# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0293 numbered 1 through 250 Created new target T0293 from T0293.a2m # command:CPU_time= 6.370 sec, elapsed time= 6.440 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nv8A/T0293-1nv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nv8A expands to /projects/compbio/data/pdb/1nv8.pdb.gz 1nv8A:Skipped atom 799, because occupancy 0.5 <= 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/T0293-1nv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nv8A read from 1nv8A/T0293-1nv8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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 # choosing archetypes in rotamer library 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=11 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nv8A/T0293-1nv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1nv8A/T0293-1nv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nv8A read from 1nv8A/T0293-1nv8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=27 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nv8A/T0293-1nv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1nv8A/T0293-1nv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nv8A read from 1nv8A/T0293-1nv8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=37 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dusA/T0293-1dusA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dusA expands to /projects/compbio/data/pdb/1dus.pdb.gz 1dusA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1dusA/T0293-1dusA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dusA read from 1dusA/T0293-1dusA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dusA to template set # found chain 1dusA in template 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=50 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dusA/T0293-1dusA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1dusA/T0293-1dusA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dusA read from 1dusA/T0293-1dusA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dusA in template 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=64 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dusA/T0293-1dusA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1dusA/T0293-1dusA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dusA read from 1dusA/T0293-1dusA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dusA in template 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=74 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg1A/T0293-1jg1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1jg1A/T0293-1jg1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg1A read from 1jg1A/T0293-1jg1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=83 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg1A/T0293-1jg1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1jg1A/T0293-1jg1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg1A read from 1jg1A/T0293-1jg1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=93 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg1A/T0293-1jg1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1jg1A/T0293-1jg1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jg1A read from 1jg1A/T0293-1jg1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=101 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o54A/T0293-1o54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o54A expands to /projects/compbio/data/pdb/1o54.pdb.gz 1o54A:Skipped atom 202, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 204, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 206, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 208, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 210, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1056, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1058, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1060, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1062, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1458, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1460, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1462, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1464, because occupancy 0.350 <= existing 0.650 in 1o54A Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1o54A Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1o54A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1o54A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1o54A Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1o54A # T0293 read from 1o54A/T0293-1o54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o54A read from 1o54A/T0293-1o54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o54A to template set # found chain 1o54A in template 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=114 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o54A/T0293-1o54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1o54A/T0293-1o54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o54A read from 1o54A/T0293-1o54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o54A in template 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=129 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o54A/T0293-1o54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1o54A/T0293-1o54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o54A read from 1o54A/T0293-1o54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o54A in template 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=136 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl5A/T0293-1dl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dl5A expands to /projects/compbio/data/pdb/1dl5.pdb.gz 1dl5A:Skipped atom 638, because occupancy 0.490 <= existing 0.510 in 1dl5A Skipped atom 640, because occupancy 0.490 <= existing 0.510 in 1dl5A Skipped atom 642, because occupancy 0.490 <= existing 0.510 in 1dl5A Skipped atom 1419, because occupancy 0.450 <= existing 0.550 in 1dl5A Skipped atom 1421, because occupancy 0.450 <= existing 0.550 in 1dl5A Skipped atom 2357, because occupancy 0.490 <= existing 0.510 in 1dl5A Skipped atom 2359, because occupancy 0.490 <= existing 0.510 in 1dl5A # T0293 read from 1dl5A/T0293-1dl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl5A read from 1dl5A/T0293-1dl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dl5A to template set # found chain 1dl5A in template 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=146 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl5A/T0293-1dl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1dl5A/T0293-1dl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl5A read from 1dl5A/T0293-1dl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dl5A in template 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=156 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl5A/T0293-1dl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1dl5A/T0293-1dl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl5A read from 1dl5A/T0293-1dl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dl5A in template 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=163 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3lA/T0293-1f3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f3lA expands to /projects/compbio/data/pdb/1f3l.pdb.gz 1f3lA:# T0293 read from 1f3lA/T0293-1f3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3lA read from 1f3lA/T0293-1f3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f3lA to template set # 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=172 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3lA/T0293-1f3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1f3lA/T0293-1f3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3lA read from 1f3lA/T0293-1f3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=184 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3lA/T0293-1f3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1f3lA/T0293-1f3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f3lA read from 1f3lA/T0293-1f3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=193 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1im8A/T0293-1im8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1im8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1im8A read from 1im8A/T0293-1im8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1im8A to template set # 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=205 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1im8A/T0293-1im8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1im8A/T0293-1im8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1im8A read from 1im8A/T0293-1im8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=217 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1im8A/T0293-1im8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1im8A/T0293-1im8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1im8A read from 1im8A/T0293-1im8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=224 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9gA/T0293-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i9gA expands to /projects/compbio/data/pdb/1i9g.pdb.gz 1i9gA:# T0293 read from 1i9gA/T0293-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0293-1i9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=237 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9gA/T0293-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1i9gA/T0293-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0293-1i9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=248 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9gA/T0293-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1i9gA/T0293-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i9gA read from 1i9gA/T0293-1i9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=257 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g38A/T0293-1g38A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g38A expands to /projects/compbio/data/pdb/1g38.pdb.gz 1g38A:# T0293 read from 1g38A/T0293-1g38A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g38A read from 1g38A/T0293-1g38A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g38A to template set # 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=267 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g38A/T0293-1g38A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1g38A/T0293-1g38A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g38A read from 1g38A/T0293-1g38A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=279 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g38A/T0293-1g38A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1g38A/T0293-1g38A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g38A read from 1g38A/T0293-1g38A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=288 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne2A/T0293-1ne2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ne2A expands to /projects/compbio/data/pdb/1ne2.pdb.gz 1ne2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1ne2A/T0293-1ne2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ne2A read from 1ne2A/T0293-1ne2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ne2A to template set # found chain 1ne2A in template 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=298 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne2A/T0293-1ne2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ne2A/T0293-1ne2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ne2A read from 1ne2A/T0293-1ne2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ne2A in template 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=310 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne2A/T0293-1ne2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ne2A/T0293-1ne2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ne2A read from 1ne2A/T0293-1ne2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ne2A in template 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=322 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/T0293-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sqgA expands to /projects/compbio/data/pdb/1sqg.pdb.gz 1sqgA:Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 1sqgA # T0293 read from 1sqgA/T0293-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0293-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sqgA to template set # found chain 1sqgA in template 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=331 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/T0293-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1sqgA/T0293-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0293-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sqgA in template 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=342 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/T0293-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1sqgA/T0293-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0293-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sqgA in template 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=349 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/T0293-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0293-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2as0A to template set # 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=358 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/T0293-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2as0A/T0293-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0293-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=373 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/T0293-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2as0A/T0293-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0293-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=379 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1nA/T0293-1i1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i1nA expands to /projects/compbio/data/pdb/1i1n.pdb.gz 1i1nA:# T0293 read from 1i1nA/T0293-1i1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1nA read from 1i1nA/T0293-1i1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i1nA to template set # found chain 1i1nA in template 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=387 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1nA/T0293-1i1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1i1nA/T0293-1i1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1nA read from 1i1nA/T0293-1i1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1nA in template set T0293 13 :ALTCTLL 1i1nA 35 :DRSHYAK 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=398 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1nA/T0293-1i1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1i1nA/T0293-1i1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1nA read from 1i1nA/T0293-1i1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1nA in template 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=405 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/T0293-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ufkA expands to /projects/compbio/data/pdb/1ufk.pdb.gz 1ufkA:# T0293 read from 1ufkA/T0293-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0293-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ufkA to template set # 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=416 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/T0293-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ufkA/T0293-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0293-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=426 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/T0293-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ufkA/T0293-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0293-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=435 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixkA/T0293-1ixkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1ixkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixkA read from 1ixkA/T0293-1ixkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ixkA to template set # 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=444 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixkA/T0293-1ixkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ixkA/T0293-1ixkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixkA read from 1ixkA/T0293-1ixkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=456 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixkA/T0293-1ixkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ixkA/T0293-1ixkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixkA read from 1ixkA/T0293-1ixkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=464 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1dA/T0293-1h1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h1dA expands to /projects/compbio/data/pdb/1h1d.pdb.gz 1h1dA:# T0293 read from 1h1dA/T0293-1h1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1dA read from 1h1dA/T0293-1h1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h1dA to template set # 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=472 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1dA/T0293-1h1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1h1dA/T0293-1h1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1dA read from 1h1dA/T0293-1h1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=479 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1dA/T0293-1h1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1h1dA/T0293-1h1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1dA read from 1h1dA/T0293-1h1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=487 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wznA/T0293-1wznA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wznA expands to /projects/compbio/data/pdb/1wzn.pdb.gz 1wznA:# T0293 read from 1wznA/T0293-1wznA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wznA read from 1wznA/T0293-1wznA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wznA to template set # 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=499 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wznA/T0293-1wznA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wznA/T0293-1wznA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wznA read from 1wznA/T0293-1wznA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=513 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wznA/T0293-1wznA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wznA/T0293-1wznA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wznA read from 1wznA/T0293-1wznA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=521 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l3iA/T0293-1l3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1l3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l3iA read from 1l3iA/T0293-1l3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l3iA to template set # 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=530 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l3iA/T0293-1l3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1l3iA/T0293-1l3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l3iA read from 1l3iA/T0293-1l3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=541 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l3iA/T0293-1l3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1l3iA/T0293-1l3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l3iA read from 1l3iA/T0293-1l3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=550 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xdzA/T0293-1xdzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xdzA expands to /projects/compbio/data/pdb/1xdz.pdb.gz 1xdzA:# T0293 read from 1xdzA/T0293-1xdzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdzA read from 1xdzA/T0293-1xdzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xdzA to template set # found chain 1xdzA in template 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=560 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xdzA/T0293-1xdzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xdzA/T0293-1xdzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdzA read from 1xdzA/T0293-1xdzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xdzA in template 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=570 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xdzA/T0293-1xdzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xdzA/T0293-1xdzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdzA read from 1xdzA/T0293-1xdzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xdzA in template 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=579 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve3A/T0293-1ve3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1ve3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve3A read from 1ve3A/T0293-1ve3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ve3A to template set # 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=589 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve3A/T0293-1ve3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ve3A/T0293-1ve3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve3A read from 1ve3A/T0293-1ve3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=601 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve3A/T0293-1ve3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ve3A/T0293-1ve3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ve3A read from 1ve3A/T0293-1ve3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=612 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxxA/T0293-1wxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1wxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxxA read from 1wxxA/T0293-1wxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wxxA to template set # 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=625 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxxA/T0293-1wxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wxxA/T0293-1wxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxxA read from 1wxxA/T0293-1wxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=638 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wxxA/T0293-1wxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wxxA/T0293-1wxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wxxA read from 1wxxA/T0293-1wxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=645 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1inlA/T0293-1inlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1inlA expands to /projects/compbio/data/pdb/1inl.pdb.gz 1inlA:# T0293 read from 1inlA/T0293-1inlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1inlA read from 1inlA/T0293-1inlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1inlA to template set # found chain 1inlA in template 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=655 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1inlA/T0293-1inlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1inlA/T0293-1inlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1inlA read from 1inlA/T0293-1inlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1inlA in template 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=668 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1inlA/T0293-1inlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1inlA/T0293-1inlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1inlA read from 1inlA/T0293-1inlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1inlA in template 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=680 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0293-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qzzA expands to /projects/compbio/data/pdb/1qzz.pdb.gz 1qzzA:# T0293 read from 1qzzA/T0293-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0293-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=691 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0293-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1qzzA/T0293-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0293-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=702 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0293-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1qzzA/T0293-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0293-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=709 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxlA/T0293-1xxlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1xxlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xxlA read from 1xxlA/T0293-1xxlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xxlA to template set # 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=718 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxlA/T0293-1xxlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xxlA/T0293-1xxlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xxlA read from 1xxlA/T0293-1xxlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=728 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxlA/T0293-1xxlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xxlA/T0293-1xxlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xxlA read from 1xxlA/T0293-1xxlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=735 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl5A/T0293-1vl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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 0.500 <= 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 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/T0293-1vl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl5A read from 1vl5A/T0293-1vl5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vl5A to template set # 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=746 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl5A/T0293-1vl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1vl5A/T0293-1vl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl5A read from 1vl5A/T0293-1vl5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=758 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl5A/T0293-1vl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1vl5A/T0293-1vl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vl5A read from 1vl5A/T0293-1vl5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=767 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kpgA/T0293-1kpgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1kpgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kpgA read from 1kpgA/T0293-1kpgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kpgA to template set # 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=777 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kpgA/T0293-1kpgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1kpgA/T0293-1kpgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kpgA read from 1kpgA/T0293-1kpgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=792 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kpgA/T0293-1kpgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1kpgA/T0293-1kpgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kpgA read from 1kpgA/T0293-1kpgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=799 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fytA/T0293-2fytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2fytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fytA read from 2fytA/T0293-2fytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fytA to template set # 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=810 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fytA/T0293-2fytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fytA/T0293-2fytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fytA read from 2fytA/T0293-2fytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=822 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fytA/T0293-2fytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fytA/T0293-2fytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fytA read from 2fytA/T0293-2fytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=831 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ej0A/T0293-1ej0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ej0A expands to /projects/compbio/data/pdb/1ej0.pdb.gz 1ej0A:# T0293 read from 1ej0A/T0293-1ej0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej0A read from 1ej0A/T0293-1ej0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ej0A to template set # found chain 1ej0A in template 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=843 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ej0A/T0293-1ej0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ej0A/T0293-1ej0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej0A read from 1ej0A/T0293-1ej0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ej0A in template 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=855 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ej0A/T0293-1ej0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ej0A/T0293-1ej0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ej0A read from 1ej0A/T0293-1ej0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ej0A in template 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=867 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0293-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0293-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wy7A to template set # 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=878 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0293-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wy7A/T0293-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0293-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=892 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0293-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1wy7A/T0293-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0293-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=902 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwvA/T0293-1uwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1uwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uwvA read from 1uwvA/T0293-1uwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uwvA to template set # 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=914 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwvA/T0293-1uwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1uwvA/T0293-1uwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uwvA read from 1uwvA/T0293-1uwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=928 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwvA/T0293-1uwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1uwvA/T0293-1uwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uwvA read from 1uwvA/T0293-1uwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=936 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fk8A/T0293-2fk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fk8A expands to /projects/compbio/data/pdb/2fk8.pdb.gz 2fk8A:# T0293 read from 2fk8A/T0293-2fk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fk8A read from 2fk8A/T0293-2fk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=946 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fk8A/T0293-2fk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fk8A/T0293-2fk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fk8A read from 2fk8A/T0293-2fk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=961 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fk8A/T0293-2fk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fk8A/T0293-2fk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fk8A read from 2fk8A/T0293-2fk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=969 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2frnA/T0293-2frnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2frnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2frnA read from 2frnA/T0293-2frnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2frnA to template set # 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=981 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2frnA/T0293-2frnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2frnA/T0293-2frnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2frnA read from 2frnA/T0293-2frnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=994 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2frnA/T0293-2frnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2frnA/T0293-2frnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2frnA read from 2frnA/T0293-2frnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1002 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1eA/T0293-1l1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l1eA expands to /projects/compbio/data/pdb/1l1e.pdb.gz 1l1eA:# T0293 read from 1l1eA/T0293-1l1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1eA read from 1l1eA/T0293-1l1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l1eA to template set # 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=1011 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1eA/T0293-1l1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1l1eA/T0293-1l1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1eA read from 1l1eA/T0293-1l1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1023 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1eA/T0293-1l1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1l1eA/T0293-1l1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1eA read from 1l1eA/T0293-1l1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1029 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp2A/T0293-1fp2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fp2A expands to /projects/compbio/data/pdb/1fp2.pdb.gz 1fp2A:# T0293 read from 1fp2A/T0293-1fp2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp2A read from 1fp2A/T0293-1fp2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fp2A to template set # found chain 1fp2A in template 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=1042 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp2A/T0293-1fp2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1fp2A/T0293-1fp2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp2A read from 1fp2A/T0293-1fp2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fp2A in template 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=1055 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp2A/T0293-1fp2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1fp2A/T0293-1fp2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fp2A read from 1fp2A/T0293-1fp2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fp2A in template 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=1065 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gh1A/T0293-2gh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2gh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gh1A read from 2gh1A/T0293-2gh1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gh1A to template set # 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=1073 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gh1A/T0293-2gh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2gh1A/T0293-2gh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gh1A read from 2gh1A/T0293-2gh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1084 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gh1A/T0293-2gh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2gh1A/T0293-2gh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gh1A read from 2gh1A/T0293-2gh1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1091 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fhpA/T0293-2fhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2fhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fhpA read from 2fhpA/T0293-2fhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fhpA to template set # 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=1099 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fhpA/T0293-2fhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fhpA/T0293-2fhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fhpA read from 2fhpA/T0293-2fhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1111 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fhpA/T0293-2fhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2fhpA/T0293-2fhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fhpA read from 2fhpA/T0293-2fhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1121 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ws6A/T0293-1ws6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1ws6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ws6A read from 1ws6A/T0293-1ws6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ws6A to template set # 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=1129 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ws6A/T0293-1ws6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ws6A/T0293-1ws6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ws6A read from 1ws6A/T0293-1ws6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1140 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ws6A/T0293-1ws6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ws6A/T0293-1ws6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ws6A read from 1ws6A/T0293-1ws6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1151 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o9gA/T0293-1o9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o9gA expands to /projects/compbio/data/pdb/1o9g.pdb.gz 1o9gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1o9gA/T0293-1o9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o9gA read from 1o9gA/T0293-1o9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o9gA to template set # found chain 1o9gA in template 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=1164 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o9gA/T0293-1o9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1o9gA/T0293-1o9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o9gA read from 1o9gA/T0293-1o9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o9gA in template 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=1179 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o9gA/T0293-1o9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1o9gA/T0293-1o9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o9gA read from 1o9gA/T0293-1o9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o9gA in template 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=1191 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f8lA/T0293-2f8lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2f8lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f8lA read from 2f8lA/T0293-2f8lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1206 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f8lA/T0293-2f8lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2f8lA/T0293-2f8lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f8lA read from 2f8lA/T0293-2f8lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=1223 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f8lA/T0293-2f8lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2f8lA/T0293-2f8lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f8lA read from 2f8lA/T0293-2f8lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1236 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvaA/T0293-1xvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xvaA expands to /projects/compbio/data/pdb/1xva.pdb.gz 1xvaA:# T0293 read from 1xvaA/T0293-1xvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvaA read from 1xvaA/T0293-1xvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xvaA to template set # 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=1254 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvaA/T0293-1xvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xvaA/T0293-1xvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvaA read from 1xvaA/T0293-1xvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1270 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvaA/T0293-1xvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1xvaA/T0293-1xvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xvaA read from 1xvaA/T0293-1xvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1284 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6yA/T0293-1m6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1m6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6yA read from 1m6yA/T0293-1m6yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m6yA to template set # 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=1292 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6yA/T0293-1m6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1m6yA/T0293-1m6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6yA read from 1m6yA/T0293-1m6yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1306 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6yA/T0293-1m6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1m6yA/T0293-1m6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6yA read from 1m6yA/T0293-1m6yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1312 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8cA/T0293-1y8cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1y8cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8cA read from 1y8cA/T0293-1y8cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y8cA to template set # 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=1323 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8cA/T0293-1y8cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1y8cA/T0293-1y8cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8cA read from 1y8cA/T0293-1y8cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1337 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8cA/T0293-1y8cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1y8cA/T0293-1y8cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y8cA read from 1y8cA/T0293-1y8cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1347 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri5A/T0293-1ri5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ri5A expands to /projects/compbio/data/pdb/1ri5.pdb.gz 1ri5A:# T0293 read from 1ri5A/T0293-1ri5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri5A read from 1ri5A/T0293-1ri5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ri5A to template set # 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=1355 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri5A/T0293-1ri5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ri5A/T0293-1ri5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri5A read from 1ri5A/T0293-1ri5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1367 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri5A/T0293-1ri5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1ri5A/T0293-1ri5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri5A read from 1ri5A/T0293-1ri5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1376 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avdA/T0293-2avdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2avdA expands to /projects/compbio/data/pdb/2avd.pdb.gz 2avdA:# T0293 read from 2avdA/T0293-2avdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avdA read from 2avdA/T0293-2avdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2avdA to template set # 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=1385 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avdA/T0293-2avdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2avdA/T0293-2avdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avdA read from 2avdA/T0293-2avdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1395 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avdA/T0293-2avdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2avdA/T0293-2avdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avdA read from 2avdA/T0293-2avdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1405 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avnA/T0293-2avnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2avnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avnA read from 2avnA/T0293-2avnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2avnA to template set # 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=1416 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avnA/T0293-2avnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2avnA/T0293-2avnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avnA read from 2avnA/T0293-2avnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1434 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avnA/T0293-2avnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2avnA/T0293-2avnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2avnA read from 2avnA/T0293-2avnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1446 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jsxA/T0293-1jsxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jsxA expands to /projects/compbio/data/pdb/1jsx.pdb.gz 1jsxA:# T0293 read from 1jsxA/T0293-1jsxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jsxA read from 1jsxA/T0293-1jsxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1455 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jsxA/T0293-1jsxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1jsxA/T0293-1jsxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jsxA read from 1jsxA/T0293-1jsxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1466 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jsxA/T0293-1jsxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1jsxA/T0293-1jsxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jsxA read from 1jsxA/T0293-1jsxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1476 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esrA/T0293-2esrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-2esrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2esrA read from 2esrA/T0293-2esrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2esrA to template set # 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=1483 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esrA/T0293-2esrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2esrA/T0293-2esrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2esrA read from 2esrA/T0293-2esrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1494 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2esrA/T0293-2esrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2esrA/T0293-2esrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2esrA read from 2esrA/T0293-2esrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1502 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/T0293-1vlmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1vlmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vlmA read from 1vlmA/T0293-1vlmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vlmA to template set # 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=1515 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/T0293-1vlmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1vlmA/T0293-1vlmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vlmA read from 1vlmA/T0293-1vlmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1532 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/T0293-1vlmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1vlmA/T0293-1vlmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vlmA read from 1vlmA/T0293-1vlmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1542 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b25A/T0293-2b25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b25A expands to /projects/compbio/data/pdb/2b25.pdb.gz 2b25A:# T0293 read from 2b25A/T0293-2b25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b25A read from 2b25A/T0293-2b25A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1556 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b25A/T0293-2b25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2b25A/T0293-2b25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b25A read from 2b25A/T0293-2b25A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1572 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b25A/T0293-2b25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 2b25A/T0293-2b25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b25A read from 2b25A/T0293-2b25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1583 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2gA/T0293-1d2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d2gA expands to /projects/compbio/data/pdb/1d2g.pdb.gz 1d2gA:# T0293 read from 1d2gA/T0293-1d2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2gA read from 1d2gA/T0293-1d2gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d2gA to template set # 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=1599 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2gA/T0293-1d2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1d2gA/T0293-1d2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2gA read from 1d2gA/T0293-1d2gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1614 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2gA/T0293-1d2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1d2gA/T0293-1d2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d2gA read from 1d2gA/T0293-1d2gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1624 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aqjA/T0293-1aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aqjA expands to /projects/compbio/data/pdb/1aqj.pdb.gz 1aqjA:# T0293 read from 1aqjA/T0293-1aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aqjA read from 1aqjA/T0293-1aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1632 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aqjA/T0293-1aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1aqjA/T0293-1aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aqjA read from 1aqjA/T0293-1aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1643 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aqjA/T0293-1aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1aqjA/T0293-1aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aqjA read from 1aqjA/T0293-1aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1651 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6q2/T0293-1g6q2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g6q2 expands to /projects/compbio/data/pdb/1g6q.pdb.gz 1g6q2:# T0293 read from 1g6q2/T0293-1g6q2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g6q2 read from 1g6q2/T0293-1g6q2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=1661 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6q2/T0293-1g6q2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1g6q2/T0293-1g6q2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g6q2 read from 1g6q2/T0293-1g6q2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=1674 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6q2/T0293-1g6q2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1g6q2/T0293-1g6q2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g6q2 read from 1g6q2/T0293-1g6q2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1685 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kr5A/T0293-1kr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0293-1kr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kr5A read from 1kr5A/T0293-1kr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kr5A to template set # 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=1694 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kr5A/T0293-1kr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1kr5A/T0293-1kr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kr5A read from 1kr5A/T0293-1kr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=1705 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kr5A/T0293-1kr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0293 read from 1kr5A/T0293-1kr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kr5A read from 1kr5A/T0293-1kr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=1712 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t43A/T0293-1t43A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t43A expands to /projects/compbio/data/pdb/1t43.pdb.gz 1t43A:# T0293 read from 1t43A/T0293-1t43A-t06-local-adpstyle5.a2m # 1t43A read from 1t43A/T0293-1t43A-t06-local-adpstyle5.a2m # adding 1t43A to template set # found chain 1t43A in template set Warning: unaligning (T0293)F23 because of BadResidue code BAD_PEPTIDE in next template residue (1t43A)S79 Warning: unaligning (T0293)G24 because of BadResidue code BAD_PEPTIDE at template residue (1t43A)S79 Warning: unaligning (T0293)E32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t43A)T88 Warning: unaligning (T0293)R33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t43A)T88 Warning: unaligning (T0293)G237 because of BadResidue code BAD_PEPTIDE in next template residue (1t43A)N267 Warning: unaligning (T0293)R238 because of BadResidue code BAD_PEPTIDE at template residue (1t43A)N267 T0293 6 :KDPEAVRALTCTLL 1t43A 60 :TRRRDGEPIAHLTG T0293 20 :RED 1t43A 75 :REF T0293 25 :LSIDIPL 1t43A 80 :LPLFVSP T0293 34 :LIPT 1t43A 89 :LIPR T0293 43 :NYIHWVEDLIGHQD 1t43A 93 :PDTECLVEQALARL T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 1t43A 107 :PEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKN T0293 114 :IKVVKVPQATL 1t43A 161 :IHILQSDWFSA T0293 126 :MD 1t43A 172 :LA T0293 134 :EIIYDFCMCNPPFFANQLEAKG 1t43A 174 :GQQFAMIVSNPPYIDEQDPHLQ T0293 158 :SRNPRRPPP 1t43A 196 :QGDVRFEPL T0293 168 :SVNTGGITEIMAEGGELEF 1t43A 218 :VHIIEQSRNALVSGGFLLL T0293 207 :MLGKACS 1t43A 237 :EHGWQQG T0293 215 :APLKEELRIQGVPKVTYTEFCQ 1t43A 244 :EAVRQAFILAGYHDVETCRDYG T0293 239 :TMRWALA 1t43A 268 :ERVTLGR Number of specific fragments extracted= 14 number of extra gaps= 3 total=1726 Will force an alignment to be made, even if fragment is small Number of alignments=160 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3tA/T0293-2b3tA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b3tA expands to /projects/compbio/data/pdb/2b3t.pdb.gz 2b3tA:# T0293 read from 2b3tA/T0293-2b3tA-t06-local-adpstyle5.a2m # 2b3tA read from 2b3tA/T0293-2b3tA-t06-local-adpstyle5.a2m # adding 2b3tA to template set # found chain 2b3tA in template set T0293 6 :KDPEAVRALTCTLL 2b3tA 60 :TRRRDGEPIAHLTG T0293 20 :REDFGLSIDIPLERLIPT 2b3tA 75 :REFWSLPLFVSPATLIPR T0293 43 :NYIHWVEDLIGHQD 2b3tA 93 :PDTECLVEQALARL T0293 59 :KSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSD 2b3tA 107 :PEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKN T0293 114 :IKVVKVPQATL 2b3tA 161 :IHILQSDWFSA T0293 126 :MD 2b3tA 172 :LA T0293 134 :EIIYDFCMCNPPFFANQLEAKG 2b3tA 174 :GQQFAMIVSNPPYIDEQDPHLQ T0293 158 :SRNPRRPPP 2b3tA 196 :QGDVRFEPL T0293 168 :SVNTGGITEIMAEGGELEF 2b3tA 218 :VHIIEQSRNALVSGGFLLL T0293 207 :MLGKACS 2b3tA 237 :EHGWQQG T0293 215 :APLKEELRIQGVPKVTYTEFCQGRTMRWALA 2b3tA 244 :EAVRQAFILAGYHDVETCRDYGDNERVTLGR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1737 Will force an alignment to be made, even if fragment is small Number of alignments=161 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sg9A/T0293-1sg9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sg9A expands to /projects/compbio/data/pdb/1sg9.pdb.gz 1sg9A:# T0293 read from 1sg9A/T0293-1sg9A-t06-local-adpstyle5.a2m # 1sg9A read from 1sg9A/T0293-1sg9A-t06-local-adpstyle5.a2m # adding 1sg9A to template set # found chain 1sg9A in template set T0293 6 :KDPEAVRALTCTLL 1sg9A 71 :EKRASGYPLHYILG T0293 20 :REDFGLSIDIPLERLIPT 1sg9A 86 :KEFMGLSFLVEEGVFVPR T0293 39 :PLRLNYIHWVEDLIG 1sg9A 104 :PETEELVELALELIR T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1sg9A 119 :KYGIKTVADIGTGSGAIGVSVAKF T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDA 1sg9A 143 :SDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEK T0293 134 :EIIYDFCMCNPPFFANQLEAK 1sg9A 188 :FASIEMILSNPPYVKSSAHLP T0293 158 :SRNPRRPP 1sg9A 209 :KDVLFEPP T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKRLRWYSC 1sg9A 226 :LDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVF Number of specific fragments extracted= 8 number of extra gaps= 0 total=1745 Will force an alignment to be made, even if fragment is small Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vq1A/T0293-1vq1A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vq1A expands to /projects/compbio/data/pdb/1vq1.pdb.gz 1vq1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1vq1A/T0293-1vq1A-t06-local-adpstyle5.a2m # 1vq1A read from 1vq1A/T0293-1vq1A-t06-local-adpstyle5.a2m # adding 1vq1A to template set # found chain 1vq1A in template set Warning: unaligning (T0293)C142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vq1A)N197 Warning: unaligning (T0293)N143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vq1A)N197 Warning: unaligning (T0293)E152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vq1A)L212 Warning: unaligning (T0293)A153 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vq1A)L212 Warning: unaligning (T0293)R162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vq1A)F213 T0293 6 :KDPEAVRALTCTLL 1vq1A 71 :EKRASGYPLHYILG T0293 20 :REDFGLSIDIPLERLIPT 1vq1A 86 :KEFMGLSFLVEEGVFVPR T0293 39 :PLRLNYIHWVEDLIG 1vq1A 104 :PETEELVELALELIR T0293 59 :KSTLRRGIDIGTGASCIYPLLGAT 1vq1A 119 :KYGIKTVADIGTGSGAIGVSVAKF T0293 84 :NGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQATLLMDA 1vq1A 143 :SDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEK T0293 134 :EIIYDFCM 1vq1A 188 :FASIEMIL T0293 144 :PPFFANQL 1vq1A 198 :PPYVKSSA T0293 163 :RPP 1vq1A 214 :EPP T0293 168 :SVNTGGITEIMAEGGELEFVKRIIHDSLQLGKRLRWYSC 1vq1A 226 :LDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVF Number of specific fragments extracted= 9 number of extra gaps= 2 total=1754 Will force an alignment to be made, even if fragment is small Number of alignments=163 # command:CPU_time= 43.595 sec, elapsed time= 48.082 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 163 Adding 31125 constraints to all_contacts Done adding distance constraints # command:CPU_time= 43.796 sec, elapsed time= 48.292 sec. # command:Reading probabilities from T0293.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 80.669 Optimizing... Probability sum: -428.573, CN propb: -428.573 weights: 0.322 constraints: 536 # command:CPU_time= 566.689 sec, elapsed time= 571.771 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 536 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 536 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 4863 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 4863 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 23762 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 23762 # command:CPU_time= 567.228 sec, elapsed time= 572.688 sec. # command: