T0293 131 :EESEIIYDFCMCN 1inlA 158 :RKFKNEFDVIIID T0293 160 :N 1inlA 183 :F T0293 183 :ELEF 1inlA 184 :TEEF T0293 191 :IHDSLQLGKRLRWYSCMLG 1inlA 188 :YQACYDALKEDGVFSAETE T0293 210 :KACSLAPLKEELRI 1inlA 208 :PFYDIGWFKLAYRR T0293 224 :QGVPKVTYTE 1inlA 224 :KVFPITRVYL T0293 234 :FCQGRTMRWALAW 1inlA 238 :TYPSGMWSYTFAS Number of specific fragments extracted= 12 number of extra gaps= 0 total=298 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2frnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2frnA expands to /projects/compbio/data/pdb/2frn.pdb.gz 2frnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 2frnA/merged-good-all-a2m # 2frnA read from 2frnA/merged-good-all-a2m # adding 2frnA to template set # found chain 2frnA in template set T0293 16 :CTLLREDFGLSIDIPLE 2frnA 88 :TVTVHVENGIKYKLDVA T0293 37 :TVPLRLNYIHWVEDLIGH 2frnA 105 :KIMFSPANVKERVRMAKV T0293 57 :S 2frnA 123 :A T0293 60 :STLRRGIDIGTGASCIYPLLGAT 2frnA 124 :KPDELVVDMFAGIGHLSLPIAVY T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 2frnA 147 :GKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMD T0293 125 :LMD 2frnA 184 :NRD T0293 132 :ES 2frnA 187 :FP T0293 134 :EIIYDFCMCNPP 2frnA 190 :ENIADRILMGYV T0293 151 :LEAKG 2frnA 202 :VRTHE T0293 190 :IIHDSLQLGKRLRWYSCMLG 2frnA 207 :FIPKALSIAKDGAIIHYHNT T0293 210 :KACSLAPLKEELRIQGV 2frnA 233 :PREPFETFKRITKEYGY T0293 228 :KVTYTEFC 2frnA 250 :DVEKLNEL T0293 236 :QGRTMRWALAWSF 2frnA 263 :APGVWHVVLDLRV Number of specific fragments extracted= 13 number of extra gaps= 0 total=311 Number of alignments=28 # 2frnA read from 2frnA/merged-good-all-a2m # found chain 2frnA in template set Warning: unaligning (T0293)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2frnA)P43 Warning: unaligning (T0293)P39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2frnA)P43 Warning: unaligning (T0293)L40 because of BadResidue code BAD_PEPTIDE at template residue (2frnA)E44 Warning: unaligning (T0293)R41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2frnA)E46 Warning: unaligning (T0293)L42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2frnA)E46 Warning: unaligning (T0293)N43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2frnA)P47 Warning: unaligning (T0293)Y44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2frnA)Y48 Warning: unaligning (T0293)I45 because of BadResidue code BAD_PEPTIDE at template residue (2frnA)K49 Warning: unaligning (T0293)H46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2frnA)H50 Warning: unaligning (T0293)D50 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2frnA)V55 Warning: unaligning (T0293)L51 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2frnA)V55 T0293 26 :SIDIPLER 2frnA 29 :RWVRIGDV T0293 34 :LI 2frnA 38 :LL T0293 47 :WVE 2frnA 51 :RIA T0293 52 :IGHQDS 2frnA 56 :YAEVLG T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 2frnA 123 :AKPDELVVDMFAGIGHLSLPIAVY T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLM 2frnA 147 :GKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPG T0293 134 :EIIYDFCMC 2frnA 190 :ENIADRILM T0293 162 :RRPPPSSVNTGGITEIMAEGGELEF 2frnA 199 :GYVVRTHEFIPKALSIAKDGAIIHY T0293 189 :RIIH 2frnA 226 :TVPE T0293 207 :MLGKACSLAPLKEELRIQGVPK 2frnA 230 :KLMPREPFETFKRITKEYGYDV T0293 229 :VTYTEFCQGRTMRWALAWS 2frnA 256 :ELKIKRYAPGVWHVVLDLR T0293 248 :FYD 2frnA 276 :FKS Number of specific fragments extracted= 12 number of extra gaps= 1 total=323 Number of alignments=29 # 2frnA read from 2frnA/merged-good-all-a2m # found chain 2frnA in template set T0293 23 :FGLSIDIPLERLIPTVPLRLNYIHWVEDL 2frnA 95 :NGIKYKLDVAKIMFSPANVKERVRMAKVA T0293 60 :STLRRGIDIGTGASCIYPLLGA 2frnA 124 :KPDELVVDMFAGIGHLSLPIAV T0293 83 :LNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 2frnA 146 :YGKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFP T0293 133 :SEIIYDFCMCN 2frnA 189 :GENIADRILMG T0293 170 :NTGGITEI 2frnA 200 :YVVRTHEF T0293 191 :IHDSLQLGKRLRWYSCMLG 2frnA 208 :IPKALSIAKDGAIIHYHNT T0293 210 :KACSLAPLKEELRIQGVP 2frnA 233 :PREPFETFKRITKEYGYD T0293 228 :KVTYTEFCQGRTMRWALAWSFYD 2frnA 255 :NELKIKRYAPGVWHVVLDLRVFK Number of specific fragments extracted= 8 number of extra gaps= 0 total=331 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vl5A expands to /projects/compbio/data/pdb/1vl5.pdb.gz 1vl5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 535, because occupancy 0.5 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1vl5A/merged-good-all-a2m # 1vl5A read from 1vl5A/merged-good-all-a2m # adding 1vl5A to template set # found chain 1vl5A in template set Warning: unaligning (T0293)R41 because first residue in template chain is (1vl5A)G28 Warning: unaligning (T0293)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0293)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0293)M126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0293)D127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0293 42 :LNYIHWVE 1vl5A 29 :SDLAKLMQ T0293 56 :DSDKSTL 1vl5A 37 :IAALKGN T0293 65 :GIDIGTGASCIYPLLGATLN 1vl5A 46 :VLDVATGGGHVANAFAPFVK T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSD 1vl5A 66 :KVVAFDLTEDILKVARAFIEGNGHQQ T0293 114 :IKVVKVP 1vl5A 92 :VEYVQGD T0293 125 :L 1vl5A 99 :A T0293 130 :KEESEIIYDFCMCNPP 1vl5A 102 :MPFTDERFHIVTCRIA T0293 147 :FANQLEAKGVNSRNPRRPPPSSVN 1vl5A 118 :AHHFPNPASFVSEAYRVLKKGGQL T0293 171 :TGG 1vl5A 148 :APE T0293 180 :EGGELEFVKRIIHDSLQL 1vl5A 151 :NDAFDVFYNYVEKERDYS T0293 208 :LGKACSLAPLKEELRIQGV 1vl5A 169 :HHRAWKKSDWLKMLEEAGF T0293 237 :GRTMRWALAWSF 1vl5A 188 :ELEELHCFHKTF Number of specific fragments extracted= 12 number of extra gaps= 2 total=343 Number of alignments=31 # 1vl5A read from 1vl5A/merged-good-all-a2m # found chain 1vl5A in template set Warning: unaligning (T0293)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0293)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0293)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0293)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0293 43 :NYIHWVEDLIG 1vl5A 29 :SDLAKLMQIAA T0293 59 :KSTL 1vl5A 40 :LKGN T0293 65 :GIDIGTGASCIYPLLGAT 1vl5A 46 :VLDVATGGGHVANAFAPF T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1vl5A 64 :VKKVVAFDLTEDILKVARAFIEGNGHQQ T0293 114 :IKVVKVPQ 1vl5A 92 :VEYVQGDA T0293 124 :LLMD 1vl5A 102 :MPFT T0293 134 :EIIYDFCMC 1vl5A 106 :DERFHIVTC T0293 158 :SRNPRRPPPSSVNTGGITEIMAEGGELEF 1vl5A 115 :RIAAHHFPNPASFVSEAYRVLKKGGQLLL T0293 187 :VKRIIHDSLQLGKRL 1vl5A 147 :SAPENDAFDVFYNYV T0293 202 :RWYSCMLGKACSLAPLKEELRIQGVPKV 1vl5A 163 :KERDYSHHRAWKKSDWLKMLEEAGFELE T0293 240 :MRWALAWS 1vl5A 191 :ELHCFHKT Number of specific fragments extracted= 11 number of extra gaps= 2 total=354 Number of alignments=32 # 1vl5A read from 1vl5A/merged-good-all-a2m # found chain 1vl5A in template set Warning: unaligning (T0293)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0293)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0293)A122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0293)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0293 40 :LRLNYIHW 1vl5A 31 :LAKLMQIA T0293 58 :DKSTL 1vl5A 39 :ALKGN T0293 65 :GIDIGTGASCIYPLLGATL 1vl5A 46 :VLDVATGGGHVANAFAPFV T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1vl5A 66 :KVVAFDLTEDILKVARAFIEGNGHQ T0293 113 :LIKVVKVPQ 1vl5A 91 :QVEYVQGDA T0293 124 :LL 1vl5A 102 :MP T0293 132 :ESEIIYDFCMCN 1vl5A 104 :FTDERFHIVTCR T0293 166 :PSSVNTGG 1vl5A 116 :IAAHHFPN T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRI 1vl5A 124 :PASFVSEAYRVLKKGGQLLLVDNSAPENDAFDVFYNY Number of specific fragments extracted= 9 number of extra gaps= 2 total=363 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dusA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1dusA/merged-good-all-a2m # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set Warning: unaligning (T0293)G209 because of BadResidue code BAD_PEPTIDE in next template residue (1dusA)T162 Warning: unaligning (T0293)K210 because of BadResidue code BAD_PEPTIDE at template residue (1dusA)T162 T0293 16 :CTLLREDFGLS 1dusA 15 :KIVEDILRGKK T0293 27 :IDIPL 1dusA 28 :FKTDS T0293 37 :TVPLRLNYIHWVEDLI 1dusA 33 :GVFSYGKVDKGTKILV T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLN 1dusA 49 :ENVVVDKDDDILDLGCGYGVIGIALADEVK T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDL 1dusA 79 :STTMADINRRAIKLAKENIKLNNLDNY T0293 114 :IKVVKVP 1dusA 107 :IRVVHSD T0293 125 :LM 1dusA 114 :LY T0293 130 :KEESEIIYDFCMCNPP 1dusA 116 :ENVKDRKYNKIITNPP T0293 147 :FA 1dusA 132 :IR T0293 181 :GG 1dusA 134 :AG T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCML 1dusA 136 :KEVLHRIIEEGKELLKDNGEIWVVI T0293 211 :ACSLAPLKEELRIQ 1dusA 163 :KQGAKSLAKYMKDV T0293 226 :VPKVTYTEFCQG 1dusA 177 :FGNVETVTIKGG T0293 241 :RWALAWSF 1dusA 189 :YRVLKSKK Number of specific fragments extracted= 14 number of extra gaps= 1 total=377 Number of alignments=34 # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set Warning: unaligning (T0293)R189 because of BadResidue code BAD_PEPTIDE in next template residue (1dusA)T162 Warning: unaligning (T0293)I190 because of BadResidue code BAD_PEPTIDE at template residue (1dusA)T162 T0293 12 :RALT 1dusA 15 :KIVE T0293 20 :REDFGLSIDIPLERL 1dusA 19 :DILRGKKLKFKTDSG T0293 38 :VPLRLNYIHWVEDLIGHQD 1dusA 34 :VFSYGKVDKGTKILVENVV T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1dusA 53 :VDKDDDILDLGCGYGVIGIALADEV T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSD 1dusA 78 :KSTTMADINRRAIKLAKENIKLNNLDN T0293 113 :LIKVVKVP 1dusA 106 :DIRVVHSD T0293 125 :LMDALK 1dusA 114 :LYENVK T0293 134 :EIIYDFCMCNPPFFANQLEA 1dusA 120 :DRKYNKIITNPPIRAGKEVL T0293 168 :SVNTGGITEIMAEGGELEFVK 1dusA 140 :HRIIEEGKELLKDNGEIWVVI T0293 191 :IHDS 1dusA 163 :KQGA T0293 215 :APLKEELRIQ 1dusA 167 :KSLAKYMKDV T0293 226 :VPKVTYTEFCQG 1dusA 177 :FGNVETVTIKGG T0293 241 :RWALAWSF 1dusA 189 :YRVLKSKK Number of specific fragments extracted= 13 number of extra gaps= 1 total=390 Number of alignments=35 # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set Warning: unaligning (T0293)G209 because of BadResidue code BAD_PEPTIDE in next template residue (1dusA)T162 Warning: unaligning (T0293)K210 because of BadResidue code BAD_PEPTIDE at template residue (1dusA)T162 T0293 24 :GLSIDIPLERL 1dusA 25 :KLKFKTDSGVF T0293 45 :IHWVEDLIGHQ 1dusA 41 :DKGTKILVENV T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1dusA 52 :VVDKDDDILDLGCGYGVIGIALADEV T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDL 1dusA 79 :STTMADINRRAIKLAKENIKLNNLDNY T0293 114 :IKVVKVPQATLL 1dusA 107 :IRVVHSDLYENV T0293 133 :SEIIYDFCMCNPPF 1dusA 119 :KDRKYNKIITNPPI T0293 181 :GGELEFVKRIIHDSLQLGKRLRWYSCML 1dusA 133 :RAGKEVLHRIIEEGKELLKDNGEIWVVI T0293 211 :ACSLAPLKEELRIQGV 1dusA 163 :KQGAKSLAKYMKDVFG T0293 228 :KVTYTEFCQG 1dusA 179 :NVETVTIKGG T0293 242 :WALAWS 1dusA 189 :YRVLKS Number of specific fragments extracted= 10 number of extra gaps= 1 total=400 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2avdA expands to /projects/compbio/data/pdb/2avd.pdb.gz 2avdA:# T0293 read from 2avdA/merged-good-all-a2m # 2avdA read from 2avdA/merged-good-all-a2m # adding 2avdA to template set # found chain 2avdA in template set Warning: unaligning (T0293)R202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avdA)I247 Warning: unaligning (T0293)W203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avdA)I247 T0293 40 :LRLNYIHWVEDLIGHQDS 2avdA 65 :EHPALRSLRLLTLEQPQG T0293 60 :STLRRGIDIGTGASCIYPLLGATLNG 2avdA 101 :IQAKKALDLGTFTGYSALALALALPA T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCNP 2avdA 128 :GRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAAGEAGTFDVAVVDA T0293 149 :NQLEAKGVNSRNPRRPPPSSVN 2avdA 187 :DKENCSAYYERCLQLLRPGGIL T0293 171 :TGG 2avdA 220 :LQP T0293 180 :EGG 2avdA 223 :PKG T0293 183 :ELEFVKRIIHDSLQ 2avdA 228 :AAECVRNLNERIRR T0293 198 :GKRL 2avdA 242 :DVRV T0293 204 :YSCMLG 2avdA 248 :SLLPLG T0293 239 :TMRWALAW 2avdA 254 :DGLTLAFK Number of specific fragments extracted= 10 number of extra gaps= 1 total=410 Number of alignments=37 # 2avdA read from 2avdA/merged-good-all-a2m # found chain 2avdA in template set Warning: unaligning (T0293)K228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avdA)I247 Warning: unaligning (T0293)V229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avdA)I247 T0293 5 :FKDPEAVRALTCT 2avdA 50 :EDSRLWQYLLSRS T0293 39 :PLRLNYIHWVEDLIGHQDSD 2avdA 63 :MREHPALRSLRLLTLEQPQG T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 2avdA 100 :LIQAKKALDLGTFTGYSALALALALP T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCNP 2avdA 127 :DGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAAGEAGTFDVAVVDA T0293 163 :RPPPSSVNTGGITEIMAEGGELEF 2avdA 187 :DKENCSAYYERCLQLLRPGGILAV T0293 187 :VKRIIHDSLQLGK 2avdA 219 :VLQPPKGDVAAEC T0293 214 :LAPLKEELRIQGVP 2avdA 232 :VRNLNERIRRDVRV T0293 230 :TYTEFCQG 2avdA 248 :SLLPLGDG T0293 241 :RWALAW 2avdA 256 :LTLAFK Number of specific fragments extracted= 9 number of extra gaps= 1 total=419 Number of alignments=38 # 2avdA read from 2avdA/merged-good-all-a2m # found chain 2avdA in template set Warning: unaligning (T0293)K228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avdA)I247 Warning: unaligning (T0293)V229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avdA)I247 T0293 5 :FKDPEAVRALTCTLLREDFGLS 2avdA 63 :MREHPALRSLRLLTLEQPQGDS T0293 40 :LRLNYIHWVEDLIG 2avdA 87 :TCEQAQLLANLARL T0293 60 :STLRRGIDIGTGASCIYPLLGATL 2avdA 101 :IQAKKALDLGTFTGYSALALALAL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCN 2avdA 126 :ADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAAGEAGTFDVAVVD T0293 156 :VNS 2avdA 186 :ADK T0293 180 :EG 2avdA 189 :EN T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACS 2avdA 191 :CSAYYERCLQLLRPGGILAVLRVLWRG T0293 214 :LAPLKEELRIQGVP 2avdA 232 :VRNLNERIRRDVRV T0293 230 :TYTEFCQG 2avdA 248 :SLLPLGDG T0293 242 :WALAW 2avdA 256 :LTLAF Number of specific fragments extracted= 10 number of extra gaps= 1 total=429 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xdzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1xdzA/merged-good-all-a2m # 1xdzA read from 1xdzA/merged-good-all-a2m # found chain 1xdzA in training set Warning: unaligning (T0293)G172 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xdzA)A177 Warning: unaligning (T0293)E180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xdzA)A177 T0293 44 :YIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 1xdzA 52 :LKHFYDSITAAFYVDFNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQLEN T0293 114 :IKVVKVP 1xdzA 121 :TTFCHDR T0293 125 :LMDALKE 1xdzA 128 :AETFGQR T0293 133 :SE 1xdzA 135 :KD T0293 135 :IIYDFCMCNPP 1xdzA 139 :ESYDIVTARAV T0293 151 :LEAKGVNSRNPRRPPPSSVN 1xdzA 150 :ARLSVLSELCLPLVKKNGLF T0293 181 :G 1xdzA 178 :E T0293 189 :RIIHDSLQLGKRLRWYSCMLG 1xdzA 179 :EELNAGKKAITTLGGELENIH T0293 231 :YTE 1xdzA 200 :SFK T0293 234 :FCQGRTMRWALAWSFYD 1xdzA 204 :PIEESDRNIMVIRKIKN Number of specific fragments extracted= 10 number of extra gaps= 0 total=439 Number of alignments=40 # 1xdzA read from 1xdzA/merged-good-all-a2m # found chain 1xdzA in training set Warning: unaligning (T0293)I190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xdzA)A177 Warning: unaligning (T0293)H192 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xdzA)A177 T0293 38 :VPLRLNYIHWVEDLIGHQDSD 1xdzA 18 :SPRQLEQFELYYDMLVEWNEK T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 1xdzA 67 :FNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQLEN T0293 114 :IKVVKVPQATLLMDA 1xdzA 121 :TTFCHDRAETFGQRK T0293 131 :EE 1xdzA 136 :DV T0293 134 :EIIYDFCMC 1xdzA 138 :RESYDIVTA T0293 162 :RRPPPSSVNTGGITEIMAEGGELEFVKR 1xdzA 147 :RAVARLSVLSELCLPLVKKNGLFVALKA T0293 193 :DSLQ 1xdzA 178 :EEEL T0293 215 :APLKEELRIQGVPKVTYTE 1xdzA 182 :NAGKKAITTLGGELENIHS T0293 234 :F 1xdzA 203 :L T0293 235 :CQGRTMRWALAWSFYD 1xdzA 205 :IEESDRNIMVIRKIKN Number of specific fragments extracted= 10 number of extra gaps= 0 total=449 Number of alignments=41 # 1xdzA read from 1xdzA/merged-good-all-a2m # found chain 1xdzA in training set Warning: unaligning (T0293)K210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xdzA)A177 T0293 6 :KDPEAVRALTCTLLREDFGLS 1xdzA 20 :RQLEQFELYYDMLVEWNEKIN T0293 34 :LIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLS 1xdzA 42 :TSITEKKEVYLKHFYDSITAAFYVDFNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQLE T0293 113 :LIKVVKVPQATLL 1xdzA 120 :NTTFCHDRAETFG T0293 129 :LKEESEIIYDFCMCN 1xdzA 133 :QRKDVRESYDIVTAR T0293 171 :TGGITEIM 1xdzA 148 :AVARLSVL T0293 188 :KRI 1xdzA 156 :SEL T0293 194 :SLQLGKRLRWYSCML 1xdzA 159 :CLPLVKKNGLFVALK T0293 211 :ACSLAPLKEELRIQG 1xdzA 178 :EEELNAGKKAITTLG T0293 226 :VPKVTYTEFCQGRTMRWALAWSFYD 1xdzA 195 :LENIHSFKLPIEESDRNIMVIRKIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=458 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ej0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1ej0A/merged-good-all-a2m # 1ej0A read from 1ej0A/merged-good-all-a2m # found chain 1ej0A in training set T0293 40 :LRLNYIHWVEDLIGHQDS 1ej0A 31 :LRSRAWFKLDEIQQSDKL T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNG 1ej0A 49 :FKPGMTVVDLGAAPGGWSQYVVTQIGG T0293 86 :WYFLATEVD 1ej0A 77 :GRIIACDLL T0293 109 :NLSD 1ej0A 86 :PMDP T0293 113 :LIKVVKVPQA 1ej0A 92 :GVDFLQGDFR T0293 123 :TLLMDALKEE 1ej0A 103 :ELVMKALLER T0293 133 :SEIIYDFCMCN 1ej0A 114 :GDSKVQVVMSD T0293 146 :FFANQ 1ej0A 125 :MAPNM T0293 151 :LEAKGVNSRN 1ej0A 131 :GTPAVDIPRA T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQ 1ej0A 141 :MYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSL T0293 226 :VPKVTYTEFC 1ej0A 182 :FTKVKVRKPD T0293 236 :QGRTMRWALAWSFYD 1ej0A 195 :ARSREVYIVATGRKP Number of specific fragments extracted= 12 number of extra gaps= 0 total=470 Number of alignments=43 # 1ej0A read from 1ej0A/merged-good-all-a2m # found chain 1ej0A in training set T0293 40 :LRLNYIHWVEDLIGHQDS 1ej0A 31 :LRSRAWFKLDEIQQSDKL T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1ej0A 49 :FKPGMTVVDLGAAPGGWSQYVVTQIG T0293 85 :GWYFLATEVD 1ej0A 76 :KGRIIACDLL T0293 109 :NLS 1ej0A 86 :PMD T0293 112 :D 1ej0A 92 :G T0293 114 :IKVVKVPQ 1ej0A 93 :VDFLQGDF T0293 122 :ATLLMDALK 1ej0A 106 :MKALLERVG T0293 134 :EIIYDFCMC 1ej0A 115 :DSKVQVVMS T0293 158 :SRNPRRPPPS 1ej0A 124 :DMAPNMSGTP T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKRLRWYSC 1ej0A 145 :ELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSLFT T0293 228 :KVTYTE 1ej0A 184 :KVKVRK T0293 234 :FCQGRTMRWALAWSFY 1ej0A 193 :SRARSREVYIVATGRK Number of specific fragments extracted= 12 number of extra gaps= 0 total=482 Number of alignments=44 # 1ej0A read from 1ej0A/merged-good-all-a2m # found chain 1ej0A in training set T0293 44 :YIHWVEDLIGHQD 1ej0A 35 :AWFKLDEIQQSDK T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1ej0A 48 :LFKPGMTVVDLGAAPGGWSQYVVTQI T0293 84 :NGWYFLATEVD 1ej0A 75 :GKGRIIACDLL T0293 109 :NLS 1ej0A 86 :PMD T0293 112 :DLIKVVKVPQATLLM 1ej0A 91 :VGVDFLQGDFRDELV T0293 127 :DALK 1ej0A 107 :KALL T0293 133 :SEIIYDFCMCN 1ej0A 114 :GDSKVQVVMSD T0293 155 :GVNSRN 1ej0A 125 :MAPNMS T0293 172 :GGITEIMA 1ej0A 131 :GTPAVDIP T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQ 1ej0A 139 :RAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSL T0293 227 :PKVTYTEF 1ej0A 183 :TKVKVRKP T0293 235 :CQGRTMRWALA 1ej0A 194 :RARSREVYIVA Number of specific fragments extracted= 12 number of extra gaps= 0 total=494 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fk8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fk8A expands to /projects/compbio/data/pdb/2fk8.pdb.gz 2fk8A:# T0293 read from 2fk8A/merged-good-all-a2m # 2fk8A read from 2fk8A/merged-good-all-a2m # adding 2fk8A to template set # found chain 2fk8A in template set Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0293)T70 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 Warning: unaligning (T0293)C212 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)S216 Warning: unaligning (T0293)S213 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)S216 T0293 7 :DPEAVRALTCTLL 2fk8A 22 :QAHYDVSDDFFAL T0293 20 :REDFGLS 2fk8A 36 :QDPTRTY T0293 27 :IDIPLER 2fk8A 45 :AYFEPPE T0293 38 :VPLRLNYIHWVEDLI 2fk8A 52 :LTLEEAQYAKVDLNL T0293 55 :QDSDKSTLRRGIDI 2fk8A 67 :DKLDLKPGMTLLDI T0293 71 :GASCIYPLLGATL 2fk8A 83 :GWGTTMRRAVERF T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 2fk8A 96 :DVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQG T0293 125 :LMD 2fk8A 132 :WED T0293 129 :LKE 2fk8A 135 :FAE T0293 136 :IYDFCMCNPPFFANQ 2fk8A 138 :PVDRIVSIEAFEHFG T0293 151 :LEAKGVNSRNPRRPPPSSVN 2fk8A 154 :ENYDDFFKRCFNIMPADGRM T0293 171 :TGGITEIMAEGG 2fk8A 179 :VSYHPYEMAARG T0293 183 :ELEFVKRIIHDSLQLGKRLRW 2fk8A 193 :LSFETARFIKFIVTEIFPGGR T0293 211 :A 2fk8A 214 :L T0293 214 :LAPLKEELRIQGVP 2fk8A 217 :TEMMVEHGEKAGFT Number of specific fragments extracted= 15 number of extra gaps= 2 total=509 Number of alignments=46 # 2fk8A read from 2fk8A/merged-good-all-a2m # found chain 2fk8A in template set Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0293)T70 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 Warning: unaligning (T0293)C212 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)S216 Warning: unaligning (T0293)S213 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)S216 T0293 20 :REDFGLSIDIPLERLIPT 2fk8A 22 :QAHYDVSDDFFALFQDPT T0293 38 :VPLRLNYIHWVEDLIGHQDSD 2fk8A 47 :FEPPELTLEEAQYAKVDLNLD T0293 59 :KSTLRRGIDI 2fk8A 71 :LKPGMTLLDI T0293 71 :GASCIYPLLGATL 2fk8A 83 :GWGTTMRRAVERF T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 2fk8A 96 :DVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWEDF T0293 134 :EIIYDFCMC 2fk8A 136 :AEPVDRIVS T0293 158 :SRNPRRPPPS 2fk8A 145 :IEAFEHFGHE T0293 168 :SVNTGGITEIMAEGGELEF 2fk8A 157 :DDFFKRCFNIMPADGRMTV T0293 195 :LQLGKRLRWYSCMLGKA 2fk8A 198 :ARFIKFIVTEIFPGGRL T0293 214 :LAPLKEELRIQGVPKVTY 2fk8A 217 :TEMMVEHGEKAGFTVPEP Number of specific fragments extracted= 10 number of extra gaps= 2 total=519 Number of alignments=47 # 2fk8A read from 2fk8A/merged-good-all-a2m # found chain 2fk8A in template set Warning: unaligning (T0293)G69 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0293)T70 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 T0293 36 :PTVPLRLNYIHWVEDLIGHQ 2fk8A 50 :PELTLEEAQYAKVDLNLDKL T0293 58 :DKSTLRRGIDI 2fk8A 70 :DLKPGMTLLDI T0293 71 :GASCIYPLLG 2fk8A 83 :GWGTTMRRAV T0293 82 :TLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 2fk8A 93 :ERFDVNVIGLTLSKNQHARCEQVLASIDTNRSRQVLLQGWEDFA T0293 135 :IIYDFCMCNPPFFA 2fk8A 137 :EPVDRIVSIEAFEH T0293 156 :VNSRN 2fk8A 151 :FGHEN T0293 187 :VKRIIHDSLQLGKRLRWYSCMLG 2fk8A 156 :YDDFFKRCFNIMPADGRMTVQSS T0293 210 :KACSLAPLKEELR 2fk8A 187 :AARGKKLSFETAR Number of specific fragments extracted= 8 number of extra gaps= 1 total=527 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xvaA expands to /projects/compbio/data/pdb/1xva.pdb.gz 1xvaA:# T0293 read from 1xvaA/merged-good-all-a2m # 1xvaA read from 1xvaA/merged-good-all-a2m # adding 1xvaA to template set # found chain 1xvaA in template set Warning: unaligning (T0293)T37 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)T37 Warning: unaligning (T0293)T82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0293)G85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0293)V169 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)L170 Warning: unaligning (T0293)N170 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)L170 Warning: unaligning (T0293)E180 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)D230 Warning: unaligning (T0293)G181 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)D230 Warning: unaligning (T0293)G182 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G231 Warning: unaligning (T0293)T232 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)G268 Warning: unaligning (T0293)R238 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)C282 T0293 38 :VPLRLNYIHWVEDLI 1xvaA 38 :RSRTAEYKAWLLGLL T0293 55 :QDS 1xvaA 53 :RQH T0293 61 :TLRRGIDIGTGASCIYPLLGA 1xvaA 56 :GCHRVLDVACGTGVDSIMLVE T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLS 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRRKE T0293 112 :DLIKVVKVPQAT 1xvaA 108 :DKWVIEEANWLT T0293 125 :LMDAL 1xvaA 120 :LDKDV T0293 131 :EESE 1xvaA 125 :PAGD T0293 136 :IYDFCMCNP 1xvaA 129 :GFDAVICLG T0293 145 :PFFANQ 1xvaA 139 :SFAHLP T0293 151 :LEAKGVNSRNPRRPPPSS 1xvaA 151 :SEHRLALKNIASMVRPGG T0293 172 :GG 1xvaA 227 :AG T0293 183 :E 1xvaA 232 :A T0293 199 :KRLRWYSCMLG 1xvaA 233 :PGFSKFRLSYY T0293 211 :ACSLAPLKEELRIQGVPKVTY 1xvaA 244 :PHCLASFTELVQEAFGGRCQH T0293 233 :EFCQG 1xvaA 272 :PYRPG T0293 239 :TMRWALAWS 1xvaA 283 :YFIHVLKKT Number of specific fragments extracted= 16 number of extra gaps= 6 total=543 Number of alignments=49 # 1xvaA read from 1xvaA/merged-good-all-a2m # found chain 1xvaA in template set Warning: unaligning (T0293)E32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)I17 Warning: unaligning (T0293)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)I17 Warning: unaligning (T0293)P36 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)Y21 Warning: unaligning (T0293)T37 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)Y21 Warning: unaligning (T0293)T82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0293)G85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0293)E183 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)L170 Warning: unaligning (T0293)L184 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)L170 Warning: unaligning (T0293)M207 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xvaA)P188 Warning: unaligning (T0293)L208 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xvaA)P188 Warning: unaligning (T0293)G209 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G189 Warning: unaligning (T0293)T239 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)C282 Warning: unaligning (T0293)M240 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)C282 T0293 28 :DIPL 1xvaA 12 :VAAE T0293 34 :LI 1xvaA 18 :PD T0293 38 :VPLRLNYIHWVEDLIGHQ 1xvaA 38 :RSRTAEYKAWLLGLLRQH T0293 61 :TLRRGIDIGTGASCIYPLLGA 1xvaA 56 :GCHRVLDVACGTGVDSIMLVE T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLS 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRRKE T0293 112 :D 1xvaA 109 :K T0293 114 :IKVVKVPQATL 1xvaA 110 :WVIEEANWLTL T0293 126 :MDALKE 1xvaA 121 :DKDVPA T0293 134 :EIIYDFCMC 1xvaA 127 :GDGFDAVIC T0293 157 :NSRNPRRPPPS 1xvaA 136 :LGNSFAHLPDS T0293 168 :SVNTGGITEIMAEGG 1xvaA 154 :RLALKNIASMVRPGG T0293 185 :EFVKRIIHDSLQLGK 1xvaA 171 :VIDHRNYDYILSTGC T0293 206 :C 1xvaA 186 :A T0293 212 :CS 1xvaA 192 :IY T0293 214 :LAPLKEELRIQ 1xvaA 247 :LASFTELVQEA T0293 225 :GVPKVTY 1xvaA 260 :GRCQHSV T0293 232 :TEFCQGR 1xvaA 274 :RPGQAYV T0293 241 :RWALAWSFYD 1xvaA 283 :YFIHVLKKTG Number of specific fragments extracted= 18 number of extra gaps= 6 total=561 Number of alignments=50 # 1xvaA read from 1xvaA/merged-good-all-a2m # found chain 1xvaA in template set Warning: unaligning (T0293)E21 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)T37 Warning: unaligning (T0293)D22 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)T37 Warning: unaligning (T0293)N84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0293)G85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0293)E183 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)Q150 Warning: unaligning (T0293)L184 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)Q150 Warning: unaligning (T0293)W203 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)L170 Warning: unaligning (T0293)Y204 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)L170 Warning: unaligning (T0293)P227 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xvaA)P188 Warning: unaligning (T0293)Q236 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)N210 Warning: unaligning (T0293)G237 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)N210 Warning: unaligning (T0293)R238 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)N211 T0293 11 :VRALTCTLLR 1xvaA 26 :AARVWQLYIG T0293 23 :FGLS 1xvaA 38 :RSRT T0293 42 :LNYIHWVEDLIG 1xvaA 42 :AEYKAWLLGLLR T0293 59 :KSTLRRGIDIGTGASCIYPLLGA 1xvaA 54 :QHGCHRVLDVACGTGVDSIMLVE T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLS 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRRKE T0293 112 :DLIKVVKVPQATLL 1xvaA 108 :DKWVIEEANWLTLD T0293 127 :DAL 1xvaA 122 :KDV T0293 132 :ESEIIYDFCMCN 1xvaA 125 :PAGDGFDAVICL T0293 171 :TGGITEIMAEGG 1xvaA 137 :GNSFAHLPDSKG T0293 185 :EFVKRIIHDSLQLGKRLR 1xvaA 151 :SEHRLALKNIASMVRPGG T0293 205 :SCMLG 1xvaA 171 :VIDHR T0293 216 :PLKEELRIQGV 1xvaA 176 :NYDYILSTGCA T0293 228 :KVTYTEFC 1xvaA 201 :DITTSVLT T0293 239 :TMRWALA 1xvaA 212 :KAHMVTL Number of specific fragments extracted= 14 number of extra gaps= 6 total=575 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ri5A expands to /projects/compbio/data/pdb/1ri5.pdb.gz 1ri5A:# T0293 read from 1ri5A/merged-good-all-a2m # 1ri5A read from 1ri5A/merged-good-all-a2m # adding 1ri5A to template set # found chain 1ri5A in template set T0293 44 :YIHWVEDLIGHQDSD 1ri5A 49 :ANNFIKACLIRLYTK T0293 61 :TLRRGIDIGTGASCIYPLLGAT 1ri5A 64 :RGDSVLDLGCGKGGDLLKYERA T0293 85 :G 1ri5A 86 :G T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 1ri5A 88 :GEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQD T0293 125 :LMD 1ri5A 123 :SYG T0293 130 :KEES 1ri5A 126 :RHMD T0293 134 :EIIYDFCMCNPPFFANQ 1ri5A 131 :GKEFDVISSQFSFHYAF T0293 151 :LEAKGVNSRNPRRPPPSSVN 1ri5A 151 :ESLDIAQRNIARHLRPGGYF T0293 171 :TGGITEIMAEGGE 1ri5A 177 :RDVILERYKQGRM T0293 199 :KRLRWYSCMLGKACS 1ri5A 207 :ESVREYRFTLLDSVN T0293 214 :LAPLKEELRIQG 1ri5A 230 :FTRMVDGFKRLG T0293 229 :VTYTE 1ri5A 242 :LSLVE Number of specific fragments extracted= 12 number of extra gaps= 0 total=587 Number of alignments=52 # 1ri5A read from 1ri5A/merged-good-all-a2m # found chain 1ri5A in template set Warning: unaligning (T0293)P36 because first residue in template chain is (1ri5A)S41 T0293 37 :TVPLRLNYIHWVEDLIGHQD 1ri5A 42 :KTINIRNANNFIKACLIRLY T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1ri5A 62 :TKRGDSVLDLGCGKGGDLLKYERA T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQ 1ri5A 86 :GIGEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDS T0293 122 :ATLLM 1ri5A 126 :RHMDL T0293 134 :EIIYDFCMCNPPF 1ri5A 131 :GKEFDVISSQFSF T0293 158 :SRNPRRP 1ri5A 144 :HYAFSTS T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKRL 1ri5A 154 :DIAQRNIARHLRPGGYFIMTVPSRDVILERYKQG T0293 214 :LAPLKEELRIQGVPKVTYTE 1ri5A 230 :FTRMVDGFKRLGLSLVERKG Number of specific fragments extracted= 8 number of extra gaps= 0 total=595 Number of alignments=53 # 1ri5A read from 1ri5A/merged-good-all-a2m # found chain 1ri5A in template set T0293 10 :AVRALT 1ri5A 45 :NIRNAN T0293 45 :IHWVEDLIGH 1ri5A 51 :NFIKACLIRL T0293 58 :DKSTLRRGIDIGTG 1ri5A 61 :YTKRGDSVLDLGCG T0293 78 :LLGATLNGW 1ri5A 79 :LLKYERAGI T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1ri5A 89 :EYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDSYGRH T0293 131 :EESEIIYDFCMCNPPFF 1ri5A 128 :MDLGKEFDVISSQFSFH T0293 176 :EIM 1ri5A 145 :YAF T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCMLG 1ri5A 148 :STSESLDIAQRNIARHLRPGGYFIMTVP T0293 213 :SLAPLKEELRIQGVPK 1ri5A 176 :SRDVILERYKQGRMSN Number of specific fragments extracted= 9 number of extra gaps= 0 total=604 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t43A/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/T0293/1t43A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0293/1t43A/merged-good-all-a2m.gz for input Trying 1t43A/merged-good-all-a2m Error: Couldn't open file 1t43A/merged-good-all-a2m or 1t43A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wznA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wznA expands to /projects/compbio/data/pdb/1wzn.pdb.gz 1wznA:# T0293 read from 1wznA/merged-good-all-a2m # 1wznA read from 1wznA/merged-good-all-a2m # adding 1wznA to template set # found chain 1wznA in template set T0293 43 :NYIHWVEDLI 1wznA 25 :AEIDFVEEIF T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGAT 1wznA 35 :KEDAKREVRRVLDLACGTGIPTLELAER T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1wznA 63 :GYEVVGLDLHEEMLRVARRKAKERNLK T0293 114 :IKVVKVP 1wznA 90 :IEFLQGD T0293 125 :LMD 1wznA 97 :VLE T0293 130 :KEESE 1wznA 100 :IAFKN T0293 136 :IYDFCMCNPPFFANQ 1wznA 105 :EFDAVTMFFSTIMYF T0293 151 :LEAKGVNSRNPRRPPPSSVN 1wznA 122 :EDLRKLFSKVAEALKPGGVF T0293 173 :G 1wznA 193 :R T0293 180 :EGGEL 1wznA 194 :PNGEV T0293 200 :RLRWYSCMLG 1wznA 199 :KAFLVDDELN T0293 211 :ACSLAPLKEELRIQ 1wznA 209 :IYTPREVRLLAEKY T0293 226 :VPKVTY 1wznA 223 :FEKVKI T0293 232 :TEFCQGRTMRWALAW 1wznA 234 :RELSPNDMRYWIVGI Number of specific fragments extracted= 14 number of extra gaps= 0 total=618 Number of alignments=55 # 1wznA read from 1wznA/merged-good-all-a2m # found chain 1wznA in template set T0293 43 :NYIHWVEDLIGHQD 1wznA 25 :AEIDFVEEIFKEDA T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1wznA 39 :KREVRRVLDLACGTGIPTLELAER T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1wznA 63 :GYEVVGLDLHEEMLRVARRKAKERNLK T0293 114 :IKVVKVPQATLLM 1wznA 90 :IEFLQGDVLEIAF T0293 134 :EIIYDFCMC 1wznA 103 :KNEFDAVTM T0293 157 :NSRNPRRPPPS 1wznA 112 :FFSTIMYFDEE T0293 168 :SVNTGGITEIMAEGGELEF 1wznA 125 :RKLFSKVAEALKPGGVFIT T0293 187 :VKR 1wznA 191 :ILR T0293 207 :MLG 1wznA 194 :PNG T0293 210 :KACSLAPLKEELRIQ 1wznA 208 :NIYTPREVRLLAEKY T0293 226 :VPKVTY 1wznA 223 :FEKVKI T0293 232 :TEFCQGRTMRWALAW 1wznA 234 :RELSPNDMRYWIVGI Number of specific fragments extracted= 12 number of extra gaps= 0 total=630 Number of alignments=56 # 1wznA read from 1wznA/merged-good-all-a2m # found chain 1wznA in template set Warning: unaligning (T0293)K210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wznA)G155 Warning: unaligning (T0293)K228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wznA)G155 T0293 44 :YIHWVEDLIGHQ 1wznA 26 :EIDFVEEIFKED T0293 58 :DKSTLRRGIDIGTGASCIYPLLGA 1wznA 38 :AKREVRRVLDLACGTGIPTLELAE T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1wznA 62 :RGYEVVGLDLHEEMLRVARRKAKERNLK T0293 114 :IKVVKVPQATLL 1wznA 90 :IEFLQGDVLEIA T0293 133 :SEIIYDFCMCN 1wznA 102 :FKNEFDAVTMF T0293 172 :GGITEIM 1wznA 113 :FSTIMYF T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCMLG 1wznA 120 :DEEDLRKLFSKVAEALKPGGVFITDFP T0293 229 :VTYTEFCQGRTMRWALAWS 1wznA 156 :PVVWNEQKGEEKLVIMDWR Number of specific fragments extracted= 8 number of extra gaps= 0 total=638 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ws6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ws6A expands to /projects/compbio/data/pdb/1ws6.pdb.gz 1ws6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1ws6A/merged-good-all-a2m # 1ws6A read from 1ws6A/merged-good-all-a2m # adding 1ws6A to template set # found chain 1ws6A in template set T0293 18 :LLREDFGLSIDIPLER 1ws6A 19 :LGGKARGVALKVPASA T0293 41 :RLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1ws6A 35 :RPSPVRLRKALFDYLRLRYPRRGRFLDPFAGSGAVGLEAASE T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ws6A 77 :GWEAVLVEKDPEAVRLLKENVRRTGLG T0293 114 :IKVVKVP 1ws6A 104 :ARVVALP T0293 125 :LMDALKEE 1ws6A 111 :VEVFLPEA T0293 133 :SEIIYDFCMCNPPFFA 1ws6A 121 :QGERFTVAFMAPPYAM T0293 152 :EAKGV 1ws6A 137 :DLAAL T0293 174 :ITEIMAEGG 1ws6A 142 :FGELLASGL T0293 199 :KRLRWYSCMLGKACSLAP 1ws6A 152 :EAGGLYVLQHPKDLYLPL T0293 237 :GRTMRW 1ws6A 170 :GERRVY T0293 243 :ALAW 1ws6A 180 :LTLV Number of specific fragments extracted= 11 number of extra gaps= 0 total=649 Number of alignments=58 # 1ws6A read from 1ws6A/merged-good-all-a2m # found chain 1ws6A in template set T0293 17 :TLLREDFGLSIDIPLERL 1ws6A 18 :ILGGKARGVALKVPASAR T0293 39 :PLRLNYIHWVEDLIGHQ 1ws6A 36 :PSPVRLRKALFDYLRLR T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1ws6A 53 :YPRRGRFLDPFAGSGAVGLEAASE T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ws6A 77 :GWEAVLVEKDPEAVRLLKENVRRTGLG T0293 114 :IKVVKVPQATLLMDALKE 1ws6A 104 :ARVVALPVEVFLPEAKAQ T0293 134 :EIIYDFCMCNPPFF 1ws6A 122 :GERFTVAFMAPPYA T0293 165 :PPSSVNTGGITEI 1ws6A 136 :MDLAALFGELLAS T0293 178 :MAEGGELEFVKRII 1ws6A 151 :VEAGGLYVLQHPKD Number of specific fragments extracted= 8 number of extra gaps= 0 total=657 Number of alignments=59 # 1ws6A read from 1ws6A/merged-good-all-a2m # found chain 1ws6A in template set T0293 23 :FGLSIDIPLERLIPTVPLRLNYIHWVED 1ws6A 24 :RGVALKVPASARPSPVRLRKALFDYLRL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGA 1ws6A 52 :RYPRRGRFLDPFAGSGAVGLEAAS T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1ws6A 76 :EGWEAVLVEKDPEAVRLLKENVRRTGLG T0293 114 :IKVVKVPQATLL 1ws6A 104 :ARVVALPVEVFL T0293 130 :K 1ws6A 116 :P T0293 131 :EESEIIYDFCMCNPPF 1ws6A 119 :KAQGERFTVAFMAPPY T0293 171 :TGGITE 1ws6A 135 :AMDLAA T0293 190 :IIHDSLQL 1ws6A 141 :LFGELLAS T0293 198 :GKRLRWYSCMLGKACSLAP 1ws6A 151 :VEAGGLYVLQHPKDLYLPL T0293 237 :GRTMR 1ws6A 170 :GERRV T0293 242 :WALAW 1ws6A 178 :NALTL Number of specific fragments extracted= 11 number of extra gaps= 0 total=668 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1im8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1im8A expands to /projects/compbio/data/pdb/1im8.pdb.gz 1im8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1im8A/merged-good-all-a2m # 1im8A read from 1im8A/merged-good-all-a2m # adding 1im8A to template set # found chain 1im8A in template set Warning: unaligning (T0293)V38 because first residue in template chain is (1im8A)F17 T0293 39 :PLRLNYIHWVEDLIGHQDSDK 1im8A 18 :IFDENVAEVFPDMIQRSVPGY T0293 60 :STLRRGIDIGTGASCIYPLLGATL 1im8A 54 :TADSNVYDLGCSRGAATLSARRNI T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1im8A 80 :PNVKIIGIDNSQPMVERCRQHIAAYHSE T0293 113 :LIKVVKVP 1im8A 109 :PVEILCND T0293 125 :LMD 1im8A 117 :IRH T0293 130 :KEES 1im8A 120 :VEIK T0293 136 :IYDFCMCNPP 1im8A 124 :NASMVILNFT T0293 147 :FANQ 1im8A 134 :LQFL T0293 151 :LEAKGVNSRNPRRPPPSSVN 1im8A 140 :EDRIALLTKIYEGLNPNGVL T0293 171 :TGG 1im8A 167 :FED T0293 184 :LEFVKRIIHDSLQLGKRLRW 1im8A 170 :TKINHLLIDLHHQFKRANGY T0293 209 :GKACSLAPLKEELRIQGVPKVTYTEFCQGRTMRWAL 1im8A 205 :MRTDSIETHKVRLKNVGFSQVELWFQCFNFGSMIAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=680 Number of alignments=61 # 1im8A read from 1im8A/merged-good-all-a2m # found chain 1im8A in template set Warning: unaligning (T0293)R33 because first residue in template chain is (1im8A)F17 T0293 34 :LIPT 1im8A 18 :IFDE T0293 38 :VPLRLNYIHWVEDLIGHQ 1im8A 35 :VPGYSNIITAIGMLAERF T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1im8A 53 :VTADSNVYDLGCSRGAATLSARRNI T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1im8A 80 :PNVKIIGIDNSQPMVERCRQHIAAYHSE T0293 112 :D 1im8A 109 :P T0293 114 :IKVVKVPQATL 1im8A 110 :VEILCNDIRHV T0293 127 :D 1im8A 121 :E T0293 134 :EIIYDFCMC 1im8A 122 :IKNASMVIL T0293 158 :SRNPRRPPPS 1im8A 131 :NFTLQFLPPE T0293 168 :SVNTGGITEIMAEGGELEF 1im8A 143 :IALLTKIYEGLNPNGVLVL T0293 187 :VKRIIHDSLQLGKRLRWYSCMLG 1im8A 166 :RFEDTKINHLLIDLHHQFKRANG T0293 210 :KACSLAPLKEELRIQGVPKVTYTEFCQGRTMRWAL 1im8A 206 :RTDSIETHKVRLKNVGFSQVELWFQCFNFGSMIAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=692 Number of alignments=62 # 1im8A read from 1im8A/merged-good-all-a2m # found chain 1im8A in template set T0293 5 :FKDPEAVRALTCTLLREDFG 1im8A 18 :IFDENVAEVFPDMIQRSVPG T0293 41 :RLNYIHWVEDLIGHQ 1im8A 38 :YSNIITAIGMLAERF T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1im8A 53 :VTADSNVYDLGCSRGAATLSARRNI T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1im8A 80 :PNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVE T0293 134 :EIIYDFCMCN 1im8A 122 :IKNASMVILN T0293 159 :RNPRRPPPSS 1im8A 132 :FTLQFLPPED T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRI 1im8A 142 :RIALLTKIYEGLNPNGVLVLSEKFRFEDTKINHLLID Number of specific fragments extracted= 7 number of extra gaps= 0 total=699 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1dl5A/merged-good-all-a2m # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0293 23 :FGLSIDIPLERLIPTVP 1dl5A 44 :IVLVSYDDGEEYSTSSQ T0293 45 :IHWVEDLI 1dl5A 61 :PSLMALFM T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNG 1dl5A 69 :EWVGLDKGMRVLEIGGGTGYNAAVMSRVVGE T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSD 1dl5A 101 :GLVVSVEYSRKICEIAKRNVERLGIEN T0293 114 :IKVVKVP 1dl5A 128 :VIFVCGD T0293 125 :LMDALKEES 1dl5A 135 :GYYGVPEFS T0293 136 :IYDFCMCNPP 1dl5A 144 :PYDVIFVTVG T0293 147 :FANQL 1dl5A 154 :VDEVP T0293 192 :HDSLQLGKRLRWYSCMLG 1dl5A 159 :ETWFTQLKEGGRVIVPIN T0293 232 :TEFCQGRTMRWALAWS 1dl5A 177 :LKLSRRQPAFLFKKKD Number of specific fragments extracted= 10 number of extra gaps= 0 total=709 Number of alignments=64 # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0293 54 :HQDSD 1dl5A 24 :EIPRE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1dl5A 73 :LDKGMRVLEIGGGTGYNAAVMSRVVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1dl5A 100 :KGLVVSVEYSRKICEIAKRNVERLGIEN T0293 114 :IKVVKVPQATLLMD 1dl5A 128 :VIFVCGDGYYGVPE T0293 134 :EIIYDFCMC 1dl5A 142 :FSPYDVIFV T0293 158 :SRNPRRPP 1dl5A 151 :TVGVDEVP T0293 172 :GGITEIMAEGGELEF 1dl5A 159 :ETWFTQLKEGGRVIV T0293 187 :VKRIIHDSLQLGKRLRWYSCMLG 1dl5A 205 :FITAGGNLGNLLERNRKLLREFP T0293 210 :K 1dl5A 235 :V T0293 214 :LAPLKEELRIQGVPKVT 1dl5A 283 :IENLLTQWESCGYRSFE Number of specific fragments extracted= 10 number of extra gaps= 0 total=719 Number of alignments=65 # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0293 42 :LNYIHWVEDL 1dl5A 62 :SLMALFMEWV T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1dl5A 72 :GLDKGMRVLEIGGGTGYNAAVMSRVV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1dl5A 99 :EKGLVVSVEYSRKICEIAKRNVERLGIE T0293 113 :LIKVVKVPQATLL 1dl5A 127 :NVIFVCGDGYYGV T0293 132 :ESEIIYDFCMCNP 1dl5A 140 :PEFSPYDVIFVTV T0293 192 :HDSLQLGKRLRWYSCMLGKACS 1dl5A 159 :ETWFTQLKEGGRVIVPINLKLS T0293 238 :RTMRWALA 1dl5A 181 :RRQPAFLF Number of specific fragments extracted= 7 number of extra gaps= 0 total=726 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qzzA expands to /projects/compbio/data/pdb/1qzz.pdb.gz 1qzzA:# T0293 read from 1qzzA/merged-good-all-a2m # 1qzzA read from 1qzzA/merged-good-all-a2m # adding 1qzzA to template set # found chain 1qzzA in template set Warning: unaligning (T0293)Y249 because last residue in template chain is (1qzzA)S357 T0293 60 :STLRRGIDIGTGASCIYPLLGATLNGWYFLATEV 1qzzA 181 :SAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVEL T0293 95 :DMCFNYAKKNVEQNNLSDLIKVVKVP 1qzzA 215 :AGPAERARRRFADAGLADRVTVAEGD T0293 125 :LMD 1qzzA 241 :FFK T0293 131 :EESE 1qzzA 244 :PLPV T0293 136 :IYDFCMCNPP 1qzzA 248 :TADVVLLSFV T0293 147 :FANQ 1qzzA 258 :LLNW T0293 151 :LEAKGVNSRNPRRPPPSSVN 1qzzA 264 :EDALTILRGCVRALEPGGRL T0293 185 :EFVKRIIHDSLQLGKR 1qzzA 298 :RFFSTLLDLRMLTFMG T0293 209 :GKACSLAPLKEELRIQG 1qzzA 314 :GRVRTRDEVVDLAGSAG T0293 229 :VTYTE 1qzzA 331 :LALAS T0293 234 :FCQGRTMRWALAWSF 1qzzA 342 :TTLPFDFSILEFTAV Number of specific fragments extracted= 11 number of extra gaps= 0 total=737 Number of alignments=67 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set Warning: unaligning (T0293)Y249 because last residue in template chain is (1qzzA)S357 T0293 29 :IPLERLIPTVPLRL 1qzzA 93 :RLGMLLADGHPAQQ T0293 45 :IHWV 1qzzA 107 :RAWL T0293 49 :EDLIGHQDSD 1qzzA 116 :VSHADLAFTG T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEV 1qzzA 180 :WSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVEL T0293 95 :DMCFNYAKKNVEQNNLSDLIKVVKVP 1qzzA 215 :AGPAERARRRFADAGLADRVTVAEGD T0293 125 :LMDAL 1qzzA 241 :FFKPL T0293 134 :EIIYDFCMC 1qzzA 246 :PVTADVVLL T0293 158 :SRNPRRPPPS 1qzzA 255 :SFVLLNWSDE T0293 168 :SVNTGGITEIMAEGGELEF 1qzzA 267 :LTILRGCVRALEPGGRLLV T0293 193 :DSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTE 1qzzA 298 :RFFSTLLDLRMLTFMGGRVRTRDEVVDLAGSAGLALASERT T0293 234 :FCQGRTMRWALAWSF 1qzzA 342 :TTLPFDFSILEFTAV Number of specific fragments extracted= 11 number of extra gaps= 0 total=748 Number of alignments=68 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set Warning: unaligning (T0293)G209 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)A296 Warning: unaligning (T0293)K210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qzzA)A296 T0293 53 :GHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEV 1qzzA 174 :PADAYDWSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVEL T0293 95 :DMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1qzzA 215 :AGPAERARRRFADAGLADRVTVAEGDFFKPL T0293 134 :EIIYDFCMCN 1qzzA 246 :PVTADVVLLS T0293 166 :PSSVNT 1qzzA 256 :FVLLNW T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCML 1qzzA 262 :SDEDALTILRGCVRALEPGGRLLVLD T0293 211 :A 1qzzA 297 :D T0293 219 :EELRI 1qzzA 298 :RFFST Number of specific fragments extracted= 7 number of extra gaps= 1 total=755 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufkA expands to /projects/compbio/data/pdb/1ufk.pdb.gz 1ufkA:# T0293 read from 1ufkA/merged-good-all-a2m # 1ufkA read from 1ufkA/merged-good-all-a2m # adding 1ufkA to template set # found chain 1ufkA in template set Warning: unaligning (T0293)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ufkA)G102 Warning: unaligning (T0293)T37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ufkA)G102 T0293 20 :REDFGLSI 1ufkA 84 :WEGAEIPL T0293 33 :RLI 1ufkA 92 :VIE T0293 44 :YIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1ufkA 103 :HHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKL T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ufkA 142 :GGKALGVDIDPMVLPQAEANAKRNGVR T0293 114 :IKVVKVP 1ufkA 169 :PRFLEGS T0293 126 :MDALKEE 1ufkA 176 :LEAALPF T0293 135 :IIYDFCMCN 1ufkA 183 :GPFDLLVAN T0293 147 :FA 1ufkA 192 :LY T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGV 1ufkA 194 :AELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGF T0293 230 :TYTEFCQGRTMRWALAW 1ufkA 237 :RPLEEAAEGEWVLLAYG Number of specific fragments extracted= 10 number of extra gaps= 1 total=765 Number of alignments=70 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set Warning: unaligning (T0293)L31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ufkA)G102 Warning: unaligning (T0293)E32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ufkA)G102 T0293 20 :REDFGLSIDIP 1ufkA 84 :WEGAEIPLVIE T0293 41 :RLNYIHWVEDLIGHQ 1ufkA 103 :HHETTRLALKALARH T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1ufkA 118 :LRPGDKVLDLGTGSGVLAIAAEKL T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ufkA 142 :GGKALGVDIDPMVLPQAEANAKRNGVR T0293 114 :IKVVKVPQATL 1ufkA 169 :PRFLEGSLEAA T0293 126 :MD 1ufkA 180 :LP T0293 134 :EIIYDFCMCNP 1ufkA 182 :FGPFDLLVANL T0293 163 :RPP 1ufkA 193 :YAE T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDS 1ufkA 198 :AALAPRYREALVPGGRALLTGILKDRA T0293 215 :APLKEELRIQGVPKVTYTEFCQ 1ufkA 225 :PLVREAMAGAGFRPLEEAAEGE T0293 241 :RWALAW 1ufkA 247 :WVLLAY Number of specific fragments extracted= 11 number of extra gaps= 1 total=776 Number of alignments=71 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set Warning: unaligning (T0293)L31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ufkA)G102 Warning: unaligning (T0293)E32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ufkA)G102 T0293 24 :GLSIDIP 1ufkA 88 :EIPLVIE T0293 37 :TVPLR 1ufkA 103 :HHETT T0293 45 :IHWVEDLIGH 1ufkA 108 :RLALKALARH T0293 59 :KSTLRRGIDIGTGASCIYPLLGA 1ufkA 118 :LRPGDKVLDLGTGSGVLAIAAEK T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1ufkA 141 :LGGKALGVDIDPMVLPQAEANAKRNGVR T0293 114 :IKVVKVPQATLL 1ufkA 169 :PRFLEGSLEAAL T0293 133 :SEIIYDFCMCN 1ufkA 181 :PFGPFDLLVAN T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTEFCQ 1ufkA 192 :LYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGE T0293 241 :RWALAWS 1ufkA 247 :WVLLAYG Number of specific fragments extracted= 9 number of extra gaps= 1 total=785 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2esrA expands to /projects/compbio/data/pdb/2esr.pdb.gz 2esrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 2esrA/merged-good-all-a2m # 2esrA read from 2esrA/merged-good-all-a2m # adding 2esrA to template set # found chain 2esrA in template set Warning: unaligning (T0293)W47 because first residue in template chain is (2esrA)V28 T0293 48 :VEDLIGHQDSDK 2esrA 29 :RGAIFNMIGPYF T0293 61 :TLRRGIDIGTGASCIYPLLGAT 2esrA 41 :NGGRVLDLFAGSGGLAIEAVSR T0293 85 :G 2esrA 63 :G T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 2esrA 65 :SAAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKME T0293 125 :LMDALKEESE 2esrA 100 :AERAIDCLTG T0293 136 :IYDFCMCNPPFFA 2esrA 110 :RFDLVFLDPPYAK T0293 151 :LEAKGV 2esrA 123 :ETIVAT T0293 174 :ITEIMAEGG 2esrA 129 :IEALAAKNL T0293 198 :GKRLRWYSCMLGKACSLA 2esrA 138 :LSEQVMVVCETDKTVLLP T0293 231 :YTEFC 2esrA 163 :IWKEK T0293 236 :QGRTMRWALAWSFYD 2esrA 169 :YGISKVTVYVNEGHH Number of specific fragments extracted= 11 number of extra gaps= 0 total=796 Number of alignments=73 # 2esrA read from 2esrA/merged-good-all-a2m # found chain 2esrA in template set Warning: unaligning (T0293)V48 because first residue in template chain is (2esrA)V28 T0293 49 :EDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 2esrA 29 :RGAIFNMIGPYFNGGRVLDLFAGSGGLAIEAVSR T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 2esrA 63 :GMSAAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKMEAERA T0293 126 :MDAL 2esrA 104 :IDCL T0293 134 :EIIYDFCMCNPPFFA 2esrA 108 :TGRFDLVFLDPPYAK T0293 168 :SVNTGGITEIMAEG 2esrA 123 :ETIVATIEALAAKN T0293 182 :GELEF 2esrA 142 :VMVVC T0293 232 :TEFCQGRTMRWALAW 2esrA 165 :KEKIYGISKVTVYVN Number of specific fragments extracted= 7 number of extra gaps= 0 total=803 Number of alignments=74 # 2esrA read from 2esrA/merged-good-all-a2m # found chain 2esrA in template set T0293 45 :IHWVEDL 2esrA 30 :GAIFNMI T0293 57 :SDKSTLRRGIDIGTGASCIYPL 2esrA 37 :GPYFNGGRVLDLFAGSGGLAIE T0293 80 :GATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 2esrA 59 :AVSRGMSAAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKMEAERAI T0293 131 :EESEIIYDFCMCNPPFFAN 2esrA 105 :DCLTGRFDLVFLDPPYAKE T0293 186 :FVKRIIHDSLQL 2esrA 124 :TIVATIEALAAK T0293 198 :GKRLRWYSCMLGKACSLA 2esrA 138 :LSEQVMVVCETDKTVLLP T0293 228 :K 2esrA 156 :K T0293 229 :VTYTEFCQGRTMRWAL 2esrA 163 :IWKEKIYGISKVTVYV Number of specific fragments extracted= 8 number of extra gaps= 0 total=811 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jsxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jsxA expands to /projects/compbio/data/pdb/1jsx.pdb.gz 1jsxA:# T0293 read from 1jsxA/merged-good-all-a2m # 1jsxA read from 1jsxA/merged-good-all-a2m # adding 1jsxA to template set # found chain 1jsxA in template set Warning: unaligning (T0293)L42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)E48 Warning: unaligning (T0293)F234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jsxA)D194 Warning: unaligning (T0293)G237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)D194 T0293 43 :NYIHWVEDLI 1jsxA 49 :MLVRHILDSI T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 1jsxA 59 :VVAPYLQGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLEN T0293 114 :IKVVKVPQATL 1jsxA 117 :IEPVQSRVEEF T0293 131 :EESE 1jsxA 128 :PSEP T0293 136 :IYDFCMCNP 1jsxA 132 :PFDGVISRA T0293 147 :FANQLEAKGVNS 1jsxA 141 :FASLNDMVSWCH T0293 169 :VNTGG 1jsxA 153 :HLPGE T0293 201 :LRWYSCMLGKACS 1jsxA 158 :QGRFYALKGQMPE T0293 215 :AP 1jsxA 171 :DE T0293 222 :RIQGVPKVTYTE 1jsxA 173 :IALLPEEYQVES T0293 238 :RTMRWALAWSFYD 1jsxA 195 :GERHLVVIKANKI Number of specific fragments extracted= 11 number of extra gaps= 0 total=822 Number of alignments=76 # 1jsxA read from 1jsxA/merged-good-all-a2m # found chain 1jsxA in template set Warning: unaligning (T0293)L42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)E48 Warning: unaligning (T0293)C235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jsxA)D194 Warning: unaligning (T0293)G237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)D194 T0293 43 :NYIHWVEDLIG 1jsxA 49 :MLVRHILDSIV T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 1jsxA 60 :VAPYLQGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLEN T0293 114 :IKVVKVPQATLLM 1jsxA 117 :IEPVQSRVEEFPS T0293 134 :EIIYDFCMC 1jsxA 130 :EPPFDGVIS T0293 162 :RRPPPSSVNTGGITEIMAEGGELEF 1jsxA 139 :RAFASLNDMVSWCHHLPGEQGRFYA T0293 187 :VKRIIHDSLQL 1jsxA 165 :KGQMPEDEIAL T0293 226 :VPK 1jsxA 176 :LPE T0293 229 :VTYTEF 1jsxA 183 :ESVVKL T0293 238 :RTMRWALAWSF 1jsxA 195 :GERHLVVIKAN Number of specific fragments extracted= 9 number of extra gaps= 0 total=831 Number of alignments=77 # 1jsxA read from 1jsxA/merged-good-all-a2m # found chain 1jsxA in template set Warning: unaligning (T0293)D22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jsxA)E48 Warning: unaligning (T0293)R41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)E48 Warning: unaligning (T0293)C235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jsxA)D194 Warning: unaligning (T0293)R238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jsxA)D194 T0293 9 :EAVRALTCTLLRE 1jsxA 22 :NQLIAYVNMLHKW T0293 42 :LNYIHWVEDLIGH 1jsxA 49 :MLVRHILDSIVVA T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLS 1jsxA 62 :PYLQGERFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLE T0293 113 :LIKVVKVPQATLL 1jsxA 116 :NIEPVQSRVEEFP T0293 133 :SEIIYDFCMCN 1jsxA 129 :SEPPFDGVISR T0293 170 :NTGG 1jsxA 140 :AFAS T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSL 1jsxA 144 :LNDMVSWCHHLPGEQGRFYALKGQMPED T0293 221 :LRIQGVPK 1jsxA 172 :EIALLPEE T0293 229 :VTYTEF 1jsxA 185 :VVKLQV T0293 239 :TMRWALAWSFY 1jsxA 195 :GERHLVVIKAN Number of specific fragments extracted= 10 number of extra gaps= 0 total=841 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o9gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1o9gA/merged-good-all-a2m # 1o9gA read from 1o9gA/merged-good-all-a2m # found chain 1o9gA in training set T0293 12 :RALTCT 1o9gA 11 :MDSSDL T0293 22 :DFGLSIDIPLER 1o9gA 17 :ACGVVLHSAPGY T0293 36 :PTVPLR 1o9gA 29 :PAFPVR T0293 43 :NYIHWVEDLI 1o9gA 35 :LATEIFQRAL T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNG 1o9gA 45 :ARLPGDGPVTLWDPCCGSGYLLTVLGLLHRR T0293 86 :WYFLATEVDDMCFNYA 1o9gA 78 :RQVIASDVDPAPLELA T0293 102 :KKNVEQNN 1o9gA 135 :RERLTAEG T0293 110 :LS 1o9gA 145 :LP T0293 114 :IKVVKVPQ 1o9gA 147 :CAIRTADV T0293 122 :ATLLMDALKE 1o9gA 157 :PRALSAVLAG T0293 135 :IIYDFCMCNPPFFA 1o9gA 167 :SAPDVVLTDLPYGE T0293 150 :QLEAKGVNS 1o9gA 181 :RTHWEGQVP T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLG 1o9gA 190 :GQPVAGLLRSLASALPAHAVIAVTDR T0293 211 :ACSL 1o9gA 216 :SRKI T0293 225 :GVPKVTYTEFCQGRTMRWALAW 1o9gA 220 :PVAPVKALERLKIGTRSAVMVR Number of specific fragments extracted= 15 number of extra gaps= 0 total=856 Number of alignments=79 # 1o9gA read from 1o9gA/merged-good-all-a2m # found chain 1o9gA in training set T0293 21 :EDFGLSIDIPL 1o9gA 5 :RHAVERMDSSD T0293 32 :ERLIPT 1o9gA 20 :VVLHSA T0293 38 :VPLRLNYIHWVEDLIGHQDS 1o9gA 29 :PAFPVRLATEIFQRALARLP T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1o9gA 49 :GDGPVTLWDPCCGSGYLLTVLGLLH T0293 85 :GWYFLATEVDDMCFNYAKKNVEQ 1o9gA 77 :LRQVIASDVDPAPLELAAKNLAL T0293 108 :NN 1o9gA 141 :EG T0293 110 :LS 1o9gA 145 :LP T0293 114 :IKVVKVPQ 1o9gA 147 :CAIRTADV T0293 122 :ATLLMDALK 1o9gA 157 :PRALSAVLA T0293 134 :EIIYDFCMCNPPFFAN 1o9gA 166 :GSAPDVVLTDLPYGER T0293 159 :R 1o9gA 182 :T T0293 163 :RPPPS 1o9gA 183 :HWEGQ T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHD 1o9gA 194 :AGLLRSLASALPAHAVIAVTDRSRKI Number of specific fragments extracted= 13 number of extra gaps= 0 total=869 Number of alignments=80 # 1o9gA read from 1o9gA/merged-good-all-a2m # found chain 1o9gA in training set T0293 35 :IPTVPLRL 1o9gA 28 :YPAFPVRL T0293 44 :YIHWVEDLIGHQ 1o9gA 36 :ATEIFQRALARL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1o9gA 48 :PGDGPVTLWDPCCGSGYLLTVLGLLH T0293 87 :YFLATEVDDMCFNYAKKNVEQNN 1o9gA 79 :QVIASDVDPAPLELAAKNLALLS T0293 110 :LS 1o9gA 145 :LP T0293 114 :IKVVKVPQATLL 1o9gA 147 :CAIRTADVFDPR T0293 127 :DALKEESEIIYDFCMCNPPFFA 1o9gA 159 :ALSAVLAGSAPDVVLTDLPYGE T0293 159 :RN 1o9gA 181 :RT T0293 170 :NTGGIT 1o9gA 183 :HWEGQV T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCMLGKACSL 1o9gA 189 :PGQPVAGLLRSLASALPAHAVIAVTDRSRKIP T0293 224 :QGVPKVT 1o9gA 222 :APVKALE T0293 233 :EFCQGRTMRWAL 1o9gA 229 :RLKIGTRSAVMV Number of specific fragments extracted= 12 number of extra gaps= 0 total=881 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aqjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aqjA expands to /projects/compbio/data/pdb/1aqj.pdb.gz 1aqjA:# T0293 read from 1aqjA/merged-good-all-a2m # 1aqjA read from 1aqjA/merged-good-all-a2m # adding 1aqjA to template set # found chain 1aqjA in template set Warning: unaligning (T0293)L42 because first residue in template chain is (1aqjA)V21 Warning: unaligning (T0293)E152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1aqjA)A124 T0293 43 :NY 1aqjA 22 :ET T0293 45 :IHWVEDLI 1aqjA 25 :PEVVDFMV T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATL 1aqjA 33 :SLAEAPRGGRVLEPACAHGPFLRAFREAH T0293 84 :NGWYFLATEVDD 1aqjA 63 :TGYRFVGVEIDP T0293 109 :NLSDLIKVVKVP 1aqjA 78 :DLPPWAEGILAD T0293 125 :L 1aqjA 90 :F T0293 129 :LKEESEIIYDFCMCNPPF 1aqjA 91 :LLWEPGEAFDLILGNPPY T0293 153 :AKGVNSRNPRRPPPSSV 1aqjA 125 :VKDLYKKAFSTWKGKYN T0293 186 :FVKRIIHDSLQLGKRLRWYSCMLGKAC 1aqjA 142 :LYGAFLEKAVRLLKPGGVLVFVVPATW T0293 213 :SLAPLKEELRIQGVPKVTYTEFC 1aqjA 173 :DFALLREFLAREGKTSVYYLGEV T0293 236 :QGRTMRWALAWSFYD 1aqjA 198 :QKKVSAVVIRFQKSG Number of specific fragments extracted= 11 number of extra gaps= 0 total=892 Number of alignments=82 # 1aqjA read from 1aqjA/merged-good-all-a2m # found chain 1aqjA in template set Warning: unaligning (T0293)L42 because first residue in template chain is (1aqjA)V21 Warning: unaligning (T0293)A148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1aqjA)A124 T0293 43 :NYIHWVEDLIGHQDS 1aqjA 22 :ETPPEVVDFMVSLAE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1aqjA 37 :APRGGRVLEPACAHGPFLRAFREAHG T0293 85 :GWYFLATEVDDM 1aqjA 64 :GYRFVGVEIDPK T0293 107 :QNNLSDLIKVVKVPQATLLM 1aqjA 76 :ALDLPPWAEGILADFLLWEP T0293 134 :EIIYDFCMCNPPF 1aqjA 96 :GEAFDLILGNPPY T0293 149 :NQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLG 1aqjA 125 :VKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDF T0293 215 :APLKEELRIQGVPKVTYTE 1aqjA 175 :ALLREFLAREGKTSVYYLG T0293 234 :FCQGRTMRWALAWSFYD 1aqjA 196 :FPQKKVSAVVIRFQKSG Number of specific fragments extracted= 8 number of extra gaps= 0 total=900 Number of alignments=83 # 1aqjA read from 1aqjA/merged-good-all-a2m # found chain 1aqjA in template set Warning: unaligning (T0293)N149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1aqjA)A124 Warning: unaligning (T0293)P165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1aqjA)A124 T0293 46 :HWVEDLIGHQ 1aqjA 26 :EVVDFMVSLA T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1aqjA 36 :EAPRGGRVLEPACAHGPFLRAFREAH T0293 84 :NGWYFLATEVDD 1aqjA 63 :TGYRFVGVEIDP T0293 107 :QNNLSDLIKVVKVPQATLL 1aqjA 76 :ALDLPPWAEGILADFLLWE T0293 133 :SEIIYDFCMCNPPFFA 1aqjA 95 :PGEAFDLILGNPPYGI T0293 166 :PSSVNTGGITE 1aqjA 134 :STWKGKYNLYG T0293 189 :RIIHDSLQLGKRLRWYSCMLGKA 1aqjA 145 :AFLEKAVRLLKPGGVLVFVVPAT T0293 212 :CSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFY 1aqjA 172 :EDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=908 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m6yA expands to /projects/compbio/data/pdb/1m6y.pdb.gz 1m6yA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 94, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 1m6yA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1m6yA/merged-good-all-a2m # 1m6yA read from 1m6yA/merged-good-all-a2m # adding 1m6yA to template set # found chain 1m6yA in template set T0293 34 :LIP 1m6yA 8 :HIP T0293 42 :L 1m6yA 11 :V T0293 47 :WVEDLI 1m6yA 12 :MVREVI T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVE 1m6yA 18 :EFLKPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLK T0293 109 :NLSDLIKVVKVPQAT 1m6yA 70 :EFSDRVSLFKVSYRE T0293 125 :LMDALKEESEIIYDFCMCNPP 1m6yA 85 :ADFLLKTLGIEKVDGILMDLG T0293 147 :FA 1m6yA 106 :VS T0293 151 :LEAKGVNSRNPR 1m6yA 108 :TYQLKGENRGFT T0293 164 :PPPSSVN 1m6yA 120 :FEREEPL T0293 171 :TGGITEIMAE 1m6yA 208 :FQAIRIYVNR T0293 182 :G 1m6yA 218 :E T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRI 1m6yA 219 :LENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRN T0293 226 :VPKVTYT 1m6yA 259 :SKKLRIL T0293 233 :EFCQGRTMRWALAW 1m6yA 280 :NPRARSGRLRAAER Number of specific fragments extracted= 14 number of extra gaps= 0 total=922 Number of alignments=85 # 1m6yA read from 1m6yA/merged-good-all-a2m # found chain 1m6yA in template set Warning: unaligning (T0293)S247 because last residue in template chain is (1m6yA)I294 T0293 37 :TVPLRLNYIHWVEDLIG 1m6yA 5 :SQRHIPVMVREVIEFLK T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNN 1m6yA 22 :PEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFS T0293 112 :DLIKVVKVPQATL 1m6yA 73 :DRVSLFKVSYREA T0293 126 :MDALKEESEIIYDFCMCNP 1m6yA 86 :DFLLKTLGIEKVDGILMDL T0293 147 :FANQLEAKGVNSRNPRRPPPS 1m6yA 105 :GVSTYQLKGENRGFTFEREEP T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKRL 1m6yA 223 :KEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETF T0293 202 :RWYSCMLGKACSLAPLKE 1m6yA 262 :LRILTEKPVRPSEEEIRE T0293 233 :EFCQGRTMRWALAW 1m6yA 280 :NPRARSGRLRAAER Number of specific fragments extracted= 8 number of extra gaps= 0 total=930 Number of alignments=86 # 1m6yA read from 1m6yA/merged-good-all-a2m # found chain 1m6yA in template set T0293 43 :NYIHWVEDL 1m6yA 12 :MVREVIEFL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVE 1m6yA 21 :KPEDEKIILDCTVGEGGHSRAILEHCPGCRIIGIDVDSEVLRIAEEKLK T0293 109 :NLSDLIKVVKVPQATLL 1m6yA 70 :EFSDRVSLFKVSYREAD T0293 127 :DALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPP 1m6yA 87 :FLLKTLGIEKVDGILMDLGVSTYQLKGENRGFTFEREEP T0293 176 :EIM 1m6yA 213 :IYV T0293 181 :GGELEFVKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRI 1m6yA 216 :NRELENLKEFLKKAEDLLNPGGRIVVISFHSLEDRIVKETFRN Number of specific fragments extracted= 6 number of extra gaps= 0 total=936 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1ne2A/merged-good-all-a2m # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0293)V38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)Y27 Warning: unaligning (T0293)F146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 Warning: unaligning (T0293)K154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)D125 Warning: unaligning (T0293)K228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)R182 Warning: unaligning (T0293)V229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)R182 T0293 39 :PLRLNYIHWV 1ne2A 28 :PTDASTAAYF T0293 51 :LIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1ne2A 38 :LIEIYNDGNIGGRSVIDAGTGNGILACGSYLL T0293 85 :G 1ne2A 70 :G T0293 86 :WYFLATEVDDMCFNYAKKN 1ne2A 72 :ESVTAFDIDPDAIETAKRN T0293 110 :LSD 1ne2A 91 :CGG T0293 114 :IKVVKVP 1ne2A 94 :VNFMVAD T0293 125 :L 1ne2A 101 :V T0293 127 :DALKE 1ne2A 102 :SEISG T0293 136 :IYDFCMCNPP 1ne2A 107 :KYDTWIMNPP T0293 192 :HDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQ 1ne2A 126 :RAFIDKAFETSMWIYSIGNAKARDFLRREFSAR T0293 225 :GVP 1ne2A 172 :PRI T0293 236 :QGRTMRWALAWSFY 1ne2A 183 :ARIEAVIFGVRNHS Number of specific fragments extracted= 12 number of extra gaps= 1 total=948 Number of alignments=88 # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0293)D28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)Y27 Warning: unaligning (T0293)V38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)Y27 Warning: unaligning (T0293)F146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 Warning: unaligning (T0293)S167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)D125 T0293 39 :PLRLNYIHWVEDLIGH 1ne2A 28 :PTDASTAAYFLIEIYN T0293 57 :SDKSTLRRGIDIGTGASCIYPLLGAT 1ne2A 44 :DGNIGGRSVIDAGTGNGILACGSYLL T0293 84 :NGWYFLATEVDDMCFNYAKKN 1ne2A 70 :GAESVTAFDIDPDAIETAKRN T0293 110 :LSD 1ne2A 91 :CGG T0293 114 :IKVVKVPQATL 1ne2A 94 :VNFMVADVSEI T0293 134 :EIIYDFCMCNPP 1ne2A 105 :SGKYDTWIMNPP T0293 168 :SVNTGGITEIMA 1ne2A 126 :RAFIDKAFETSM T0293 183 :ELEFVKRIIHD 1ne2A 138 :WIYSIGNAKAR T0293 215 :APLKEELRIQ 1ne2A 149 :DFLRREFSAR T0293 238 :RTMRWALAWSFY 1ne2A 161 :VFREEKVYITVP Number of specific fragments extracted= 10 number of extra gaps= 0 total=958 Number of alignments=89 # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0293)L25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)Y27 Warning: unaligning (T0293)L34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)Y27 Warning: unaligning (T0293)F146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 Warning: unaligning (T0293)K154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)D125 Warning: unaligning (T0293)V229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)R182 Warning: unaligning (T0293)T230 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)R182 T0293 11 :VRALTCTLLREDFG 1ne2A 4 :KNDLEIRLQKLQQQ T0293 35 :IPTVPLRLNYIHWVEDL 1ne2A 28 :PTDASTAAYFLIEIYND T0293 58 :DKSTLRRGIDIGTGASCIYPL 1ne2A 45 :GNIGGRSVIDAGTGNGILACG T0293 80 :GATLNGWYFLATEVDDMCFNYAKKNV 1ne2A 66 :SYLLGAESVTAFDIDPDAIETAKRNC T0293 112 :DLIKVVKVPQATLL 1ne2A 92 :GGVNFMVADVSEIS T0293 135 :IIYDFCMCNPP 1ne2A 106 :GKYDTWIMNPP T0293 184 :L 1ne2A 126 :R T0293 189 :RIIHDSLQL 1ne2A 127 :AFIDKAFET T0293 201 :LRWYSCMLGKAC 1ne2A 136 :SMWIYSIGNAKA T0293 214 :LAPLKEELRIQ 1ne2A 148 :RDFLRREFSAR T0293 225 :GVPK 1ne2A 171 :VPRI T0293 237 :GRTMRWALAWSFYD 1ne2A 183 :ARIEAVIFGVRNHS Number of specific fragments extracted= 12 number of extra gaps= 1 total=970 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2avnA expands to /projects/compbio/data/pdb/2avn.pdb.gz 2avnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 161, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2avnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1025, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2avnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2avnA Skipped atom 1905, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1911, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1913, because occupancy 0.500 <= existing 0.500 in 2avnA # T0293 read from 2avnA/merged-good-all-a2m # 2avnA read from 2avnA/merged-good-all-a2m # adding 2avnA to template set # found chain 2avnA in template set Warning: unaligning (T0293)V169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0293)N170 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 T0293 44 :YIHWVEDLIG 2avnA 28 :YHRLIGSFLE T0293 55 :QDSD 2avnA 38 :EYLK T0293 61 :TLRRGIDIGTGASCIYPLLGAT 2avnA 42 :NPCRVLDLGGGTGKWSLFLQER T0293 85 :GWYFLATEVDDMCFNYAKKN 2avnA 64 :GFEVVLVDPSKEMLEVAREK T0293 109 :NLSD 2avnA 84 :GVKN T0293 116 :VVKVP 2avnA 88 :VVEAK T0293 125 :LMD 2avnA 93 :AED T0293 130 :KEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSS 2avnA 96 :LPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDG T0293 171 :T 2avnA 146 :F T0293 174 :ITEIMAEGG 2avnA 147 :LQQMIEKDA T0293 184 :L 2avnA 156 :W T0293 189 :RIIHDSLQLG 2avnA 157 :DQITRFLKTQ T0293 199 :K 2avnA 191 :E T0293 202 :RWYSCMLG 2avnA 192 :GFETVDIR T0293 210 :KACS 2avnA 204 :MEYP T0293 214 :LAPLKEELRIQ 2avnA 215 :EETIFRLEQEL T0293 225 :GV 2avnA 227 :RD T0293 232 :TEFCQGRTMRWALAWSF 2avnA 229 :RNIIWKADHIFFVLKKK Number of specific fragments extracted= 18 number of extra gaps= 1 total=988 Number of alignments=91 # 2avnA read from 2avnA/merged-good-all-a2m # found chain 2avnA in template set Warning: unaligning (T0293)E183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0293)L184 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 Warning: unaligning (T0293)Y249 because last residue in template chain is (2avnA)R246 T0293 31 :LERLI 2avnA 17 :DSMYE T0293 39 :PLRLNYIHWVEDLIGHQD 2avnA 22 :TPKWKLYHRLIGSFLEEY T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 2avnA 40 :LKNPCRVLDLGGGTGKWSLFLQER T0293 85 :GWYFLATEVDDMCFNYAKKN 2avnA 64 :GFEVVLVDPSKEMLEVAREK T0293 109 :NLSD 2avnA 84 :GVKN T0293 116 :VVKVPQATLLMD 2avnA 88 :VVEAKAEDLPFP T0293 134 :EIIYDFCMC 2avnA 100 :SGAFEAVLA T0293 157 :NSRNPRRPPPSSVNTGGITEIMAEGG 2avnA 109 :LGDVLSYVENKDKAFSEIRRVLVPDG T0293 185 :EF 2avnA 137 :IA T0293 214 :LAPLKEELRIQ 2avnA 215 :EETIFRLEQEL T0293 232 :TEFCQGRTMRWALAWSF 2avnA 229 :RNIIWKADHIFFVLKKK Number of specific fragments extracted= 11 number of extra gaps= 1 total=999 Number of alignments=92 # 2avnA read from 2avnA/merged-good-all-a2m # found chain 2avnA in template set Warning: unaligning (T0293)W203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0293)Y204 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 T0293 10 :AVRALTCTLLREDFGL 2avnA 5 :SWEFYDRIARAYDSMY T0293 37 :TVPLRLNYIHWVEDLIGHQ 2avnA 21 :ETPKWKLYHRLIGSFLEEY T0293 59 :KSTLRRGIDIGTGASCIYPLLGA 2avnA 40 :LKNPCRVLDLGGGTGKWSLFLQE T0293 84 :NGWYFLATEVDDMCFNYAKKN 2avnA 63 :RGFEVVLVDPSKEMLEVAREK T0293 109 :NLS 2avnA 84 :GVK T0293 115 :KVVKVPQATLL 2avnA 87 :NVVEAKAEDLP T0293 132 :ESEIIYDFCMCN 2avnA 98 :FPSGAFEAVLAL T0293 172 :GG 2avnA 110 :GD T0293 175 :TEIMAEG 2avnA 112 :VLSYVEN T0293 187 :VKRIIHDSLQLGKRLR 2avnA 119 :KDKAFSEIRRVLVPDG T0293 205 :SCMLG 2avnA 137 :IATVD T0293 213 :SLAPLKEELRIQGV 2avnA 142 :NFYTFLQQMIEKDA Number of specific fragments extracted= 12 number of extra gaps= 1 total=1011 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nv8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nv8A expands to /projects/compbio/data/pdb/1nv8.pdb.gz 1nv8A:Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1786, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1788, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1790, because occupancy 0.500 <= existing 0.500 in 1nv8A # T0293 read from 1nv8A/merged-good-all-a2m # 1nv8A read from 1nv8A/merged-good-all-a2m # adding 1nv8A to template set # found chain 1nv8A in template set Warning: unaligning (T0293)A148 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)S203 Warning: unaligning (T0293)N149 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)S203 Warning: unaligning (T0293)E180 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)D224 Warning: unaligning (T0293)G181 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)D224 Warning: unaligning (T0293)G209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nv8A)E249 Warning: unaligning (T0293)A211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nv8A)E249 T0293 3 :LNFKDPEAVRALTCTLL 1nv8A 68 :ELVEKRASGYPLHYILG T0293 20 :REDFGLSIDIPLERLIP 1nv8A 86 :KEFMGLSFLVEEGVFVP T0293 41 :RLNYIHWVEDLI 1nv8A 103 :RPETEELVELAL T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATL 1nv8A 115 :ELIRKYGIKTVADIGTGSGAIGVSVAKFS T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 1nv8A 144 :DAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEP T0293 129 :LKEESE 1nv8A 184 :FKEKFA T0293 136 :IYDFCMCNPPFF 1nv8A 190 :SIEMILSNPPYV T0293 150 :Q 1nv8A 204 :S T0293 163 :RPPPSSVN 1nv8A 205 :AHLPKDVL T0293 171 :TGG 1nv8A 220 :FGG T0293 182 :G 1nv8A 225 :G T0293 184 :LEFVKRIIHD 1nv8A 226 :LDFYREFFGR T0293 198 :GK 1nv8A 236 :YD T0293 200 :RLRWYSCML 1nv8A 239 :SGKIVLMEI T0293 212 :CSLAPLK 1nv8A 250 :DQVEELK T0293 224 :QGVPKVTYTEFCQGRTMRWALAW 1nv8A 257 :KIVSDTVFLKDSAGKYRFLLLNR Number of specific fragments extracted= 16 number of extra gaps= 3 total=1027 Number of alignments=94 # 1nv8A read from 1nv8A/merged-good-all-a2m # found chain 1nv8A in template set Warning: unaligning (T0293)A148 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)S203 Warning: unaligning (T0293)N149 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)S203 Warning: unaligning (T0293)I190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nv8A)E249 Warning: unaligning (T0293)I191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nv8A)E249 T0293 10 :AVRALTCTLL 1nv8A 75 :SGYPLHYILG T0293 20 :REDFGLSIDIPLERLIPT 1nv8A 86 :KEFMGLSFLVEEGVFVPR T0293 39 :PLRLNYIHWVEDLIGHQDSD 1nv8A 104 :PETEELVELALELIRKYGIK T0293 64 :RGIDIGTGASCIYPLLGATL 1nv8A 124 :TVADIGTGSGAIGVSVAKFS T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEES 1nv8A 144 :DAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIE T0293 139 :FCMCNPPFF 1nv8A 193 :MILSNPPYV T0293 150 :Q 1nv8A 204 :S T0293 158 :SRNPRRPPP 1nv8A 205 :AHLPKDVLF T0293 168 :SVNTGGITEIMAEGGELEFVKR 1nv8A 226 :LDFYREFFGRYDTSGKIVLMEI T0293 192 :HDSLQLGKR 1nv8A 250 :DQVEELKKI T0293 226 :VPKVTYTEFCQGRTMRWALAWS 1nv8A 259 :VSDTVFLKDSAGKYRFLLLNRR Number of specific fragments extracted= 11 number of extra gaps= 2 total=1038 Number of alignments=95 # 1nv8A read from 1nv8A/merged-good-all-a2m # found chain 1nv8A in template set Warning: unaligning (T0293)A148 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)S203 Warning: unaligning (T0293)N149 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)S203 Warning: unaligning (T0293)G181 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)D224 Warning: unaligning (T0293)G182 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)D224 Warning: unaligning (T0293)G209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nv8A)E249 Warning: unaligning (T0293)K210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nv8A)E249 T0293 13 :ALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIG 1nv8A 79 :LHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRK T0293 60 :STLRRGIDIGTGASCIYPLLGA 1nv8A 120 :YGIKTVADIGTGSGAIGVSVAK T0293 83 :LNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1nv8A 142 :FSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPF T0293 131 :EESEIIYDFCMCNPPFF 1nv8A 185 :KEKFASIEMILSNPPYV T0293 150 :QL 1nv8A 204 :SA T0293 164 :PPPSSVNTGGITEIMAE 1nv8A 206 :HLPKDVLFEPPEALFGG T0293 183 :ELEFVKRIIHD 1nv8A 225 :GLDFYREFFGR T0293 199 :KRLRWYSCML 1nv8A 238 :TSGKIVLMEI T0293 211 :ACSLAP 1nv8A 250 :DQVEEL T0293 223 :IQGVPKVTYTEFCQGRTMRWAL 1nv8A 256 :KKIVSDTVFLKDSAGKYRFLLL Number of specific fragments extracted= 10 number of extra gaps= 3 total=1048 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1dA expands to /projects/compbio/data/pdb/1h1d.pdb.gz 1h1dA:# T0293 read from 1h1dA/merged-good-all-a2m # 1h1dA read from 1h1dA/merged-good-all-a2m # adding 1h1dA to template set # found chain 1h1dA in template set Warning: unaligning (T0293)Y249 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1dA)S216 Warning: unaligning (T0293)D250 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h1dA)S216 T0293 60 :STLRRGIDIGTGASCIYPLLGATL 1h1dA 57 :YSPSLVLELGAYCGYSAVRMARLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCNP 1h1dA 82 :PGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDH T0293 146 :FFANQLEAKGVNSR 1h1dA 143 :WKDRYLPDTLLLEK T0293 161 :PRRPPPSSVNT 1h1dA 157 :CGLLRKGTVLL T0293 172 :GGIT 1h1dA 169 :DNVI T0293 188 :KRIIHDSLQLGKRLRWYSCMLGKA 1h1dA 173 :VPGTPDFLAYVRGSSSFECTHYSS T0293 231 :YTEFCQGRTMRWALAWSF 1h1dA 197 :YLEYMKVVDGLEKAIYQG Number of specific fragments extracted= 7 number of extra gaps= 1 total=1055 Number of alignments=97 # 1h1dA read from 1h1dA/merged-good-all-a2m # found chain 1h1dA in template set T0293 42 :LNYIHWVEDLIGHQDSD 1h1dA 19 :PGDPQSVLEAIDTYCTQ T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1h1dA 56 :EYSPSLVLELGAYCGYSAVRMARLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCN 1h1dA 82 :PGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLD T0293 163 :RPPPS 1h1dA 142 :HWKDR T0293 168 :SVNTGGITEI 1h1dA 148 :LPDTLLLEKC T0293 178 :MAEGGELEF 1h1dA 160 :LRKGTVLLA T0293 214 :LAPLKEELRIQG 1h1dA 176 :TPDFLAYVRGSS T0293 226 :VPKVTYTEFCQGRTMRWALAWSFYD 1h1dA 191 :CTHYSSYLEYMKVVDGLEKAIYQGP Number of specific fragments extracted= 8 number of extra gaps= 0 total=1063 Number of alignments=98 # 1h1dA read from 1h1dA/merged-good-all-a2m # found chain 1h1dA in template set T0293 6 :KDPEAVRALTCTLLREDFGLS 1h1dA 20 :GDPQSVLEAIDTYCTQKEWAM T0293 41 :RLNYIHWVEDLIG 1h1dA 43 :GDAKGQIMDAVIR T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1h1dA 56 :EYSPSLVLELGAYCGYSAVRMARLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKEESEIIYDFCMCN 1h1dA 82 :PGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLD T0293 156 :VNSRN 1h1dA 142 :HWKDR T0293 187 :VKRIIHDSLQL 1h1dA 147 :YLPDTLLLEKC T0293 198 :GKRLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTEF 1h1dA 160 :LRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSS T0293 235 :CQGRTMRWALAWS 1h1dA 200 :YMKVVDGLEKAIY Number of specific fragments extracted= 8 number of extra gaps= 0 total=1071 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1fp2A/merged-good-all-a2m # 1fp2A read from 1fp2A/merged-good-all-a2m # found chain 1fp2A in training set T0293 41 :RLNYIHWVEDLIGHQDSD 1fp2A 157 :NPEYNTSFNDAMASDSKL T0293 60 :STLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMC 1fp2A 187 :DGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVV T0293 108 :NNLS 1fp2A 225 :ENLS T0293 112 :DLIKVVKVP 1fp2A 231 :NNLTYVGGD T0293 125 :LMD 1fp2A 240 :MFT T0293 131 :EES 1fp2A 243 :SIP T0293 136 :IYDFCMCNPPFFAN 1fp2A 246 :NADAVLLKYILHNW T0293 151 :LEAKGVNSRNPRRPPPSSVN 1fp2A 262 :KDCLRILKKCKEAVTNDGKR T0293 171 :TGG 1fp2A 291 :IDK T0293 180 :EGGELE 1fp2A 294 :KKDENQ T0293 187 :VKRIIHDSLQLGKRLR 1fp2A 300 :VTQIKLLMDVNMACLN T0293 209 :GKACSLAPLKEELRIQGVPKVTYTEFCQ 1fp2A 316 :GKERNEEEWKKLFIEAGFQHYKISPLTG T0293 238 :RTMRWALA 1fp2A 344 :FLSLIEIY Number of specific fragments extracted= 13 number of extra gaps= 0 total=1084 Number of alignments=100 # 1fp2A read from 1fp2A/merged-good-all-a2m # found chain 1fp2A in training set T0293 45 :IHWVEDLIGHQDSD 1fp2A 68 :IGNVRRLMRYLAHN T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEV 1fp2A 186 :FDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDR T0293 95 :DMCF 1fp2A 221 :PQVV T0293 108 :NNLS 1fp2A 225 :ENLS T0293 112 :DLIKVVKVP 1fp2A 231 :NNLTYVGGD T0293 125 :LMDAL 1fp2A 240 :MFTSI T0293 135 :IIYDFCMC 1fp2A 245 :PNADAVLL T0293 158 :SRNPRRPPPS 1fp2A 253 :KYILHNWTDK T0293 168 :SVNTGGITEIMAEG 1fp2A 265 :LRILKKCKEAVTND T0293 182 :GELEF 1fp2A 282 :GKVTI T0293 187 :VKR 1fp2A 290 :VID T0293 190 :IIHDSLQLGK 1fp2A 296 :DENQVTQIKL T0293 200 :RLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTEFCQGRTMRWAL 1fp2A 307 :MDVNMACLNGKERNEEEWKKLFIEAGFQHYKISPLTGFLSLIEIY Number of specific fragments extracted= 13 number of extra gaps= 0 total=1097 Number of alignments=101 # 1fp2A read from 1fp2A/merged-good-all-a2m # found chain 1fp2A in training set T0293 7 :DPEAVRALTCTLLRE 1fp2A 157 :NPEYNTSFNDAMASD T0293 44 :YIHWVEDLIG 1fp2A 172 :SKLINLALRD T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDM 1fp2A 182 :CDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQV T0293 105 :VEQNNLSDLIKVVKVPQATLL 1fp2A 224 :VENLSGSNNLTYVGGDMFTSI T0293 135 :IIYDFCMCN 1fp2A 245 :PNADAVLLK T0293 166 :PSSVNT 1fp2A 254 :YILHNW T0293 183 :ELEFVKRIIHDSLQLGK 1fp2A 260 :TDKDCLRILKKCKEAVT T0293 200 :RLRWYSCML 1fp2A 280 :KRGKVTIID T0293 209 :GKACSLAPLKEELRIQGVPKVTYTEFCQG 1fp2A 316 :GKERNEEEWKKLFIEAGFQHYKISPLTGF T0293 241 :RWALAW 1fp2A 345 :LSLIEI Number of specific fragments extracted= 10 number of extra gaps= 0 total=1107 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kpgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kpgA expands to /projects/compbio/data/pdb/1kpg.pdb.gz 1kpgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1kpgA/merged-good-all-a2m # 1kpgA read from 1kpgA/merged-good-all-a2m # adding 1kpgA to template set # found chain 1kpgA in template set T0293 38 :VPLRLNY 1kpgA 37 :YFERDDM T0293 45 :IHWVEDLI 1kpgA 50 :IAKIDLAL T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATL 1kpgA 58 :GKLGLQPGMTLLDVGCGWGATMMRAVEKY T0293 85 :GWYFLATEVDDMCFNYAKKNVE 1kpgA 87 :DVNVVGLTLSKNQANHVQQLVA T0293 109 :NLSD 1kpgA 109 :NSEN T0293 114 :IKVVKVP 1kpgA 116 :KRVLLAG T0293 125 :LMD 1kpgA 123 :WEQ T0293 129 :LKE 1kpgA 126 :FDE T0293 136 :IYDFCMCNPPF 1kpgA 129 :PVDRIVSIGAF T0293 148 :ANQ 1kpgA 140 :EHF T0293 151 :LEAKGVNSRNPRRPPPSSVN 1kpgA 145 :ERYDAFFSLAHRLLPADGVM T0293 172 :GGITEIMAEGG 1kpgA 171 :GLHPKEIHERG T0293 183 :ELEFVKRIIHDSLQLGKRLRW 1kpgA 184 :MSFTFARFLKFIVTEIFPGGR T0293 211 :ACSLAPLKEELRIQGV 1kpgA 205 :LPSIPMVQECASANGF T0293 230 :TYTE 1kpgA 221 :TVTR Number of specific fragments extracted= 15 number of extra gaps= 0 total=1122 Number of alignments=103 # 1kpgA read from 1kpgA/merged-good-all-a2m # found chain 1kpgA in template set T0293 32 :ERLIPTVPLRLNYIHWVEDLIGHQDS 1kpgA 36 :AYFERDDMTLQEAQIAKIDLALGKLG T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1kpgA 62 :LQPGMTLLDVGCGWGATMMRAVEKY T0293 85 :GWYFLATEVDDMCFNYAKKN 1kpgA 87 :DVNVVGLTLSKNQANHVQQL T0293 107 :QNNLS 1kpgA 107 :VANSE T0293 112 :D 1kpgA 115 :S T0293 114 :IKVVKVPQATL 1kpgA 116 :KRVLLAGWEQF T0293 134 :EIIYDFCMC 1kpgA 127 :DEPVDRIVS T0293 158 :SRNPRRPPPS 1kpgA 136 :IGAFEHFGHE T0293 168 :SVNTGGITEIMAEGGELEF 1kpgA 148 :DAFFSLAHRLLPADGVMLL T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVPKVTYTEF 1kpgA 181 :GLPMSFTFARFLKFIVTEIFPGGRLPSIPMVQECASANGFTVTRVQSL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1132 Number of alignments=104 # 1kpgA read from 1kpgA/merged-good-all-a2m # found chain 1kpgA in template set T0293 38 :VPLRLNYIHWVEDLIGHQ 1kpgA 43 :MTLQEAQIAKIDLALGKL T0293 58 :DKSTLRRGIDIGTGASCIYPL 1kpgA 61 :GLQPGMTLLDVGCGWGATMMR T0293 80 :GATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1kpgA 82 :AVEKYDVNVVGLTLSKNQANHVQQLVANSENLRSKRVLLAGWEQFD T0293 135 :IIYDFCMCN 1kpgA 128 :EPVDRIVSI T0293 173 :GITEIMAEGG 1kpgA 137 :GAFEHFGHER T0293 187 :VKRIIHDSLQLGKRLRWYSCML 1kpgA 147 :YDAFFSLAHRLLPADGVMLLHT T0293 209 :GKACSLAPLKEEL 1kpgA 180 :RGLPMSFTFARFL Number of specific fragments extracted= 7 number of extra gaps= 0 total=1139 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d2gA expands to /projects/compbio/data/pdb/1d2g.pdb.gz 1d2gA:# T0293 read from 1d2gA/merged-good-all-a2m # 1d2gA read from 1d2gA/merged-good-all-a2m # adding 1d2gA to template set # found chain 1d2gA in template set T0293 38 :VPLRLNYIHWVEDLI 1d2gA 38 :RSRTAEYKAWLLGLL T0293 55 :QDS 1d2gA 53 :RQH T0293 61 :TLRRGIDIGTGASCIYPLLGAT 1d2gA 56 :GCHRVLDVACGTGVDSIMLVEE T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1d2gA 78 :GFSVTSVDASDKMLKYALKERWNRRKE T0293 112 :DLIKVVKVP 1d2gA 108 :DKWVIEEAN T0293 125 :LMDALKEES 1d2gA 117 :WLTLDKDVP T0293 134 :EIIYDFCMCNP 1d2gA 127 :GDGFDAVICLG T0293 145 :PFFANQ 1d2gA 139 :SFAHLP T0293 151 :LEAKGVNSRNPRRPPPSSVN 1d2gA 151 :SEHRLALKNIASMVRPGGLL T0293 171 :TGG 1d2gA 226 :GAG T0293 180 :EGGE 1d2gA 229 :RDGA T0293 199 :KRLRWYSCMLG 1d2gA 233 :PGFSKFRLSYY T0293 211 :ACSLAPLKEELRIQGVPKVTY 1d2gA 244 :PHCLASFTELVQEAFGGRCQH T0293 233 :EFCQG 1d2gA 272 :PYRPG T0293 238 :RTMRWALAWS 1d2gA 282 :CYFIHVLKKT Number of specific fragments extracted= 15 number of extra gaps= 0 total=1154 Number of alignments=106 # 1d2gA read from 1d2gA/merged-good-all-a2m # found chain 1d2gA in template set T0293 26 :SIDIPLERLIPT 1d2gA 10 :LGVAAEGIPDQY T0293 38 :VPLRLNYIHWVEDLIGHQ 1d2gA 38 :RSRTAEYKAWLLGLLRQH T0293 61 :TLRRGIDIGTGASCIYPLLGAT 1d2gA 56 :GCHRVLDVACGTGVDSIMLVEE T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1d2gA 78 :GFSVTSVDASDKMLKYALKERWNRRKE T0293 112 :D 1d2gA 109 :K T0293 114 :IKVVKVPQATL 1d2gA 110 :WVIEEANWLTL T0293 126 :MDALKE 1d2gA 121 :DKDVPA T0293 134 :EIIYDFCMC 1d2gA 127 :GDGFDAVIC T0293 157 :NSRNPRRPPPS 1d2gA 136 :LGNSFAHLPDS T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKR 1d2gA 154 :RLALKNIASMVRPGGLLVIDHKNYDYILSTGCA T0293 207 :MLG 1d2gA 187 :PPG T0293 210 :KACS 1d2gA 194 :YKSD T0293 214 :LAPLKEELRIQ 1d2gA 247 :LASFTELVQEA T0293 225 :GVPK 1d2gA 259 :GGRC T0293 229 :VTY 1d2gA 264 :HSV T0293 232 :TEFCQGRTMRWALAWSFY 1d2gA 274 :RPGQAYVPCYFIHVLKKT Number of specific fragments extracted= 16 number of extra gaps= 0 total=1170 Number of alignments=107 # 1d2gA read from 1d2gA/merged-good-all-a2m # found chain 1d2gA in template set T0293 10 :AVRALTCTLLREDFGLS 1d2gA 25 :EAARVWQLYIGDTRSRT T0293 42 :LNYIHWVEDLIG 1d2gA 42 :AEYKAWLLGLLR T0293 59 :KSTLRRGIDIGTGASCIYPLLGA 1d2gA 54 :QHGCHRVLDVACGTGVDSIMLVE T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1d2gA 77 :EGFSVTSVDASDKMLKYALKERWNRRKE T0293 112 :DLIKVVKVPQATLL 1d2gA 108 :DKWVIEEANWLTLD T0293 127 :DA 1d2gA 122 :KD T0293 131 :EESEIIYDFCMCN 1d2gA 124 :VPAGDGFDAVICL T0293 171 :TGGITEIMAEGGELEFVKRIIHDSLQLGKRLRWYSCMLG 1d2gA 137 :GNSFAHLPDSKGDQSEHRLALKNIASMVRPGGLLVIDHK T0293 216 :PLKEELRIQGVP 1d2gA 176 :NYDYILSTGCAP T0293 228 :KVTYTEFCQGRTMRWALA 1d2gA 201 :DITTSVLTVNNKAHMVTL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1180 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3tA/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/T0293/2b3tA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0293/2b3tA/merged-good-all-a2m.gz for input Trying 2b3tA/merged-good-all-a2m Error: Couldn't open file 2b3tA/merged-good-all-a2m or 2b3tA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1sqgA/merged-good-all-a2m # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0293 30 :PLERL 1sqgA 216 :PVHAL T0293 36 :PTVPLRL 1sqgA 221 :PGFEDGW T0293 44 :YIHWVEDLI 1sqgA 231 :QDASAQGCM T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLS 1sqgA 240 :TWLAPQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMK T0293 114 :IKVVKVP 1sqgA 297 :ATVKQGD T0293 125 :LMDALKEESEIIYDFCMCNPPFFANQ 1sqgA 304 :GRYPSQWCGEQQFDRILLDAPCSATG T0293 151 :LEAKGVNSRN 1sqgA 333 :RHPDIKWLRR T0293 171 :TGGITEI 1sqgA 343 :DRDIPEL T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLG 1sqgA 350 :AQLQSEILDAIWPHLKTGGTLVYATC T0293 210 :KACSLAPLKEELRI 1sqgA 379 :PEENSLQIKAFLQR T0293 226 :VPKVTYTEFCQGRT 1sqgA 393 :TADAELCETGTPEQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=1191 Number of alignments=109 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0293 29 :IPLERLIPT 1sqgA 139 :SDARYLHPS T0293 47 :WVEDLIGHQDSD 1sqgA 148 :WLLKRLQKAYPE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLS 1sqgA 244 :PQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMK T0293 114 :IKVVKVPQATL 1sqgA 297 :ATVKQGDGRYP T0293 126 :MDALK 1sqgA 308 :SQWCG T0293 134 :EIIYDFCMCNPPFFA 1sqgA 313 :EQQFDRILLDAPCSA T0293 158 :SRNPRRPPPS 1sqgA 328 :TGVIRRHPDI T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDS 1sqgA 354 :SEILDAIWPHLKTGGTLVYATCSVLPE T0293 195 :LQLGKRL 1sqgA 383 :SLQIKAF Number of specific fragments extracted= 9 number of extra gaps= 0 total=1200 Number of alignments=110 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0293 30 :PLERLIPTVPLRLNYIHWV 1sqgA 224 :EDGWVTVQDASAQGCMTWL T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLS 1sqgA 243 :APQNGEHILDLCAAPGGKTTHILEVAPEAQVVAVDIDEQRLSRVYDNLKRLGMK T0293 114 :IKVVKVPQATLL 1sqgA 297 :ATVKQGDGRYPS T0293 130 :KEESEIIYDFCMCN 1sqgA 309 :QWCGEQQFDRILLD T0293 161 :PRRPPPSSVNTGGITEIMAEGGE 1sqgA 323 :APCSATGVIRRHPDIKWLRRDRD T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLG 1sqgA 350 :AQLQSEILDAIWPHLKTGGTLVYATC T0293 210 :KACSLAPLKEELRI 1sqgA 379 :PEENSLQIKAFLQR Number of specific fragments extracted= 7 number of extra gaps= 0 total=1207 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ve3A expands to /projects/compbio/data/pdb/1ve3.pdb.gz 1ve3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1ve3A/merged-good-all-a2m # 1ve3A read from 1ve3A/merged-good-all-a2m # adding 1ve3A to template set # found chain 1ve3A in template set T0293 40 :LRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1ve3A 17 :NSQEYRSRIETLEPLLMKYMKKRGKVLDLACGVGGFSFLLEDY T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ve3A 60 :GFEVVGVDISEDMIRKAREYAKSRESN T0293 114 :IKVVKVP 1ve3A 87 :VEFIVGD T0293 125 :LMD 1ve3A 94 :ARK T0293 130 :KEESEIIYDFCMCNPP 1ve3A 97 :LSFEDKTFDYVIFIDS T0293 147 :FANQ 1ve3A 113 :IVHF T0293 151 :LEAKGVNSRNPRRPPPSSVN 1ve3A 119 :LELNQVFKEVRRVLKPSGKF T0293 202 :RWYSC 1ve3A 187 :FRVRF T0293 209 :G 1ve3A 192 :N T0293 211 :ACSLAPLKEELRIQ 1ve3A 193 :VWGKTGVELLAKLY T0293 229 :VTYT 1ve3A 207 :FTKE T0293 233 :EFCQGRTMRWALAW 1ve3A 213 :EKVGNYSYLTVYNP Number of specific fragments extracted= 12 number of extra gaps= 0 total=1219 Number of alignments=112 # 1ve3A read from 1ve3A/merged-good-all-a2m # found chain 1ve3A in template set Warning: unaligning (T0293)R200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ve3A)I164 Warning: unaligning (T0293)C212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ve3A)I164 T0293 37 :TVPLRLNYIHWVEDLIGHQ 1ve3A 17 :NSQEYRSRIETLEPLLMKY T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1ve3A 36 :MKKRGKVLDLACGVGGFSFLLEDY T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 1ve3A 60 :GFEVVGVDISEDMIRKAREYAKSRESN T0293 114 :IKVVKVPQATLLMD 1ve3A 87 :VEFIVGDARKLSFE T0293 134 :EIIYDFCMC 1ve3A 101 :DKTFDYVIF T0293 158 :SRNPRRPPPS 1ve3A 110 :IDSIVHFEPL T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGK 1ve3A 122 :NQVFKEVRRVLKPSGKFIMYFTDLRELLPRLK T0293 213 :S 1ve3A 165 :S T0293 214 :LAPLKEELRIQ 1ve3A 196 :KTGVELLAKLY T0293 229 :VTYTEFCQGRTMRWALAW 1ve3A 209 :KEAEEKVGNYSYLTVYNP Number of specific fragments extracted= 10 number of extra gaps= 0 total=1229 Number of alignments=113 # 1ve3A read from 1ve3A/merged-good-all-a2m # found chain 1ve3A in template set Warning: unaligning (T0293)A215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ve3A)I164 Warning: unaligning (T0293)V226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ve3A)I164 T0293 40 :LRLNYIHWVEDLIGH 1ve3A 20 :EYRSRIETLEPLLMK T0293 58 :DKSTLRRGIDIGTGASCIYPLLGA 1ve3A 35 :YMKKRGKVLDLACGVGGFSFLLED T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1ve3A 59 :YGFEVVGVDISEDMIRKAREYAKSRESN T0293 114 :IKVVKVPQATLL 1ve3A 87 :VEFIVGDARKLS T0293 132 :ESEIIYDFCMCN 1ve3A 99 :FEDKTFDYVIFI T0293 166 :PSSVNT 1ve3A 111 :DSIVHF T0293 183 :ELEFVKRIIHDSLQLGKRLRWYSCMLG 1ve3A 117 :EPLELNQVFKEVRRVLKPSGKFIMYFT T0293 210 :KACSL 1ve3A 149 :LPRLK T0293 227 :PKVTY 1ve3A 165 :SKVIP T0293 234 :F 1ve3A 170 :D T0293 236 :QGRTMRWA 1ve3A 171 :QEERTVVI Number of specific fragments extracted= 11 number of extra gaps= 0 total=1240 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gh1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gh1A expands to /projects/compbio/data/pdb/2gh1.pdb.gz 2gh1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 2gh1A/merged-good-all-a2m # 2gh1A read from 2gh1A/merged-good-all-a2m # adding 2gh1A to template set # found chain 2gh1A in template set T0293 45 :IHWVEDLIG 2gh1A 24 :DDYVSFLVN T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNG 2gh1A 33 :TVWKITKPVHIVDYGCGYGYLGLVLMPLLPE T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLS 2gh1A 65 :SKYTGIDSGETLLAEARELFRLLPYD T0293 114 :IKVVKVP 2gh1A 91 :SEFLEGD T0293 125 :LMD 2gh1A 98 :ATE T0293 130 :KEESE 2gh1A 101 :IELND T0293 136 :IYDFCMCNP 2gh1A 106 :KYDIAICHA T0293 146 :FFANQLEAKGVNSRNPRRPPPSSVN 2gh1A 115 :FLLHMTTPETMLQKMIHSVKKGGKI T0293 173 :GITEIMA 2gh1A 159 :KQSEFIQ T0293 184 :LEFVKRIIHDSLQLGKRLR 2gh1A 166 :LGVLQKLFESDTQRNGKDG T0293 212 :CSLAPLKEELRIQGVPKVTYT 2gh1A 185 :NIGMKIPIYLSELGVKNIECR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1251 Number of alignments=115 # 2gh1A read from 2gh1A/merged-good-all-a2m # found chain 2gh1A in template set T0293 45 :IHWVEDLIGH 2gh1A 24 :DDYVSFLVNT T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATLN 2gh1A 34 :VWKITKPVHIVDYGCGYGYLGLVLMPLLP T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 2gh1A 64 :GSKYTGIDSGETLLAEARELFRLLPYD T0293 114 :IKVVKVPQATLLM 2gh1A 91 :SEFLEGDATEIEL T0293 134 :EIIYDFCMC 2gh1A 104 :NDKYDIAIC T0293 158 :SRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDS 2gh1A 113 :HAFLLHMTTPETMLQKMIHSVKKGGKIICFEPHWISN T0293 195 :LQLGKRLRWYSCMLGKACSL 2gh1A 166 :LGVLQKLFESDTQRNGKDGN T0293 215 :APLKEELRIQGVPKVTYTE 2gh1A 188 :MKIPIYLSELGVKNIECRV Number of specific fragments extracted= 8 number of extra gaps= 0 total=1259 Number of alignments=116 # 2gh1A read from 2gh1A/merged-good-all-a2m # found chain 2gh1A in template set T0293 45 :IHWVEDLIGH 2gh1A 24 :DDYVSFLVNT T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATL 2gh1A 34 :VWKITKPVHIVDYGCGYGYLGLVLMPLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 2gh1A 63 :EGSKYTGIDSGETLLAEARELFRLLPYD T0293 114 :IKVVKVPQATLL 2gh1A 91 :SEFLEGDATEIE T0293 133 :SEIIYDFCMCN 2gh1A 103 :LNDKYDIAICH T0293 166 :PSSVNTGG 2gh1A 114 :AFLLHMTT T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGK 2gh1A 122 :PETMLQKMIHSVKKGGKIICFEPH Number of specific fragments extracted= 7 number of extra gaps= 0 total=1266 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vlmA expands to /projects/compbio/data/pdb/1vlm.pdb.gz 1vlmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1022, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 1vlmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1vlmA/merged-good-all-a2m # 1vlmA read from 1vlmA/merged-good-all-a2m # adding 1vlmA to template set # found chain 1vlmA in template set Warning: unaligning (T0293)R200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 Warning: unaligning (T0293)R202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vlmA)V146 Warning: unaligning (T0293)C212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)S155 Warning: unaligning (T0293)S213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)S155 T0293 45 :IHWVEDLIGHQD 1vlmA 23 :YLSELQAVKCLL T0293 61 :TLRRGIDIGTGASCIYPLL 1vlmA 35 :PEGRGVEIGVGTGRFAVPL T0293 85 :GW 1vlmA 54 :KI T0293 89 :LATEVDDMCFNYAKKN 1vlmA 57 :IGVEPSERMAEIARKR T0293 109 :N 1vlmA 73 :G T0293 114 :IKVVKVP 1vlmA 74 :VFVLKGT T0293 125 :LMD 1vlmA 81 :AEN T0293 130 :KEESEIIYDFCMCNPP 1vlmA 84 :LPLKDESFDFALMVTT T0293 147 :FANQLEAKGVNSRNPRRPPPSSVN 1vlmA 100 :ICFVDDPERALKEAYRILKKGGYL T0293 171 :TGG 1vlmA 129 :DRE T0293 184 :L 1vlmA 132 :S T0293 189 :RIIHDSLQLGK 1vlmA 133 :FLGREYEKNKE T0293 203 :W 1vlmA 147 :F T0293 209 :GKA 1vlmA 151 :ARF T0293 214 :LAPLKEELRIQGVPKVTY 1vlmA 156 :TEELMDLMRKAGFEEFKV T0293 233 :EFC 1vlmA 182 :SEL T0293 237 :GRTMRWALAW 1vlmA 195 :GEGAFVVIRG Number of specific fragments extracted= 17 number of extra gaps= 1 total=1283 Number of alignments=118 # 1vlmA read from 1vlmA/merged-good-all-a2m # found chain 1vlmA in template set Warning: unaligning (T0293)V187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)V128 Warning: unaligning (T0293)W203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 Warning: unaligning (T0293)S205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vlmA)V146 Warning: unaligning (T0293)C212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)S155 Warning: unaligning (T0293)S213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)S155 T0293 42 :LNYIHWVEDLIGHQ 1vlmA 20 :RFAYLSELQAVKCL T0293 59 :KSTL 1vlmA 34 :LPEG T0293 64 :RGIDIGTGASCIYPLLG 1vlmA 38 :RGVEIGVGTGRFAVPLK T0293 83 :LN 1vlmA 55 :IK T0293 89 :LATEVDDMCFNYAKKN 1vlmA 57 :IGVEPSERMAEIARKR T0293 112 :D 1vlmA 73 :G T0293 114 :IKVVKVPQATLLMD 1vlmA 74 :VFVLKGTAENLPLK T0293 134 :EIIYDFCMC 1vlmA 88 :DESFDFALM T0293 158 :SRNPRRPPPSSVNTGGITEIMAEGGELEF 1vlmA 97 :VTTICFVDDPERALKEAYRILKKGGYLIV T0293 188 :KRIIHDSLQLGKRLR 1vlmA 129 :DRESFLGREYEKNKE T0293 206 :CMLG 1vlmA 147 :FYKN T0293 210 :KA 1vlmA 152 :RF T0293 214 :LAPLKEELRIQGVPKVTY 1vlmA 156 :TEELMDLMRKAGFEEFKV Number of specific fragments extracted= 13 number of extra gaps= 2 total=1296 Number of alignments=119 # 1vlmA read from 1vlmA/merged-good-all-a2m # found chain 1vlmA in template set Warning: unaligning (T0293)L208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)V128 Warning: unaligning (T0293)G209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)V128 Warning: unaligning (T0293)V226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 Warning: unaligning (T0293)K228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vlmA)V146 T0293 12 :RALTCTLLREDF 1vlmA 10 :NEYERWFLVHRF T0293 40 :LRLNYIHWVEDL 1vlmA 22 :AYLSELQAVKCL T0293 60 :STLRRGIDIGTGASCI 1vlmA 34 :LPEGRGVEIGVGTGRF T0293 80 :GATLN 1vlmA 50 :AVPLK T0293 89 :LATEVDDMCFNYAKK 1vlmA 57 :IGVEPSERMAEIARK T0293 112 :DLIKVVKVPQATLL 1vlmA 72 :RGVFVLKGTAENLP T0293 132 :ESEIIYDFCMCN 1vlmA 86 :LKDESFDFALMV T0293 166 :PSSVNTGG 1vlmA 98 :TTICFVDD T0293 187 :VKRIIHDSLQLGKRLRWYSCM 1vlmA 106 :PERALKEAYRILKKGGYLIVG T0293 211 :ACSLAPLKEELRIQG 1vlmA 129 :DRESFLGREYEKNKE Number of specific fragments extracted= 10 number of extra gaps= 1 total=1306 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2as0A expands to /projects/compbio/data/pdb/2as0.pdb.gz 2as0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 2as0A/merged-good-all-a2m # 2as0A read from 2as0A/merged-good-all-a2m # adding 2as0A to template set # found chain 2as0A in template set T0293 16 :CTLLREDFGLSIDIPLERLIPTVPLRL 2as0A 178 :YRTIIQEGRAKFIVDMRGQKTGFFLDQ T0293 45 :IHWVEDLI 2as0A 205 :RENRLALE T0293 55 :QDSD 2as0A 213 :KWVQ T0293 61 :TLRRGIDIGTGASCIYPLLGAT 2as0A 217 :PGDRVLDVFTYTGGFAIHAAIA T0293 85 :GW 2as0A 239 :GA T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 2as0A 242 :EVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGS T0293 125 :LMDALKEE 2as0A 276 :AFEEMEKL T0293 133 :SEIIYDFCMCNPP 2as0A 286 :KGEKFDIVVLDPP T0293 146 :FFANQLEAKGV 2as0A 300 :FVQHEKDLKAG T0293 184 :LEFVKRIIHDSLQLGKRLRWYS 2as0A 311 :LRAYFNVNFAGLNLVKDGGILV T0293 206 :CMLGKACSLAPLKEELRI 2as0A 334 :CSCSQHVDLQMFKDMIIA T0293 224 :QG 2as0A 356 :AG T0293 226 :VPKVTYT 2as0A 363 :LEPYRTQ T0293 233 :EFC 2as0A 371 :PDH T0293 236 :QGRTMRWALAWSFY 2as0A 382 :TEYLKCLFLYVEDM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1321 Number of alignments=121 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0293 26 :SIDIPLERL 2as0A 30 :EGDIKPGDI T0293 35 :IPTVPLRLNYIHWVEDLIGHQDSD 2as0A 68 :DKDVEINKDLFKRRIKKANEYRKK T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 2as0A 215 :VQPGDRVLDVFTYTGGFAIHAAIA T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKE 2as0A 239 :GADEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQKK T0293 134 :EIIYDFCMCNPP 2as0A 287 :GEKFDIVVLDPP T0293 146 :FF 2as0A 300 :FV T0293 162 :RRPPPSSVNTGGITEIM 2as0A 302 :QHEKDLKAGLRAYFNVN T0293 179 :AEGGELEFVKRI 2as0A 326 :KDGGILVTCSCS T0293 210 :KACSLAPLKEELRIQ 2as0A 338 :QHVDLQMFKDMIIAA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1330 Number of alignments=122 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0293 24 :GLSIDIPLERLIPTVPLRL 2as0A 186 :RAKFIVDMRGQKTGFFLDQ T0293 49 :EDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 2as0A 205 :RENRLALEKWVQPGDRVLDVFTYTGGFAIHAAIA T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDAL 2as0A 239 :GADEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQ T0293 132 :ESEIIYDFCMCNPPFFANQLEAKG 2as0A 285 :KKGEKFDIVVLDPPAFVQHEKDLK T0293 182 :GELEFVKRIIHDSLQLGKRLRWYSCML 2as0A 309 :AGLRAYFNVNFAGLNLVKDGGILVTCS T0293 209 :GKACSLAPLKEELRI 2as0A 337 :SQHVDLQMFKDMIIA Number of specific fragments extracted= 6 number of extra gaps= 0 total=1336 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l3iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l3iA expands to /projects/compbio/data/pdb/1l3i.pdb.gz 1l3iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1l3iA/merged-good-all-a2m # 1l3iA read from 1l3iA/merged-good-all-a2m # adding 1l3iA to template set # found chain 1l3iA in template set T0293 29 :IPLERLI 1l3iA 2 :IPDDEFI T0293 36 :PTVPLRLNYI 1l3iA 11 :PSVPGPTAME T0293 47 :WVEDLI 1l3iA 21 :VRCLIM T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLN 1l3iA 27 :CLAEPGKNDVAVDVGCGTGGVTLELAGRVR T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 1l3iA 57 :RVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGD T0293 125 :LMDALKEES 1l3iA 91 :APEALCKIP T0293 136 :IYDFCMCNPP 1l3iA 100 :DIDIAVVGGS T0293 180 :EGG 1l3iA 110 :GGE T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVP 1l3iA 113 :LQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFD T0293 229 :VT 1l3iA 154 :VN T0293 239 :TMRWALAWS 1l3iA 156 :ITELNIARG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1347 Number of alignments=124 # 1l3iA read from 1l3iA/merged-good-all-a2m # found chain 1l3iA in template set T0293 29 :IPLERLIPT 1l3iA 2 :IPDDEFIKN T0293 38 :VPLRLNYIHWVEDLIG 1l3iA 15 :GPTAMEVRCLIMCLAE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1l3iA 31 :PGKNDVAVDVGCGTGGVTLELAGRVR T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMD 1l3iA 57 :RVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEALCK T0293 134 :EIIYDFCMC 1l3iA 98 :IPDIDIAVV T0293 158 :SRNP 1l3iA 107 :GGSG T0293 165 :PPSSVNTGGITEIMAEGGELEFVKRIIHDS 1l3iA 111 :GELQEILRIIKDKLKPGGRIIVTAILLETK T0293 215 :APLKEELRIQGVPK 1l3iA 141 :FEAMECLRDLGFDV T0293 239 :TMRWALAW 1l3iA 156 :ITELNIAR Number of specific fragments extracted= 9 number of extra gaps= 0 total=1356 Number of alignments=125 # 1l3iA read from 1l3iA/merged-good-all-a2m # found chain 1l3iA in template set T0293 29 :IPLERLIPTVP 1l3iA 2 :IPDDEFIKNPS T0293 40 :LRLNYIHWVEDLI 1l3iA 17 :TAMEVRCLIMCLA T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1l3iA 30 :EPGKNDVAVDVGCGTGGVTLELAGRV T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 1l3iA 57 :RVYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGDAPEAL T0293 132 :ESEIIYDFCMCN 1l3iA 96 :CKIPDIDIAVVG T0293 178 :MAEGG 1l3iA 108 :GSGGE T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVP 1l3iA 113 :LQEILRIIKDKLKPGGRIIVTAILLETKFEAMECLRDLGFD T0293 228 :KVTYTEFCQGRTMR 1l3iA 160 :NIARGRALDRGTMM T0293 242 :WALAW 1l3iA 179 :VALIY Number of specific fragments extracted= 9 number of extra gaps= 0 total=1365 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fytA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fytA expands to /projects/compbio/data/pdb/2fyt.pdb.gz 2fytA:Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 688, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2418, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2424, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2426, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2428, because occupancy 0.500 <= existing 0.500 in 2fytA # T0293 read from 2fytA/merged-good-all-a2m # 2fytA read from 2fytA/merged-good-all-a2m # adding 2fytA to template set # found chain 2fytA in template set T0293 41 :RLNYIHWVEDLIG 2fytA 253 :DKIRTESYRDFIY T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGAT 2fytA 266 :QNPHIFKDKVVLDVGCGTGILSMFAAKA T0293 84 :NGWYFLATEVDDM 2fytA 294 :GAKKVLGVDQSEI T0293 98 :FNYAKKNVEQNNLSDLIKVVKVP 2fytA 307 :LYQAMDIIRLNKLEDTITLIKGK T0293 125 :LMD 2fytA 330 :IEE T0293 130 :KEESEIIYDFCMCNP 2fytA 333 :VHLPVEKVDVIISEW T0293 146 :FFAN 2fytA 348 :MGYF T0293 169 :VNTGG 2fytA 352 :LLFES T0293 183 :ELEFVKRIIHDS 2fytA 357 :MLDSVLYAKNKY T0293 198 :GKRLRWYS 2fytA 369 :LAKGGSVY T0293 206 :CMLGKACSLAPLKEE 2fytA 382 :ISLVAVSDVNKHADR T0293 229 :VTYTEFCQGRT 2fytA 397 :IAFWDDVYGFK Number of specific fragments extracted= 12 number of extra gaps= 0 total=1377 Number of alignments=127 # 2fytA read from 2fytA/merged-good-all-a2m # found chain 2fytA in template set Warning: unaligning (T0293)F5 because first residue in template chain is (2fytA)F238 Warning: unaligning (T0293)K6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fytA)S239 Warning: unaligning (T0293)E233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fytA)V510 Warning: unaligning (T0293)F234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fytA)V510 T0293 7 :DPEAVRALTCTLLR 2fytA 240 :SYGHYGIHEEMLKD T0293 42 :LNYIHWVEDLIGH 2fytA 254 :KIRTESYRDFIYQ T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGAT 2fytA 267 :NPHIFKDKVVLDVGCGTGILSMFAAKA T0293 84 :NGWYFLATEVD 2fytA 294 :GAKKVLGVDQS T0293 96 :MCFNYAKKNVEQNNLSDLIKVVKVPQATLLMD 2fytA 305 :EILYQAMDIIRLNKLEDTITLIKGKIEEVHLP T0293 134 :EIIYDFCMC 2fytA 337 :VEKVDVIIS T0293 155 :GVNSRNPRRPPPSSVNTGGITEIMAEGGELEF 2fytA 346 :EWMGYFLLFESMLDSVLYAKNKYLAKGGSVYP T0293 187 :VKRIIHD 2fytA 386 :AVSDVNK T0293 197 :LGKRLRWYSCMLGKACS 2fytA 393 :HADRIAFWDDVYGFKMS T0293 229 :VTYT 2fytA 505 :EKPF T0293 235 :CQGRTMRWALAWSFYD 2fytA 511 :KAGEALKGKVTVHKNK Number of specific fragments extracted= 11 number of extra gaps= 1 total=1388 Number of alignments=128 # 2fytA read from 2fytA/merged-good-all-a2m # found chain 2fytA in template set T0293 42 :LNYIHWVEDLIGHQ 2fytA 254 :KIRTESYRDFIYQN T0293 57 :SDKSTLRRGIDIGTGASCIYPLLG 2fytA 268 :PHIFKDKVVLDVGCGTGILSMFAA T0293 82 :TLNGWYFLATEVDDM 2fytA 292 :KAGAKKVLGVDQSEI T0293 98 :FNYAKKNVEQNNLSDLIKVVKVPQATLL 2fytA 307 :LYQAMDIIRLNKLEDTITLIKGKIEEVH T0293 132 :ESEIIYDFCMCN 2fytA 335 :LPVEKVDVIISE T0293 163 :RPPPSSVNT 2fytA 347 :WMGYFLLFE T0293 173 :G 2fytA 356 :S T0293 186 :FVKRIIHDSLQLGKRLRWYS 2fytA 357 :MLDSVLYAKNKYLAKGGSVY T0293 238 :RTMRWALAWSFY 2fytA 377 :PDICTISLVAVS Number of specific fragments extracted= 9 number of extra gaps= 0 total=1397 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fhpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fhpA expands to /projects/compbio/data/pdb/2fhp.pdb.gz 2fhpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 91, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 297, because occupancy 0.300 <= existing 0.300 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 408, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 513, because occupancy 0.350 <= existing 0.350 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1083, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fhpA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fhpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1178, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1180, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1182, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1184, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1186, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1188, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1190, because occupancy 0.400 <= existing 0.600 in 2fhpA Skipped atom 1192, because occupancy 0.400 <= existing 0.600 in 2fhpA # T0293 read from 2fhpA/merged-good-all-a2m # 2fhpA read from 2fhpA/merged-good-all-a2m # adding 2fhpA to template set # found chain 2fhpA in template set Warning: unaligning (T0293)W246 because last residue in template chain is (2fhpA)Q182 T0293 20 :REDFGLSIDIP 2fhpA 6 :GEYGGRRLKAL T0293 36 :PTVPLRLNYIHWVEDLIGHQDSDK 2fhpA 17 :DGDNTRPTTDKVKESIFNMIGPYF T0293 61 :TLRRGIDIGTGASCIYPLLGAT 2fhpA 41 :DGGMALDLYSGSGGLAIEAVSR T0293 85 :G 2fhpA 63 :G T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 2fhpA 65 :DKSICIEKNFAALKVIKENIAITKEPEKFEVRKMD T0293 125 :LMDALKEE 2fhpA 100 :ANRALEQF T0293 133 :SEIIYDFCMCNPPFFA 2fhpA 110 :EKLQFDLVLLDPPYAK T0293 151 :LEAKGV 2fhpA 126 :QEIVSQ T0293 174 :ITEIMAEGG 2fhpA 132 :LEKMLERQL T0293 198 :GKRLRWYSCMLGKACSLA 2fhpA 141 :LTNEAVIVCETDKTVKLP T0293 228 :KVTYT 2fhpA 163 :TLKKT T0293 233 :EFCQGRTMRWALA 2fhpA 169 :ETVYGITQVTIYR Number of specific fragments extracted= 12 number of extra gaps= 0 total=1409 Number of alignments=130 # 2fhpA read from 2fhpA/merged-good-all-a2m # found chain 2fhpA in template set T0293 26 :SIDIPLERLIPT 2fhpA 5 :SGEYGGRRLKAL T0293 38 :VPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 2fhpA 18 :GDNTRPTTDKVKESIFNMIGPYFDGGMALDLYSGSGGLAIEAVSR T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDALKE 2fhpA 63 :GMDKSICIEKNFAALKVIKENIAITKEPEKFEVRKMDANRALEQFYEE T0293 134 :EIIYDFCMCNPPFFA 2fhpA 111 :KLQFDLVLLDPPYAK T0293 165 :PPSSVNTGGITEI 2fhpA 126 :QEIVSQLEKMLER T0293 178 :MAEGGELEFVKR 2fhpA 141 :LTNEAVIVCETD T0293 224 :QGVPK 2fhpA 153 :KTVKL T0293 229 :VTYTEFCQGRTMRWALA 2fhpA 165 :KKTRETVYGITQVTIYR Number of specific fragments extracted= 8 number of extra gaps= 0 total=1417 Number of alignments=131 # 2fhpA read from 2fhpA/merged-good-all-a2m # found chain 2fhpA in template set T0293 41 :RLNYIHWVEDL 2fhpA 26 :DKVKESIFNMI T0293 57 :SDKSTLRRGIDIGTGASCIYPLLGATLNG 2fhpA 37 :GPYFDGGMALDLYSGSGGLAIEAVSRGMD T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLL 2fhpA 66 :KSICIEKNFAALKVIKENIAITKEPEKFEVRKMDANRAL T0293 127 :D 2fhpA 105 :E T0293 129 :LKEESEIIYDFCMCNPPFFA 2fhpA 106 :QFYEEKLQFDLVLLDPPYAK T0293 159 :RN 2fhpA 126 :QE T0293 187 :VKRIIHDSLQL 2fhpA 128 :IVSQLEKMLER T0293 198 :GKRLRWYSCMLGKACSLA 2fhpA 141 :LTNEAVIVCETDKTVKLP T0293 228 :K 2fhpA 159 :E T0293 229 :VTYTEFCQGRTMRWA 2fhpA 166 :KTRETVYGITQVTIY Number of specific fragments extracted= 10 number of extra gaps= 0 total=1427 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xxlA expands to /projects/compbio/data/pdb/1xxl.pdb.gz 1xxlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1xxlA/merged-good-all-a2m # 1xxlA read from 1xxlA/merged-good-all-a2m # adding 1xxlA to template set # found chain 1xxlA in template set Warning: unaligning (T0293)Y44 because first residue in template chain is (1xxlA)H-3 T0293 45 :IHWVEDLI 1xxlA -2 :HHSLGLMI T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLN 1xxlA 6 :KTAECRAEHRVLDIGAGAGHTALAFSPYVQ T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSD 1xxlA 36 :ECIGVDATKEMVEVASSFAQEKGVEN T0293 114 :IKVVKVP 1xxlA 62 :VRFQQGT T0293 125 :LMD 1xxlA 69 :AES T0293 130 :KEESEIIYDFCMCNPP 1xxlA 72 :LPFPDDSFDIITCRYA T0293 147 :FANQLEAKGVNSRNPRRPPPSSVN 1xxlA 88 :AHHFSDVRKAVREVARVLKQDGRF T0293 171 :TGGITEIMAEGG 1xxlA 128 :VNHLNRLRDPSH T0293 190 :IIHDSLQLGKRLRWYSCMLGKA 1xxlA 144 :SLSEWQAMFSANQLAYQDIQKW T0293 217 :LKEELRIQGVP 1xxlA 171 :YDSWIKRGGTP Number of specific fragments extracted= 10 number of extra gaps= 0 total=1437 Number of alignments=133 # 1xxlA read from 1xxlA/merged-good-all-a2m # found chain 1xxlA in template set Warning: unaligning (T0293)R41 because first residue in template chain is (1xxlA)H-3 T0293 42 :LNYIHWVEDLIG 1xxlA -2 :HHSLGLMIKTAE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1xxlA 10 :CRAEHRVLDIGAGAGHTALAFSPYVQ T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSD 1xxlA 36 :ECIGVDATKEMVEVASSFAQEKGVEN T0293 114 :IKVVKVPQATLLMD 1xxlA 62 :VRFQQGTAESLPFP T0293 134 :EIIYDFCMC 1xxlA 76 :DDSFDIITC T0293 158 :SRNPRRPPPSSVNTGGITEIMAEGGELEF 1xxlA 85 :RYAAHHFSDVRKAVREVARVLKQDGRFLL T0293 187 :VKRIIHDSLQLGKRL 1xxlA 117 :YAPEDPVLDEFVNHL T0293 202 :RWYSCMLGKACSLAPLKEELRIQG 1xxlA 133 :RLRDPSHVRESSLSEWQAMFSANQ T0293 238 :RTMRWALAWSF 1xxlA 157 :LAYQDIQKWNL Number of specific fragments extracted= 9 number of extra gaps= 0 total=1446 Number of alignments=134 # 1xxlA read from 1xxlA/merged-good-all-a2m # found chain 1xxlA in template set T0293 45 :IHWVEDLIGHQ 1xxlA -2 :HHSLGLMIKTA T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATL 1xxlA 9 :ECRAEHRVLDIGAGAGHTALAFSPYV T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1xxlA 36 :ECIGVDATKEMVEVASSFAQEKGVE T0293 113 :LIKVVKVPQATLL 1xxlA 61 :NVRFQQGTAESLP T0293 132 :ESEIIYDFCMCN 1xxlA 74 :FPDDSFDIITCR T0293 166 :PSSVNTGG 1xxlA 86 :YAAHHFSD T0293 187 :VKRIIHDSLQLGKRLRWYSCMLGKACSLAPLKEELRI 1xxlA 94 :VRKAVREVARVLKQDGRFLLVDHYAPEDPVLDEFVNH Number of specific fragments extracted= 7 number of extra gaps= 0 total=1453 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0293 read from 1jg1A/merged-good-all-a2m # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set T0293 20 :REDFGLSIDIPLERLIP 1jg1A 59 :YAHIDEPLPIPAGQTVS T0293 44 :YIHWVEDLI 1jg1A 76 :APHMVAIML T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATL 1jg1A 85 :EIANLKPGMNILEVGTGSGWNAALISEIV T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1jg1A 114 :KTDVYTIERIPELVEFAKRNLERAGVKN T0293 114 :IKVVKVP 1jg1A 142 :VHVILGD T0293 125 :LMDALKE 1jg1A 149 :GSKGFPP T0293 134 :EIIYDFCMCNPP 1jg1A 156 :KAPYDVIIVTAG T0293 147 :FANQ 1jg1A 168 :APKI T0293 191 :IHDSLQLGKRLRWYSCMLGKAC 1jg1A 172 :PEPLIEQLKIGGKLIIPVGSYH T0293 237 :GRTMRWALAWSF 1jg1A 194 :LWQELLEVRKTK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1463 Number of alignments=136 # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set Warning: unaligning (T0293)R41 because first residue in template chain is (1jg1A)E14 Warning: unaligning (T0293)L42 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1jg1A)K15 T0293 43 :NYIHWVEDLIGHQDSD 1jg1A 16 :ELYEKWMRTVEMLKAE T0293 59 :KSTLRRGIDIGTGASCIYPLLGATL 1jg1A 89 :LKPGMNILEVGTGSGWNAALISEIV T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1jg1A 114 :KTDVYTIERIPELVEFAKRNLERAGVKN T0293 114 :IKVVKVPQATLLMD 1jg1A 142 :VHVILGDGSKGFPP T0293 134 :EIIYDFCMC 1jg1A 156 :KAPYDVIIV T0293 158 :SRNPRRPPPS 1jg1A 165 :TAGAPKIPEP T0293 174 :ITEIMAEGGELEF 1jg1A 175 :LIEQLKIGGKLII T0293 187 :VK 1jg1A 189 :VG T0293 235 :CQGRTMRWALAWSFYD 1jg1A 191 :SYHLWQELLEVRKTKD Number of specific fragments extracted= 9 number of extra gaps= 0 total=1472 Number of alignments=137 # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set T0293 22 :DFGLSIDIPLERLIPTVPLRLNYIHWV 1jg1A 61 :HIDEPLPIPAGQTVSAPHMVAIMLEIA T0293 58 :DKSTLRRGIDIGTGASCIYPLLGATLNG 1jg1A 88 :NLKPGMNILEVGTGSGWNAALISEIVKT T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1jg1A 116 :DVYTIERIPELVEFAKRNLERAGVK T0293 113 :LIKVVKVPQATLL 1jg1A 141 :NVHVILGDGSKGF T0293 132 :ESEIIYDFCMCN 1jg1A 154 :PPKAPYDVIIVT T0293 159 :RNPRRPP 1jg1A 166 :AGAPKIP T0293 192 :HDSLQLGKRLRWYSCMLGKACSL 1jg1A 173 :EPLIEQLKIGGKLIIPVGSYHLW T0293 227 :PKVTYTEFCQGRTMR 1jg1A 196 :QELLEVRKTKDGIKI Number of specific fragments extracted= 8 number of extra gaps= 0 total=1480 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vq1A/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/T0293/1vq1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0293/1vq1A/merged-good-all-a2m.gz for input Trying 1vq1A/merged-good-all-a2m Error: Couldn't open file 1vq1A/merged-good-all-a2m or 1vq1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6q2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g6q2 expands to /projects/compbio/data/pdb/1g6q.pdb.gz 1g6q2:# T0293 read from 1g6q2/merged-good-all-a2m # 1g6q2 read from 1g6q2/merged-good-all-a2m # adding 1g6q2 to template set # found chain 1g6q2 in template set Warning: unaligning (T0293)T61 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0293)L62 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 Warning: unaligning (T0293)E180 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)E141 Warning: unaligning (T0293)G181 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)E141 T0293 41 :RLNYIHWVEDLIG 1g6q2 39 :DTVRTLSYRNAII T0293 55 :QDSDKS 1g6q2 52 :QNKDLF T0293 63 :RRGIDIGTGASCIYPLLGAT 1g6q2 60 :KIVLDVGCGTGILSMFAAKH T0293 84 :NGWYFLATEVDDM 1g6q2 80 :GAKHVIGVDMSSI T0293 98 :FNYAKKNVEQNNLSDLIKVVKVP 1g6q2 93 :IEMAKELVELNGFSDKITLLRGK T0293 125 :LMD 1g6q2 116 :LED T0293 130 :KEESEIIYDFCMCNP 1g6q2 119 :VHLPFPKVDIIISEW T0293 146 :FFANQ 1g6q2 134 :MGYFL T0293 171 :T 1g6q2 139 :L T0293 182 :GELEFVKRIIHD 1g6q2 142 :SMMDTVLYARDH T0293 197 :LGKRLRWYS 1g6q2 154 :YLVEGGLIF T0293 206 :CMLGKACSLAPLKEELR 1g6q2 168 :IHLAGLEDSQYKDEKLN T0293 231 :YTEFCQGRT 1g6q2 185 :YWQDVYGFD Number of specific fragments extracted= 13 number of extra gaps= 2 total=1493 Number of alignments=139 # 1g6q2 read from 1g6q2/merged-good-all-a2m # found chain 1g6q2 in template set Warning: unaligning (T0293)T61 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0293)L62 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 Warning: unaligning (T0293)R163 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)E141 Warning: unaligning (T0293)P164 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)E141 T0293 42 :LNYIHWVEDLIGHQDS 1g6q2 40 :TVRTLSYRNAIIQNKD T0293 59 :KS 1g6q2 56 :LF T0293 63 :RRGIDIGTGASCIYPLLGAT 1g6q2 60 :KIVLDVGCGTGILSMFAAKH T0293 84 :NGWYFLATEVD 1g6q2 80 :GAKHVIGVDMS T0293 96 :MCFNYAKKNVEQNNLSDLIKVVKVPQATLLMD 1g6q2 91 :SIIEMAKELVELNGFSDKITLLRGKLEDVHLP T0293 134 :EIIYDFCMC 1g6q2 123 :FPKVDIIIS T0293 155 :GVNSRNPR 1g6q2 132 :EWMGYFLL T0293 165 :PPSSVNTGGITEIMAEGGELEF 1g6q2 142 :SMMDTVLYARDHYLVEGGLIFP T0293 187 :VKRI 1g6q2 172 :GLED T0293 194 :SLQLGKRLRWYSCMLGKACS 1g6q2 176 :SQYKDEKLNYWQDVYGFDYS Number of specific fragments extracted= 10 number of extra gaps= 2 total=1503 Number of alignments=140 # 1g6q2 read from 1g6q2/merged-good-all-a2m # found chain 1g6q2 in template set Warning: unaligning (T0293)T61 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0293)L62 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 Warning: unaligning (T0293)E180 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)E141 Warning: unaligning (T0293)G181 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)E141 T0293 42 :LNYIHWVEDLIGHQ 1g6q2 40 :TVRTLSYRNAIIQN T0293 57 :SDKS 1g6q2 54 :KDLF T0293 63 :RRGIDIGTGASCIYPLLG 1g6q2 60 :KIVLDVGCGTGILSMFAA T0293 82 :TLNGWYFLATEVDDM 1g6q2 78 :KHGAKHVIGVDMSSI T0293 98 :FNYAKKNVEQNNLSDLIKVVKVPQATLL 1g6q2 93 :IEMAKELVELNGFSDKITLLRGKLEDVH T0293 132 :ESEIIYDFCMCN 1g6q2 121 :LPFPKVDIIISE T0293 163 :RPP 1g6q2 133 :WMG T0293 176 :EIMA 1g6q2 136 :YFLL T0293 182 :GELEFVK 1g6q2 142 :SMMDTVL T0293 192 :HDSLQLGKRLRWYS 1g6q2 149 :YARDHYLVEGGLIF T0293 239 :TMRWALAWSF 1g6q2 164 :DKCSIHLAGL Number of specific fragments extracted= 11 number of extra gaps= 2 total=1514 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g38A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g38A expands to /projects/compbio/data/pdb/1g38.pdb.gz 1g38A:# T0293 read from 1g38A/merged-good-all-a2m # 1g38A read from 1g38A/merged-good-all-a2m # adding 1g38A to template set # found chain 1g38A in template set T0293 45 :IHWVEDLI 1g38A 25 :PEVVDFMV T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATLNG 1g38A 33 :SLAEAPRGGRVLEPACAHGPFLRAFREAHGT T0293 86 :WYFLATEVDD 1g38A 65 :YRFVGVEIDP T0293 109 :NLSDLIKVVKVP 1g38A 78 :DLPPWAEGILAD T0293 125 :LMD 1g38A 90 :FLL T0293 130 :KE 1g38A 93 :WE T0293 133 :SEIIYDFCMCNPPF 1g38A 95 :PGEAFDLILGNPPY T0293 147 :F 1g38A 111 :V T0293 149 :NQLEAKGVNSRNPRRPPPS 1g38A 121 :VFKAVKDLYKKAFSTWKGK T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLGKAC 1g38A 140 :YNLYGAFLEKAVRLLKPGGVLVFVVPATW T0293 213 :SLAPLKEELRIQGVPKVTYTEFC 1g38A 173 :DFALLREFLAREGKTSVYYLGEV T0293 236 :QGRTMRWALAWSFYD 1g38A 198 :QKKVSAVVIRFQKSG Number of specific fragments extracted= 12 number of extra gaps= 0 total=1526 Number of alignments=142 # 1g38A read from 1g38A/merged-good-all-a2m # found chain 1g38A in template set T0293 43 :NYIHWVEDLIGH 1g38A 22 :ETPPEVVDFMVS T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATLN 1g38A 34 :LAEAPRGGRVLEPACAHGPFLRAFREAHG T0293 85 :GWYFLATEVDDM 1g38A 64 :GYRFVGVEIDPK T0293 107 :QNNLSDLIKVVKVPQATLLM 1g38A 76 :ALDLPPWAEGILADFLLWEP T0293 134 :EIIYDFCMCNPPFFA 1g38A 96 :GEAFDLILGNPPYGI T0293 158 :SRNPRRPPPS 1g38A 111 :VGEASKYPIH T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLG 1g38A 144 :GAFLEKAVRLLKPGGVLVFVVPATWLVLEDF T0293 215 :APLKEELRIQGVPKVTY 1g38A 175 :ALLREFLAREGKTSVYY T0293 232 :TEFCQG 1g38A 193 :GEVFPQ T0293 238 :RTMRWALAWSFYD 1g38A 200 :KVSAVVIRFQKSG Number of specific fragments extracted= 10 number of extra gaps= 0 total=1536 Number of alignments=143 # 1g38A read from 1g38A/merged-good-all-a2m # found chain 1g38A in template set T0293 46 :HWVEDLIGHQDS 1g38A 26 :EVVDFMVSLAEA T0293 60 :STLRRGIDIGTGASCIYPLLGATL 1g38A 38 :PRGGRVLEPACAHGPFLRAFREAH T0293 84 :NGWYFLATEVDD 1g38A 63 :TGYRFVGVEIDP T0293 107 :QNNLSDLIKVVKVPQATLL 1g38A 76 :ALDLPPWAEGILADFLLWE T0293 133 :SEIIYDFCMCNPPFFAN 1g38A 95 :PGEAFDLILGNPPYGIV T0293 156 :VNSRNPR 1g38A 112 :GEASKYP T0293 166 :PSSVNTGGITEIM 1g38A 134 :STWKGKYNLYGAF T0293 191 :IHDSLQLGKRLRWYSCMLGKA 1g38A 147 :LEKAVRLLKPGGVLVFVVPAT T0293 212 :CSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD 1g38A 172 :EDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1545 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wxxA expands to /projects/compbio/data/pdb/1wxx.pdb.gz 1wxxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1wxxA/merged-good-all-a2m # 1wxxA read from 1wxxA/merged-good-all-a2m # adding 1wxxA to template set # found chain 1wxxA in template set T0293 15 :TCTLLREDFGLSIDIPLERLIPTVPL 1wxxA 172 :RVQVQEGRVRYLVDLRAGQKTGAYLD T0293 47 :WVEDLI 1wxxA 198 :QRENRL T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATLN 1wxxA 204 :YMERFRGERALDVFSYAGGFALHLALGFR T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLSD 1wxxA 233 :EVVAVDSSAEALRRAEENARLNGLGN T0293 114 :IKVVKVP 1wxxA 259 :VRVLEAN T0293 125 :LMDALKEE 1wxxA 266 :AFDLLRRL T0293 133 :SEIIYDFCMCNPP 1wxxA 276 :EGERFDLVVLDPP T0293 146 :FFANQLEAKGV 1wxxA 290 :FAKGKKDVERA T0293 184 :LEFVKRIIHDSLQLGKRLRWYSCMLG 1wxxA 301 :YRAYKEVNLRAIKLLKEGGILATASC T0293 210 :KACSLAPLKEELRI 1wxxA 328 :HHMTEPLFYAMVAE T0293 224 :QGVP 1wxxA 346 :AHRL T0293 229 :VTYT 1wxxA 350 :LRVV T0293 243 :AL 1wxxA 354 :EK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1558 Number of alignments=145 # 1wxxA read from 1wxxA/merged-good-all-a2m # found chain 1wxxA in template set T0293 24 :GLSIDIPLERL 1wxxA 15 :SRHLWVFRRDV T0293 38 :VPLRLNYIHWVEDLIGHQDSD 1wxxA 62 :FAPAEDPVAALLENLAQALAR T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1wxxA 207 :RFRGERALDVFSYAGGFALHLALG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSD 1wxxA 231 :FREVVAVDSSAEALRRAEENARLNGLGN T0293 114 :IKVVKVPQATLLMDALKE 1wxxA 259 :VRVLEANAFDLLRRLEKE T0293 134 :EIIYDFCMCNPP 1wxxA 277 :GERFDLVVLDPP T0293 146 :FF 1wxxA 290 :FA T0293 162 :RRPPPSSVNTGGITEIM 1wxxA 292 :KGKKDVERAYRAYKEVN T0293 179 :AEGGELEFVKRIIH 1wxxA 316 :KEGGILATASCSHH T0293 212 :CSLAPLKEELRI 1wxxA 330 :MTEPLFYAMVAE T0293 224 :QGVPK 1wxxA 346 :AHRLL T0293 229 :VTYTEFCQ 1wxxA 353 :VEKRGQPF T0293 237 :GRTMRWALAW 1wxxA 372 :HYLKFAVFQV Number of specific fragments extracted= 13 number of extra gaps= 0 total=1571 Number of alignments=146 # 1wxxA read from 1wxxA/merged-good-all-a2m # found chain 1wxxA in template set T0293 25 :LSIDIPLERLIPTVPLRLNYIHW 1wxxA 182 :YLVDLRAGQKTGAYLDQRENRLY T0293 57 :SDKSTLRRGIDIGTGASCIYPLLGATL 1wxxA 205 :MERFRGERALDVFSYAGGFALHLALGF T0293 87 :YFLATEVDDMCFNYAKKNVEQNNLS 1wxxA 233 :EVVAVDSSAEALRRAEENARLNGLG T0293 113 :LIKVVKVPQATLLMDA 1wxxA 258 :NVRVLEANAFDLLRRL T0293 131 :EESEIIYDFCMCNPPFFANQLEAK 1wxxA 274 :EKEGERFDLVVLDPPAFAKGKKDV T0293 181 :GGELEFVKRIIHDSLQLGKRLRWYSCML 1wxxA 298 :ERAYRAYKEVNLRAIKLLKEGGILATAS T0293 209 :GKACSLAPLKEELRI 1wxxA 327 :SHHMTEPLFYAMVAE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1578 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sg9A/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/T0293/1sg9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0293/1sg9A/merged-good-all-a2m.gz for input Trying 1sg9A/merged-good-all-a2m Error: Couldn't open file 1sg9A/merged-good-all-a2m or 1sg9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kr5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kr5A expands to /projects/compbio/data/pdb/1kr5.pdb.gz 1kr5A:Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1kr5A # T0293 read from 1kr5A/merged-good-all-a2m # 1kr5A read from 1kr5A/merged-good-all-a2m # adding 1kr5A to template set # found chain 1kr5A in template set T0293 13 :ALTCTLL 1kr5A 35 :DRSHYAK T0293 20 :REDFGLSIDIPLERLIP 1kr5A 43 :NPYMDSPQSIGFQATIS T0293 41 :RL 1kr5A 60 :AP T0293 46 :HWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNG 1kr5A 62 :HMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMVGC T0293 86 :WYFLATEVDDMCFNYAKKNVEQNN 1kr5A 103 :GKVIGIDHIKELVDDSVNNVRKDD T0293 112 :DLIKVVKVP 1kr5A 133 :GRVQLVVGD T0293 125 :LMDALKEE 1kr5A 142 :GRMGYAEE T0293 135 :IIYDFCMCNPP 1kr5A 150 :APYDAIHVGAA T0293 147 :FANQL 1kr5A 161 :APVVP T0293 192 :HDSLQLGKRLRWYSCMLGKA 1kr5A 166 :QALIDQLKPGGRLILPVGPA T0293 237 :GRTMRWALAWSFY 1kr5A 186 :GGNQMLEQYDKLQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=1589 Number of alignments=148 # 1kr5A read from 1kr5A/merged-good-all-a2m # found chain 1kr5A in template set T0293 55 :QDSD 1kr5A 34 :TDRS T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLN 1kr5A 75 :LHEGAKALDVGSGSGILTACFARMVG T0293 85 :GWYFLATEVDDMCFNYAKKNVEQ 1kr5A 102 :TGKVIGIDHIKELVDDSVNNVRK T0293 112 :DLIKVVKVPQATLLMD 1kr5A 133 :GRVQLVVGDGRMGYAE T0293 134 :EIIYDFCMC 1kr5A 149 :EAPYDAIHV T0293 158 :SRNPRRPP 1kr5A 158 :GAAAPVVP T0293 172 :GGITEIMAEGGELEF 1kr5A 166 :QALIDQLKPGGRLIL T0293 187 :VKR 1kr5A 182 :VGP T0293 235 :CQGRTMRWALAWSFYD 1kr5A 185 :AGGNQMLEQYDKLQDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=1598 Number of alignments=149 # 1kr5A read from 1kr5A/merged-good-all-a2m # found chain 1kr5A in template set T0293 46 :HWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATL 1kr5A 62 :HMHAYALELLFDQLHEGAKALDVGSGSGILTACFARMV T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 1kr5A 101 :CTGKVIGIDHIKELVDDSVNNVRKDDPT T0293 112 :DLIKVVKVPQATLL 1kr5A 133 :GRVQLVVGDGRMGY T0293 132 :ESEIIYDFCMCNP 1kr5A 147 :AEEAPYDAIHVGA T0293 155 :GVNSRN 1kr5A 160 :AAPVVP T0293 192 :HDSLQLGKRLRWYSCMLGKA 1kr5A 166 :QALIDQLKPGGRLILPVGPA T0293 224 :QGVPKVTYTEFCQGRTM 1kr5A 186 :GGNQMLEQYDKLQDGSI Number of specific fragments extracted= 7 number of extra gaps= 0 total=1605 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l1eA expands to /projects/compbio/data/pdb/1l1e.pdb.gz 1l1eA:# T0293 read from 1l1eA/merged-good-all-a2m # 1l1eA read from 1l1eA/merged-good-all-a2m # adding 1l1eA to template set # found chain 1l1eA in template set Warning: unaligning (T0293)E180 because of BadResidue code BAD_PEPTIDE at template residue (1l1eA)H186 T0293 37 :TVPLRLNY 1l1eA 36 :AYFERDDM T0293 45 :IHWVEDLI 1l1eA 50 :IAKIDLAL T0293 55 :QDSDKSTLRRGIDIGTGASCIYPLLGATL 1l1eA 58 :GKLNLEPGMTLLDIGCGWGATMRRAIEKY T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVP 1l1eA 87 :DVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEG T0293 125 :LMD 1l1eA 123 :WEK T0293 129 :LKE 1l1eA 126 :FDE T0293 136 :IYDFCMCNPPFFANQ 1l1eA 129 :PVDRIVSIGAFEHFG T0293 151 :LEAKGVNSRNPRRPPPSSVN 1l1eA 145 :QRYHHFFEVTHRTLPADGKM T0293 181 :GG 1l1eA 187 :EL T0293 188 :KRIIHDSLQLGKRLRW 1l1eA 189 :VHFTKFILAEIFPGGW T0293 211 :ACSLAPLKEELRIQGV 1l1eA 205 :LPSIPTVHEYAEKVGF T0293 240 :MRWAL 1l1eA 221 :RVTAV Number of specific fragments extracted= 12 number of extra gaps= 1 total=1617 Number of alignments=151 # 1l1eA read from 1l1eA/merged-good-all-a2m # found chain 1l1eA in template set Warning: unaligning (T0293)F23 because first residue in template chain is (1l1eA)Y16 Warning: unaligning (T0293)I191 because of BadResidue code BAD_PEPTIDE in next template residue (1l1eA)H186 Warning: unaligning (T0293)H192 because of BadResidue code BAD_PEPTIDE at template residue (1l1eA)H186 T0293 24 :GLSIDIPLERLIPT 1l1eA 17 :DLSDDFFRLFLDPT T0293 38 :VPLRLNYIHWVEDLIGH 1l1eA 42 :DMTLQEAQIAKIDLALG T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGATL 1l1eA 59 :KLNLEPGMTLLDIGCGWGATMRRAIEKY T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 1l1eA 87 :DVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKF T0293 134 :EIIYDFCMC 1l1eA 127 :DEPVDRIVS T0293 158 :SRNPRRPPPS 1l1eA 136 :IGAFEHFGHQ T0293 168 :SVNTGGITEIMAEGGELEF 1l1eA 148 :HHFFEVTHRTLPADGKMLL T0293 187 :VKRI 1l1eA 181 :GLTL T0293 193 :DSLQLGKRLRWYSCMLGKACSLAPLKEELRIQGVPK 1l1eA 187 :ELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRV Number of specific fragments extracted= 9 number of extra gaps= 1 total=1626 Number of alignments=152 # 1l1eA read from 1l1eA/merged-good-all-a2m # found chain 1l1eA in template set T0293 38 :VPLRLNYIHWVEDLIGHQ 1l1eA 43 :MTLQEAQIAKIDLALGKL T0293 58 :DKSTLRRGIDIGTGASCIYPLLG 1l1eA 61 :NLEPGMTLLDIGCGWGATMRRAI T0293 82 :TLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATL 1l1eA 84 :EKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKF T0293 134 :EIIYDFCMCNPPFFA 1l1eA 127 :DEPVDRIVSIGAFEH T0293 156 :VNSRN 1l1eA 142 :FGHQR T0293 187 :VKRIIHDSLQLGKRLRWYSCML 1l1eA 147 :YHHFFEVTHRTLPADGKMLLHT Number of specific fragments extracted= 6 number of extra gaps= 0 total=1632 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wy7A expands to /projects/compbio/data/pdb/1wy7.pdb.gz 1wy7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0293 read from 1wy7A/merged-good-all-a2m # 1wy7A read from 1wy7A/merged-good-all-a2m # adding 1wy7A to template set # found chain 1wy7A in template set T0293 30 :PLE 1wy7A 22 :KVW T0293 37 :TVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGAT 1wy7A 25 :LEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVE 1wy7A 71 :GAKEVICVEVDKEAVDVLIENLG T0293 109 :NLSDLIKVVKVP 1wy7A 94 :EFKGKFKVFIGD T0293 125 :LMD 1wy7A 106 :VSE T0293 132 :ESE 1wy7A 109 :FNS T0293 136 :IYDFCMCNPPFFA 1wy7A 112 :RVDIVIMNPPFGS T0293 152 :EA 1wy7A 125 :QR T0293 180 :EGGE 1wy7A 127 :KHAD T0293 188 :KRIIHDSLQLGK 1wy7A 131 :RPFLLKAFEISD T0293 203 :WYSCMLG 1wy7A 143 :VVYSIHL T0293 210 :KACSLAPLKEELRIQG 1wy7A 151 :KPEVRRFIEKFSWEHG T0293 229 :VTYT 1wy7A 167 :FVVT T0293 240 :MRWALAWS 1wy7A 171 :HRLTTKIE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1646 Number of alignments=154 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set Warning: unaligning (T0293)T232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy7A)H186 Warning: unaligning (T0293)E233 because of BadResidue code BAD_PEPTIDE in next template residue (1wy7A)K188 Warning: unaligning (T0293)F234 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K188 Warning: unaligning (T0293)C235 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K189 T0293 24 :GL 1wy7A 14 :KL T0293 26 :SIDIPLERLIPT 1wy7A 17 :GFKNPKVWLEQY T0293 39 :PLRLNYIHWVEDLIG 1wy7A 29 :RTPGNAASELLWLAY T0293 56 :DSDKSTLRRGIDIGTGASCIYPLLGAT 1wy7A 44 :SLGDIEGKVVADLGAGTGVLSYGALLL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNN 1wy7A 71 :GAKEVICVEVDKEAVDVLIENLGEFK T0293 112 :DLIKVVKVPQATL 1wy7A 97 :GKFKVFIGDVSEF T0293 134 :EIIYDFCMCNPPFFA 1wy7A 110 :NSRVDIVIMNPPFGS T0293 162 :RRPPPSSVNTGGITEIMA 1wy7A 125 :QRKHADRPFLLKAFEISD T0293 183 :ELEFVKRIIHDSL 1wy7A 143 :VVYSIHLAKPEVR T0293 215 :APLKEELRIQGVPK 1wy7A 156 :RFIEKFSWEHGFVV T0293 236 :QGRTMRWALAWSFY 1wy7A 190 :LERITVDIYRFSKV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1657 Number of alignments=155 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set Warning: unaligning (T0293)P227 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy7A)H186 Warning: unaligning (T0293)F234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy7A)H186 Warning: unaligning (T0293)C235 because of BadResidue code BAD_PEPTIDE in next template residue (1wy7A)K188 Warning: unaligning (T0293)Q236 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K188 Warning: unaligning (T0293)G237 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K189 T0293 41 :RLNYIHWVEDLIGH 1wy7A 32 :GNAASELLWLAYSL T0293 58 :DKSTLRRGIDIGTGASCIYPL 1wy7A 46 :GDIEGKVVADLGAGTGVLSYG T0293 80 :GATLNGWYFLATEVDDMCFNYAKKNVE 1wy7A 67 :ALLLGAKEVICVEVDKEAVDVLIENLG T0293 109 :NLSDLIKVVKVPQATLL 1wy7A 94 :EFKGKFKVFIGDVSEFN T0293 135 :IIYDFCMCNPPFFANQ 1wy7A 111 :SRVDIVIMNPPFGSQR T0293 180 :EGGELE 1wy7A 127 :KHADRP T0293 190 :IIHDSLQLG 1wy7A 133 :FLLKAFEIS T0293 201 :LRWYSCMLGKACSLAPLKEELRIQG 1wy7A 142 :DVVYSIHLAKPEVRRFIEKFSWEHG T0293 226 :V 1wy7A 179 :I T0293 238 :RTMRWALAWSF 1wy7A 190 :LERITVDIYRF Number of specific fragments extracted= 10 number of extra gaps= 0 total=1667 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f8lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f8lA expands to /projects/compbio/data/pdb/2f8l.pdb.gz 2f8lA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 726, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 738, because occupancy 0.350 <= existing 0.350 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1763, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1765, because occupancy 0.500 <= existing 0.500 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1767, because occupancy 0.400 <= existing 0.400 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 2f8lA Skipped atom 1771, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1773, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1775, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1777, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1779, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1781, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1783, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1785, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1787, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1789, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 1791, because occupancy 0.350 <= existing 0.650 in 2f8lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2099, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2101, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2103, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2105, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2107, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2109, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2111, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2113, because occupancy 0.350 <= existing 0.650 in 2f8lA Skipped atom 2115, because occupancy 0.350 <= existing 0.650 in 2f8lA # T0293 read from 2f8lA/merged-good-all-a2m # 2f8lA read from 2f8lA/merged-good-all-a2m # adding 2f8lA to template set # found chain 2f8lA in template set Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8lA)C127 Warning: unaligning (T0293)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)C127 Warning: unaligning (T0293)Q236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f8lA)Q282 Warning: unaligning (T0293)G237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)A283 T0293 29 :IPLERLIP 2f8lA 91 :IQVNHQMT T0293 41 :RLNYIHWVEDLIG 2f8lA 99 :PDSIGFIVAYLLE T0293 55 :QDSDKSTLRRGIDI 2f8lA 112 :KVIQKKKNVSILDP T0293 71 :GASCIYPLLGATL 2f8lA 128 :GTANLLTTVINQL T0293 84 :NG 2f8lA 143 :KG T0293 86 :WYFLATEVDDMCFNYAKKNVEQNNLS 2f8lA 148 :VHASGVDVDDLLISLALVGADLQRQK T0293 114 :IKVVKVP 2f8lA 174 :MTLLHQD T0293 125 :LMD 2f8lA 181 :GLA T0293 131 :EESEIIYDFCMCNPP 2f8lA 184 :NLLVDPVDVVISDLP T0293 147 :FANQLEAKGV 2f8lA 199 :VGYYPDDENA T0293 159 :RNPRRPPPSSVNTGG 2f8lA 209 :KTFELCREEGHSFAH T0293 184 :LEFV 2f8lA 224 :FLFI T0293 192 :HDSLQLGKRLRWYSCMLG 2f8lA 228 :EQGMRYTKPGGYLFFLVP T0293 210 :KACSLAPLKEELRIQ 2f8lA 250 :GTSDFAKVDKFIKKN T0293 229 :VTYT 2f8lA 265 :GHIE T0293 233 :EFC 2f8lA 275 :ETL T0293 238 :RTMRWALAWSFYD 2f8lA 284 :RKSILILEKADVD Number of specific fragments extracted= 17 number of extra gaps= 1 total=1684 Number of alignments=157 # 2f8lA read from 2f8lA/merged-good-all-a2m # found chain 2f8lA in template set Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8lA)C127 Warning: unaligning (T0293)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)C127 Warning: unaligning (T0293)G237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)A283 T0293 21 :EDFGLSIDIPL 2f8lA 85 :KGMKHGIQVNH T0293 33 :RL 2f8lA 96 :QM T0293 40 :LRLNYIHWVEDLIGHQDS 2f8lA 98 :TPDSIGFIVAYLLEKVIQ T0293 59 :KSTLRRGIDI 2f8lA 116 :KKKNVSILDP T0293 71 :GASCIYPLLGATL 2f8lA 128 :GTANLLTTVINQL T0293 85 :GWYFLATEVDDMCFNYAKKNVEQNNLS 2f8lA 147 :DVHASGVDVDDLLISLALVGADLQRQK T0293 114 :IKVVKVP 2f8lA 174 :MTLLHQD T0293 125 :LMDALK 2f8lA 181 :GLANLL T0293 134 :EIIYDFCMCNPP 2f8lA 187 :VDPVDVVISDLP T0293 146 :FFANQLEAK 2f8lA 201 :YYPDDENAK T0293 158 :SRNPRRPPPS 2f8lA 210 :TFELCREEGH T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDS 2f8lA 224 :FLFIEQGMRYTKPGGYLFFLVPDAMFG T0293 211 :ACSLAPLKEELRIQG 2f8lA 251 :TSDFAKVDKFIKKNG T0293 229 :VTYTEFCQ 2f8lA 271 :IKLPETLF T0293 238 :RTMRWALAWSF 2f8lA 284 :RKSILILEKAD Number of specific fragments extracted= 15 number of extra gaps= 2 total=1699 Number of alignments=158 # 2f8lA read from 2f8lA/merged-good-all-a2m # found chain 2f8lA in template set Warning: unaligning (T0293)G69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8lA)C127 Warning: unaligning (T0293)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)C127 Warning: unaligning (T0293)Q236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f8lA)Q282 Warning: unaligning (T0293)R238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f8lA)Q282 Warning: unaligning (T0293)T239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8lA)A283 T0293 5 :FKDPEAVRALTCTLLREDFG 2f8lA 70 :FSNEEIRKGLQLALLKGMKH T0293 28 :DIPLERLIPTVPLRLNYIHWVEDLIG 2f8lA 90 :GIQVNHQMTPDSIGFIVAYLLEKVIQ T0293 59 :KSTLRRGIDI 2f8lA 116 :KKKNVSILDP T0293 71 :GASCIYPLLGATL 2f8lA 128 :GTANLLTTVINQL T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLS 2f8lA 146 :VDVHASGVDVDDLLISLALVGADLQRQK T0293 114 :IKVVKVPQATLL 2f8lA 174 :MTLLHQDGLANL T0293 133 :SEIIYDFCMCNPP 2f8lA 186 :LVDPVDVVISDLP T0293 146 :FFANQLEAKGVNSRN 2f8lA 201 :YYPDDENAKTFELCR T0293 170 :NTGGITEI 2f8lA 216 :EEGHSFAH T0293 188 :KRIIHDSLQLGKRLRWYSCMLGKAC 2f8lA 224 :FLFIEQGMRYTKPGGYLFFLVPDAM T0293 213 :SLAPLKEELRIQGVPKVTYTE 2f8lA 253 :DFAKVDKFIKKNGHIEGIIKL T0293 234 :FC 2f8lA 278 :FK T0293 240 :MRWALAWSFYD 2f8lA 284 :RKSILILEKAD Number of specific fragments extracted= 13 number of extra gaps= 1 total=1712 Number of alignments=159 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0293//projects/compbio/experiments/protein-predict/casp7/T0293/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0293//projects/compbio/experiments/protein-predict/casp7/T0293/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0293/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0293/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)L89.CB) [> 3.7868 = 6.3113 < 8.2046] w=1.0000 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)F139.CB) [> 2.7777 = 4.6294 < 6.0183] w=1.0000 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)C140.CB) [> 4.0978 = 6.8296 < 8.8785] w=1.0000 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)M141.CB) [> 4.3080 = 7.1800 < 9.3340] w=1.0000 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)L89.CB) [> 2.9044 = 4.8407 < 6.2929] w=1.0000 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)F139.CB) [> 4.3874 = 7.3123 < 9.5060] w=1.0000 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)C140.CB) [> 2.9770 = 4.9617 < 6.4502] w=1.0000 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)M141.CB) [> 4.2931 = 7.1552 < 9.3018] w=1.0000 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)L89.CB) [> 4.1627 = 6.9378 < 9.0192] w=1.0000 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)A90.CB) [> 2.6589 = 4.4316 < 5.7611] w=1.0000 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)T91.CB) [> 4.1950 = 6.9917 < 9.0892] w=1.0000 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)M141.CB) [> 2.9998 = 4.9997 < 6.4996] w=1.0000 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)E92.CB) [> 3.0397 = 5.0661 < 6.5859] w=1.0000 to align # Constraint # added constraint: constraint((T0293)A90.CB, (T0293)V116.CB) [> 2.9755 = 4.9591 < 6.4468] w=1.0000 to align # Constraint # added constraint: constraint((T0293)A90.CB, (T0293)V117.CB) [> 4.2761 = 7.1268 < 9.2648] w=1.0000 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)V117.CB) [> 2.9938 = 4.9898 < 6.4867] w=1.0000 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)V119.CB) [> 3.1997 = 5.3328 < 6.9326] w=1.0000 to align # Constraint # added constraint: constraint((T0293)E92.CB, (T0293)K118.CB) [> 3.8135 = 6.3558 < 8.2625] w=1.0000 to align # Constraint # added constraint: constraint((T0293)V93.CB, (T0293)K118.CB) [> 4.1703 = 6.9505 < 9.0356] w=1.0000 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)Y137.CB) [> 3.0357 = 5.0594 < 6.5772] w=0.9935 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)D138.CB) [> 3.6334 = 6.0557 < 7.8724] w=0.9935 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)Y137.CB) [> 2.7845 = 4.6408 < 6.0331] w=0.9935 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)A90.CB) [> 2.8639 = 4.7731 < 6.2050] w=0.9871 to align # Constraint # added constraint: constraint((T0293)A90.CB, (T0293)K115.CB) [> 4.2637 = 7.1061 < 9.2380] w=0.9871 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)K115.CB) [> 3.0547 = 5.0911 < 6.6184] w=0.9871 to align # Constraint # added constraint: constraint((T0293)V93.CB, (T0293)P120.CB) [> 3.1626 = 5.2709 < 6.8522] w=0.9871 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)F88.CB) [> 3.8220 = 6.3700 < 8.2810] w=0.9807 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)F88.CB) [> 3.2186 = 5.3643 < 6.9736] w=0.9807 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)V117.CB) [> 4.0012 = 6.6686 < 8.6692] w=0.9806 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)T91.CB) [> 4.2570 = 7.0950 < 9.2234] w=0.9806 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)F88.CB) [> 3.1293 = 5.2155 < 6.7801] w=0.9742 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)Y76.CB) [> 2.8047 = 4.6745 < 6.0768] w=0.9742 to align # Constraint # added constraint: constraint((T0293)I75.CB, (T0293)M141.CB) [> 3.4906 = 5.8177 < 7.5630] w=0.9742 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)D138.CB) [> 3.1398 = 5.2330 < 6.8029] w=0.9742 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)Y137.CB) [> 3.0362 = 5.0603 < 6.5784] w=0.9742 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)K115.CB) [> 4.3162 = 7.1937 < 9.3518] w=0.9678 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)D138.CB) [> 2.5756 = 4.2926 < 5.5804] w=0.9677 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)Y87.CB) [> 2.9513 = 4.9189 < 6.3945] w=0.9613 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)Y87.CB) [> 3.9906 = 6.6510 < 8.6463] w=0.9613 to align # Constraint # added constraint: constraint((T0293)V93.CB, (T0293)V119.CB) [> 3.9855 = 6.6425 < 8.6353] w=0.9613 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)A90.CB) [> 3.4593 = 5.7655 < 7.4951] w=0.9548 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)I114.CB) [> 2.7903 = 4.6506 < 6.0458] w=0.9420 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)C142.CB) [> 3.0067 = 5.0112 < 6.5145] w=0.9420 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)T91.CB) [> 3.1093 = 5.1822 < 6.7368] w=0.9420 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)E92.CB) [> 2.9447 = 4.9079 < 6.3802] w=0.9419 to align # Constraint # added constraint: constraint((T0293)D95.CB, (T0293)K118.CB) [> 3.5246 = 5.8743 < 7.6365] w=0.9370 to align # Constraint # added constraint: constraint((T0293)L79.CB, (T0293)F88.CB) [> 3.4067 = 5.6778 < 7.3812] w=0.9313 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)A101.CB) [> 3.6941 = 6.1569 < 8.0039] w=0.9248 to align # Constraint # added constraint: constraint((T0293)F98.CB, (T0293)K118.CB) [> 3.0876 = 5.1459 < 6.6897] w=0.9248 to align # Constraint # added constraint: constraint((T0293)F98.CB, (T0293)V116.CB) [> 3.2986 = 5.4977 < 7.1471] w=0.9248 to align # Constraint # added constraint: constraint((T0293)A90.CB, (T0293)I114.CB) [> 3.7395 = 6.2326 < 8.1023] w=0.9226 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)C140.CB) [> 4.0609 = 6.7682 < 8.7987] w=0.9226 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)A90.CB) [> 2.2067 = 3.6779 < 4.7812] w=0.9226 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)L89.CB) [> 4.4057 = 7.3429 < 9.5457] w=0.9206 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)A101.CB) [> 2.2713 = 3.7854 < 4.9211] w=0.9184 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)I114.CB) [> 3.5763 = 5.9605 < 7.7487] w=0.9097 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)C97.CB) [> 2.6705 = 4.4509 < 5.7861] w=0.9085 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)E92.CB) [> 3.0959 = 5.1598 < 6.7077] w=0.9033 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)T91.CB) [> 3.6020 = 6.0034 < 7.8044] w=0.9033 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)T91.CB) [> 3.7277 = 6.2129 < 8.0768] w=0.9032 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)A101.CB) [> 3.4295 = 5.7158 < 7.4306] w=0.8990 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)N104.CB) [> 3.2367 = 5.3945 < 7.0128] w=0.8861 to align # Constraint # added constraint: constraint((T0293)A101.CB, (T0293)V116.CB) [> 3.2336 = 5.3893 < 7.0061] w=0.8861 to align # Constraint # added constraint: constraint((T0293)E92.CB, (T0293)A101.CB) [> 4.1416 = 6.9027 < 8.9735] w=0.8861 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)F88.CB) [> 4.5641 = 7.6069 < 9.8890] w=0.8839 to align # Constraint # added constraint: constraint((T0293)K102.CB, (T0293)V116.CB) [> 3.3623 = 5.6038 < 7.2850] w=0.8797 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)Y100.CB) [> 3.0681 = 5.1136 < 6.6476] w=0.8797 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)C142.CB) [> 4.0031 = 6.6718 < 8.6733] w=0.8645 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)D94.CB) [> 4.2306 = 7.0510 < 9.1663] w=0.8645 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)W86.CB) [> 4.1170 = 6.8616 < 8.9201] w=0.8581 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)C97.CB) [> 3.7440 = 6.2400 < 8.1121] w=0.8569 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)N104.CB) [> 3.8479 = 6.4132 < 8.3371] w=0.8539 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)L79.CB) [> 4.0792 = 6.7987 < 8.8384] w=0.8516 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)W86.CB) [> 3.4412 = 5.7354 < 7.4560] w=0.8516 to align # Constraint # added constraint: constraint((T0293)L79.CB, (T0293)M141.CB) [> 4.2829 = 7.1382 < 9.2796] w=0.8339 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)I114.CB) [> 4.4971 = 7.4952 < 9.7437] w=0.8323 to align # Constraint # added constraint: constraint((T0293)L62.CB, (T0293)W86.CB) [> 3.6746 = 6.1244 < 7.9617] w=0.8239 to align # Constraint # added constraint: constraint((T0293)V105.CB, (T0293)I114.CB) [> 3.1150 = 5.1917 < 6.7492] w=0.8217 to align # Constraint # added constraint: constraint((T0293)E92.CB, (T0293)V116.CB) [> 4.2193 = 7.0321 < 9.1417] w=0.8080 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)A90.CB) [> 4.3934 = 7.3224 < 9.5191] w=0.8065 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)K118.CB) [> 4.5297 = 7.5495 < 9.8144] w=0.8065 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)V105.CB) [> 3.6518 = 6.0864 < 7.9123] w=0.8023 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)I136.CB) [> 4.2800 = 7.1333 < 9.2733] w=0.8016 to align # Constraint # added constraint: constraint((T0293)I75.CB, (T0293)N143.CB) [> 3.6683 = 6.1138 < 7.9479] w=0.7885 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)V116.CB) [> 4.0557 = 6.7594 < 8.7872] w=0.7871 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)L79.CB) [> 4.1969 = 6.9949 < 9.0933] w=0.7700 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)N104.CB) [> 3.7516 = 6.2526 < 8.1284] w=0.7700 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)M141.CB) [> 4.1730 = 6.9550 < 9.0415] w=0.7507 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)A90.CB) [> 4.5712 = 7.6186 < 9.9042] w=0.7484 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)F139.CB) [> 3.5330 = 5.8883 < 7.6548] w=0.7435 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)Y137.CB) [> 4.3945 = 7.3242 < 9.5215] w=0.7422 to align # Constraint # added constraint: constraint((T0293)G80.CA, (T0293)I114.CB) [> 3.9337 = 6.5562 < 8.5230] w=0.7378 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)C97.CB) [> 4.3281 = 7.2135 < 9.3776] w=0.7294 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)V116.CB) [> 4.5704 = 7.6173 < 9.9025] w=0.7291 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)N108.CB) [> 3.6743 = 6.1238 < 7.9609] w=0.7194 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)V105.CB) [> 3.8582 = 6.4303 < 8.3594] w=0.7136 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)A90.CB) [> 4.4676 = 7.4460 < 9.6797] w=0.7097 to align # Constraint # added constraint: constraint((T0293)V105.CB, (T0293)V116.CB) [> 4.1894 = 6.9823 < 9.0770] w=0.7055 to align # Constraint # added constraint: constraint((T0293)Y87.CB, (T0293)K115.CB) [> 4.3481 = 7.2468 < 9.4208] w=0.6984 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)V93.CB) [> 4.5318 = 7.5531 < 9.8190] w=0.6964 to align # Constraint # added constraint: constraint((T0293)E92.CB, (T0293)V117.CB) [> 4.5776 = 7.6293 < 9.9181] w=0.6945 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)V116.CB) [> 4.1746 = 6.9577 < 9.0449] w=0.6903 to align # Constraint # added constraint: constraint((T0293)E92.CB, (T0293)V119.CB) [> 4.4952 = 7.4919 < 9.7395] w=0.6710 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)Q121.CB) [> 2.9585 = 4.9308 < 6.4101] w=0.6667 to align # Constraint # added constraint: constraint((T0293)G80.CA, (T0293)L110.CB) [> 3.6604 = 6.1006 < 7.9307] w=0.6665 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)Q121.CB) [> 3.4281 = 5.7134 < 7.4275] w=0.6613 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)Y100.CB) [> 4.4094 = 7.3491 < 9.5538] w=0.6565 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)I114.CB) [> 4.1710 = 6.9517 < 9.0372] w=0.6532 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)Y100.CB) [> 4.3519 = 7.2532 < 9.4291] w=0.6500 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)W86.CB) [> 3.9439 = 6.5731 < 8.5451] w=0.6433 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)N143.CB) [> 4.0329 = 6.7216 < 8.7381] w=0.6401 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)Y87.CB) [> 4.1723 = 6.9539 < 9.0401] w=0.6284 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)L110.CB) [> 3.7251 = 6.2085 < 8.0710] w=0.6149 to align # Constraint # added constraint: constraint((T0293)Y87.CB, (T0293)I114.CB) [> 4.4550 = 7.4250 < 9.6524] w=0.6149 to align # Constraint # added constraint: constraint((T0293)L62.CB, (T0293)G85.CA) [> 3.6785 = 6.1308 < 7.9700] w=0.5990 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)V116.CB) [> 4.6538 = 7.7564 < 10.0833] w=0.5936 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)C142.CB) [> 4.2104 = 7.0173 < 9.1225] w=0.5916 to align # Constraint # added constraint: constraint((T0293)D94.CB, (T0293)K118.CB) [> 4.4660 = 7.4434 < 9.6764] w=0.5910 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)F98.CB) [> 4.3856 = 7.3093 < 9.5021] w=0.5765 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)L113.CB) [> 3.9132 = 6.5221 < 8.4787] w=0.5694 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)V105.CB) [> 4.1915 = 6.9858 < 9.0815] w=0.5523 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)I75.CB) [> 3.8058 = 6.3430 < 8.2458] w=0.5501 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)Q121.CB) [> 3.8876 = 6.4793 < 8.4231] w=0.5482 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)C140.CB) [> 4.6439 = 7.7398 < 10.0617] w=0.5396 to align # Constraint # added constraint: constraint((T0293)F98.CB, (T0293)V117.CB) [> 4.4864 = 7.4774 < 9.7206] w=0.5394 to align # Constraint # added constraint: constraint((T0293)Y87.CB, (T0293)L113.CB) [> 3.4068 = 5.6780 < 7.3814] w=0.5383 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)F98.CB) [> 4.3101 = 7.1835 < 9.3386] w=0.5377 to align # Constraint # added constraint: constraint((T0293)S60.CB, (T0293)D138.CB) [> 4.2699 = 7.1165 < 9.2514] w=0.5282 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)S205.CB) [> 4.3076 = 7.1793 < 9.3330] w=0.5253 to align # Constraint # added constraint: constraint((T0293)T61.CB, (T0293)W86.CB) [> 3.9863 = 6.6439 < 8.6370] w=0.5223 to align # Constraint # added constraint: constraint((T0293)M141.CB, (T0293)S205.CB) [> 3.1677 = 5.2796 < 6.8634] w=0.5188 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)L78.CB) [> 3.5695 = 5.9492 < 7.7339] w=0.5163 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)Y204.CB) [> 2.9172 = 4.8620 < 6.3207] w=0.5124 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)W203.CB) [> 3.1197 = 5.1995 < 6.7594] w=0.5124 to align # Constraint # added constraint: constraint((T0293)K59.CB, (T0293)L79.CB) [> 3.8040 = 6.3400 < 8.2420] w=0.5116 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)W203.CB) [> 4.3702 = 7.2836 < 9.4687] w=0.5059 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)R202.CB) [> 3.6919 = 6.1532 < 7.9992] w=0.4930 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)C206.CB) [> 2.9911 = 4.9851 < 6.4807] w=0.4896 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)L79.CB) [> 4.0475 = 6.7459 < 8.7697] w=0.4892 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)S205.CB) [> 4.3319 = 7.2198 < 9.3857] w=0.4801 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)G198.CA) [> 3.0510 = 5.0849 < 6.6104] w=0.4737 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)S194.CB) [> 3.1840 = 5.3066 < 6.8986] w=0.4687 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)G198.CA) [> 3.5055 = 5.8425 < 7.5953] w=0.4672 to align # Constraint # added constraint: constraint((T0293)E49.CB, (T0293)L78.CB) [> 3.7252 = 6.2087 < 8.0713] w=0.4642 to align # Constraint # added constraint: constraint((T0293)V93.CB, (T0293)Q121.CB) [> 4.3640 = 7.2733 < 9.4553] w=0.4633 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)W203.CB) [> 4.3174 = 7.1957 < 9.3544] w=0.4608 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)M207.CB) [> 4.1711 = 6.9519 < 9.0375] w=0.4444 to align # Constraint # added constraint: constraint((T0293)N143.CB, (T0293)M207.CB) [> 2.8369 = 4.7282 < 6.1466] w=0.4367 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)L125.CB) [> 3.4349 = 5.7249 < 7.4423] w=0.4314 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)L197.CB) [> 3.3637 = 5.6062 < 7.2880] w=0.4285 to align # Constraint # added constraint: constraint((T0293)G80.CA, (T0293)L113.CB) [> 3.5247 = 5.8745 < 7.6368] w=0.4232 to align # Constraint # added constraint: constraint((T0293)S194.CB, (T0293)Y204.CB) [> 3.5108 = 5.8514 < 7.6068] w=0.4171 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)M141.CB) [> 4.4024 = 7.3373 < 9.5385] w=0.4126 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)Y204.CB) [> 4.5560 = 7.5934 < 9.8714] w=0.4078 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)L197.CB) [> 3.9183 = 6.5305 < 8.4896] w=0.3963 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)L124.CB) [> 4.3326 = 7.2210 < 9.3872] w=0.3938 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)L197.CB) [> 3.7447 = 6.2412 < 8.1136] w=0.3898 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)A90.CB) [> 4.5636 = 7.6060 < 9.8878] w=0.3890 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)Y204.CB) [> 4.3914 = 7.3191 < 9.5148] w=0.3841 to align # Constraint # added constraint: constraint((T0293)L51.CB, (T0293)S205.CB) [> 3.5401 = 5.9001 < 7.6701] w=0.3833 to align # Constraint # added constraint: constraint((T0293)Y76.CB, (T0293)V116.CB) [> 4.5052 = 7.5087 < 9.7613] w=0.3829 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)L78.CB) [> 3.4783 = 5.7972 < 7.5364] w=0.3824 to align # Constraint # added constraint: constraint((T0293)L62.CB, (T0293)D138.CB) [> 3.1862 = 5.3103 < 6.9033] w=0.3791 to align # Constraint # added constraint: constraint((T0293)W86.CB, (T0293)L113.CB) [> 4.0617 = 6.7695 < 8.8004] w=0.3781 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)K102.CB) [> 4.5135 = 7.5225 < 9.7793] w=0.3761 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)T82.CB) [> 3.5715 = 5.9525 < 7.7383] w=0.3710 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)F186.CB) [> 3.1913 = 5.3187 < 6.9144] w=0.3705 to align # Constraint # added constraint: constraint((T0293)T61.CB, (T0293)L83.CB) [> 3.8473 = 6.4121 < 8.3358] w=0.3632 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)L83.CB) [> 3.5152 = 5.8587 < 7.6163] w=0.3632 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)P120.CB) [> 4.3783 = 7.2972 < 9.4864] w=0.3503 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)P144.CB) [> 3.8313 = 6.3855 < 8.3011] w=0.3395 to align # Constraint # added constraint: constraint((T0293)R64.CB, (T0293)I135.CB) [> 3.9463 = 6.5771 < 8.5503] w=0.3345 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)E185.CB) [> 4.2791 = 7.1319 < 9.2715] w=0.3333 to align # Constraint # added constraint: constraint((T0293)M141.CB, (T0293)E185.CB) [> 3.1072 = 5.1787 < 6.7323] w=0.3269 to align # Constraint # added constraint: constraint((T0293)Y231.CB, (T0293)W242.CB) [> 3.7919 = 6.3199 < 8.2158] w=0.3265 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)L184.CB) [> 2.8702 = 4.7837 < 6.2188] w=0.3204 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)E183.CB) [> 3.1890 = 5.3150 < 6.9095] w=0.3204 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)N170.CB) [> 4.0426 = 6.7377 < 8.7590] w=0.3198 to align # Constraint # added constraint: constraint((T0293)V229.CB, (T0293)L244.CB) [> 3.4988 = 5.8314 < 7.5808] w=0.3193 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)M141.CB) [> 4.1247 = 6.8744 < 8.9368] w=0.3181 to align # Constraint # added constraint: constraint((T0293)Q121.CB, (T0293)I190.CB) [> 3.5333 = 5.8888 < 7.6555] w=0.3084 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)M178.CB) [> 3.5223 = 5.8706 < 7.6317] w=0.3075 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)I174.CB) [> 3.1772 = 5.2953 < 6.8839] w=0.3075 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)E185.CB) [> 4.3141 = 7.1902 < 9.3473] w=0.3075 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)G182.CA) [> 3.9218 = 6.5364 < 8.4973] w=0.3075 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)G182.CA) [> 3.3758 = 5.6264 < 7.3143] w=0.3075 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)N143.CB) [> 4.3753 = 7.2922 < 9.4799] w=0.3045 to align # Constraint # added constraint: constraint((T0293)Y231.CB, (T0293)A243.CB) [> 3.8856 = 6.4760 < 8.4189] w=0.3022 to align # Constraint # added constraint: constraint((T0293)V229.CB, (T0293)A245.CB) [> 3.6615 = 6.1026 < 7.9333] w=0.3014 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)A179.CB) [> 3.5749 = 5.9582 < 7.7456] w=0.3011 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)M178.CB) [> 3.4532 = 5.7553 < 7.4819] w=0.3011 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)I177.CB) [> 3.4729 = 5.7882 < 7.5247] w=0.3011 to align # Constraint # added constraint: constraint((T0293)I135.CB, (T0293)L197.CB) [> 4.0273 = 6.7122 < 8.7259] w=0.2951 to align # Constraint # added constraint: constraint((T0293)I174.CB, (T0293)L184.CB) [> 3.4297 = 5.7161 < 7.4309] w=0.2946 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)A179.CB) [> 3.9519 = 6.5865 < 8.5625] w=0.2946 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)I177.CB) [> 3.9079 = 6.5132 < 8.4672] w=0.2946 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)P144.CB) [> 4.1452 = 6.9086 < 8.9812] w=0.2943 to align # Constraint # added constraint: constraint((T0293)L51.CB, (T0293)I75.CB) [> 4.0494 = 6.7489 < 8.7736] w=0.2901 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)M141.CB) [> 4.1945 = 6.9908 < 9.0880] w=0.2900 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)A179.CB) [> 3.1468 = 5.2447 < 6.8181] w=0.2882 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)E185.CB) [> 4.2486 = 7.0811 < 9.2054] w=0.2875 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)L110.CB) [> 4.5423 = 7.5704 < 9.8415] w=0.2858 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)I174.CB) [> 4.0621 = 6.7702 < 8.8013] w=0.2827 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)E183.CB) [> 4.4019 = 7.3364 < 9.5373] w=0.2817 to align # Constraint # added constraint: constraint((T0293)Y231.CB, (T0293)L244.CB) [> 4.0172 = 6.6954 < 8.7040] w=0.2815 to align # Constraint # added constraint: constraint((T0293)T230.CB, (T0293)L244.CB) [> 3.7229 = 6.2049 < 8.0663] w=0.2806 to align # Constraint # added constraint: constraint((T0293)L51.CB, (T0293)M141.CB) [> 3.8049 = 6.3416 < 8.2440] w=0.2772 to align # Constraint # added constraint: constraint((T0293)Y137.CB, (T0293)G182.CA) [> 4.3556 = 7.2593 < 9.4371] w=0.2768 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)R202.CB) [> 4.2777 = 7.1295 < 9.2684] w=0.2767 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)L184.CB) [> 4.5350 = 7.5584 < 9.8259] w=0.2746 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)L79.CB) [> 4.1759 = 6.9598 < 9.0478] w=0.2710 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)I190.CB) [> 3.9117 = 6.5195 < 8.4754] w=0.2679 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)L83.CB) [> 3.8699 = 6.4498 < 8.3847] w=0.2664 to align # Constraint # added constraint: constraint((T0293)Y204.CB, (T0293)A245.CB) [> 3.8560 = 6.4267 < 8.3547] w=0.2644 to align # Constraint # added constraint: constraint((T0293)S205.CB, (T0293)A243.CB) [> 3.7821 = 6.3035 < 8.1946] w=0.2644 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)I177.CB) [> 3.8404 = 6.4006 < 8.3208] w=0.2624 to align # Constraint # added constraint: constraint((T0293)T232.CB, (T0293)W242.CB) [> 3.8038 = 6.3396 < 8.2415] w=0.2622 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)L201.CB) [> 4.4453 = 7.4088 < 9.6314] w=0.2594 to align # Constraint # added constraint: constraint((T0293)S205.CB, (T0293)L244.CB) [> 3.9741 = 6.6235 < 8.6106] w=0.2580 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)I75.CB) [> 4.3012 = 7.1687 < 9.3193] w=0.2577 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)L184.CB) [> 4.3381 = 7.2301 < 9.3992] w=0.2567 to align # Constraint # added constraint: constraint((T0293)T232.CB, (T0293)A243.CB) [> 3.6048 = 6.0079 < 7.8103] w=0.2553 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)I190.CB) [> 3.9418 = 6.5696 < 8.5405] w=0.2551 to align # Constraint # added constraint: constraint((T0293)Y87.CB, (T0293)D112.CB) [> 3.3344 = 5.5573 < 7.2245] w=0.2530 to align # Constraint # added constraint: constraint((T0293)T230.CB, (T0293)A243.CB) [> 3.6357 = 6.0595 < 7.8773] w=0.2501 to align # Constraint # added constraint: constraint((T0293)Y231.CB, (T0293)R241.CB) [> 3.8518 = 6.4197 < 8.3456] w=0.2452 to align # Constraint # added constraint: constraint((T0293)M207.CB, (T0293)W242.CB) [> 4.0409 = 6.7348 < 8.7553] w=0.2451 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)A101.CB) [> 4.4855 = 7.4758 < 9.7185] w=0.2436 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)D112.CB) [> 3.9226 = 6.5376 < 8.4989] w=0.2387 to align # Constraint # added constraint: constraint((T0293)L208.CB, (T0293)W242.CB) [> 3.7803 = 6.3004 < 8.1906] w=0.2386 to align # Constraint # added constraint: constraint((T0293)Q121.CB, (T0293)N170.CB) [> 3.4706 = 5.7843 < 7.5196] w=0.2374 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)V187.CB) [> 3.9385 = 6.5642 < 8.5335] w=0.2365 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)E134.CB) [> 3.6591 = 6.0985 < 7.9280] w=0.2355 to align # Constraint # added constraint: constraint((T0293)C206.CB, (T0293)A243.CB) [> 3.8455 = 6.4091 < 8.3318] w=0.2321 to align # Constraint # added constraint: constraint((T0293)K218.CB, (T0293)Y231.CB) [> 4.0786 = 6.7976 < 8.8369] w=0.2312 to align # Constraint # added constraint: constraint((T0293)T232.CB, (T0293)R241.CB) [> 3.4905 = 5.8175 < 7.5628] w=0.2307 to align # Constraint # added constraint: constraint((T0293)Y44.CB, (T0293)C74.CB) [> 3.7674 = 6.2789 < 8.1626] w=0.2307 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)I135.CB) [> 4.1842 = 6.9737 < 9.0658] w=0.2258 to align # Constraint # added constraint: constraint((T0293)I75.CB, (T0293)C142.CB) [> 4.3981 = 7.3302 < 9.5293] w=0.2255 to align # Constraint # added constraint: constraint((T0293)V229.CB, (T0293)A243.CB) [> 3.8317 = 6.3862 < 8.3020] w=0.2243 to align # Constraint # added constraint: constraint((T0293)I136.CB, (T0293)M178.CB) [> 4.2042 = 7.0070 < 9.1091] w=0.2237 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)P145.CB) [> 3.7123 = 6.1872 < 8.0434] w=0.2230 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)L124.CB) [> 4.1574 = 6.9290 < 9.0077] w=0.2207 to align # Constraint # added constraint: constraint((T0293)Y44.CB, (T0293)I75.CB) [> 3.9324 = 6.5540 < 8.5202] w=0.2194 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)I174.CB) [> 4.1158 = 6.8597 < 8.9176] w=0.2181 to align # Constraint # added constraint: constraint((T0293)A122.CB, (T0293)R189.CB) [> 3.6068 = 6.0113 < 7.8146] w=0.2181 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)M207.CB) [> 4.1053 = 6.8422 < 8.8948] w=0.2142 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)V119.CB) [> 4.5210 = 7.5349 < 9.7954] w=0.2133 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)L125.CB) [> 3.7821 = 6.3035 < 8.1946] w=0.2128 to align # Constraint # added constraint: constraint((T0293)M207.CB, (T0293)R241.CB) [> 3.8277 = 6.3795 < 8.2934] w=0.2128 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)N160.CB) [> 3.6049 = 6.0081 < 7.8105] w=0.2125 to align # Constraint # added constraint: constraint((T0293)T171.CB, (T0293)E220.CB) [> 3.4035 = 5.6725 < 7.3743] w=0.2124 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)N143.CB) [> 4.2524 = 7.0874 < 9.2136] w=0.2078 to align # Constraint # added constraint: constraint((T0293)G85.CA, (T0293)D112.CB) [> 3.9210 = 6.5351 < 8.4956] w=0.2065 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)N160.CB) [> 4.0327 = 6.7211 < 8.7374] w=0.2059 to align # Constraint # added constraint: constraint((T0293)I135.CB, (T0293)I177.CB) [> 4.0939 = 6.8231 < 8.8700] w=0.2056 to align # Constraint # added constraint: constraint((T0293)T171.CB, (T0293)L221.CB) [> 3.8291 = 6.3818 < 8.2964] w=0.2052 to align # Constraint # added constraint: constraint((T0293)D138.CB, (T0293)M178.CB) [> 4.5161 = 7.5268 < 9.7848] w=0.2048 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)M240.CB) [> 3.5906 = 5.9844 < 7.7797] w=0.1999 to align # Constraint # added constraint: constraint((T0293)T175.CB, (T0293)Q224.CB) [> 3.0081 = 5.0135 < 6.5176] w=0.1987 to align # Constraint # added constraint: constraint((T0293)I191.CB, (T0293)E220.CB) [> 3.4744 = 5.7906 < 7.5278] w=0.1936 to align # Constraint # added constraint: constraint((T0293)P77.CB, (T0293)F88.CB) [> 4.5208 = 7.5346 < 9.7950] w=0.1936 to align # Constraint # added constraint: constraint((T0293)S168.CB, (T0293)E220.CB) [> 3.4765 = 5.7941 < 7.5323] w=0.1930 to align # Constraint # added constraint: constraint((T0293)K218.CB, (T0293)V229.CB) [> 3.5653 = 5.9422 < 7.7248] w=0.1930 to align # Constraint # added constraint: constraint((T0293)V93.CB, (T0293)L125.CB) [> 4.3213 = 7.2022 < 9.3629] w=0.1929 to align # Constraint # added constraint: constraint((T0293)Y44.CB, (T0293)N143.CB) [> 4.0973 = 6.8288 < 8.8775] w=0.1890 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)L129.CB) [> 4.1321 = 6.8869 < 8.9530] w=0.1872 to align # Constraint # added constraint: constraint((T0293)E185.CB, (T0293)A243.CB) [> 3.8326 = 6.3876 < 8.3039] w=0.1865 to align # Constraint # added constraint: constraint((T0293)I191.CB, (T0293)L221.CB) [> 4.0134 = 6.6890 < 8.6957] w=0.1856 to align # Constraint # added constraint: constraint((T0293)V119.CB, (T0293)A128.CB) [> 3.0274 = 5.0457 < 6.5595] w=0.1855 to align # Constraint # added constraint: constraint((T0293)V229.CB, (T0293)W246.CB) [> 3.5929 = 5.9882 < 7.7846] w=0.1853 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)C97.CB) [> 4.6079 = 7.6798 < 9.9837] w=0.1806 to align # Constraint # added constraint: constraint((T0293)G172.CA, (T0293)Q224.CB) [> 3.2328 = 5.3880 < 7.0044] w=0.1801 to align # Constraint # added constraint: constraint((T0293)P161.CB, (T0293)N170.CB) [> 4.2959 = 7.1598 < 9.3078] w=0.1796 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)N170.CB) [> 4.0282 = 6.7136 < 8.7277] w=0.1784 to align # Constraint # added constraint: constraint((T0293)T171.CB, (T0293)L184.CB) [> 4.1837 = 6.9728 < 9.0646] w=0.1784 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)C97.CB) [> 4.5686 = 7.6143 < 9.8986] w=0.1742 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)M178.CB) [> 4.4492 = 7.4152 < 9.6398] w=0.1737 to align # Constraint # added constraint: constraint((T0293)Q121.CB, (T0293)G173.CA) [> 4.1974 = 6.9956 < 9.0943] w=0.1714 to align # Constraint # added constraint: constraint((T0293)T171.CB, (T0293)Q224.CB) [> 2.9907 = 4.9845 < 6.4799] w=0.1672 to align # Constraint # added constraint: constraint((T0293)N160.CB, (T0293)N170.CB) [> 3.4454 = 5.7423 < 7.4650] w=0.1672 to align # Constraint # added constraint: constraint((T0293)L184.CB, (T0293)A245.CB) [> 3.7296 = 6.2160 < 8.0808] w=0.1671 to align # Constraint # added constraint: constraint((T0293)V117.CB, (T0293)A128.CB) [> 3.7147 = 6.1911 < 8.0484] w=0.1667 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)L208.CB) [> 3.6974 = 6.1623 < 8.0110] w=0.1662 to align # Constraint # added constraint: constraint((T0293)V226.CB, (T0293)W246.CB) [> 3.4632 = 5.7720 < 7.5037] w=0.1662 to align # Constraint # added constraint: constraint((T0293)M141.CB, (T0293)F186.CB) [> 4.4881 = 7.4801 < 9.7242] w=0.1614 to align # Constraint # added constraint: constraint((T0293)K102.CB, (T0293)S111.CB) [> 4.3235 = 7.2058 < 9.3675] w=0.1613 to align # Constraint # added constraint: constraint((T0293)C74.CB, (T0293)N143.CB) [> 4.3709 = 7.2849 < 9.4704] w=0.1613 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)T239.CB) [> 3.4949 = 5.8249 < 7.5724] w=0.1612 to align # Constraint # added constraint: constraint((T0293)L214.CB, (T0293)Y231.CB) [> 3.9053 = 6.5089 < 8.4616] w=0.1608 to align # Constraint # added constraint: constraint((T0293)E185.CB, (T0293)L244.CB) [> 3.8828 = 6.4714 < 8.4128] w=0.1607 to align # Constraint # added constraint: constraint((T0293)E183.CB, (T0293)A245.CB) [> 3.8139 = 6.3565 < 8.2634] w=0.1607 to align # Constraint # added constraint: constraint((T0293)F186.CB, (T0293)A243.CB) [> 3.7944 = 6.3240 < 8.2213] w=0.1600 to align # Constraint # added constraint: constraint((T0293)K228.CB, (T0293)A245.CB) [> 3.4839 = 5.8065 < 7.5484] w=0.1598 to align # Constraint # added constraint: constraint((T0293)I191.CB, (T0293)L217.CB) [> 4.1781 = 6.9636 < 9.0526] w=0.1598 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)N143.CB) [> 4.1469 = 6.9115 < 8.9849] w=0.1561 to align # Constraint # added constraint: constraint((T0293)T175.CB, (T0293)V226.CB) [> 3.7727 = 6.2878 < 8.1741] w=0.1548 to align # Constraint # added constraint: constraint((T0293)L208.CB, (T0293)L217.CB) [> 3.5727 = 5.9546 < 7.7409] w=0.1543 to align # Constraint # added constraint: constraint((T0293)L184.CB, (T0293)L244.CB) [> 3.6351 = 6.0585 < 7.8761] w=0.1542 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)L217.CB) [> 3.5156 = 5.8594 < 7.6172] w=0.1536 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)M141.CB) [> 4.4994 = 7.4990 < 9.7487] w=0.1533 to align # Constraint # added constraint: constraint((T0293)I52.CB, (T0293)E185.CB) [> 3.5092 = 5.8487 < 7.6033] w=0.1526 to align # Constraint # added constraint: constraint((T0293)G53.CA, (T0293)L78.CB) [> 4.2424 = 7.0706 < 9.1918] w=0.1496 to align # Constraint # added constraint: constraint((T0293)F186.CB, (T0293)W242.CB) [> 3.7372 = 6.2287 < 8.0974] w=0.1490 to align # Constraint # added constraint: constraint((T0293)E185.CB, (T0293)W242.CB) [> 4.0541 = 6.7568 < 8.7839] w=0.1490 to align # Constraint # added constraint: constraint((T0293)T91.CB, (T0293)L129.CB) [> 3.7762 = 6.2937 < 8.1818] w=0.1485 to align # Constraint # added constraint: constraint((T0293)H46.CB, (T0293)L78.CB) [> 4.1838 = 6.9730 < 9.0649] w=0.1484 to align # Constraint # added constraint: constraint((T0293)C206.CB, (T0293)L217.CB) [> 3.6625 = 6.1041 < 7.9354] w=0.1484 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)I190.CB) [> 3.5705 = 5.9508 < 7.7360] w=0.1469 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)G182.CA) [> 4.6227 = 7.7045 < 10.0159] w=0.1462 to align # Constraint # added constraint: constraint((T0293)E183.CB, (T0293)L244.CB) [> 3.9812 = 6.6353 < 8.6259] w=0.1426 to align # Constraint # added constraint: constraint((T0293)W86.CB, (T0293)F139.CB) [> 4.5101 = 7.5168 < 9.7719] w=0.1419 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)P164.CB) [> 3.4610 = 5.7684 < 7.4989] w=0.1414 to align # Constraint # added constraint: constraint((T0293)I66.CB, (T0293)R163.CB) [> 3.9429 = 6.5715 < 8.5430] w=0.1414 to align # Constraint # added constraint: constraint((T0293)L40.CB, (T0293)C74.CB) [> 3.6893 = 6.1488 < 7.9935] w=0.1409 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)W242.CB) [> 3.7691 = 6.2818 < 8.1664] w=0.1404 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)F186.CB) [> 3.7648 = 6.2746 < 8.1570] w=0.1389 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)S205.CB) [> 3.8616 = 6.4360 < 8.3668] w=0.1384 to align # Constraint # added constraint: constraint((T0293)M141.CB, (T0293)L184.CB) [> 4.6193 = 7.6989 < 10.0085] w=0.1361 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)P161.CB) [> 3.5420 = 5.9034 < 7.6744] w=0.1356 to align # Constraint # added constraint: constraint((T0293)I27.CB, (T0293)P77.CB) [> 4.1735 = 6.9559 < 9.0427] w=0.1355 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)L217.CB) [> 3.8977 = 6.4962 < 8.4450] w=0.1355 to align # Constraint # added constraint: constraint((T0293)L184.CB, (T0293)V226.CB) [> 4.1155 = 6.8592 < 8.9169] w=0.1355 to align # Constraint # added constraint: constraint((T0293)L221.CB, (T0293)A243.CB) [> 3.8292 = 6.3819 < 8.2965] w=0.1350 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)N160.CB) [> 3.0982 = 5.1636 < 6.7126] w=0.1349 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)R241.CB) [> 3.5603 = 5.9338 < 7.7139] w=0.1349 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)W242.CB) [> 4.1569 = 6.9282 < 9.0067] w=0.1349 to align # Constraint # added constraint: constraint((T0293)E49.CB, (T0293)I75.CB) [> 3.8446 = 6.4076 < 8.3299] w=0.1347 to align # Constraint # added constraint: constraint((T0293)L221.CB, (T0293)L244.CB) [> 3.7020 = 6.1700 < 8.0210] w=0.1344 to align # Constraint # added constraint: constraint((T0293)L51.CB, (T0293)E185.CB) [> 3.7741 = 6.2901 < 8.1772] w=0.1334 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)F88.CB) [> 4.5719 = 7.6199 < 9.9059] w=0.1332 to align # Constraint # added constraint: constraint((T0293)V119.CB, (T0293)L129.CB) [> 3.9892 = 6.6487 < 8.6433] w=0.1292 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)S158.CB) [> 3.7404 = 6.2339 < 8.1041] w=0.1292 to align # Constraint # added constraint: constraint((T0293)I27.CB, (T0293)A72.CB) [> 3.6168 = 6.0280 < 7.8365] w=0.1290 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)R163.CB) [> 3.8587 = 6.4311 < 8.3605] w=0.1285 to align # Constraint # added constraint: constraint((T0293)T171.CB, (T0293)F186.CB) [> 3.7002 = 6.1670 < 8.0172] w=0.1283 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)C206.CB) [> 3.9583 = 6.5971 < 8.5762] w=0.1283 to align # Constraint # added constraint: constraint((T0293)F146.CB, (T0293)L208.CB) [> 3.8043 = 6.3405 < 8.2427] w=0.1275 to align # Constraint # added constraint: constraint((T0293)V48.CB, (T0293)E185.CB) [> 3.6471 = 6.0785 < 7.9021] w=0.1270 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)N143.CB) [> 4.5501 = 7.5834 < 9.8585] w=0.1239 to align # Constraint # added constraint: constraint((T0293)A148.CB, (T0293)G209.CA) [> 3.6728 = 6.1214 < 7.9578] w=0.1232 to align # Constraint # added constraint: constraint((T0293)G182.CA, (T0293)W246.CB) [> 3.4719 = 5.7865 < 7.5225] w=0.1232 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)E220.CB) [> 3.3027 = 5.5045 < 7.1558] w=0.1226 to align # Constraint # added constraint: constraint((T0293)L34.CB, (T0293)A72.CB) [> 3.8784 = 6.4640 < 8.4032] w=0.1226 to align # Constraint # added constraint: constraint((T0293)I27.CB, (T0293)C74.CB) [> 3.8184 = 6.3639 < 8.2731] w=0.1226 to align # Constraint # added constraint: constraint((T0293)H192.CB, (T0293)Q224.CB) [> 3.6996 = 6.1660 < 8.0159] w=0.1226 to align # Constraint # added constraint: constraint((T0293)L195.CB, (T0293)V226.CB) [> 3.7953 = 6.3254 < 8.2231] w=0.1226 to align # Constraint # added constraint: constraint((T0293)P144.CB, (T0293)C206.CB) [> 3.6572 = 6.0953 < 7.9239] w=0.1224 to align # Constraint # added constraint: constraint((T0293)N143.CB, (T0293)F186.CB) [> 4.4448 = 7.4079 < 9.6303] w=0.1218 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)V156.CB) [> 3.8512 = 6.4186 < 8.3442] w=0.1217 to align # Constraint # added constraint: constraint((T0293)F186.CB, (T0293)L244.CB) [> 3.8926 = 6.4876 < 8.4339] w=0.1213 to align # Constraint # added constraint: constraint((T0293)G181.CA, (T0293)W246.CB) [> 3.5126 = 5.8544 < 7.6107] w=0.1168 to align # Constraint # added constraint: constraint((T0293)Q121.CB, (T0293)P144.CB) [> 4.3263 = 7.2104 < 9.3735] w=0.1168 to align # Constraint # added constraint: constraint((T0293)P161.CB, (T0293)F186.CB) [> 3.6600 = 6.0999 < 7.9299] w=0.1162 to align # Constraint # added constraint: constraint((T0293)L214.CB, (T0293)R241.CB) [> 3.8007 = 6.3346 < 8.2349] w=0.1161 to align # Constraint # added constraint: constraint((T0293)L89.CB, (T0293)L124.CB) [> 4.4745 = 7.4576 < 9.6948] w=0.1161 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)I114.CB) [> 4.5918 = 7.6531 < 9.9490] w=0.1161 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)M141.CB) [> 4.4504 = 7.4173 < 9.6425] w=0.1161 to align # Constraint # added constraint: constraint((T0293)L25.CB, (T0293)L78.CB) [> 3.8919 = 6.4865 < 8.4325] w=0.1156 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)V169.CB) [> 3.0820 = 5.1367 < 6.6777] w=0.1156 to align # Constraint # added constraint: constraint((T0293)A153.CB, (T0293)E220.CB) [> 3.6971 = 6.1618 < 8.0104] w=0.1156 to align # Constraint # added constraint: constraint((T0293)K154.CB, (T0293)E220.CB) [> 3.4538 = 5.7563 < 7.4832] w=0.1156 to align # Constraint # added constraint: constraint((T0293)N157.CB, (T0293)E220.CB) [> 3.4800 = 5.8000 < 7.5400] w=0.1156 to align # Constraint # added constraint: constraint((T0293)M126.CB, (T0293)R159.CB) [> 4.1476 = 6.9127 < 8.9865] w=0.1156 to align # Constraint # added constraint: constraint((T0293)L221.CB, (T0293)Y231.CB) [> 4.0814 = 6.8024 < 8.8431] w=0.1141 to align # Constraint # added constraint: constraint((T0293)F147.CB, (T0293)L208.CB) [> 3.5708 = 5.9514 < 7.7368] w=0.1098 to align # Constraint # added constraint: constraint((T0293)F147.CB, (T0293)G209.CA) [> 3.9421 = 6.5701 < 8.5412] w=0.1098 to align # Constraint # added constraint: constraint((T0293)W86.CB, (T0293)D138.CB) [> 4.7242 = 7.8737 < 10.2359] w=0.1097 to align # Constraint # added constraint: constraint((T0293)L62.CB, (T0293)T82.CB) [> 3.9246 = 6.5411 < 8.5034] w=0.1097 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)S167.CB) [> 3.2297 = 5.3828 < 6.9976] w=0.1097 to align # Constraint # added constraint: constraint((T0293)N157.CB, (T0293)L221.CB) [> 3.7172 = 6.1953 < 8.0539] w=0.1091 to align # Constraint # added constraint: constraint((T0293)G181.CA, (T0293)S247.CB) [> 3.4861 = 5.8102 < 7.5532] w=0.1090 to align # Constraint # added constraint: constraint((T0293)V38.CB, (T0293)A72.CB) [> 3.4876 = 5.8126 < 7.5564] w=0.1086 to align # Constraint # added constraint: constraint((T0293)E185.CB, (T0293)A245.CB) [> 3.8592 = 6.4319 < 8.3615] w=0.1084 to align # Constraint # added constraint: constraint((T0293)F146.CB, (T0293)G209.CA) [> 3.6866 = 6.1444 < 7.9877] w=0.1082 to align # Constraint # added constraint: constraint((T0293)K228.CB, (T0293)S247.CB) [> 3.5379 = 5.8965 < 7.6654] w=0.1079 to align # Constraint # added constraint: constraint((T0293)I27.CB, (T0293)N104.CB) [> 3.1041 = 5.1735 < 6.7256] w=0.1032 to align # Constraint # added constraint: constraint((T0293)F147.CB, (T0293)C212.CB) [> 3.6298 = 6.0497 < 7.8647] w=0.1027 to align # Constraint # added constraint: constraint((T0293)V38.CB, (T0293)C74.CB) [> 3.7835 = 6.3058 < 8.1976] w=0.1022 to align # Constraint # added constraint: constraint((T0293)H192.CB, (T0293)E220.CB) [> 4.2194 = 7.0323 < 9.1420] w=0.1017 to align # Constraint # added constraint: constraint((T0293)L25.CB, (T0293)N108.CB) [> 3.3640 = 5.6067 < 7.2888] w=0.0968 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)P216.CB) [> 3.8309 = 6.3848 < 8.3003] w=0.0968 to align # Constraint # added constraint: constraint((T0293)G80.CA, (T0293)N108.CB) [> 4.3728 = 7.2879 < 9.4743] w=0.0968 to align # Constraint # added constraint: constraint((T0293)L201.CB, (T0293)W246.CB) [> 4.1367 = 6.8946 < 8.9629] w=0.0968 to align # Constraint # added constraint: constraint((T0293)R189.CB, (T0293)T239.CB) [> 3.6197 = 6.0329 < 7.8427] w=0.0967 to align # Constraint # added constraint: constraint((T0293)G69.CA, (T0293)N160.CB) [> 2.8993 = 4.8322 < 6.2819] w=0.0962 to align # Constraint # added constraint: constraint((T0293)F139.CB, (T0293)P164.CB) [> 4.5191 = 7.5318 < 9.7914] w=0.0962 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)C212.CB) [> 4.0556 = 6.7593 < 8.7871] w=0.0960 to align # Constraint # added constraint: constraint((T0293)Y44.CB, (T0293)V187.CB) [> 3.9885 = 6.6474 < 8.6416] w=0.0960 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)W242.CB) [> 3.9031 = 6.5052 < 8.4568] w=0.0955 to align # Constraint # added constraint: constraint((T0293)R189.CB, (T0293)M240.CB) [> 4.2320 = 7.0533 < 9.1693] w=0.0955 to align # Constraint # added constraint: constraint((T0293)R63.CB, (T0293)T82.CB) [> 4.6552 = 7.7586 < 10.0862] w=0.0922 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)M240.CB) [> 4.0449 = 6.7415 < 8.7639] w=0.0910 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)R238.CB) [> 3.7365 = 6.2274 < 8.0957] w=0.0910 to align # Constraint # added constraint: constraint((T0293)L124.CB, (T0293)I174.CB) [> 4.0724 = 6.7873 < 8.8235] w=0.0904 to align # Constraint # added constraint: constraint((T0293)L208.CB, (T0293)T239.CB) [> 3.8253 = 6.3754 < 8.2881] w=0.0903 to align # Constraint # added constraint: constraint((T0293)F147.CB, (T0293)V156.CB) [> 3.8421 = 6.4034 < 8.3244] w=0.0903 to align # Constraint # added constraint: constraint((T0293)G181.CA, (T0293)F248.CB) [> 3.4504 = 5.7507 < 7.4759] w=0.0897 to align # Constraint # added constraint: constraint((T0293)V117.CB, (T0293)S133.CB) [> 4.3003 = 7.1672 < 9.3174] w=0.0896 to align # Constraint # added constraint: constraint((T0293)E49.CB, (T0293)C74.CB) [> 4.0194 = 6.6991 < 8.7088] w=0.0896 to align # Constraint # added constraint: constraint((T0293)R33.CB, (T0293)G71.CA) [> 3.7410 = 6.2350 < 8.1055] w=0.0845 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)M240.CB) [> 3.5121 = 5.8535 < 7.6095] w=0.0845 to align # Constraint # added constraint: constraint((T0293)R33.CB, (T0293)A72.CB) [> 3.8330 = 6.3884 < 8.3049] w=0.0839 to align # Constraint # added constraint: constraint((T0293)C142.CB, (T0293)T171.CB) [> 4.1178 = 6.8630 < 8.9219] w=0.0839 to align # Constraint # added constraint: constraint((T0293)N84.CB, (T0293)D112.CB) [> 4.2373 = 7.0621 < 9.1807] w=0.0839 to align # Constraint # added constraint: constraint((T0293)W47.CB, (T0293)F234.CB) [> 3.7310 = 6.2184 < 8.0839] w=0.0839 to align # Constraint # added constraint: constraint((T0293)E180.CB, (T0293)F248.CB) [> 3.2732 = 5.4553 < 7.0919] w=0.0832 to align # Constraint # added constraint: constraint((T0293)M178.CB, (T0293)W246.CB) [> 3.6009 = 6.0015 < 7.8019] w=0.0832 to align # Constraint # added constraint: constraint((T0293)F234.CB, (T0293)A243.CB) [> 3.9977 = 6.6629 < 8.6617] w=0.0826 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)E220.CB) [> 3.8284 = 6.3807 < 8.2949] w=0.0774 to align # Constraint # added constraint: constraint((T0293)F23.CB, (T0293)L78.CB) [> 3.2204 = 5.3674 < 6.9776] w=0.0774 to align # Constraint # added constraint: constraint((T0293)R162.CB, (T0293)A211.CB) [> 3.6396 = 6.0660 < 7.8858] w=0.0774 to align # Constraint # added constraint: constraint((T0293)L214.CB, (T0293)W242.CB) [> 3.5247 = 5.8744 < 7.6367] w=0.0769 to align # Constraint # added constraint: constraint((T0293)S167.CB, (T0293)F186.CB) [> 3.8260 = 6.3767 < 8.2897] w=0.0767 to align # Constraint # added constraint: constraint((T0293)S167.CB, (T0293)E220.CB) [> 3.5448 = 5.9079 < 7.6803] w=0.0766 to align # Constraint # added constraint: constraint((T0293)R189.CB, (T0293)R241.CB) [> 3.9111 = 6.5184 < 8.4740] w=0.0761 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)L110.CB) [> 4.1233 = 6.8721 < 8.9337] w=0.0751 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)C142.CB) [> 4.4225 = 7.3709 < 9.5822] w=0.0751 to align # Constraint # added constraint: constraint((T0293)N99.CB, (T0293)K118.CB) [> 4.5044 = 7.5073 < 9.7595] w=0.0729 to align # Constraint # added constraint: constraint((T0293)E180.CB, (T0293)S247.CB) [> 3.6195 = 6.0324 < 7.8422] w=0.0716 to align # Constraint # added constraint: constraint((T0293)N160.CB, (T0293)V187.CB) [> 3.8320 = 6.3867 < 8.3027] w=0.0711 to align # Constraint # added constraint: constraint((T0293)A148.CB, (T0293)L208.CB) [> 4.0671 = 6.7785 < 8.8120] w=0.0711 to align # Constraint # added constraint: constraint((T0293)T37.CB, (T0293)A72.CB) [> 4.0671 = 6.7785 < 8.8120] w=0.0710 to align # Constraint # added constraint: constraint((T0293)L40.CB, (T0293)N143.CB) [> 3.6061 = 6.0102 < 7.8132] w=0.0710 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)F186.CB) [> 4.6073 = 7.6788 < 9.9824] w=0.0709 to align # Constraint # added constraint: constraint((T0293)F146.CB, (T0293)C212.CB) [> 4.2701 = 7.1168 < 9.2518] w=0.0705 to align # Constraint # added constraint: constraint((T0293)F146.CB, (T0293)K188.CB) [> 4.1295 = 6.8825 < 8.9473] w=0.0702 to align # Constraint # added constraint: constraint((T0293)K188.CB, (T0293)T239.CB) [> 3.6585 = 6.0975 < 7.9268] w=0.0652 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)S158.CB) [> 4.2809 = 7.1348 < 9.2753] w=0.0652 to align # Constraint # added constraint: constraint((T0293)L214.CB, (T0293)A243.CB) [> 3.8586 = 6.4311 < 8.3604] w=0.0645 to align # Constraint # added constraint: constraint((T0293)L184.CB, (T0293)S213.CB) [> 3.3042 = 5.5070 < 7.1591] w=0.0645 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)P145.CB) [> 4.4272 = 7.3787 < 9.5923] w=0.0645 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)S167.CB) [> 4.1163 = 6.8604 < 8.9186] w=0.0645 to align # Constraint # added constraint: constraint((T0293)G173.CA, (T0293)R189.CB) [> 3.3695 = 5.6158 < 7.3005] w=0.0638 to align # Constraint # added constraint: constraint((T0293)G182.CA, (T0293)A245.CB) [> 3.8048 = 6.3413 < 8.2437] w=0.0587 to align # Constraint # added constraint: constraint((T0293)R162.CB, (T0293)G209.CA) [> 3.6963 = 6.1605 < 8.0086] w=0.0581 to align # Constraint # added constraint: constraint((T0293)L34.CB, (T0293)G71.CA) [> 3.9730 = 6.6216 < 8.6081] w=0.0581 to align # Constraint # added constraint: constraint((T0293)L201.CB, (T0293)A245.CB) [> 4.1394 = 6.8990 < 8.9686] w=0.0581 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)L89.CB) [> 4.7654 = 7.9424 < 10.3251] w=0.0581 to align # Constraint # added constraint: constraint((T0293)V187.CB, (T0293)L244.CB) [> 4.3618 = 7.2696 < 9.4505] w=0.0575 to align # Constraint # added constraint: constraint((T0293)F146.CB, (T0293)V187.CB) [> 3.9092 = 6.5153 < 8.4700] w=0.0573 to align # Constraint # added constraint: constraint((T0293)P145.CB, (T0293)F186.CB) [> 3.5977 = 5.9961 < 7.7949] w=0.0573 to align # Constraint # added constraint: constraint((T0293)P166.CB, (T0293)E220.CB) [> 4.3078 = 7.1797 < 9.3336] w=0.0573 to align # Constraint # added constraint: constraint((T0293)L19.CB, (T0293)I29.CB) [> 4.0117 = 6.6862 < 8.6921] w=0.0523 to align # Constraint # added constraint: constraint((T0293)N160.CB, (T0293)K188.CB) [> 4.0872 = 6.8120 < 8.8557] w=0.0523 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)C74.CB) [> 4.0189 = 6.6982 < 8.7077] w=0.0522 to align # Constraint # added constraint: constraint((T0293)R20.CB, (T0293)I29.CB) [> 3.7379 = 6.2299 < 8.0989] w=0.0516 to align # Constraint # added constraint: constraint((T0293)N143.CB, (T0293)K188.CB) [> 3.9808 = 6.6346 < 8.6250] w=0.0516 to align # Constraint # added constraint: constraint((T0293)F23.CB, (T0293)A81.CB) [> 4.3311 = 7.2185 < 9.3840] w=0.0516 to align # Constraint # added constraint: constraint((T0293)V105.CB, (T0293)K115.CB) [> 4.5163 = 7.5272 < 9.7853] w=0.0516 to align # Constraint # added constraint: constraint((T0293)I27.CB, (T0293)S73.CB) [> 4.1525 = 6.9209 < 8.9971] w=0.0516 to align # Constraint # added constraint: constraint((T0293)L34.CB, (T0293)C74.CB) [> 3.5294 = 5.8824 < 7.6471] w=0.0516 to align # Constraint # added constraint: constraint((T0293)F147.CB, (T0293)A211.CB) [> 3.4779 = 5.7965 < 7.5354] w=0.0511 to align # Constraint # added constraint: constraint((T0293)P161.CB, (T0293)K188.CB) [> 3.9432 = 6.5720 < 8.5436] w=0.0510 to align # Constraint # added constraint: constraint((T0293)P145.CB, (T0293)I190.CB) [> 4.1342 = 6.8904 < 8.9575] w=0.0501 to align # Constraint # added constraint: constraint((T0293)V117.CB, (T0293)M126.CB) [> 4.2582 = 7.0969 < 9.2260] w=0.0501 to align # Constraint # added constraint: constraint((T0293)R189.CB, (T0293)R238.CB) [> 3.8759 = 6.4598 < 8.3977] w=0.0458 to align # Constraint # added constraint: constraint((T0293)P145.CB, (T0293)G209.CA) [> 3.7627 = 6.2712 < 8.1525] w=0.0458 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)A72.CB) [> 3.7066 = 6.1776 < 8.0309] w=0.0458 to align # Constraint # added constraint: constraint((T0293)V38.CB, (T0293)G71.CA) [> 3.5474 = 5.9124 < 7.6861] w=0.0452 to align # Constraint # added constraint: constraint((T0293)P145.CB, (T0293)G182.CA) [> 3.6810 = 6.1350 < 7.9755] w=0.0452 to align # Constraint # added constraint: constraint((T0293)C16.CB, (T0293)L31.CB) [> 3.6484 = 6.0806 < 7.9048] w=0.0452 to align # Constraint # added constraint: constraint((T0293)L19.CB, (T0293)D28.CB) [> 3.6672 = 6.1120 < 7.9456] w=0.0452 to align # Constraint # added constraint: constraint((T0293)T37.CB, (T0293)M96.CB) [> 3.4219 = 5.7032 < 7.4141] w=0.0452 to align # Constraint # added constraint: constraint((T0293)F23.CB, (T0293)I45.CB) [> 3.6090 = 6.0150 < 7.8195] w=0.0452 to align # Constraint # added constraint: constraint((T0293)S73.CB, (T0293)N108.CB) [> 3.8618 = 6.4364 < 8.3673] w=0.0452 to align # Constraint # added constraint: constraint((T0293)W47.CB, (T0293)M240.CB) [> 3.8776 = 6.4627 < 8.4015] w=0.0452 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)F146.CB) [> 3.9469 = 6.5782 < 8.5516] w=0.0452 to align # Constraint # added constraint: constraint((T0293)L14.CB, (T0293)A72.CB) [> 3.8131 = 6.3551 < 8.2617] w=0.0452 to align # Constraint # added constraint: constraint((T0293)D22.CB, (T0293)C74.CB) [> 3.7072 = 6.1787 < 8.0323] w=0.0446 to align # Constraint # added constraint: constraint((T0293)L124.CB, (T0293)C140.CB) [> 4.1911 = 6.9851 < 9.0806] w=0.0400 to align # Constraint # added constraint: constraint((T0293)L34.CB, (T0293)M96.CB) [> 3.9495 = 6.5825 < 8.5572] w=0.0387 to align # Constraint # added constraint: constraint((T0293)I68.CB, (T0293)P120.CB) [> 4.6118 = 7.6864 < 9.9923] w=0.0387 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)A90.CB) [> 3.4476 = 5.7460 < 7.4698] w=0.0387 to align # Constraint # added constraint: constraint((T0293)Y44.CB, (T0293)M240.CB) [> 4.0684 = 6.7806 < 8.8148] w=0.0387 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)C235.CB) [> 4.2732 = 7.1220 < 9.2586] w=0.0387 to align # Constraint # added constraint: constraint((T0293)R20.CB, (T0293)I35.CB) [> 3.7516 = 6.2527 < 8.1286] w=0.0387 to align # Constraint # added constraint: constraint((T0293)T15.CB, (T0293)C74.CB) [> 3.9418 = 6.5697 < 8.5406] w=0.0387 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)N108.CB) [> 3.4095 = 5.6825 < 7.3873] w=0.0372 to align # Constraint # added constraint: constraint((T0293)N108.CB, (T0293)K118.CB) [> 3.8021 = 6.3368 < 8.2379] w=0.0372 to align # Constraint # added constraint: constraint((T0293)T17.CB, (T0293)I29.CB) [> 4.3966 = 7.3276 < 9.5259] w=0.0329 to align # Constraint # added constraint: constraint((T0293)T15.CB, (T0293)I29.CB) [> 3.6648 = 6.1080 < 7.9404] w=0.0323 to align # Constraint # added constraint: constraint((T0293)E183.CB, (T0293)G209.CA) [> 4.1274 = 6.8790 < 8.9427] w=0.0323 to align # Constraint # added constraint: constraint((T0293)D22.CB, (T0293)A72.CB) [> 4.1433 = 6.9054 < 8.9771] w=0.0323 to align # Constraint # added constraint: constraint((T0293)L14.CB, (T0293)C97.CB) [> 4.1857 = 6.9761 < 9.0689] w=0.0322 to align # Constraint # added constraint: constraint((T0293)D67.CB, (T0293)G80.CA) [> 4.4170 = 7.3616 < 9.5701] w=0.0322 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)E220.CB) [> 4.3493 = 7.2489 < 9.4236] w=0.0317 to align # Constraint # added constraint: constraint((T0293)C140.CB, (T0293)P161.CB) [> 4.5828 = 7.6380 < 9.9294] w=0.0317 to align # Constraint # added constraint: constraint((T0293)I45.CB, (T0293)F234.CB) [> 4.1314 = 6.8857 < 8.9514] w=0.0315 to align # Constraint # added constraint: constraint((T0293)E176.CB, (T0293)I191.CB) [> 4.0205 = 6.7008 < 8.7111] w=0.0315 to align # Constraint # added constraint: constraint((T0293)A90.CB, (T0293)N108.CB) [> 4.2938 = 7.1563 < 9.3032] w=0.0307 to align # Constraint # added constraint: constraint((T0293)L14.CB, (T0293)C74.CB) [> 3.9614 = 6.6024 < 8.5831] w=0.0264 to align # Constraint # added constraint: constraint((T0293)A13.CB, (T0293)L31.CB) [> 4.4137 = 7.3561 < 9.5629] w=0.0258 to align # Constraint # added constraint: constraint((T0293)C16.CB, (T0293)I29.CB) [> 3.5176 = 5.8626 < 7.6214] w=0.0258 to align # Constraint # added constraint: constraint((T0293)P145.CB, (T0293)G181.CA) [> 3.3695 = 5.6158 < 7.3005] w=0.0258 to align # Constraint # added constraint: constraint((T0293)L34.CB, (T0293)S73.CB) [> 4.3848 = 7.3080 < 9.5004] w=0.0258 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)L42.CB) [> 4.0437 = 6.7395 < 8.7613] w=0.0258 to align # Constraint # added constraint: constraint((T0293)T15.CB, (T0293)I35.CB) [> 3.6253 = 6.0422 < 7.8548] w=0.0258 to align # Constraint # added constraint: constraint((T0293)K210.CB, (T0293)C235.CB) [> 3.3579 = 5.5965 < 7.2755] w=0.0258 to align # Constraint # added constraint: constraint((T0293)P161.CB, (T0293)L201.CB) [> 3.0509 = 5.0849 < 6.6104] w=0.0258 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)N108.CB) [> 4.3707 = 7.2845 < 9.4698] w=0.0243 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)N108.CB) [> 3.2613 = 5.4355 < 7.0661] w=0.0243 to align # Constraint # added constraint: constraint((T0293)A122.CB, (T0293)I174.CB) [> 4.5910 = 7.6516 < 9.9471] w=0.0200 to align # Constraint # added constraint: constraint((T0293)A13.CB, (T0293)N108.CB) [> 3.5320 = 5.8866 < 7.6526] w=0.0200 to align # Constraint # added constraint: constraint((T0293)R12.CB, (T0293)L42.CB) [> 4.0597 = 6.7661 < 8.7960] w=0.0194 to align # Constraint # added constraint: constraint((T0293)A72.CB, (T0293)V116.CB) [> 4.1657 = 6.9428 < 9.0257] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)P145.CB) [> 3.4925 = 5.8209 < 7.5671] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)V93.CB) [> 4.5269 = 7.5448 < 9.8083] w=0.0194 to align # Constraint # added constraint: constraint((T0293)C74.CB, (T0293)N108.CB) [> 2.4102 = 4.0171 < 5.2222] w=0.0194 to align # Constraint # added constraint: constraint((T0293)G71.CA, (T0293)V93.CB) [> 4.7597 = 7.9329 < 10.3128] w=0.0194 to align # Constraint # added constraint: constraint((T0293)V11.CB, (T0293)L31.CB) [> 3.8785 = 6.4642 < 8.4035] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T17.CB, (T0293)S26.CB) [> 4.0190 = 6.6983 < 8.7078] w=0.0194 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)I45.CB) [> 3.9052 = 6.5087 < 8.4613] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)L89.CB) [> 4.5104 = 7.5174 < 9.7726] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T70.CB, (T0293)F88.CB) [> 4.7701 = 7.9501 < 10.3351] w=0.0194 to align # Constraint # added constraint: constraint((T0293)R12.CB, (T0293)I45.CB) [> 4.2198 = 7.0331 < 9.1430] w=0.0194 to align # Constraint # added constraint: constraint((T0293)V11.CB, (T0293)N108.CB) [> 3.3076 = 5.5127 < 7.1665] w=0.0194 to align # Constraint # added constraint: constraint((T0293)L14.CB, (T0293)N108.CB) [> 4.1493 = 6.9154 < 8.9900] w=0.0194 to align # Constraint # added constraint: constraint((T0293)G209.CA, (T0293)K218.CB) [> 4.0371 = 6.7285 < 8.7470] w=0.0194 to align # Constraint # added constraint: constraint((T0293)T17.CB, (T0293)A72.CB) [> 3.2546 = 5.4243 < 7.0516] w=0.0135 to align # Constraint # added constraint: constraint((T0293)A13.CB, (T0293)I35.CB) [> 3.5570 = 5.9283 < 7.7068] w=0.0129 to align # Constraint # added constraint: constraint((T0293)G65.CA, (T0293)L201.CB) [> 4.6451 = 7.7418 < 10.0643] w=0.0129 to align # Constraint # added constraint: constraint((T0293)R12.CB, (T0293)R41.CB) [> 3.9145 = 6.5241 < 8.4813] w=0.0129 to align # Constraint # added constraint: constraint((T0293)P161.CB, (T0293)E220.CB) [> 4.1398 = 6.8997 < 8.9696] w=0.0129 to align # Constraint # added constraint: constraint((T0293)F88.CB, (T0293)N108.CB) [> 4.4709 = 7.4515 < 9.6869] w=0.0129 to align # Constraint # added constraint: constraint((T0293)D94.CB, (T0293)V119.CB) [> 4.4540 = 7.4233 < 9.6503] w=0.0129 to align # Constraint # added constraint: constraint((T0293)V11.CB, (T0293)A72.CB) [> 3.6855 = 6.1425 < 7.9853] w=0.0129 to align # Constraint # added constraint: constraint((T0293)V11.CB, (T0293)W47.CB) [> 3.8677 = 6.4461 < 8.3799] w=0.0129 to align # Constraint # added constraint: constraint((T0293)T17.CB, (T0293)L40.CB) [> 3.8461 = 6.4101 < 8.3331] w=0.0129 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)G71.CA) [> 4.7509 = 7.9182 < 10.2937] w=0.0129 to align # Constraint # added constraint: constraint((T0293)F5.CB, (T0293)T17.CB) [> 4.0787 = 6.7979 < 8.8373] w=0.0129 to align # Constraint # added constraint: constraint((T0293)F5.CB, (T0293)L14.CB) [> 4.1676 = 6.9459 < 9.0297] w=0.0129 to align # Constraint # added constraint: constraint((T0293)N143.CB, (T0293)E183.CB) [> 4.6938 = 7.8230 < 10.1699] w=0.0099 to align # Constraint # added constraint: constraint((T0293)T17.CB, (T0293)C74.CB) [> 2.3866 = 3.9777 < 5.1711] w=0.0071 to align # Constraint # added constraint: constraint((T0293)C16.CB, (T0293)N108.CB) [> 2.7011 = 4.5019 < 5.8524] w=0.0071 to align # Constraint # added constraint: constraint((T0293)C16.CB, (T0293)C74.CB) [> 4.6680 = 7.7800 < 10.1140] w=0.0071 to align # Constraint # added constraint: constraint((T0293)K115.CB, (T0293)L125.CB) [> 4.7697 = 7.9495 < 10.3344] w=0.0065 to align # Constraint # added constraint: constraint((T0293)F5.CB, (T0293)L19.CB) [> 3.4182 = 5.6969 < 7.4060] w=0.0065 to align # Constraint # added constraint: constraint((T0293)F5.CB, (T0293)C16.CB) [> 3.2137 = 5.3561 < 6.9629] w=0.0065 to align # Constraint # added constraint: constraint((T0293)N4.CB, (T0293)T17.CB) [> 3.2081 = 5.3469 < 6.9510] w=0.0065 to align # Constraint # added constraint: constraint((T0293)F5.CB, (T0293)D94.CB) [> 4.6570 = 7.7617 < 10.0902] w=0.0065 to align # Constraint # added constraint: constraint((T0293)N143.CB, (T0293)G209.CA) [> 3.5556 = 5.9260 < 7.7037] w=0.0065 to align # Constraint # added constraint: constraint((T0293)L25.CB, (T0293)N84.CB) [> 4.7141 = 7.8568 < 10.2138] w=0.0065 to align # Constraint # added constraint: constraint((T0293)C16.CB, (T0293)C235.CB) [> 4.5892 = 7.6487 < 9.9433] w=0.0065 to align # Constraint # added constraint: constraint((T0293)L18.CB, (T0293)L34.CB) [> 3.5655 = 5.9426 < 7.7253] w=0.0065 to align # Constraint # added constraint: constraint((T0293)A13.CB, (T0293)F248.CB) [> 4.1148 = 6.8580 < 8.9153] w=0.0065 to align # Constraint # added constraint: constraint((T0293)A13.CB, (T0293)I45.CB) [> 3.4993 = 5.8322 < 7.5819] w=0.0065 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0293/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0293/decoys/ # ReadConformPDB reading from PDB file chimera1.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file fromTry4.proto.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file lineup230and245take1.2rotateNterminusAndMove.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file lineup230and245take1.9rotateNtermSlide33-37helix.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file shift232over1.1FromTry8.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file shift232over1.2FromTry8.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file shift232over1.2andMoveH33-37.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file shift232over1FromTry8.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file shift232over2FromTry8.renum.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 213 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 225 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 215 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0293)A179.C and (T0293)E180.N only 0.000 apart, marking (T0293)E180.N as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.CA only 0.000 apart, marking (T0293)E180.CA as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.CA only 0.000 apart, marking (T0293)E180.CA as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.CB only 0.000 apart, marking (T0293)E180.CB as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.CB only 0.000 apart, marking (T0293)E180.CB as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.CB only 0.000 apart, marking (T0293)E180.CB as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.CG only 0.000 apart, marking (T0293)E180.CG as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.CG only 0.000 apart, marking (T0293)E180.CG as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.CG only 0.000 apart, marking (T0293)E180.CG as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.CG only 0.000 apart, marking (T0293)E180.CG as missing WARNING: atoms too close: (T0293)E180.CG and (T0293)E180.CD only 0.000 apart, marking (T0293)E180.CD as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.CD only 0.000 apart, marking (T0293)E180.CD as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.CD only 0.000 apart, marking (T0293)E180.CD as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.CD only 0.000 apart, marking (T0293)E180.CD as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.CD only 0.000 apart, marking (T0293)E180.CD as missing WARNING: atoms too close: (T0293)E180.CD and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)E180.CG and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.OE1 only 0.000 apart, marking (T0293)E180.OE1 as missing WARNING: atoms too close: (T0293)E180.OE1 and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.CD and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.CG and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.OE2 only 0.000 apart, marking (T0293)E180.OE2 as missing WARNING: atoms too close: (T0293)E180.OE2 and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.OE1 and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.CD and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.CG and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.O only 0.000 apart, marking (T0293)E180.O as missing WARNING: atoms too close: (T0293)E180.O and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.OE2 and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.OE1 and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.CD and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.CG and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.CB and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.CA and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)E180.N and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing WARNING: atoms too close: (T0293)A179.C and (T0293)E180.C only 0.000 apart, marking (T0293)E180.C as missing # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 193 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 220 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 178 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 241 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 212 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 246 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 242 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 209 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 204 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 247 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 233 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 222 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 211 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 240 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 204 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 249 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 236 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 244 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 239 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 242 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 243 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 245 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0293 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.0931 model score -0.0744 model score -0.0924 model score -0.0926 model score -0.0757 model score -0.0819 model score -0.0832 model score -0.0800 model score -0.0684 model score 0.1647 model score 0.1724 model score 0.1782 model score 0.1515 model score 0.1892 model score 0.1074 model score 0.0980 model score 0.1048 model score 0.1517 model score -0.0473 model score 0.1505 model score 0.1196 model score 0.0696 model score 0.0707 model score 0.1079 model score 0.2295 model score 0.1180 model score 0.1911 model score 0.4884 model score 0.9008 model score 1.4670 model score 1.4301 model score 1.6241 model score 1.7187 model score 1.5024 model score -0.2902 model score -0.1264 model score -0.1266 model score -0.1337 model score 0.0319 model score -0.1267 model score -0.1317 model score -0.1450 model score -0.1828 model score -0.1805 model score -0.1596 model score -0.1073 model score -0.2138 model score 0.1127 model score -0.2044 model score 0.5842 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.2134 model score -0.0422 model score -0.1192 model score -0.1450 model score -0.2105 model score -0.1961 model score -0.1315 model score -0.1450 model score -0.1450 model score -0.1317 model score 0.2295 model score 0.4131 model score 0.1274 model score 0.2334 model score 0.8490 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.6016 model score 0.0376 model score 0.1598 model score -0.0709 model score 0.0252 model score 0.9442 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.1961 model score -0.2237 model score -0.1315 model score 0.1955 model score 0.1943 model score 0.0454 model score -0.1302 model score -0.1691 model score -0.2147 model score -0.2585 model score -0.2551 model score -0.2479 model score 1.8207 model score 1.3829 model score 1.6642 model score 1.6261 model score 1.5415 model score -0.1807 model score -0.0074 model score -0.1747 model score -0.1108 model score -0.1832 model score -0.2003 model score -0.0256 model score -0.1615 model score -0.0654 model score -0.0131 model score -0.1321 model score -0.1196 model score -0.1373 model score -0.2120 model score -0.1306 model score -0.1709 model score 2.0575 model score 2.2111 model score 2.2316 model score 2.2360 model score 2.0866 model score -0.0877 model score -0.0894 model score -0.1040 model score -0.0952 model score -0.1789 model score -0.1838 model score -0.0758 model score 0.0590 model score 0.1334 model score -0.1725 model score -0.1641 model score -0.1464 model score -0.1635 model score 0.0636 model score -0.1413 model score -0.1650 model score -0.2105 model score -0.1576 model score -0.1360 model score -0.2146 model score -0.1430 model score -0.1139 model score -0.1253 model score -0.1471 model score -0.0936 model score -0.1276 model score 0.0181 model score -0.1877 model score -0.1394 model score -0.1246 model score -0.0701 model score -0.1273 model score 0.0171 model score -0.0754 model score 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max: 0.0237 USE_EVALUE, weight: 0.1000 eval: 0.0237 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0237 USE_EVALUE, weight: 0.9998 eval: 0.0000 min: 0.0000 max: 0.0237 Number of contacts in models: 260 Number of contacts in alignments: 159 NUMB_ALIGNS: 159 Adding 13406 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -434.7088, CN propb: -434.7088 weights: 0.2977 constraints: 700 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 700 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 700 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 12706 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 12706 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 13406 # command: