# 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 T0296 numbered 1 through 445 Created new target T0296 from T0296.a2m # command:CPU_time= 6.620 sec, elapsed time= 6.745 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i60A/T0296-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i60A expands to /projects/compbio/data/pdb/1i60.pdb.gz 1i60A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0296 read from 1i60A/T0296-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0296-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i60A to template set # found chain 1i60A in template set T0296 7 :TETIAMIEEQNFDIRTITMGISLLDC 1i60A 49 :DDLAEYFQTHHIKPLALNALVFFNNR # choosing archetypes in rotamer library T0296 34 :DP 1i60A 75 :DE T0296 43 :KIYQKITTKAANLVAVGDEI 1i60A 77 :KGHNEIITEFKGMMETCKTL T0296 67 :GIPIVNKRVSVT 1i60A 97 :GVKYVVAVPLVT T0296 85 :AATDATD 1i60A 110 :QKIVKEE T0296 92 :YVVLAKALDKAAKEIGVDFIGGF 1i60A 121 :SVDVLTELSDIAEPYGVKIALEF T0296 121 :GYQKG 1i60A 144 :VGHPQ T0296 130 :INSIPRALAE 1i60A 154 :FEQAYEIVNT T0296 140 :TDKVCSSVNI 1i60A 166 :RDNVGLVLDS T0296 154 :SGINMTAVAD 1i60A 181 :MGSNIESLKQ T0296 174 :LSD 1i60A 191 :ADG T0296 178 :GVAKLVVFANAVED 1i60A 194 :KKIFIYHIDDTEDF T0296 192 :NPFM 1i60A 209 :IGFL T0296 196 :AGAFHGVGEA 1i60A 214 :DEDRVWPGQG T0296 228 :GQSFDVVAETVKK 1i60A 224 :AIDLDAHLSALKE T0296 260 :LGVE 1i60A 237 :IGFS T0296 265 :GIVDLSL 1i60A 241 :DVVSVEL T0296 273 :PTPAVGD 1i60A 248 :FRPEYYK T0296 280 :SVARVL 1i60A 256 :TAEEAI T0296 299 :TAALALLNDQVKKG 1i60A 262 :QTAKKTTVDVVSKY Number of specific fragments extracted= 20 number of extra gaps= 0 total=20 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 1i60A/T0296-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1i60A/T0296-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0296-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i60A in template set T0296 7 :TETIAMIEEQNFDIRTITMGISLLD 1i60A 49 :DDLAEYFQTHHIKPLALNALVFFNN T0296 33 :IDPD 1i60A 74 :RDEK T0296 44 :IYQKITTKAANLVAVGDEI 1i60A 78 :GHNEIITEFKGMMETCKTL T0296 67 :GIPIVNKRVSVT 1i60A 97 :GVKYVVAVPLVT T0296 85 :AATDATD 1i60A 110 :QKIVKEE T0296 92 :YVVLAKALDKAAKEIGVDFIGGF 1i60A 121 :SVDVLTELSDIAEPYGVKIALEF T0296 121 :GYQKG 1i60A 144 :VGHPQ T0296 130 :INSIPRALAE 1i60A 154 :FEQAYEIVNT T0296 140 :TDKVCSSVNI 1i60A 166 :RDNVGLVLDS T0296 154 :SGINMTAVAD 1i60A 181 :MGSNIESLKQ T0296 174 :L 1i60A 191 :A T0296 176 :DMGVAKLVVFANAVED 1i60A 192 :DGKKIFIYHIDDTEDF T0296 192 :NPFM 1i60A 209 :IGFL T0296 196 :AGAFHGVGEA 1i60A 214 :DEDRVWPGQG T0296 228 :GQSFDVVAETVKK 1i60A 224 :AIDLDAHLSALKE T0296 260 :LGVEF 1i60A 237 :IGFSD T0296 266 :IVDLSL 1i60A 242 :VVSVEL T0296 273 :PTPAVGD 1i60A 248 :FRPEYYK T0296 280 :SVARVL 1i60A 256 :TAEEAI T0296 299 :TAALALLNDQVKKG 1i60A 262 :QTAKKTTVDVVSKY Number of specific fragments extracted= 20 number of extra gaps= 0 total=40 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i60A/T0296-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1i60A/T0296-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0296-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i60A in template set T0296 3 :IR 1i60A 48 :LD T0296 8 :ETIAMIEEQNFDIRTITMGISLLDC 1i60A 50 :DLAEYFQTHHIKPLALNALVFFNNR T0296 34 :D 1i60A 75 :D T0296 42 :EKIYQKITTKAANLVAVGDEI 1i60A 76 :EKGHNEIITEFKGMMETCKTL T0296 67 :GIPIVNKRVSVTPI 1i60A 97 :GVKYVVAVPLVTEQ T0296 86 :ATDATDY 1i60A 111 :KIVKEEI T0296 93 :VVLAKALDKAAKEIGVDFIGGFSA 1i60A 122 :VDVLTELSDIAEPYGVKIALEFVG T0296 119 :QKGYQ 1i60A 146 :HPQCT T0296 124 :KGDEILINSIPRAL 1i60A 152 :NTFEQAYEIVNTVN T0296 140 :TDKVCSSVN 1i60A 166 :RDNVGLVLD T0296 154 :SGINMTAVA 1i60A 181 :MGSNIESLK T0296 173 :NLSD 1i60A 190 :QADG T0296 178 :GVAKLVVFANAVEDNPFMAGA 1i60A 194 :KKIFIYHIDDTEDFPIGFLTD T0296 199 :FHGVGEA 1i60A 217 :RVWPGQG T0296 228 :GQSFDVVAETVK 1i60A 224 :AIDLDAHLSALK T0296 259 :RLGVE 1i60A 236 :EIGFS T0296 266 :IVDLSL 1i60A 242 :VVSVEL T0296 289 :GLETVGTHGTTAALALLNDQVKKGG 1i60A 248 :FRPEYYKLTAEEAIQTAKKTTVDVV Number of specific fragments extracted= 18 number of extra gaps= 0 total=58 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c93A/T0296-1c93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c93A expands to /projects/compbio/data/pdb/1c93.pdb.gz 1c93A:# T0296 read from 1c93A/T0296-1c93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c93A read from 1c93A/T0296-1c93A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c93A to template set # found chain 1c93A in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE in next template residue (1c93A)A45 T0296 18 :FDIRTI 1c93A 38 :FDVAVI T0296 25 :MGISLLD 1c93A 46 :ANINYDT T0296 32 :CIDPDI 1c93A 60 :HFNENV T0296 42 :EKIYQKITTKAANLV 1c93A 66 :QRVLDNAVTQIRPLQ T0296 65 :ELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIG 1c93A 81 :QQGIKVLLSVLGNHQGAGFANFPSQQAASAFAKQLSDAVAKYGLDGVD T0296 113 :GFSALVQKGYQKGD 1c93A 135 :EYGNNGTAQPNDSS T0296 127 :EILINSIPRALA 1c93A 150 :VHLVTALRANMP T0296 141 :DKVCSSVNIGSTKSGIN 1c93A 162 :DKIISLYNIGPAASRLS T0296 171 :TANLSDMGVAKLVVFANAVE 1c93A 179 :YGGVDVSDKFDYAWNPYYGT T0296 197 :GAFHGVG 1c93A 199 :WQVPGIA T0296 204 :EADVIINVGVS 1c93A 207 :PKAQLSPAAVE T0296 226 :VRGQSFDVVAETVKKTA 1c93A 218 :IGRTSRSTVADLARRTV T0296 259 :RLGVEFGIVDL 1c93A 235 :DEGYGVYLTYN T0296 272 :APTPAVGDSVARVLEEMGLE 1c93A 246 :LDGGDRTADVSAFTRELYGS Number of specific fragments extracted= 14 number of extra gaps= 1 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c93A/T0296-1c93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1c93A/T0296-1c93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c93A read from 1c93A/T0296-1c93A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c93A in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE in next template residue (1c93A)A45 T0296 18 :FDIRTI 1c93A 38 :FDVAVI T0296 25 :MGISLLD 1c93A 46 :ANINYDT T0296 32 :CIDPDINR 1c93A 60 :HFNENVQR T0296 44 :IYQKITTKAANLV 1c93A 68 :VLDNAVTQIRPLQ T0296 65 :ELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIG 1c93A 81 :QQGIKVLLSVLGNHQGAGFANFPSQQAASAFAKQLSDAVAKYGLDGVD T0296 113 :GFSALVQKGYQKGD 1c93A 135 :EYGNNGTAQPNDSS T0296 127 :EILINSIPRALA 1c93A 150 :VHLVTALRANMP T0296 141 :DKVCSSVNIGSTKSGIN 1c93A 162 :DKIISLYNIGPAASRLS T0296 171 :TANLSDMGVAKLVVFANAVE 1c93A 179 :YGGVDVSDKFDYAWNPYYGT T0296 197 :GAFHGVG 1c93A 199 :WQVPGIA T0296 204 :EADVIINVGVS 1c93A 207 :PKAQLSPAAVE T0296 226 :VRGQSFDVVAETVKKTAFK 1c93A 218 :IGRTSRSTVADLARRTVDE T0296 261 :GVEFGIVDL 1c93A 237 :GYGVYLTYN T0296 272 :APTPAVGDSVARVLEEMGLE 1c93A 246 :LDGGDRTADVSAFTRELYGS Number of specific fragments extracted= 14 number of extra gaps= 1 total=86 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 1c93A/T0296-1c93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1c93A/T0296-1c93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c93A read from 1c93A/T0296-1c93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c93A in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE at template residue (1c93A)A45 T0296 18 :FDIRTI 1c93A 38 :FDVAVI T0296 25 :MGISLLD 1c93A 46 :ANINYDT T0296 35 :PD 1c93A 53 :GT T0296 37 :INRAAEKIYQKITTKAANLV 1c93A 61 :FNENVQRVLDNAVTQIRPLQ T0296 65 :ELGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIGVDFIGGFSALVQKG 1c93A 81 :QQGIKVLLSVLGNHQGAGFANFPSQQAASAFAKQLSDAVAKYGLDGVDFNDQYAEYG T0296 122 :YQK 1c93A 141 :TAQ T0296 125 :GDE 1c93A 145 :NDS T0296 128 :ILINSIPRALA 1c93A 151 :HLVTALRANMP T0296 141 :DKVCSSVNIGSTKSGIN 1c93A 162 :DKIISLYNIGPAASRLS T0296 174 :LSDMGVAKLVVF 1c93A 182 :VDVSDKFDYAWN T0296 190 :EDNPFMAGAFHGVGEADV 1c93A 194 :PYYGTWQVPGIALPKAQL T0296 209 :INVGVSG 1c93A 212 :SPAAVEI T0296 227 :RGQS 1c93A 219 :GRTS T0296 235 :AETVKKTA 1c93A 223 :RSTVADLA T0296 254 :QMASER 1c93A 231 :RRTVDE T0296 261 :GVEFGIVDL 1c93A 237 :GYGVYLTYN T0296 272 :APTPAVGDSVARVLEEMGLE 1c93A 246 :LDGGDRTADVSAFTRELYGS Number of specific fragments extracted= 17 number of extra gaps= 1 total=103 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 1j0dA/T0296-1j0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j0dA expands to /projects/compbio/data/pdb/1j0d.pdb.gz 1j0dA:# T0296 read from 1j0dA/T0296-1j0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0dA read from 1j0dA/T0296-1j0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j0dA to template set # found chain 1j0dA in template set T0296 10 :IAMIEEQNFDIRTITMG 1j0dA 59 :VPDIVEGDYTHLVSIGG T0296 55 :LVAVGDEIAAELGIPIVNKRVS 1j0dA 80 :QTRMVAALAAKLGKKCVLIQED T0296 77 :VTPISLIGAATDATDYV 1j0dA 103 :VPIPEAEKDVYNRVGNI T0296 101 :KAAKEIGVDFIG 1j0dA 120 :ELSRIMGADVRV T0296 121 :GYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANA 1j0dA 135 :GFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVT T0296 196 :AGAFHGVGEADVIINVGVSG 1j0dA 210 :LAGMAQYGRQDDVIAIDASF T0296 230 :SFDVVAETVKK 1j0dA 230 :TSEKTKEQTLR T0296 252 :VGQMASERLGVE 1j0dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1j0dA 260 :LDTRFA T0296 273 :PTPAVGDSVARVLEEMGLETVGTH 1j0dA 272 :PNEGTIEAIRTCAEQEGVLTDPVY T0296 298 :TTAALALLNDQVKK 1j0dA 296 :EGKSMQGLIALIKE T0296 343 :G 1j0dA 310 :D Number of specific fragments extracted= 12 number of extra gaps= 0 total=115 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 1j0dA/T0296-1j0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1j0dA/T0296-1j0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0dA read from 1j0dA/T0296-1j0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j0dA in template set T0296 10 :IAMIEEQNFDIRTITMG 1j0dA 59 :VPDIVEGDYTHLVSIGG T0296 56 :VAVGDEIAAELGIPIVNKRVS 1j0dA 81 :TRMVAALAAKLGKKCVLIQED T0296 77 :VTPISLIGAATDATDYV 1j0dA 103 :VPIPEAEKDVYNRVGNI T0296 101 :KAAKEIGVDFIG 1j0dA 120 :ELSRIMGADVRV T0296 121 :GYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANA 1j0dA 135 :GFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVT T0296 196 :AGAFHGVGEADVIINVGVSG 1j0dA 210 :LAGMAQYGRQDDVIAIDASF T0296 230 :SFDVVAETVKK 1j0dA 230 :TSEKTKEQTLR T0296 252 :VGQMASERLGVE 1j0dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1j0dA 260 :LDTRFA T0296 273 :PTPAVGDSVARVLEEMGLETVGTH 1j0dA 272 :PNEGTIEAIRTCAEQEGVLTDPVY T0296 298 :TTAALALLNDQVKK 1j0dA 296 :EGKSMQGLIALIKE T0296 343 :G 1j0dA 310 :D Number of specific fragments extracted= 12 number of extra gaps= 0 total=127 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 1j0dA/T0296-1j0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1j0dA/T0296-1j0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0dA read from 1j0dA/T0296-1j0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j0dA in template set T0296 10 :IAMIEEQNFD 1j0dA 59 :VPDIVEGDYT T0296 21 :RTITMGISLLD 1j0dA 69 :HLVSIGGRQSN T0296 55 :LVAVGDEIAAELGIPIVNKRVSVTPI 1j0dA 80 :QTRMVAALAAKLGKKCVLIQEDWVPI T0296 81 :SLIGAATDATDYVVLAKA 1j0dA 107 :EAEKDVYNRVGNIELSRI T0296 106 :IGVDFIGG 1j0dA 125 :MGADVRVI T0296 119 :QKGYQ 1j0dA 133 :EDGFD T0296 124 :KGDEILINSIPRALAETDKVC 1j0dA 139 :GMRKSFANALQELEDAGHKPY T0296 146 :SVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANAVEDNPFMAGAFHGVGEADVIINVGVSG 1j0dA 160 :PIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDASF T0296 234 :VAETVKKTAFK 1j0dA 230 :TSEKTKEQTLR T0296 252 :VGQMASERLGVE 1j0dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1j0dA 260 :LDTRFA T0296 273 :PTPAVGDSVARVLEEMGLETVG 1j0dA 272 :PNEGTIEAIRTCAEQEGVLTDP T0296 296 :HGTTAALALLNDQVKK 1j0dA 294 :VYEGKSMQGLIALIKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=140 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 1edt/T0296-1edt-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1edt expands to /projects/compbio/data/pdb/1edt.pdb.gz 1edt:Warning: there is no chain 1edt will retry with 1edtA # T0296 read from 1edt/T0296-1edt-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1edt read from 1edt/T0296-1edt-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1edt to template set # found chain 1edt in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE in next template residue (1edt)A45 T0296 18 :FDIRTI 1edt 38 :FDVAVI T0296 25 :MGISLLD 1edt 46 :ANINYDT T0296 32 :CIDPD 1edt 60 :HFNEN T0296 41 :AEKIYQKITTKAANLVA 1edt 65 :VQRVLDNAVTQIRPLQQ T0296 66 :LGIPIVNK 1edt 82 :QGIKVLLS T0296 75 :VSVTPISLIGAAT 1edt 90 :VLGNHQGAGFANF T0296 88 :DATDYVVLAKALDKAAKEIGVDFIG 1edt 104 :SQQAASAFAKQLSDAVAKYGLDGVD T0296 114 :FSA 1edt 136 :YGN T0296 120 :KG 1edt 139 :NG T0296 122 :YQKGD 1edt 144 :PNDSS T0296 127 :EILINSIPRALA 1edt 150 :VHLVTALRANMP T0296 141 :DKVCSSVNIG 1edt 162 :DKIISLYNIG T0296 170 :ETANL 1edt 172 :PAASR T0296 175 :SDMGVAKLVV 1edt 183 :DVSDKFDYAW T0296 192 :NPFMAGAFH 1edt 193 :NPYYGTWQV T0296 201 :GVG 1edt 203 :GIA T0296 204 :EADVIINVGVS 1edt 207 :PKAQLSPAAVE T0296 226 :VRGQSFDVVAETVKKTA 1edt 218 :IGRTSRSTVADLARRTV T0296 258 :ER 1edt 235 :DE T0296 261 :GVEFGIVD 1edt 237 :GYGVYLTY T0296 292 :TVGTHGTTAALALLNDQVKKGGV 1edt 245 :NLDGGDRTADVSAFTRELYGSEA Number of specific fragments extracted= 21 number of extra gaps= 1 total=161 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 1edt/T0296-1edt-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1edt/T0296-1edt-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1edt read from 1edt/T0296-1edt-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1edt in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE in next template residue (1edt)A45 T0296 18 :FDIRTI 1edt 38 :FDVAVI T0296 25 :MGISLLD 1edt 46 :ANINYDT T0296 32 :CIDPDIN 1edt 60 :HFNENVQ T0296 43 :KIYQKITTKAANLVA 1edt 67 :RVLDNAVTQIRPLQQ T0296 66 :LGIPIVNK 1edt 82 :QGIKVLLS T0296 75 :VSVTPISLIGAAT 1edt 90 :VLGNHQGAGFANF T0296 88 :DATDYVVLAKALDKAAKEIGVDFIG 1edt 104 :SQQAASAFAKQLSDAVAKYGLDGVD T0296 114 :FSA 1edt 136 :YGN T0296 120 :KG 1edt 139 :NG T0296 122 :YQKGD 1edt 144 :PNDSS T0296 127 :EILINSIPRALA 1edt 150 :VHLVTALRANMP T0296 141 :DKVCSSVNIGSTKSGI 1edt 162 :DKIISLYNIGPAASRL T0296 173 :NLSD 1edt 178 :SYGG T0296 177 :MGVAKLVV 1edt 185 :SDKFDYAW T0296 192 :NPFMAGAFH 1edt 193 :NPYYGTWQV T0296 201 :GVG 1edt 203 :GIA T0296 204 :EADVIINVGVS 1edt 207 :PKAQLSPAAVE T0296 226 :VRGQSFDVVAETVKKTAFK 1edt 218 :IGRTSRSTVADLARRTVDE T0296 261 :GVEFGIVD 1edt 237 :GYGVYLTY T0296 292 :TVGTHGTTAALALLNDQVKKGGV 1edt 245 :NLDGGDRTADVSAFTRELYGSEA Number of specific fragments extracted= 20 number of extra gaps= 1 total=181 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 1edt/T0296-1edt-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1edt/T0296-1edt-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1edt read from 1edt/T0296-1edt-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1edt in template set Warning: unaligning (T0296)T24 because of BadResidue code BAD_PEPTIDE in next template residue (1edt)A45 T0296 18 :FDIRTI 1edt 38 :FDVAVI T0296 25 :MGISLLD 1edt 46 :ANINYDT T0296 35 :PD 1edt 53 :GT T0296 37 :INRAAEKIYQKITTKAANLVA 1edt 61 :FNENVQRVLDNAVTQIRPLQQ T0296 66 :LGIPIVNK 1edt 82 :QGIKVLLS T0296 75 :VSVTPISLIGAAT 1edt 90 :VLGNHQGAGFANF T0296 88 :DATDYVVLAKALDKAAKEIGVDFIGGFSA 1edt 104 :SQQAASAFAKQLSDAVAKYGLDGVDFDDE T0296 117 :LVQKGYQKGDE 1edt 136 :YGNNGTAQPND T0296 128 :ILINSIPRALAET 1edt 151 :HLVTALRANMPDK T0296 143 :VCSSVNI 1edt 164 :IISLYNI T0296 169 :KETA 1edt 171 :GPAA T0296 173 :N 1edt 181 :G T0296 177 :MGVAKLVVF 1edt 185 :SDKFDYAWN T0296 190 :EDNPFMAGAFHGVGEADV 1edt 194 :PYYGTWQVPGIALPKAQL T0296 209 :INVGVS 1edt 212 :SPAAVE T0296 226 :VRGQSFDVVAE 1edt 218 :IGRTSRSTVAD T0296 241 :TAF 1edt 229 :LAR T0296 255 :MASER 1edt 232 :RTVDE T0296 261 :GVEFGIVDL 1edt 237 :GYGVYLTYN T0296 272 :APTPAVGDSVARVLEEMGL 1edt 246 :LDGGDRTADVSAFTRELYG Number of specific fragments extracted= 20 number of extra gaps= 1 total=201 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 1p1xA/T0296-1p1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1p1xA/T0296-1p1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1xA read from 1p1xA/T0296-1p1xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p1xA in training set Warning: unaligning (T0296)L29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)F76 Warning: unaligning (T0296)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)F76 Warning: unaligning (T0296)L117 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K146 Warning: unaligning (T0296)G125 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K146 Warning: unaligning (T0296)V147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)S169 Warning: unaligning (T0296)N148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)S169 Warning: unaligning (T0296)G150 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K172 Warning: unaligning (T0296)S151 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K172 Warning: unaligning (T0296)L290 because last residue in template chain is (1p1xA)H250 T0296 1 :MDIRQVTETIAMIEEQNF 1p1xA 48 :IYPRFIPIARKTLKEQGT T0296 20 :IRTITMG 1p1xA 68 :IRIATVT T0296 31 :DCIDPDINRAAEKIYQKI 1p1xA 77 :PHGNDDIDIALAETRAAI T0296 65 :ELGIPIVNK 1p1xA 95 :AYGADEVDV T0296 77 :VTPISLIGAA 1p1xA 104 :VFPYRALMAG T0296 88 :DATDYVVLAKALDKAAKEIGVDFIG 1p1xA 114 :NEQVGFDLVKACKEACAAANVLLKV T0296 113 :GFSA 1p1xA 141 :ETGE T0296 126 :DEILINSIPRALAETDKVCSS 1p1xA 147 :DEALIRKASEISIKAGADFIK T0296 149 :I 1p1xA 170 :T T0296 152 :TKSGINMTAVADMGRIIKETANLSD 1p1xA 173 :VAVNATPESARIMMEVIRDMGVEKT T0296 180 :AKLVVFANAVE 1p1xA 198 :VGFKPAGGVRT T0296 216 :PGVVKR 1p1xA 209 :AEDAQK T0296 252 :VGQMASERLG 1p1xA 215 :YLAIADELFG T0296 264 :FGIVD 1p1xA 233 :YRFGA T0296 278 :GDSVARVLEEMG 1p1xA 238 :SSLLASLLKALG Number of specific fragments extracted= 15 number of extra gaps= 4 total=216 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 1p1xA/T0296-1p1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1p1xA/T0296-1p1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1xA read from 1p1xA/T0296-1p1xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p1xA in training set Warning: unaligning (T0296)L29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)F76 Warning: unaligning (T0296)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)F76 Warning: unaligning (T0296)L117 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K146 Warning: unaligning (T0296)G125 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K146 Warning: unaligning (T0296)V147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)S169 Warning: unaligning (T0296)N148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)S169 Warning: unaligning (T0296)G150 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K172 Warning: unaligning (T0296)S151 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K172 Warning: unaligning (T0296)L290 because last residue in template chain is (1p1xA)H250 T0296 1 :MDIRQVTETIAMIEEQN 1p1xA 48 :IYPRFIPIARKTLKEQG T0296 18 :FDIRTIT 1p1xA 68 :IRIATVT T0296 31 :DCIDPDINRAAEKIYQKI 1p1xA 77 :PHGNDDIDIALAETRAAI T0296 65 :ELGIPIVN 1p1xA 95 :AYGADEVD T0296 76 :SVTPISLIGAA 1p1xA 103 :VVFPYRALMAG T0296 88 :DATDYVVLAKALDKAAKEIGVDFIG 1p1xA 114 :NEQVGFDLVKACKEACAAANVLLKV T0296 113 :GFSA 1p1xA 141 :ETGE T0296 126 :DEILINSIPRALAETDKVCSS 1p1xA 147 :DEALIRKASEISIKAGADFIK T0296 149 :I 1p1xA 170 :T T0296 152 :TKSGINMTAVADMGRIIKETANLSD 1p1xA 173 :VAVNATPESARIMMEVIRDMGVEKT T0296 180 :AKLVVF 1p1xA 198 :VGFKPA T0296 200 :HGVGE 1p1xA 204 :GGVRT T0296 231 :FDV 1p1xA 209 :AED T0296 249 :GQLVGQMASERLG 1p1xA 212 :AQKYLAIADELFG T0296 264 :FGIVD 1p1xA 233 :YRFGA T0296 278 :GDSVARVLEEMG 1p1xA 238 :SSLLASLLKALG Number of specific fragments extracted= 16 number of extra gaps= 4 total=232 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 1p1xA/T0296-1p1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1p1xA/T0296-1p1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1xA read from 1p1xA/T0296-1p1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p1xA in training set Warning: unaligning (T0296)L29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)F76 Warning: unaligning (T0296)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)F76 Warning: unaligning (T0296)Q119 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K146 Warning: unaligning (T0296)G125 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K146 Warning: unaligning (T0296)V147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p1xA)S169 Warning: unaligning (T0296)N148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p1xA)S169 Warning: unaligning (T0296)G150 because of BadResidue code BAD_PEPTIDE in next template residue (1p1xA)K172 Warning: unaligning (T0296)S151 because of BadResidue code BAD_PEPTIDE at template residue (1p1xA)K172 Warning: unaligning (T0296)L290 because last residue in template chain is (1p1xA)H250 T0296 3 :IRQVTETIAMIEEQNFD 1p1xA 50 :PRFIPIARKTLKEQGTP T0296 20 :IRTITMG 1p1xA 68 :IRIATVT T0296 31 :DCIDPDINR 1p1xA 77 :PHGNDDIDI T0296 55 :LVAVGDEIAA 1p1xA 86 :ALAETRAAIA T0296 66 :LGIPIVN 1p1xA 96 :YGADEVD T0296 76 :SVTPISLIGA 1p1xA 103 :VVFPYRALMA T0296 87 :TDATDYVVLAKALDKAAKEIGVDFIGGFSALV 1p1xA 113 :GNEQVGFDLVKACKEACAAANVLLKVIIETGE T0296 126 :DEILINSIPRALAETDKVCSS 1p1xA 147 :DEALIRKASEISIKAGADFIK T0296 149 :I 1p1xA 170 :T T0296 152 :TKSGINMTAVADMGRIIKETANLSD 1p1xA 173 :VAVNATPESARIMMEVIRDMGVEKT T0296 180 :AKLV 1p1xA 198 :VGFK T0296 198 :AFHGVGEA 1p1xA 202 :PAGGVRTA T0296 247 :RIGQLVGQMASERLG 1p1xA 210 :EDAQKYLAIADELFG T0296 264 :FGI 1p1xA 235 :FGA T0296 270 :S 1p1xA 238 :S T0296 279 :DSVARVLEEMG 1p1xA 239 :SLLASLLKALG Number of specific fragments extracted= 16 number of extra gaps= 4 total=248 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 1qtwA/T0296-1qtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1qtwA/T0296-1qtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qtwA read from 1qtwA/T0296-1qtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qtwA in training set Warning: unaligning (T0296)G84 because of BadResidue code BAD_PEPTIDE in next template residue (1qtwA)M115 Warning: unaligning (T0296)A85 because of BadResidue code BAD_PEPTIDE at template residue (1qtwA)M115 Warning: unaligning (T0296)V213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qtwA)I263 Warning: unaligning (T0296)S214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qtwA)I263 T0296 1 :MDIRQVTETIAMIEEQNFD 1qtwA 44 :LTTQTIDEFKAACEKYHYT T0296 29 :LLDCIDPDI 1qtwA 66 :ILPHDSYLI T0296 38 :NRAAEKIYQKITTKAA 1qtwA 81 :TEALEKSRDAFIDEMQ T0296 62 :IAAELGIPIVNKRV 1qtwA 97 :RCEQLGLSLLNFHP T0296 83 :I 1qtwA 113 :H T0296 86 :ATDATDYVVLAKAL 1qtwA 116 :QISEEDCLARIAES T0296 100 :DKAAKEI 1qtwA 131 :NIALDKT T0296 107 :GVDFIG 1qtwA 139 :GVTAVI T0296 119 :QKGYQKGDEILINSIPRALAETDKVCSSVN 1qtwA 150 :QGSNLGFKFEHLAAIIDGVEDKSRVGVCID T0296 155 :GI 1qtwA 187 :GY T0296 157 :NMTAVADMGRIIKETANL 1qtwA 192 :TPAECEKTFADFARTVGF T0296 178 :GVAKLVVFANAVEDNPFMAGAFHGVGEAD 1qtwA 210 :KYLRGMHLNDAKSTFGSRVDRHHSLGEGN T0296 207 :VIINVG 1qtwA 256 :IPLILE T0296 215 :GPGVVKRALEKVRG 1qtwA 264 :NPDIWAEEIAWLKA Number of specific fragments extracted= 14 number of extra gaps= 2 total=262 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 1qtwA/T0296-1qtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1qtwA/T0296-1qtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qtwA read from 1qtwA/T0296-1qtwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qtwA in training set Warning: unaligning (T0296)G84 because of BadResidue code BAD_PEPTIDE in next template residue (1qtwA)M115 Warning: unaligning (T0296)A85 because of BadResidue code BAD_PEPTIDE at template residue (1qtwA)M115 Warning: unaligning (T0296)V213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qtwA)I263 Warning: unaligning (T0296)S214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qtwA)I263 T0296 1 :MDIRQVTETIAMIEEQNFD 1qtwA 44 :LTTQTIDEFKAACEKYHYT T0296 29 :LLDCIDPDI 1qtwA 66 :ILPHDSYLI T0296 38 :NRAAEKIYQKITTKAA 1qtwA 81 :TEALEKSRDAFIDEMQ T0296 62 :IAAELGIPIVNKRV 1qtwA 97 :RCEQLGLSLLNFHP T0296 83 :I 1qtwA 113 :H T0296 86 :ATDATDYVVLAKAL 1qtwA 116 :QISEEDCLARIAES T0296 100 :DKAAKEI 1qtwA 131 :NIALDKT T0296 107 :GVDFIG 1qtwA 139 :GVTAVI T0296 119 :QKGYQKGDEILINSIPRALAETDKVCSSVN 1qtwA 150 :QGSNLGFKFEHLAAIIDGVEDKSRVGVCID T0296 155 :GI 1qtwA 187 :GY T0296 157 :NMTAVADMGRIIKETANL 1qtwA 192 :TPAECEKTFADFARTVGF T0296 178 :GVAKLVVFANAVEDNPFMAGAFHGVGEAD 1qtwA 210 :KYLRGMHLNDAKSTFGSRVDRHHSLGEGN T0296 207 :VIINVG 1qtwA 256 :IPLILE T0296 215 :GPGVVKRALEKVRG 1qtwA 264 :NPDIWAEEIAWLKA Number of specific fragments extracted= 14 number of extra gaps= 2 total=276 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 1qtwA/T0296-1qtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1qtwA/T0296-1qtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qtwA read from 1qtwA/T0296-1qtwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qtwA in training set Warning: unaligning (T0296)G84 because of BadResidue code BAD_PEPTIDE in next template residue (1qtwA)M115 Warning: unaligning (T0296)A85 because of BadResidue code BAD_PEPTIDE at template residue (1qtwA)M115 Warning: unaligning (T0296)S270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qtwA)I263 Warning: unaligning (T0296)L271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qtwA)I263 Warning: unaligning (T0296)T292 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qtwA)V284 Warning: unaligning (T0296)V293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qtwA)V284 T0296 2 :DIRQVTETIAMIEEQNFD 1qtwA 45 :TTQTIDEFKAACEKYHYT T0296 30 :LDCIDPDI 1qtwA 67 :LPHDSYLI T0296 38 :NRAAEKIYQKITTKA 1qtwA 81 :TEALEKSRDAFIDEM T0296 57 :AVG 1qtwA 96 :QRC T0296 64 :AELGIPIVN 1qtwA 99 :EQLGLSLLN T0296 77 :VTPISL 1qtwA 108 :FHPGSH T0296 86 :ATDATDYVVLAKA 1qtwA 116 :QISEEDCLARIAE T0296 99 :LDKAAKEI 1qtwA 130 :INIALDKT T0296 107 :GVDFIGGFSA 1qtwA 139 :GVTAVIENTA T0296 118 :VQKGYQKGDEILINSIPRALAETDKVCSSVN 1qtwA 149 :GQGSNLGFKFEHLAAIIDGVEDKSRVGVCID T0296 154 :SGINMTAVADMGRIIKETANLSD 1qtwA 189 :DLRTPAECEKTFADFARTVGFKY T0296 180 :AKLVVFANAVEDNPFMAGAFHGVGEADV 1qtwA 212 :LRGMHLNDAKSTFGSRVDRHHSLGEGNI T0296 215 :GPGVVKRALE 1qtwA 240 :GHDAFRWIMQ T0296 225 :KVRG 1qtwA 252 :RFDG T0296 264 :FGIVDL 1qtwA 256 :IPLILE T0296 272 :AP 1qtwA 264 :NP T0296 275 :PAVGDSVARVLEEMGLE 1qtwA 266 :DIWAEEIAWLKAQQTEK Number of specific fragments extracted= 17 number of extra gaps= 3 total=293 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 1ur4A/T0296-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ur4A expands to /projects/compbio/data/pdb/1ur4.pdb.gz 1ur4A:# T0296 read from 1ur4A/T0296-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0296-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ur4A to template set # found chain 1ur4A in template set T0296 2 :DIRQVTETIAMIEEQNFDIRTITMGISL 1ur4A 87 :DLEKAIQIGKRATANGMKLLADFHYSDF T0296 30 :LDCIDPDINRAAEKIYQKITTKAANLVA 1ur4A 125 :KAWANLNFEDKKTALYQYTKQSLKAMKA T0296 66 :LGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIG 1ur4A 153 :AGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETD T0296 140 :TDKVCSSVNIGSTKSG 1ur4A 195 :SNILVALHFTNPETSG T0296 160 :AVADMGRIIKET 1ur4A 211 :RYAWIAETLHRH T0296 201 :GVGEA 1ur4A 223 :HVDYD T0296 208 :IINVGVSGP 1ur4A 228 :VFASSYYPF T0296 227 :RGQSFDVVAETVKK 1ur4A 237 :WHGTLKNLTSVLTS T0296 256 :ASERLGVEFGIVDLSLAPT 1ur4A 251 :VADTYGKKVMVAETSYTYT T0296 275 :PAVGD 1ur4A 281 :PKNGQ T0296 289 :GLETVGTHGTTAALALLNDQVKKGGVMACN 1ur4A 287 :LNNPVTVQGQANAVRDVIQAVSDVGEAGIG T0296 320 :VGGLSGAFIPV 1ur4A 317 :VFYWEPAWIPV T0296 331 :SEDEGMIAAVQN 1ur4A 331 :HRLEKNKALWET Number of specific fragments extracted= 13 number of extra gaps= 0 total=306 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 1ur4A/T0296-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ur4A/T0296-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0296-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0296 2 :DIRQVTETIAMIEEQNFDIRTITMGISL 1ur4A 87 :DLEKAIQIGKRATANGMKLLADFHYSDF T0296 30 :LDCIDPDINRAAEKIYQKITTKAANLVA 1ur4A 125 :KAWANLNFEDKKTALYQYTKQSLKAMKA T0296 66 :LGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEIG 1ur4A 153 :AGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRETD T0296 140 :TDKVCSSVNIGSTKSG 1ur4A 195 :SNILVALHFTNPETSG T0296 160 :AVADMGRIIKET 1ur4A 211 :RYAWIAETLHRH T0296 201 :GVGEA 1ur4A 223 :HVDYD T0296 208 :IINVGVSGP 1ur4A 228 :VFASSYYPF T0296 227 :RGQSFDVVAETVK 1ur4A 237 :WHGTLKNLTSVLT T0296 255 :MASERLGVEFGIVDLSLAPT 1ur4A 250 :SVADTYGKKVMVAETSYTYT T0296 275 :PAVGD 1ur4A 281 :PKNGQ T0296 289 :GLETVGTHGTTAALALLNDQVKKGGVMACN 1ur4A 287 :LNNPVTVQGQANAVRDVIQAVSDVGEAGIG T0296 320 :VGGLSGAFIPV 1ur4A 317 :VFYWEPAWIPV T0296 331 :SEDEGMIAAVQN 1ur4A 331 :HRLEKNKALWET Number of specific fragments extracted= 13 number of extra gaps= 0 total=319 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 1ur4A/T0296-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ur4A/T0296-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0296-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0296 2 :DIRQVTETIAMIEEQNFDIRTITMGIS 1ur4A 87 :DLEKAIQIGKRATANGMKLLADFHYSD T0296 29 :LLDCIDPDINRAAEKIYQKITTKAANLVA 1ur4A 124 :PKAWANLNFEDKKTALYQYTKQSLKAMKA T0296 66 :LGIPIVNKRVSVTPISLIGAATDATDYVVLAKALDKAAKEI 1ur4A 153 :AGIDIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRET T0296 107 :GVDFIGGFSALV 1ur4A 196 :NILVALHFTNPE T0296 153 :KSG 1ur4A 208 :TSG T0296 160 :AVADMGRIIKETA 1ur4A 211 :RYAWIAETLHRHH T0296 179 :VAKLVVFANAV 1ur4A 225 :DYDVFASSYYP T0296 226 :VRGQSFDVVAETV 1ur4A 236 :FWHGTLKNLTSVL T0296 254 :QMASERLGVEFGIVDLSL 1ur4A 249 :TSVADTYGKKVMVAETSY T0296 272 :APTPAVG 1ur4A 280 :APKNGQT T0296 289 :GLETVGTHGTTAALALLNDQVKKGGV 1ur4A 287 :LNNPVTVQGQANAVRDVIQAVSDVGE T0296 316 :ACNQVGGLSGAFIPVS 1ur4A 313 :AGIGVFYWEPAWIPVG T0296 334 :EGMIAAVQN 1ur4A 334 :EKNKALWET Number of specific fragments extracted= 13 number of extra gaps= 0 total=332 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 1z41A/T0296-1z41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z41A expands to /projects/compbio/data/pdb/1z41.pdb.gz 1z41A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0296 read from 1z41A/T0296-1z41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z41A read from 1z41A/T0296-1z41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z41A to template set # found chain 1z41A in template set T0296 3 :IRQVTETIAMIEEQNFDIRTITMGI 1z41A 82 :IEGFAKLTEQVKEQGSKIGIQLAHA T0296 29 :LLDC 1z41A 107 :GRKA T0296 33 :IDPDI 1z41A 112 :LEGDI T0296 87 :TDATDYVVLAKALDKAAK 1z41A 134 :MSAEKVKETVQEFKQAAA T0296 105 :EIGVDFIG 1z41A 155 :EAGFDVIE T0296 113 :GFSALV 1z41A 168 :GYLIHE T0296 120 :KGYQKGDE 1z41A 184 :DEYGGSPE T0296 128 :ILINSIPRALAET 1z41A 195 :RFLREIIDEVKQV T0296 141 :DKVCSSVNIG 1z41A 210 :GPLFVRVSAS T0296 151 :STKSGINMTAVADMGRIIKET 1z41A 221 :YTDKGLDIADHIGFAKWMKEQ T0296 179 :VAKLVVFANA 1z41A 242 :GVDLIDCSSG T0296 197 :GAFHGVGEADV 1z41A 255 :HADINVFPGYQ T0296 216 :PGVVKRALEKV 1z41A 266 :VSFAEKIREQA T0296 229 :QSFDVVAETVKKTAFKITRIGQL 1z41A 287 :TDGSMAEEILQNGRADLIFIGRE T0296 252 :VGQMASERLGVEF 1z41A 316 :FARTAAKQLNTEI T0296 273 :PTPAVG 1z41A 329 :PAPVQY Number of specific fragments extracted= 16 number of extra gaps= 0 total=348 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 1z41A/T0296-1z41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1z41A/T0296-1z41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z41A read from 1z41A/T0296-1z41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z41A in template set T0296 4 :RQVTETIAMIEEQNFDIRTITMGI 1z41A 39 :PFHMAHYISRAIGQVGLIIVEASA T0296 28 :SLLD 1z41A 64 :NPQG T0296 32 :CIDPDINRA 1z41A 76 :IWSDEHIEG T0296 55 :LVAVGDEIA 1z41A 85 :FAKLTEQVK T0296 65 :ELGIPIVNKRVSV 1z41A 94 :EQGSKIGIQLAHA T0296 82 :LIGA 1z41A 108 :RKAE T0296 87 :TDATDYVVLAKALDKAAK 1z41A 134 :MSAEKVKETVQEFKQAAA T0296 105 :EIGVDFIG 1z41A 155 :EAGFDVIE T0296 113 :GFSALV 1z41A 168 :GYLIHE T0296 120 :KGYQKGDE 1z41A 184 :DEYGGSPE T0296 128 :ILINSIPRALAET 1z41A 195 :RFLREIIDEVKQV T0296 141 :DKVCSSVNIG 1z41A 210 :GPLFVRVSAS T0296 151 :STKSGINMTAVADMGRIIKET 1z41A 221 :YTDKGLDIADHIGFAKWMKEQ T0296 179 :VAKLVVFANA 1z41A 242 :GVDLIDCSSG T0296 197 :GAFHGVGEADV 1z41A 255 :HADINVFPGYQ T0296 216 :PGVVKRALEKV 1z41A 266 :VSFAEKIREQA T0296 229 :QSFDVVAETVKKTA 1z41A 287 :TDGSMAEEILQNGR T0296 243 :FKITR 1z41A 308 :RELLR T0296 251 :LVGQMASERLGVE 1z41A 315 :FFARTAAKQLNTE T0296 272 :APTPAV 1z41A 328 :IPAPVQ Number of specific fragments extracted= 20 number of extra gaps= 0 total=368 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 1z41A/T0296-1z41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1z41A/T0296-1z41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z41A read from 1z41A/T0296-1z41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z41A in template set T0296 4 :RQVTETIAMIEEQNFDIRTITMG 1z41A 39 :PFHMAHYISRAIGQVGLIIVEAS T0296 27 :ISLLDCIDPD 1z41A 63 :VNPQGRITDQ T0296 38 :N 1z41A 79 :D T0296 50 :TKAANLVAVGDEIAA 1z41A 80 :EHIEGFAKLTEQVKE T0296 66 :LGIPIVNK 1z41A 95 :QGSKIGIQ T0296 77 :VTPISLIGAAT 1z41A 103 :LAHAGRKAELE T0296 88 :DATDYVVLAKALDKAAK 1z41A 135 :SAEKVKETVQEFKQAAA T0296 105 :EIGVDFIGGFSA 1z41A 155 :EAGFDVIEIHAA T0296 120 :KGYQKGDEILINSIPRALAE 1z41A 184 :DEYGGSPENRYRFLREIIDE T0296 140 :TDKVCSSVNIG 1z41A 209 :DGPLFVRVSAS T0296 151 :STKSGINMTAVADMGRIIKET 1z41A 221 :YTDKGLDIADHIGFAKWMKEQ T0296 178 :GVAKLVVFANAVEDNPFMAGAFHGVG 1z41A 242 :GVDLIDCSSGALVHADINVFPGYQVS T0296 207 :VIINVG 1z41A 279 :ATGAVG T0296 213 :VSGPGVVKRALEK 1z41A 286 :ITDGSMAEEILQN T0296 228 :GQ 1z41A 299 :GR T0296 230 :SFDVVAETVKK 1z41A 302 :DLIFIGRELLR T0296 250 :QLVGQMASERLGVE 1z41A 314 :PFFARTAAKQLNTE Number of specific fragments extracted= 17 number of extra gaps= 0 total=385 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 1mjhA/T0296-1mjhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mjhA expands to /projects/compbio/data/pdb/1mjh.pdb.gz 1mjhA:# T0296 read from 1mjhA/T0296-1mjhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mjhA read from 1mjhA/T0296-1mjhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mjhA to template set # found chain 1mjhA in template set Warning: unaligning (T0296)I33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mjhA)V66 T0296 4 :RQVTETIAMIEEQ 1mjhA 16 :ETAEIALKHVKAF T0296 17 :NFDIRTITM 1mjhA 33 :AEEVILLHV T0296 27 :ISLLDC 1mjhA 42 :IDEREI T0296 38 :NRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPIS 1mjhA 67 :EEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHE T0296 98 :ALDKAAKEIGVDFIG 1mjhA 111 :EIVKIAEDEGVDIII T0296 144 :CSS 1mjhA 127 :GSH T0296 149 :IGSTKSGI 1mjhA 130 :GKTNLKEI T0296 157 :NM 1mjhA 139 :LG T0296 163 :DMGRIIKETANLS 1mjhA 141 :SVTENVIKKSNKP T0296 183 :VVFANAV 1mjhA 154 :VLVVKRK Number of specific fragments extracted= 10 number of extra gaps= 0 total=395 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 1mjhA/T0296-1mjhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1mjhA/T0296-1mjhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mjhA read from 1mjhA/T0296-1mjhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mjhA in template set Warning: unaligning (T0296)I33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mjhA)V66 T0296 4 :RQVTETIAMIEEQ 1mjhA 16 :ETAEIALKHVKAF T0296 17 :NFDIRTI 1mjhA 33 :AEEVILL T0296 25 :MGISLLDC 1mjhA 40 :HVIDEREI T0296 38 :NRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPIS 1mjhA 67 :EEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHE T0296 98 :ALDKAAKEIGVDFIG 1mjhA 111 :EIVKIAEDEGVDIII T0296 144 :CSS 1mjhA 127 :GSH T0296 149 :IGSTKSGI 1mjhA 130 :GKTNLKEI T0296 157 :NMT 1mjhA 139 :LGS T0296 164 :MGRIIKETANLS 1mjhA 142 :VTENVIKKSNKP T0296 183 :VVFANAV 1mjhA 154 :VLVVKRK Number of specific fragments extracted= 10 number of extra gaps= 0 total=405 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 1mjhA/T0296-1mjhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1mjhA/T0296-1mjhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mjhA read from 1mjhA/T0296-1mjhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mjhA in template set Warning: unaligning (T0296)N17 because of BadResidue code BAD_PEPTIDE in next template residue (1mjhA)T30 Warning: unaligning (T0296)D34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mjhA)V66 T0296 5 :QVTETIAMIEEQ 1mjhA 17 :TAEIALKHVKAF T0296 21 :RTITMGISLLDCI 1mjhA 35 :EVILLHVIDEREI T0296 38 :NRAAEKIYQKITTKAANLVAVGDEIAAELGIPIVNKRVSVTPISL 1mjhA 67 :EEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEE T0296 99 :LDKAAKEIGVDFIGGFSA 1mjhA 112 :IVKIAEDEGVDIIIMGSH T0296 119 :QKGYQKGDEI 1mjhA 130 :GKTNLKEILL T0296 131 :NSIPRALAETDK 1mjhA 141 :SVTENVIKKSNK Number of specific fragments extracted= 6 number of extra gaps= 1 total=411 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 1o60A/T0296-1o60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o60A expands to /projects/compbio/data/pdb/1o60.pdb.gz 1o60A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1135, because occupancy 0.35 <= existing 0.650 in 1o60A Skipped atom 1137, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 1139, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 1141, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 1143, because occupancy 0.350 <= existing 0.650 in 1o60A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1609, because occupancy 0.500 <= existing 0.500 in 1o60A Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1o60A Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1o60A Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1o60A Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1o60A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2036, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 2038, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 2040, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 2042, because occupancy 0.350 <= existing 0.650 in 1o60A Skipped atom 2044, because occupancy 0.350 <= existing 0.650 in 1o60A # T0296 read from 1o60A/T0296-1o60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o60A read from 1o60A/T0296-1o60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o60A to template set # found chain 1o60A in template set Warning: unaligning (T0296)Q229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o60A)R218 T0296 20 :IRTITMGI 1o60A 20 :VLFGGMNV T0296 32 :CID 1o60A 28 :LES T0296 49 :TTKAANLVAVGDEIAAELGIPIVNKRV 1o60A 31 :RDMAMQVCEAYVKVTEKLGVPYVFKAS T0296 77 :VTP 1o60A 58 :FDK T0296 84 :GAATDA 1o60A 61 :ANRSSI T0296 90 :TDYVVLAKALDK 1o60A 75 :EEGLKIFQELKD T0296 105 :EIGVDFIG 1o60A 87 :TFGVKIIT T0296 113 :GFSA 1o60A 101 :QCQP T0296 118 :VQKGYQ 1o60A 105 :VADVVD T0296 125 :GDEIL 1o60A 120 :RQTDL T0296 134 :PRALAETDKVCSS 1o60A 125 :VEAMAKTGAVINV T0296 151 :STKSGINMTAVADMGRIIKET 1o60A 138 :KKPQFLSPSQMGNIVEKIEEC T0296 178 :GVAKLVVFANAVE 1o60A 159 :GNDKIILCDRGTN T0296 200 :HGVGEA 1o60A 172 :FGYDNL T0296 212 :GV 1o60A 178 :IV T0296 215 :GPGVVKRALEKVRG 1o60A 180 :DMLGFSVMKKASKG T0296 252 :VGQMASERLGVEFGIVDLSLAPTPAVGD 1o60A 221 :VTELARSGLAVGIAGLFLEAHPNPNQAK T0296 295 :TH 1o60A 249 :CD T0296 324 :SGAFIPVSEDEGMIAAVQN 1o60A 251 :GPSALPLSALEGFVSQMKA Number of specific fragments extracted= 19 number of extra gaps= 0 total=430 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 1o60A/T0296-1o60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1o60A/T0296-1o60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o60A read from 1o60A/T0296-1o60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o60A in template set Warning: unaligning (T0296)Q229 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o60A)R218 Warning: unaligning (T0296)A242 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o60A)R218 T0296 21 :RTITMGI 1o60A 21 :LFGGMNV T0296 30 :L 1o60A 28 :L T0296 33 :ID 1o60A 29 :ES T0296 49 :TTKAANLVAVGDEIAAELGIPIVNKRV 1o60A 31 :RDMAMQVCEAYVKVTEKLGVPYVFKAS T0296 77 :VTP 1o60A 58 :FDK T0296 84 :GA 1o60A 61 :AN T0296 86 :ATDATDYVVLAKALDK 1o60A 71 :GPGMEEGLKIFQELKD T0296 105 :EIGVDFIG 1o60A 87 :TFGVKIIT T0296 113 :GFSA 1o60A 101 :QCQP T0296 118 :VQKGYQ 1o60A 105 :VADVVD T0296 125 :GDEILI 1o60A 120 :RQTDLV T0296 135 :RALAETDKVCSS 1o60A 126 :EAMAKTGAVINV T0296 151 :STKSGINMTAVADMGRIIKET 1o60A 138 :KKPQFLSPSQMGNIVEKIEEC T0296 178 :GVAKLVVFANAVE 1o60A 159 :GNDKIILCDRGTN T0296 200 :HGVGEA 1o60A 172 :FGYDNL T0296 212 :GV 1o60A 178 :IV T0296 215 :GPGVVKRALEKVRG 1o60A 180 :DMLGFSVMKKASKG T0296 243 :FKITRIGQLVGQM 1o60A 219 :AQVTELARSGLAV T0296 263 :EFGIVDLSLAPTPAVG 1o60A 232 :GIAGLFLEAHPNPNQA T0296 294 :GTH 1o60A 248 :KCD T0296 324 :SGAFIPVSEDEGMIAAVQN 1o60A 251 :GPSALPLSALEGFVSQMKA Number of specific fragments extracted= 21 number of extra gaps= 0 total=451 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 1o60A/T0296-1o60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1o60A/T0296-1o60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o60A read from 1o60A/T0296-1o60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o60A in template set Warning: unaligning (T0296)V233 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o60A)R218 Warning: unaligning (T0296)T246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o60A)R218 T0296 4 :RQVTE 1o60A 35 :MQVCE T0296 9 :TIAMIEEQNFDI 1o60A 41 :YVKVTEKLGVPY T0296 22 :TITMGISLLDCIDPD 1o60A 53 :VFKASFDKANRSSIH T0296 52 :AANLVAVGDEIAAELGIPIVNK 1o60A 74 :MEEGLKIFQELKDTFGVKIITD T0296 77 :V 1o60A 96 :V T0296 87 :TDATDYVVLAK 1o60A 97 :HEIYQCQPVAD T0296 107 :GVDFIGGFSALV 1o60A 108 :VVDIIQLPAFLA T0296 125 :GDEILINSIPR 1o60A 120 :RQTDLVEAMAK T0296 140 :TDKVC 1o60A 131 :TGAVI T0296 148 :NIG 1o60A 136 :NVK T0296 152 :TKSGINMTAVADMGRIIKET 1o60A 139 :KPQFLSPSQMGNIVEKIEEC T0296 178 :GVAKLVVFANAVE 1o60A 159 :GNDKIILCDRGTN T0296 202 :VGEADVIIN 1o60A 172 :FGYDNLIVD T0296 216 :PGVVKRALEKVRGQSF 1o60A 181 :MLGFSVMKKASKGSPV T0296 232 :D 1o60A 204 :L T0296 247 :RIGQLVGQMASER 1o60A 219 :AQVTELARSGLAV T0296 263 :EFGIVDLSLAPTPAVGD 1o60A 232 :GIAGLFLEAHPNPNQAK T0296 293 :VGT 1o60A 249 :CDG T0296 325 :GAFIPVSEDEGMIAAVQN 1o60A 252 :PSALPLSALEGFVSQMKA Number of specific fragments extracted= 19 number of extra gaps= 0 total=470 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 1ceo/T0296-1ceo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ceo expands to /projects/compbio/data/pdb/1ceo.pdb.gz 1ceo:Warning: there is no chain 1ceo will retry with 1ceoA # T0296 read from 1ceo/T0296-1ceo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ceo read from 1ceo/T0296-1ceo-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ceo to template set # found chain 1ceo in template set Warning: unaligning (T0296)G113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ceo)S103 Warning: unaligning (T0296)Y122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ceo)S103 Warning: unaligning (T0296)G321 because of BadResidue code BAD_PEPTIDE in next template residue (1ceo)N314 Warning: unaligning (T0296)G322 because of BadResidue code BAD_PEPTIDE at template residue (1ceo)N314 T0296 7 :TETIAMIEEQNFDIRTITMGISL 1ceo 31 :EKDIETIAEAGFDHVRLPFDYPI T0296 32 :CIDPD 1ceo 54 :IESDD T0296 88 :DA 1ceo 59 :NV T0296 90 :TDYVVLAKALDKAAKEIGVDFIG 1ceo 65 :EDGLSYIDRCLEWCKKYNLGLVL T0296 123 :Q 1ceo 104 :T T0296 124 :KGDEI 1ceo 110 :NQQKR T0296 129 :LINSIPRALAETDKVCSSV 1ceo 118 :IWRFLAKRYINEREHIAFE T0296 148 :NIGSTKSGINMTAVADMGRIIKETANL 1ceo 140 :QVVEPDSTRWNKLMLECIKAIREIDST T0296 181 :K 1ceo 168 :W T0296 183 :VVFANAVEDNPFMAGAFHGVGEADVIINVGVSGPGVVK 1ceo 169 :LYIGGNNYNSPDELKNLADIDDDYIVYNFHFYNPFFFT T0296 221 :RALEKVRG 1ceo 234 :EFVKNNPK T0296 231 :FDVVAETVKK 1ceo 255 :KELLRKDLKP T0296 253 :GQMASERLGVEFGIVDLSL 1ceo 265 :AIEFREKKKCKLYCGEFGV T0296 290 :LETVGTHGTTAALALLNDQVKKGGVMAC 1ceo 284 :IAIADLESRIKWHEDYISLLEEYDIGGA T0296 320 :V 1ceo 312 :V T0296 323 :LSGAFIPVS 1ceo 315 :YKKMDFEIY T0296 332 :EDEGMIAAVQ 1ceo 330 :VSQELVNILA Number of specific fragments extracted= 17 number of extra gaps= 1 total=487 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 1ceo/T0296-1ceo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ceo/T0296-1ceo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ceo read from 1ceo/T0296-1ceo-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ceo in template set Warning: unaligning (T0296)G113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ceo)S103 Warning: unaligning (T0296)Y122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ceo)S103 Warning: unaligning (T0296)G321 because of BadResidue code BAD_PEPTIDE in next template residue (1ceo)N314 Warning: unaligning (T0296)G322 because of BadResidue code BAD_PEPTIDE at template residue (1ceo)N314 T0296 7 :TETIAMIEEQNFDIRTITMGISLL 1ceo 31 :EKDIETIAEAGFDHVRLPFDYPII T0296 33 :IDPD 1ceo 55 :ESDD T0296 88 :DA 1ceo 59 :NV T0296 90 :TDYVVLAKALDKAAKEIGVDFIG 1ceo 65 :EDGLSYIDRCLEWCKKYNLGLVL T0296 123 :Q 1ceo 104 :T T0296 124 :KGDEI 1ceo 110 :NQQKR T0296 129 :LINSIPRALAETDKVCSSV 1ceo 118 :IWRFLAKRYINEREHIAFE T0296 148 :NIGSTKSGINMTAVADMGRIIKETANLS 1ceo 140 :QVVEPDSTRWNKLMLECIKAIREIDSTM T0296 181 :K 1ceo 168 :W T0296 183 :VVFANAVEDNPFMAGAFHGVGEADVIINVGVSGPGVVK 1ceo 169 :LYIGGNNYNSPDELKNLADIDDDYIVYNFHFYNPFFFT T0296 221 :RALEKVRG 1ceo 214 :ESAMAYNR T0296 229 :QSFDVV 1ceo 230 :EGIEEF T0296 235 :AETVKKTAFKI 1ceo 255 :KELLRKDLKPA T0296 254 :QMASERLGVEFGIVDLSL 1ceo 266 :IEFREKKKCKLYCGEFGV T0296 290 :LETVGTHGTTAALALLNDQVKKGGVMAC 1ceo 284 :IAIADLESRIKWHEDYISLLEEYDIGGA T0296 320 :V 1ceo 312 :V T0296 323 :LSGAFIPVS 1ceo 315 :YKKMDFEIY T0296 332 :EDEGMIAAVQ 1ceo 330 :VSQELVNILA Number of specific fragments extracted= 18 number of extra gaps= 1 total=505 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 1ceo/T0296-1ceo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ceo/T0296-1ceo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ceo read from 1ceo/T0296-1ceo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ceo in template set Warning: unaligning (T0296)P79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ceo)S103 Warning: unaligning (T0296)Q319 because of BadResidue code BAD_PEPTIDE in next template residue (1ceo)N314 Warning: unaligning (T0296)V320 because of BadResidue code BAD_PEPTIDE at template residue (1ceo)N314 T0296 8 :ETIAMIEEQNFDI 1ceo 32 :KDIETIAEAGFDH T0296 23 :ITMGISLLDCIDPD 1ceo 45 :VRLPFDYPIIESDD T0296 37 :INRAA 1ceo 60 :VGEYK T0296 46 :QKITTKAANLVAVGD 1ceo 65 :EDGLSYIDRCLEWCK T0296 65 :ELGIPIVNKRVSVT 1ceo 80 :KYNLGLVLDMHHAP T0296 88 :DATDYVVLA 1ceo 107 :EDPNQQKRF T0296 97 :KALDKAAKEIG 1ceo 117 :DIWRFLAKRYI T0296 108 :VDFIGGFSA 1ceo 133 :IAFELLNQV T0296 122 :YQKGDEIL 1ceo 142 :VEPDSTRW T0296 158 :MTAVADMGRIIKETANLS 1ceo 150 :NKLMLECIKAIREIDSTM T0296 181 :K 1ceo 168 :W T0296 183 :VVFANAVEDNPFMAGAFHGVGEADVIINVGVSGPGVVK 1ceo 169 :LYIGGNNYNSPDELKNLADIDDDYIVYNFHFYNPFFFT T0296 221 :RALEK 1ceo 234 :EFVKN T0296 226 :VRGQSFD 1ceo 248 :LNNLKLN T0296 235 :AE 1ceo 255 :KE T0296 241 :TAFKITRIG 1ceo 257 :LLRKDLKPA T0296 254 :QMASERLGVEFGIVDLSLAPTPAV 1ceo 266 :IEFREKKKCKLYCGEFGVIAIADL T0296 279 :DSVARVLEE 1ceo 290 :ESRIKWHED T0296 305 :LNDQVKKGGVMACN 1ceo 299 :YISLLEEYDIGGAV T0296 321 :GGLSGAFI 1ceo 315 :YKKMDFEI T0296 330 :VSED 1ceo 323 :YNED T0296 334 :EGMIAAV 1ceo 332 :QELVNIL Number of specific fragments extracted= 22 number of extra gaps= 1 total=527 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 1dosA/T0296-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dosA expands to /projects/compbio/data/pdb/1dos.pdb.gz 1dosA:Skipped atom 958, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 960, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 962, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 964, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 966, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 968, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 970, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 972, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 976, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 978, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 980, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 982, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 984, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 986, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 988, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 990, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 992, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 994, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1000, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1002, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1004, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1006, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1008, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1010, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1301, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1303, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1305, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1307, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1309, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1311, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1313, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1315, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1319, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1321, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1323, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1325, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1327, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1329, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1331, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1333, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1337, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1339, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1341, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1343, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1345, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1347, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1349, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1351, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1620, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1622, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1624, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1626, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1628, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1630, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1632, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1634, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1638, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1640, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1642, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1644, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1646, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1648, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1650, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1652, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1654, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1658, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1660, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1662, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1664, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1666, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1668, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1670, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1672, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2117, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2119, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2121, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2123, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2125, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2127, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2129, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2133, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2135, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2137, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2139, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2141, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2143, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2145, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2147, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2149, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2151, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2158, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2160, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2162, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2164, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2517, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2519, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2521, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2523, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2525, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2527, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2529, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2531, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2533, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2535, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2537, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2541, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2543, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2545, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2547, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2549, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2551, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2553, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2555, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2557, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2559, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2565, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2567, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2569, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2571, because occupancy 0.400 <= existing 0.600 in 1dosA # T0296 read from 1dosA/T0296-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0296-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dosA to template set # found chain 1dosA in template set Warning: unaligning (T0296)M195 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)D191 Warning: unaligning (T0296)A196 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)D191 Warning: unaligning (T0296)D279 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)A231 T0296 4 :RQVTETIAMIEEQNFDIRTITM 1dosA 15 :DDVQKVFQVAKENNFALPAVNC T0296 33 :IDP 1dosA 37 :VGT T0296 54 :NLVAVGDEIAAELGIPIVNK 1dosA 40 :DSINAVLETAAKVKAPVIVQ T0296 75 :VSVTPISLIGAA 1dosA 60 :FSNGGASFIAGK T0296 87 :TDA 1dosA 75 :SDV T0296 90 :TDYVVLAKALDKAAKEIGVDFIGGFS 1dosA 84 :LGAISGAHHVHQMAEHYGVPVILHTD T0296 121 :GYQKGDEILINSI 1dosA 110 :HCAKKLLPWIDGL T0296 134 :PRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANL 1dosA 127 :EKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKI T0296 178 :GVAKLVVFANA 1dosA 168 :GMTLEIELGCT T0296 191 :DNPF 1dosA 186 :DNSH T0296 197 :G 1dosA 192 :A T0296 202 :VGEA 1dosA 193 :SALY T0296 214 :SGPGVVKRALEKVRGQ 1dosA 197 :TQPEDVDYAYTELSKI T0296 262 :VEFGIVDLSLAPTPAVG 1dosA 213 :SPRFTIAASFGNVHGVY T0296 291 :ETVGTHG 1dosA 232 :GNVVLTP T0296 300 :AALALLNDQVKKGGVMACNQ 1dosA 239 :TILRDSQEYVSKKHNLPHNS T0296 323 :LSGAFI 1dosA 259 :LNFVFH T0296 343 :GSLNLEKLEAMT 1dosA 267 :SGSTAQEIKDSV T0296 358 :SVGLDMIAIP 1dosA 279 :SYGVVKMNID T0296 373 :ETIAAMIADEA 1dosA 289 :TDTQWATWEGV Number of specific fragments extracted= 20 number of extra gaps= 2 total=547 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 1dosA/T0296-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1dosA/T0296-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0296-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dosA in template set Warning: unaligning (T0296)M195 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)D191 Warning: unaligning (T0296)A196 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)D191 Warning: unaligning (T0296)D279 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)A231 T0296 4 :RQVTETIAMIEEQNFDIRTITM 1dosA 15 :DDVQKVFQVAKENNFALPAVNC T0296 33 :IDPD 1dosA 37 :VGTD T0296 55 :LVAVGDEIAAELGIPIVNK 1dosA 41 :SINAVLETAAKVKAPVIVQ T0296 75 :VSVTPISLIGAA 1dosA 60 :FSNGGASFIAGK T0296 87 :TDA 1dosA 75 :SDV T0296 90 :TDYVVLAKALDKAAKEIGVDFIGGFS 1dosA 84 :LGAISGAHHVHQMAEHYGVPVILHTD T0296 121 :GYQKGDEILINSI 1dosA 110 :HCAKKLLPWIDGL T0296 134 :PRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANL 1dosA 127 :EKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKI T0296 178 :GVAKLVVFANA 1dosA 168 :GMTLEIELGCT T0296 191 :DNPF 1dosA 186 :DNSH T0296 197 :G 1dosA 192 :A T0296 202 :VGEA 1dosA 193 :SALY T0296 214 :SGPGVVKRALEKVRGQ 1dosA 197 :TQPEDVDYAYTELSKI T0296 262 :VEFGIVDLSLAPTPAVG 1dosA 213 :SPRFTIAASFGNVHGVY T0296 291 :ETVGTHG 1dosA 232 :GNVVLTP T0296 300 :AALALLNDQVKKGGVMACNQ 1dosA 239 :TILRDSQEYVSKKHNLPHNS T0296 323 :LSGAFI 1dosA 259 :LNFVFH T0296 343 :GSLNLEKLEAMT 1dosA 267 :SGSTAQEIKDSV T0296 358 :SVGLDMIAIP 1dosA 279 :SYGVVKMNID T0296 373 :ETIAAMIADEA 1dosA 289 :TDTQWATWEGV Number of specific fragments extracted= 20 number of extra gaps= 2 total=567 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 1dosA/T0296-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1dosA/T0296-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0296-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dosA in template set Warning: unaligning (T0296)V207 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)D191 Warning: unaligning (T0296)I208 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)D191 T0296 4 :RQVTETIAMIEEQNFDIRTITM 1dosA 15 :DDVQKVFQVAKENNFALPAVNC T0296 33 :ID 1dosA 37 :VG T0296 53 :ANLVAVGDEIAAELGIPIV 1dosA 39 :TDSINAVLETAAKVKAPVI T0296 75 :VSVT 1dosA 58 :VQFS T0296 79 :PISLIGAAT 1dosA 64 :GASFIAGKG T0296 89 :ATDYVVLAKALDKAAKEIGVDFIGGFSA 1dosA 83 :ILGAISGAHHVHQMAEHYGVPVILHTDH T0296 118 :VQKGYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLS 1dosA 111 :CAKKLLPWIDGLLDAGEKHFAATGKPLFSSHMIDLSEESLQENIEICSKYLERMSKIG T0296 180 :AKLVVFANAVEDNPF 1dosA 169 :MTLEIELGCTGGEED T0296 201 :GVGEAD 1dosA 184 :GVDNSH T0296 209 :INVGVSGPGVVKRALEKVRG 1dosA 192 :ASALYTQPEDVDYAYTELSK T0296 229 :QSFDVVAETVKK 1dosA 232 :GNVVLTPTILRD T0296 252 :VGQMASERLGVE 1dosA 244 :SQEYVSKKHNLP T0296 264 :FGIV 1dosA 259 :LNFV T0296 271 :LAPTPAVG 1dosA 263 :FHGGSGST T0296 306 :NDQVKKGGV 1dosA 271 :AQEIKDSVS T0296 321 :GGLSGAFI 1dosA 280 :YGVVKMNI T0296 333 :DEGMIAAVQNG 1dosA 288 :DTDTQWATWEG Number of specific fragments extracted= 17 number of extra gaps= 1 total=584 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 1gtzA/T0296-1gtzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gtzA expands to /projects/compbio/data/pdb/1gtz.pdb.gz 1gtzA:Skipped atom 65, because occupancy 0.300 <= existing 0.700 in 1gtzA Skipped atom 67, because occupancy 0.300 <= existing 0.700 in 1gtzA Skipped atom 69, because occupancy 0.300 <= existing 0.700 in 1gtzA Skipped atom 76, because occupancy 0.400 <= existing 0.600 in 1gtzA Skipped atom 78, because occupancy 0.400 <= existing 0.600 in 1gtzA Skipped atom 80, because occupancy 0.400 <= existing 0.600 in 1gtzA Skipped atom 221, because occupancy 0.400 <= existing 0.600 in 1gtzA Skipped atom 937, because occupancy 0.300 <= existing 0.700 in 1gtzA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1gtzA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1gtzA # T0296 read from 1gtzA/T0296-1gtzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gtzA read from 1gtzA/T0296-1gtzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gtzA to template set # found chain 1gtzA in template set T0296 16 :QNFDIRTITMG 1gtzA 5 :ANAPIMILNGP T0296 28 :SLLDCIDPDINRA 1gtzA 16 :NLNLLGQAQPEIY T0296 52 :AANLVAVGDEIAAELGIPIVNKR 1gtzA 33 :LADVEALCVKAAAAHGGTVDFRQ T0296 86 :ATDATDYVVLAKALDK 1gtzA 56 :SNHEGELVDWIHEARL T0296 106 :IGVDFIGGFSALVQK 1gtzA 72 :NHCGIVINPAAYSHT T0296 130 :INSIPRALAETDKV 1gtzA 87 :SVAILDALNTCDGL T0296 179 :VAKLVVFANAVEDNPFMAGAFHGVGEADVIIN 1gtzA 101 :PVVEVHISNIHQREPFRHHSYVSQRADGVVAG T0296 214 :SGPGVVKRALEKV 1gtzA 133 :CGVQGYVFGVERI T0296 235 :AE 1gtzA 146 :AA Number of specific fragments extracted= 9 number of extra gaps= 0 total=593 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 1gtzA/T0296-1gtzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1gtzA/T0296-1gtzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gtzA read from 1gtzA/T0296-1gtzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gtzA in template set T0296 17 :NFDIRTITMG 1gtzA 6 :NAPIMILNGP T0296 28 :SLLDCIDPDINRA 1gtzA 16 :NLNLLGQAQPEIY T0296 52 :AANLVAVGDEIAAELGIPIVNKR 1gtzA 33 :LADVEALCVKAAAAHGGTVDFRQ T0296 86 :ATDATDYVVLAKALDK 1gtzA 56 :SNHEGELVDWIHEARL T0296 106 :IGVDFIGGFSALVQK 1gtzA 72 :NHCGIVINPAAYSHT T0296 130 :INSIPRALAETDKV 1gtzA 87 :SVAILDALNTCDGL T0296 179 :VAKLVVFANAVEDNPFMAGAFHGVGEADVIIN 1gtzA 101 :PVVEVHISNIHQREPFRHHSYVSQRADGVVAG T0296 214 :SGPGVVKRALE 1gtzA 133 :CGVQGYVFGVE T0296 237 :TVKKT 1gtzA 144 :RIAAL Number of specific fragments extracted= 9 number of extra gaps= 0 total=602 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 1gtzA/T0296-1gtzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1gtzA/T0296-1gtzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gtzA read from 1gtzA/T0296-1gtzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gtzA in template set T0296 67 :GIPIV 1gtzA 6 :NAPIM T0296 75 :VSVTPISLIGAATDATDY 1gtzA 11 :ILNGPNLNLLGQAQPEIY T0296 93 :VVLAKALDKAAKEIGVDFIGGFS 1gtzA 34 :ADVEALCVKAAAAHGGTVDFRQS T0296 124 :KGDEILINSIPRALAETDKVCSS 1gtzA 57 :NHEGELVDWIHEARLNHCGIVIN T0296 151 :STK 1gtzA 80 :PAA T0296 161 :VADMGRIIKETANLSDMGVAKLVVFANAVEDNPFMAGAFHGVGEADVIIN 1gtzA 83 :YSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAG T0296 214 :SGPGVVKRALEKVR 1gtzA 133 :CGVQGYVFGVERIA Number of specific fragments extracted= 7 number of extra gaps= 0 total=609 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 1vhwA/T0296-1vhwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vhwA expands to /projects/compbio/data/pdb/1vhw.pdb.gz 1vhwA:Skipped atom 289, because occupancy 0.350 <= existing 0.650 in 1vhwA Skipped atom 291, because occupancy 0.350 <= existing 0.650 in 1vhwA Skipped atom 293, because occupancy 0.350 <= existing 0.650 in 1vhwA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 1vhwA Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 1vhwA # T0296 read from 1vhwA/T0296-1vhwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhwA read from 1vhwA/T0296-1vhwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vhwA to template set # found chain 1vhwA in template set T0296 145 :SSVNIGSTKSG 1vhwA 56 :RRISVMGHGMG T0296 158 :MTAVADMGRIIKETA 1vhwA 67 :IPSCSIYVTELIKDY T0296 178 :GVAKLVVFANAVE 1vhwA 82 :GVKKIIRVGSCGA T0296 198 :AFHGVGEADVIINVGVS 1vhwA 95 :VNEGIKVRDVVIGMGAC T0296 215 :GPGVV 1vhwA 113 :DSKVN T0296 223 :LEKVRGQS 1vhwA 118 :RIRFKDHD T0296 232 :DVVAETVKK 1vhwA 132 :YKMVKAAEE T0296 256 :ASERLGVEFGIVDLSLAPTPAVGD 1vhwA 141 :AAKARGIDVKVGNLFSAELFYTPD T0296 280 :SVARVLEEMGLETVGTH 1vhwA 166 :SMFDVMDKYGIVGVEME T0296 302 :LALLNDQVKKGGVMAC 1vhwA 183 :AAGIYGVAAEYGAKAL T0296 355 :AICSVG 1vhwA 199 :AICTVS T0296 362 :DMIAIPEDTPAETIAAMIADEAAIGV 1vhwA 205 :DHIKTGEQTTSEERQNTFNEMIEIAL Number of specific fragments extracted= 12 number of extra gaps= 0 total=621 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 1vhwA/T0296-1vhwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1vhwA/T0296-1vhwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhwA read from 1vhwA/T0296-1vhwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhwA in template set T0296 145 :SSVNIGSTKSG 1vhwA 56 :RRISVMGHGMG T0296 158 :MTAVADMGRIIKETA 1vhwA 67 :IPSCSIYVTELIKDY T0296 178 :GVAKLVVFANA 1vhwA 82 :GVKKIIRVGSC T0296 190 :E 1vhwA 94 :A T0296 198 :AFHGVGEADVIINVGVS 1vhwA 95 :VNEGIKVRDVVIGMGAC T0296 215 :GPGVV 1vhwA 113 :DSKVN T0296 223 :LEKVRGQS 1vhwA 118 :RIRFKDHD T0296 232 :DVVAETVKK 1vhwA 132 :YKMVKAAEE T0296 256 :ASERLGVEFGIVDLSLAPTPAVGD 1vhwA 141 :AAKARGIDVKVGNLFSAELFYTPD T0296 280 :SVARVLEEMGLETVGTH 1vhwA 166 :SMFDVMDKYGIVGVEME T0296 302 :LALLNDQVKKGGVMAC 1vhwA 183 :AAGIYGVAAEYGAKAL T0296 355 :AICSVG 1vhwA 199 :AICTVS T0296 362 :DMIAIPEDTPAETIAAMIADEAAIGV 1vhwA 205 :DHIKTGEQTTSEERQNTFNEMIEIAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=634 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 1vhwA/T0296-1vhwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1vhwA/T0296-1vhwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhwA read from 1vhwA/T0296-1vhwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhwA in template set T0296 75 :VSVTPISL 1vhwA 16 :VVLMPGDP T0296 97 :KALDKAAKEI 1vhwA 24 :LRAKYIAENF T0296 111 :IGGFSALVQKGYQK 1vhwA 34 :LDNAVQVCDVRNMF T0296 139 :ETDKVCSS 1vhwA 54 :KGRRISVM T0296 153 :KSGINMTAVADMGRIIKETAN 1vhwA 62 :GHGMGIPSCSIYVTELIKDYG T0296 179 :VAKLVVFANAVEDNP 1vhwA 83 :VKKIIRVGSCGAVNE T0296 201 :GVGEADVIINVGVS 1vhwA 98 :GIKVRDVVIGMGAC T0296 215 :GPGVVKR 1vhwA 113 :DSKVNRI T0296 225 :KVRGQSFD 1vhwA 120 :RFKDHDFA T0296 233 :VVAETVKKTAFK 1vhwA 129 :IADYKMVKAAEE T0296 256 :ASERLGVEFGIVDLSLAPTPAVGD 1vhwA 141 :AAKARGIDVKVGNLFSAELFYTPD T0296 280 :SVARVLEEMGLETVGTH 1vhwA 166 :SMFDVMDKYGIVGVEME T0296 302 :LALLNDQVKKGGV 1vhwA 183 :AAGIYGVAAEYGA T0296 325 :GA 1vhwA 196 :KA T0296 354 :TAICSVG 1vhwA 198 :LAICTVS T0296 362 :DMIAIPEDTPAETIAAMIADEAAIGV 1vhwA 205 :DHIKTGEQTTSEERQNTFNEMIEIAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=650 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 1ufoA/T0296-1ufoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ufoA expands to /projects/compbio/data/pdb/1ufo.pdb.gz 1ufoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 10, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 12, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 14, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 16, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 18, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 20, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 22, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 24, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 26, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 28, because occupancy 0.480 <= existing 0.520 in 1ufoA Skipped atom 30, because occupancy 0.480 <= existing 0.520 in 1ufoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1601, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1603, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1605, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1607, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1609, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1611, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1613, because occupancy 0.340 <= existing 0.660 in 1ufoA Skipped atom 1615, because occupancy 0.340 <= existing 0.660 in 1ufoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0296 read from 1ufoA/T0296-1ufoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufoA read from 1ufoA/T0296-1ufoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ufoA to template set # found chain 1ufoA in template set T0296 156 :INMTAV 1ufoA 35 :GSKEHI T0296 168 :IKETANLSDMG 1ufoA 41 :LALLPGYAERG T0296 180 :AKLVVF 1ufoA 52 :FLLLAF T0296 191 :DNPFMAGAFHGVGEA 1ufoA 58 :DAPRHGEREGPPPSS T0296 214 :SGPGVVKRALE 1ufoA 73 :KSPRYVEEVYR T0296 233 :VVAETVKK 1ufoA 84 :VALGFKEE T0296 249 :GQLVGQMASERLGVEFGIVDLSL 1ufoA 92 :ARRVAEEAERRFGLPLFLAGGSL T0296 297 :GTTAALALLN 1ufoA 115 :GAFVAHLLLA T0296 320 :V 1ufoA 127 :F T0296 322 :GLSGAFI 1ufoA 128 :RPRGVLA T0296 329 :PVSEDEGMIAAVQNG 1ufoA 148 :QVVEDPGVLALYQAP T0296 346 :NLEKLEAMTAICSVG 1ufoA 166 :RGEAYGGVPLLHLHG T0296 368 :EDTPAETIAAMIADE 1ufoA 184 :HIVPLARMEKTLEAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=663 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 1ufoA/T0296-1ufoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ufoA/T0296-1ufoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufoA read from 1ufoA/T0296-1ufoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufoA in template set T0296 157 :NMTAV 1ufoA 36 :SKEHI T0296 168 :IKETANLSDMGV 1ufoA 41 :LALLPGYAERGF T0296 181 :KLVVF 1ufoA 53 :LLLAF T0296 191 :DNPFMAGAFHGVGEA 1ufoA 58 :DAPRHGEREGPPPSS T0296 214 :SGPGVVKRALE 1ufoA 73 :KSPRYVEEVYR T0296 241 :TAFKITRIGQLVGQMASERLGVEFGIVDLSL 1ufoA 84 :VALGFKEEARRVAEEAERRFGLPLFLAGGSL T0296 297 :GTTAALALLN 1ufoA 115 :GAFVAHLLLA T0296 319 :QV 1ufoA 126 :GF T0296 322 :GLSGAFI 1ufoA 128 :RPRGVLA T0296 329 :PVSEDEGMIAAVQNG 1ufoA 148 :QVVEDPGVLALYQAP T0296 346 :NLEKLEAMTAICSVG 1ufoA 166 :RGEAYGGVPLLHLHG T0296 368 :EDTPAETIAAMIADE 1ufoA 184 :HIVPLARMEKTLEAL Number of specific fragments extracted= 12 number of extra gaps= 0 total=675 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 1ufoA/T0296-1ufoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1ufoA/T0296-1ufoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufoA read from 1ufoA/T0296-1ufoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufoA in template set T0296 155 :GINMTAVADM 1ufoA 34 :QGSKEHILAL T0296 174 :LSDMGVAKLVVFANAVEDNPFMAGAFHGVGEA 1ufoA 44 :LPGYAERGFLLLAFDAPRHGEREGPPPSSKSP T0296 233 :VVAETVKKTAFKITRIGQLVGQMASERLGVEFGIVDLSL 1ufoA 76 :RYVEEVYRVALGFKEEARRVAEEAERRFGLPLFLAGGSL T0296 297 :GTTAALALLN 1ufoA 115 :GAFVAHLLLA T0296 315 :MACNQVGGLSGAFIP 1ufoA 127 :FRPRGVLAFIGSGFP T0296 330 :VSEDEGMIAAVQN 1ufoA 149 :VVEDPGVLALYQA T0296 346 :NLEKLEAMTAICSVG 1ufoA 166 :RGEAYGGVPLLHLHG T0296 368 :EDTPAETIAAMIADE 1ufoA 184 :HIVPLARMEKTLEAL T0296 387 :VINMKTTAVRI 1ufoA 201 :HYPEGRLARFV Number of specific fragments extracted= 9 number of extra gaps= 0 total=684 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 1f2dA/T0296-1f2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f2dA expands to /projects/compbio/data/pdb/1f2d.pdb.gz 1f2dA:# T0296 read from 1f2dA/T0296-1f2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f2dA read from 1f2dA/T0296-1f2dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f2dA to template set # found chain 1f2dA in template set T0296 58 :VGDEIAAELGIPIVNKRVS 1f2dA 83 :MVAALAAKLGKKCVLIQED T0296 77 :VTPISLIGAATDATDYV 1f2dA 103 :VPIPEAEKDVYNRVGNI T0296 101 :KAAKEIGVDFIG 1f2dA 120 :ELSRIMGADVRV T0296 121 :GYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANA 1f2dA 135 :GFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVT T0296 196 :AGAFHGVGEADVIINVGVS 1f2dA 210 :LAGMAQYGRQDDVIAIDAS T0296 229 :QSFDVVAETVKK 1f2dA 229 :FTSEKTKEQTLR T0296 252 :VGQMASERLGVE 1f2dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1f2dA 260 :LDTRFA T0296 288 :MGLETVGTHGTTAALALLNDQ 1f2dA 266 :YPCYGVPNEGTIEAIRTCAEQ T0296 312 :GGVMAC 1f2dA 287 :EGVLTD T0296 329 :PVSED 1f2dA 293 :PVYEG T0296 334 :EGMIAAVQNGSLN 1f2dA 301 :QGLIALIKEDYFK Number of specific fragments extracted= 12 number of extra gaps= 0 total=696 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 1f2dA/T0296-1f2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1f2dA/T0296-1f2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f2dA read from 1f2dA/T0296-1f2dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f2dA in template set T0296 11 :AMIEEQNFDIRTITMG 1f2dA 60 :PDIVEGDYTHLVSIGG T0296 55 :LVAVGDEIAAELGIPIVNKRVS 1f2dA 80 :QTRMVAALAAKLGKKCVLIQED T0296 77 :VTPISLIGAATDATDYV 1f2dA 103 :VPIPEAEKDVYNRVGNI T0296 101 :KAAKEIGVDFIG 1f2dA 120 :ELSRIMGADVRV T0296 121 :GYQKGDEILINSIPRALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANA 1f2dA 135 :GFDIGMRKSFANALQELEDAGHKPYPIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVT T0296 196 :AGAFHGVGEADVIINVGVSG 1f2dA 210 :LAGMAQYGRQDDVIAIDASF T0296 230 :SFDVVAETVKK 1f2dA 230 :TSEKTKEQTLR T0296 252 :VGQMASERLGVE 1f2dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1f2dA 260 :LDTRFA T0296 288 :MGLETVGTHGTTAALALLNDQ 1f2dA 266 :YPCYGVPNEGTIEAIRTCAEQ T0296 312 :GGVMAC 1f2dA 287 :EGVLTD T0296 329 :PVSED 1f2dA 293 :PVYEG T0296 334 :EGMIAAVQNGSLN 1f2dA 301 :QGLIALIKEDYFK Number of specific fragments extracted= 13 number of extra gaps= 0 total=709 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 1f2dA/T0296-1f2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1f2dA/T0296-1f2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f2dA read from 1f2dA/T0296-1f2dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f2dA in template set T0296 10 :IAMIEEQNFD 1f2dA 59 :VPDIVEGDYT T0296 21 :RTITMGISLL 1f2dA 69 :HLVSIGGRQS T0296 54 :NLVAVGDEIAAELGIPIVNKRVSVTPI 1f2dA 79 :NQTRMVAALAAKLGKKCVLIQEDWVPI T0296 81 :SLIGAATDATDYVVLAKA 1f2dA 107 :EAEKDVYNRVGNIELSRI T0296 106 :IGVDFIGG 1f2dA 125 :MGADVRVI T0296 119 :QKGYQ 1f2dA 133 :EDGFD T0296 124 :KGDEILINSIPRALAETDKVC 1f2dA 139 :GMRKSFANALQELEDAGHKPY T0296 146 :SVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANAVEDNPFMAGAFHGVGEADVIINVGVS 1f2dA 160 :PIPAGCSEHKYGGLGFVGFADEVINQEVELGIKFDKIVVCCVTGSTTAGILAGMAQYGRQDDVIAIDAS T0296 233 :VVAETVKKTAFK 1f2dA 229 :FTSEKTKEQTLR T0296 252 :VGQMASERLGVE 1f2dA 241 :IANNTAKLIGVE T0296 267 :VDLSLA 1f2dA 260 :LDTRFA T0296 289 :GLETVGTHGTTAALALLNDQ 1f2dA 267 :PCYGVPNEGTIEAIRTCAEQ T0296 329 :PVSED 1f2dA 293 :PVYEG T0296 334 :EGMIAAVQNGSL 1f2dA 301 :QGLIALIKEDYF Number of specific fragments extracted= 14 number of extra gaps= 0 total=723 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 1e4iA/T0296-1e4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e4iA expands to /projects/compbio/data/pdb/1e4i.pdb.gz 1e4iA:# T0296 read from 1e4iA/T0296-1e4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e4iA read from 1e4iA/T0296-1e4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e4iA to template set # found chain 1e4iA in template set Warning: unaligning (T0296)C32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)D90 Warning: unaligning (T0296)I33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)D90 Warning: unaligning (T0296)S76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)W122 Warning: unaligning (T0296)V77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)W122 Warning: unaligning (T0296)A186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)N222 Warning: unaligning (T0296)N187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)N222 Warning: unaligning (T0296)A272 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1e4iA)S297 Warning: unaligning (T0296)P273 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1e4iA)S297 Warning: unaligning (T0296)I398 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)S399 Warning: unaligning (T0296)P399 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)S399 T0296 3 :IRQVTETIAMIEEQNFDIRTITM 1e4iA 58 :YHRYEEDIRLMKELGIRTYRFSV T0296 29 :LLD 1e4iA 86 :FPN T0296 34 :DPDIN 1e4iA 91 :GEVNQ T0296 47 :KITTKAANLVAVGD 1e4iA 96 :KGLDYYHRVVDLLN T0296 65 :ELGIPIVNKRV 1e4iA 110 :DNGIEPFCTLY T0296 78 :TPISLIGAA 1e4iA 123 :DLPQALQDA T0296 87 :TDATDYVVLAKAL 1e4iA 134 :WGNRRTIQAFVQF T0296 100 :DKAAKEI 1e4iA 148 :ETMFREF T0296 107 :GVDFIG 1e4iA 157 :KIQHWL T0296 113 :GFSALV 1e4iA 166 :EPWCIA T0296 119 :QKGYQKGDEILINSIPRAL 1e4iA 180 :HAPGLTNLQTAIDVGHHLL T0296 159 :TAVADMGRIIKET 1e4iA 199 :VAHGLSVRRFREL T0296 175 :SDM 1e4iA 212 :GTS T0296 180 :AKLVVF 1e4iA 215 :GQIGIA T0296 188 :AVE 1e4iA 223 :VSW T0296 210 :NVGVSGPGVVKRALEKV 1e4iA 226 :AVPYSTSEEDKAACART T0296 227 :RGQSFDVVAETVKKTAFKITRI 1e4iA 256 :QGSYPQFLVDWFAEQGATVPIQ T0296 249 :G 1e4iA 279 :G T0296 256 :ASERLGVEFGIVDLSL 1e4iA 280 :DMDIIGEPIDMIGINY T0296 274 :TPAVGD 1e4iA 304 :NPEAGF T0296 288 :MGLETVGTHGTTAALAL 1e4iA 323 :DIGWPVESRGLYEVLHY T0296 317 :CNQVGGLSGAFIPVS 1e4iA 340 :LQKYGNIDIYITENG T0296 342 :NGSLNLEKLEA 1e4iA 363 :NGKVQDDRRIS T0296 374 :TIAAMIADEAAIGVINMKTTAVRI 1e4iA 374 :YMQQHLVQVHRTIHDGLHVKGYMA Number of specific fragments extracted= 24 number of extra gaps= 5 total=747 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 1e4iA/T0296-1e4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1e4iA/T0296-1e4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e4iA read from 1e4iA/T0296-1e4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e4iA in template set Warning: unaligning (T0296)C32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)D90 Warning: unaligning (T0296)I33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)D90 Warning: unaligning (T0296)S76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)W122 Warning: unaligning (T0296)V77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)W122 Warning: unaligning (T0296)A186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)N222 Warning: unaligning (T0296)N187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)N222 Warning: unaligning (T0296)A272 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1e4iA)S297 Warning: unaligning (T0296)P273 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1e4iA)S297 Warning: unaligning (T0296)I398 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)S399 Warning: unaligning (T0296)P399 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)S399 T0296 3 :IRQVTETIAMIEEQNFDIRTITM 1e4iA 58 :YHRYEEDIRLMKELGIRTYRFSV T0296 29 :LLD 1e4iA 86 :FPN T0296 34 :DPDI 1e4iA 91 :GEVN T0296 46 :QKITTKAANLVAVGD 1e4iA 95 :QKGLDYYHRVVDLLN T0296 65 :ELGIPIVNKRV 1e4iA 110 :DNGIEPFCTLY T0296 78 :TPISLIGA 1e4iA 123 :DLPQALQD T0296 86 :ATDATDYVVLAKAL 1e4iA 133 :GWGNRRTIQAFVQF T0296 100 :DKAAKEI 1e4iA 148 :ETMFREF T0296 107 :GVDFIG 1e4iA 157 :KIQHWL T0296 113 :GFSALV 1e4iA 166 :EPWCIA T0296 119 :QKGYQKGDEILINSIPRALA 1e4iA 180 :HAPGLTNLQTAIDVGHHLLV T0296 160 :AVADMGRIIKETA 1e4iA 200 :AHGLSVRRFRELG T0296 179 :VAKLVVF 1e4iA 214 :SGQIGIA T0296 188 :AVE 1e4iA 223 :VSW T0296 210 :NVGVSGPGVVKRALEKV 1e4iA 226 :AVPYSTSEEDKAACART T0296 227 :RGQSFDVVAETVKKTAFKITR 1e4iA 256 :QGSYPQFLVDWFAEQGATVPI T0296 256 :ASERLGVEFGIVDLSL 1e4iA 280 :DMDIIGEPIDMIGINY T0296 274 :TPAVGD 1e4iA 304 :NPEAGF T0296 288 :MGLETVGTHGTTAALAL 1e4iA 323 :DIGWPVESRGLYEVLHY T0296 317 :CNQVGGLSGAFIPVS 1e4iA 340 :LQKYGNIDIYITENG T0296 342 :NGSLNLEKLEA 1e4iA 363 :NGKVQDDRRIS T0296 374 :TIAAMIADEAAIGVINMKTTAVRI 1e4iA 374 :YMQQHLVQVHRTIHDGLHVKGYMA Number of specific fragments extracted= 22 number of extra gaps= 5 total=769 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 1e4iA/T0296-1e4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1e4iA/T0296-1e4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e4iA read from 1e4iA/T0296-1e4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e4iA in template set Warning: unaligning (T0296)G84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)D90 Warning: unaligning (T0296)A85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)D90 Warning: unaligning (T0296)S270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1e4iA)N222 Warning: unaligning (T0296)L271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1e4iA)N222 T0296 49 :TTKAANLVAVGDEI 1e4iA 58 :YHRYEEDIRLMKEL T0296 67 :GIPIVNKRVSVTPISLI 1e4iA 72 :GIRTYRFSVSWPRIFPN T0296 86 :ATDATDYVVLAKALDKAAKEIGVDFIG 1e4iA 91 :GEVNQKGLDYYHRVVDLLNDNGIEPFC T0296 113 :GFSALVQKGYQKGDEI 1e4iA 124 :LPQALQDAGGWGNRRT T0296 158 :MTAVADMGRIIKETA 1e4iA 140 :IQAFVQFAETMFREF T0296 177 :MGVAKLVVFANAVE 1e4iA 155 :HGKIQHWLTFNEPW T0296 195 :MAGAFHGVGEADV 1e4iA 172 :FLSNMLGVHAPGL T0296 229 :QSFDVV 1e4iA 185 :TNLQTA T0296 239 :KKTAFKITRIGQLVGQMA 1e4iA 191 :IDVGHHLLVAHGLSVRRF T0296 258 :ERLGVEFGIVDL 1e4iA 209 :RELGTSGQIGIA T0296 272 :APT 1e4iA 223 :VSW T0296 275 :PAVGD 1e4iA 230 :STSEE T0296 280 :SVARVLEEM 1e4iA 238 :ACARTISLH T0296 298 :TTAALALLND 1e4iA 247 :SDWFLQPIYQ T0296 321 :GG 1e4iA 257 :GS T0296 332 :EDEGMIAAVQNGSLN 1e4iA 259 :YPQFLVDWFAEQGAT T0296 364 :IAIPED 1e4iA 274 :VPIQDG T0296 384 :AIGVINMKTTAVRII 1e4iA 280 :DMDIIGEPIDMIGIN Number of specific fragments extracted= 18 number of extra gaps= 2 total=787 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 1jx6A/T0296-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jx6A expands to /projects/compbio/data/pdb/1jx6.pdb.gz 1jx6A:# T0296 read from 1jx6A/T0296-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0296-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jx6A to template set # found chain 1jx6A in template set T0296 38 :NRAAEK 1jx6A 32 :QEFLDE T0296 46 :QKITTKAANLVAVGD 1jx6A 39 :PEQRNLTNALSEAVR T0296 69 :PIVNKRVSVT 1jx6A 66 :PIKISVVYPG T0296 86 :ATDATDYVVLAKALDKAAKEIGVDF 1jx6A 76 :QQVSDYWVRNIASFEKRLYKLNINY T0296 111 :IGGF 1jx6A 102 :LNQV T0296 121 :GYQKGDEILINSIPRALAETDKVC 1jx6A 108 :RPNADIKQQSLSLMEALKSKSDYL T0296 149 :IGSTKSGINMTAVAD 1jx6A 132 :IFTLDTTRHRKFVEH T0296 171 :TANLSD 1jx6A 147 :VLDSTN T0296 180 :AKLVVF 1jx6A 153 :TKLILQ T0296 194 :FMAGAFHGVGEADVIINVGVSGPGVVKRALEKV 1jx6A 159 :NITTPVREWDKHQPFLYVGFDHAEGSRELATEF T0296 227 :RGQS 1jx6A 196 :PKHT T0296 237 :TVKK 1jx6A 210 :YISD T0296 247 :RIGQLVGQMASERLGVEFGIVD 1jx6A 214 :VRGDTFIHQVNRDNNFELQSAY T0296 273 :PTPAVGDSVARVLEEMGLETVGTH 1jx6A 236 :YTKATKQSGYDAAKASLAKHPDVD T0296 297 :GTTAALALLNDQVKKGGV 1jx6A 264 :CSTDVALGAVDALAELGR T0296 324 :SGAFI 1jx6A 282 :EDIMI T0296 329 :PVSEDEGMIAAVQNGSLN 1jx6A 288 :GWGGGSAELDAIQKGDLD T0296 361 :LDMIAIP 1jx6A 306 :ITVMRMN T0296 373 :ETIAAMIADEAAIG 1jx6A 313 :DDTGIAMAEAIKWD T0296 388 :INMKTT 1jx6A 327 :LEDKPV T0296 399 :P 1jx6A 333 :P T0296 403 :E 1jx6A 334 :T T0296 404 :GDMIEFG 1jx6A 338 :GDFEIVT Number of specific fragments extracted= 23 number of extra gaps= 0 total=810 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 1jx6A/T0296-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1jx6A/T0296-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0296-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0296 37 :INRAAEK 1jx6A 31 :YQEFLDE T0296 46 :QKITTKAANLVAVGD 1jx6A 39 :PEQRNLTNALSEAVR T0296 69 :PIVNKRVSVT 1jx6A 66 :PIKISVVYPG T0296 86 :ATDATDYVVLAKALDKAAKEIGVDF 1jx6A 76 :QQVSDYWVRNIASFEKRLYKLNINY T0296 111 :IGGF 1jx6A 102 :LNQV T0296 121 :GYQKGDEILINSIPRALAETDKVC 1jx6A 108 :RPNADIKQQSLSLMEALKSKSDYL T0296 149 :IGSTKSGIN 1jx6A 132 :IFTLDTTRH T0296 165 :GRIIKETANLSD 1jx6A 141 :RKFVEHVLDSTN T0296 180 :AKLVVFA 1jx6A 153 :TKLILQN T0296 195 :MAGAFHGVGEADVIINVGVSGPGVV 1jx6A 160 :ITTPVREWDKHQPFLYVGFDHAEGS T0296 232 :DVVAETVKKTAFK 1jx6A 185 :RELATEFGKFFPK T0296 245 :ITRI 1jx6A 211 :ISDV T0296 249 :GQLVGQMASERLGVEFGIVD 1jx6A 216 :GDTFIHQVNRDNNFELQSAY T0296 273 :PTPAVGDSVARVLEEMGLETVGTH 1jx6A 236 :YTKATKQSGYDAAKASLAKHPDVD T0296 297 :GTTAALALLNDQVKKGGV 1jx6A 264 :CSTDVALGAVDALAELGR T0296 324 :SGAFI 1jx6A 282 :EDIMI T0296 329 :PVSEDEGMIAAVQNGSLN 1jx6A 288 :GWGGGSAELDAIQKGDLD T0296 361 :LDMIAIP 1jx6A 306 :ITVMRMN T0296 373 :ETIAAMIADEAAIG 1jx6A 313 :DDTGIAMAEAIKWD T0296 388 :INMKTT 1jx6A 327 :LEDKPV T0296 399 :P 1jx6A 333 :P T0296 403 :E 1jx6A 334 :T T0296 404 :GDMIEFG 1jx6A 338 :GDFEIVT Number of specific fragments extracted= 23 number of extra gaps= 0 total=833 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 1jx6A/T0296-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1jx6A/T0296-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0296-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0296 36 :DINRAAEK 1jx6A 30 :GYQEFLDE T0296 46 :QKITTKAANLVAVGD 1jx6A 39 :PEQRNLTNALSEAVR T0296 67 :GIPIVNK 1jx6A 64 :QRPIKIS T0296 75 :VSVT 1jx6A 71 :VVYP T0296 80 :ISL 1jx6A 75 :GQQ T0296 88 :DATDYVVLAKALDKAAKEIGVDFIGGFSALV 1jx6A 78 :VSDYWVRNIASFEKRLYKLNINYQLNQVFTR T0296 122 :YQKGDEILINSIPRALAETDKVCS 1jx6A 109 :PNADIKQQSLSLMEALKSKSDYLI T0296 147 :VNIGSTK 1jx6A 133 :FTLDTTR T0296 164 :MGRIIKETANLSD 1jx6A 140 :HRKFVEHVLDSTN T0296 180 :AKLVVF 1jx6A 153 :TKLILQ T0296 194 :FMAGAFHGVGEADVIINVGVSGPGVVKRALEKV 1jx6A 159 :NITTPVREWDKHQPFLYVGFDHAEGSRELATEF T0296 227 :RGQSF 1jx6A 197 :KHTYY T0296 233 :VVAE 1jx6A 210 :YISD T0296 247 :RIGQLVGQMASERLGVEFGIVDLSLAPT 1jx6A 214 :VRGDTFIHQVNRDNNFELQSAYYTKATK T0296 279 :DSVARVLEEM 1jx6A 242 :QSGYDAAKAS T0296 289 :GLETVGTH 1jx6A 257 :DVDFIYAC T0296 298 :TTAALALLNDQVKKGGV 1jx6A 265 :STDVALGAVDALAELGR T0296 316 :ACNQVGGLSG 1jx6A 282 :EDIMINGWGG T0296 333 :DEGMIAAVQNGSLN 1jx6A 292 :GSAELDAIQKGDLD T0296 361 :LDMIAIP 1jx6A 306 :ITVMRMN T0296 373 :ET 1jx6A 313 :DD T0296 376 :AAMIADEAAIGVINMKTT 1jx6A 315 :TGIAMAEAIKWDLEDKPV T0296 399 :PK 1jx6A 333 :PT T0296 403 :E 1jx6A 335 :V T0296 404 :GDMIEFGG 1jx6A 338 :GDFEIVTK T0296 423 :GASSV 1jx6A 346 :ADSPE Number of specific fragments extracted= 26 number of extra gaps= 0 total=859 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 1j0aA/T0296-1j0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j0aA expands to /projects/compbio/data/pdb/1j0a.pdb.gz 1j0aA:# T0296 read from 1j0aA/T0296-1j0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0aA read from 1j0aA/T0296-1j0aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j0aA to template set # found chain 1j0aA in template set T0296 9 :TIAMIEEQNFDIRTITMG 1j0aA 61 :LLGDALSKGADVVITVGA T0296 58 :VGDEIAAELGIPIVNKRV 1j0aA 86 :VTGLAAKKLGLDAILVLR T0296 86 :ATDATD 1j0aA 104 :GKEELK T0296 98 :ALDKAAKEIGVDFIG 1j0aA 110 :GNYLLDKIMGIETRV T0296 121 :GYQ 1j0aA 126 :DAK T0296 124 :KGDEILINSIPRALAETDKVCSSVNIGST 1j0aA 131 :FELMKYAEEIAEELKREGRKPYVIPPGGA T0296 157 :NMTAVADMGRIIKETANLSDMGVAKLVVFANA 1j0aA 160 :SPIGTLGYVRAVGEIATQSEVKFDSIVVAAGS T0296 197 :GAF 1j0aA 202 :LSI T0296 202 :VGEADVIINVGVSGPG 1j0aA 205 :LNEDIRPVGIAVGRFG T0296 228 :GQSFDVVAETV 1j0aA 221 :EVMTSKLDNLI T0296 254 :QMASERLGVEF 1j0aA 232 :KEAAELLGVKV T0296 265 :GIVDLSL 1j0aA 247 :ELYDYSF T0296 275 :PAVGD 1j0aA 254 :GEYGK T0296 280 :SVARVLEEMGLE 1j0aA 262 :EVAQIIRKVGTR T0296 292 :TVGTHGTTAALALLNDQVKKGG 1j0aA 277 :ILDPVYTGKAFYGLVDLARKGE Number of specific fragments extracted= 15 number of extra gaps= 0 total=874 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 1j0aA/T0296-1j0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1j0aA/T0296-1j0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0aA read from 1j0aA/T0296-1j0aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j0aA in template set T0296 9 :TIAMIEEQNFDIRTITMG 1j0aA 61 :LLGDALSKGADVVITVGA T0296 58 :VGDEIAAELGIPIVNKRV 1j0aA 86 :VTGLAAKKLGLDAILVLR T0296 86 :ATDATD 1j0aA 104 :GKEELK T0296 98 :ALDKAAKEIGVDFIG 1j0aA 110 :GNYLLDKIMGIETRV T0296 121 :GYQ 1j0aA 126 :DAK T0296 124 :KGDEILINSIPRALAETDKVCSSVNIGST 1j0aA 131 :FELMKYAEEIAEELKREGRKPYVIPPGGA T0296 157 :NMTAVADMGRIIKETANLSDMGVAKLVVFANA 1j0aA 160 :SPIGTLGYVRAVGEIATQSEVKFDSIVVAAGS T0296 197 :GAF 1j0aA 202 :LSI T0296 202 :VGEADVIINVGVSG 1j0aA 205 :LNEDIRPVGIAVGR T0296 216 :PG 1j0aA 221 :EV T0296 241 :TAFKITR 1j0aA 223 :MTSKLDN T0296 252 :VGQMASERLGVEF 1j0aA 230 :LIKEAAELLGVKV T0296 265 :GIVDLSL 1j0aA 247 :ELYDYSF T0296 275 :PAVGD 1j0aA 254 :GEYGK T0296 280 :SVARVLEEMGLE 1j0aA 262 :EVAQIIRKVGTR T0296 292 :TVGTHGTTAALALLNDQVKKGG 1j0aA 277 :ILDPVYTGKAFYGLVDLARKGE Number of specific fragments extracted= 16 number of extra gaps= 0 total=890 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 1j0aA/T0296-1j0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1j0aA/T0296-1j0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j0aA read from 1j0aA/T0296-1j0aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j0aA in template set T0296 8 :ETIAMIEEQNFDI 1j0aA 60 :YLLGDALSKGADV T0296 22 :TITMGISLL 1j0aA 73 :VITVGAVHS T0296 58 :VGDEIAAELGIPIV 1j0aA 86 :VTGLAAKKLGLDAI T0296 75 :VSVTPIS 1j0aA 100 :LVLRGKE T0296 88 :DATD 1j0aA 107 :ELKG T0296 99 :LDKAAKEIGVDFIGGF 1j0aA 111 :NYLLDKIMGIETRVYD T0296 119 :QKGYQKGDEILINSIPRALAETDKVCSS 1j0aA 127 :AKDSFELMKYAEEIAEELKREGRKPYVI T0296 152 :TKSGINMTAVADMGRIIKETANLSDMGVAKLVVFANAV 1j0aA 155 :PPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSG T0296 215 :GPGVVKRALEKVRGQSFDVV 1j0aA 193 :GTLAGLSLGLSILNEDIRPV T0296 245 :ITRIGQLVGQMASERLGVEF 1j0aA 223 :MTSKLDNLIKEAAELLGVKV T0296 265 :GIVDLSLAPTPAVGDSVARVLEEMG 1j0aA 247 :ELYDYSFGEYGKITGEVAQIIRKVG T0296 290 :LETVGTHGTTAALALLNDQVKKG 1j0aA 275 :GIILDPVYTGKAFYGLVDLARKG Number of specific fragments extracted= 12 number of extra gaps= 0 total=902 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 1brwA/T0296-1brwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1brwA expands to /projects/compbio/data/pdb/1brw.pdb.gz 1brwA:# T0296 read from 1brwA/T0296-1brwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brwA read from 1brwA/T0296-1brwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1brwA to template set # found chain 1brwA in template set Warning: unaligning (T0296)G113 because of BadResidue code BAD_PEPTIDE in next template residue (1brwA)T154 T0296 1 :MDIRQVTETIAMIEEQNF 1brwA 16 :LTKEEIEWIVRGYTNGDI T0296 33 :IDPDINRAAEKIY 1brwA 34 :PDYQMSALAMAIY T0296 46 :QKITTKAANLVA 1brwA 53 :EETAALTMAMVQ T0296 66 :LGIPIVNKRVS 1brwA 102 :VGVPVAKMSGR T0296 77 :VTPISLIGAA 1brwA 117 :TGGTIDKLES T0296 87 :TDATDYVVL 1brwA 134 :ISKDEFIRL T0296 103 :AKEIGVDFIG 1brwA 143 :VNENGIAIIG T0296 114 :FSALVQKGYQKGDEILINSIP 1brwA 164 :LYALRDVTATVNSIPLIASSI T0296 135 :RALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVV 1brwA 188 :KIAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVGRRTMAVIS T0296 187 :NAVE 1brwA 238 :DMSQ T0296 195 :MAGA 1brwA 242 :PLGY T0296 212 :GVSGPGVVKRALEKVRGQSFDVVAETVK 1brwA 246 :AVGNALEVKEAIETLKGNGPHDLTELCL T0296 251 :LVGQMASERLG 1brwA 274 :TLGSHMVYLAE T0296 273 :PTPAVG 1brwA 285 :KAPSLD T0296 300 :AALALLNDQVKKGGVMAC 1brwA 291 :EARRLLEEAIRSGAAIAA T0296 336 :MIAAVQNGSL 1brwA 309 :FKTFLAAQGG T0296 346 :NLEKLEAMTA 1brwA 325 :DLDKLPKAAY T0296 361 :LDMIAIPED 1brwA 335 :TSTVTAAAD T0296 375 :IAAMIADEAAIGV 1brwA 351 :ADDIGTAAMWLGA T0296 400 :KGKEGD 1brwA 365 :RAKKED T0296 406 :MIEFGGLLGT 1brwA 377 :GIVLHKKIGD T0296 420 :KVNGAS 1brwA 387 :RVQKGE Number of specific fragments extracted= 22 number of extra gaps= 1 total=924 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 1brwA/T0296-1brwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1brwA/T0296-1brwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brwA read from 1brwA/T0296-1brwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1brwA in template set Warning: unaligning (T0296)G113 because of BadResidue code BAD_PEPTIDE in next template residue (1brwA)T154 T0296 1 :MDIRQVTETIAMIEEQNF 1brwA 16 :LTKEEIEWIVRGYTNGDI T0296 33 :IDPDINRAAEKIY 1brwA 34 :PDYQMSALAMAIY T0296 46 :QKITTKAANLVA 1brwA 53 :EETAALTMAMVQ T0296 66 :LGIPIVNKRVS 1brwA 102 :VGVPVAKMSGR T0296 77 :VTPISLIGA 1brwA 117 :TGGTIDKLE T0296 86 :ATDATDYVVL 1brwA 133 :EISKDEFIRL T0296 103 :AKEIGVDFIG 1brwA 143 :VNENGIAIIG T0296 114 :FSALVQKGYQKGDEILINSIP 1brwA 164 :LYALRDVTATVNSIPLIASSI T0296 135 :RALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSDMGVAKLVV 1brwA 188 :KIAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVGRRTMAVIS T0296 187 :NAVE 1brwA 238 :DMSQ T0296 195 :MAGA 1brwA 242 :PLGY T0296 212 :GVSGPGVVKRALEKVRGQSFDVVA 1brwA 246 :AVGNALEVKEAIETLKGNGPHDLT T0296 247 :RIGQLVGQMASERLG 1brwA 270 :ELCLTLGSHMVYLAE T0296 273 :PTPAVG 1brwA 285 :KAPSLD T0296 300 :AALALLNDQVKKGGVMAC 1brwA 291 :EARRLLEEAIRSGAAIAA T0296 336 :MIAAVQNGSL 1brwA 309 :FKTFLAAQGG T0296 346 :NLEKLEAMTA 1brwA 325 :DLDKLPKAAY T0296 361 :LDMIAIPED 1brwA 335 :TSTVTAAAD T0296 375 :IAAMIADEAAIGV 1brwA 351 :ADDIGTAAMWLGA T0296 400 :KGKEGD 1brwA 365 :RAKKED T0296 406 :MIEFGGLLGT 1brwA 377 :GIVLHKKIGD T0296 420 :KVNGAS 1brwA 387 :RVQKGE Number of specific fragments extracted= 22 number of extra gaps= 1 total=946 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 1brwA/T0296-1brwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0296 read from 1brwA/T0296-1brwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brwA read from 1brwA/T0296-1brwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1brwA in template set Warning: unaligning (T0296)G113 because of BadResidue code BAD_PEPTIDE in next template residue (1brwA)T154 Warning: unaligning (T0296)F114 because of BadResidue code BAD_PEPTIDE at template residue (1brwA)T154 Warning: unaligning (T0296)K120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1brwA)D156 Warning: unaligning (T0296)G121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1brwA)D156 T0296 66 :LGIPIVN 1brwA 102 :VGVPVAK T0296 75 :VSVTPISLIGAAT 1brwA 109 :MSGRGLGHTGGTI T0296 88 :DATDY 1brwA 135 :SKDEF T0296 100 :DKAAKEIGVDFIG 1brwA 140 :IRLVNENGIAIIG T0296 122 :YQKGDEILINSIPR 1brwA 157 :LTPADKKLYALRDV T0296 136 :ALAETDKVCSSVNIGSTKSGINMTAVADMGRIIKETANLSD 1brwA 189 :IAAGADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGKRVG T0296 180 :AKLVVFANAVED 1brwA 230 :RRTMAVISDMSQ T0296 198 :AFH 1brwA 242 :PLG T0296 211 :VGVSGPGVVKRALEKVRGQSFDVVAE 1brwA 245 :YAVGNALEVKEAIETLKGNGPHDLTE T0296 248 :IGQLVGQMASERLGV 1brwA 271 :LCLTLGSHMVYLAEK T0296 272 :APTPA 1brwA 286 :APSLD T0296 300 :AALALLNDQVKKGGVMA 1brwA 291 :EARRLLEEAIRSGAAIA T0296 335 :GMIAAVQNGSL 1brwA 308 :AFKTFLAAQGG T0296 346 :NLEKLEAMT 1brwA 325 :DLDKLPKAA T0296 362 :DMIAIPED 1brwA 336 :STVTAAAD T0296 375 :IAAMIADEAAIGV 1brwA 351 :ADDIGTAAMWLGA T0296 399 :PKGKE 1brwA 364 :GRAKK T0296 404 :GDMIEFGGLLGT 1brwA 375 :AVGIVLHKKIGD T0296 420 :KVNGAS 1brwA 387 :RVQKGE Number of specific fragments extracted= 19 number of extra gaps= 1 total=965 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 24.395 sec, elapsed time= 39.158 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 98790 constraints to all_contacts Done adding distance constraints # command:CPU_time= 24.660 sec, elapsed time= 39.462 sec. # command:Reading probabilities from T0296.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 15.396 Optimizing... Probability sum: -883.551, CN propb: -883.551 weights: 0.127 constraints: 1769 # command:CPU_time= 1537.834 sec, elapsed time= 1552.999 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1769 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1769 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 5735 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 5735 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 87762 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 87762 # command:CPU_time= 1539.575 sec, elapsed time= 1555.862 sec. # command: