# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0295/ # command:# Making conformation for sequence T0295 numbered 1 through 275 Created new target T0295 from T0295.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0295/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0295//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0295/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0295//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0295/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0295/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0295/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1i1nA/merged-good-all-a2m # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0295 5 :NPGILDKIIYAAK 1i1nA 60 :APHMHAYALELLF # choosing archetypes in rotamer library T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLA 1i1nA 75 :LHEGAKALDVGSGSGILTACFARMV T0295 43 :KKVITIDIDSRMISEVKKRCL 1i1nA 103 :GKVIGIDHIKELVDDSVNNVR T0295 64 :YE 1i1nA 131 :SS T0295 68 :NNLEVYEGDAIKTVFPK 1i1nA 133 :GRVQLVVGDGRMGYAEE T0295 85 :FDVCTANIPYKISSP 1i1nA 152 :YDAIHVGAAAPVVPQ T0295 106 :SHRPLFKCAVLMFQK 1i1nA 167 :ALIDQLKPGGRLILP T0295 127 :LANVGDS 1i1nA 182 :VGPAGGN T0295 140 :INVKLF 1i1nA 189 :QMLEQY T0295 146 :CKVTKVCNVN 1i1nA 202 :IKMKPLMGVI T0295 177 :SSFLTNFDE 1i1nA 212 :YVPLTDKEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 Number of alignments=1 # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0295 3 :LKNPGILDKIIYAAK 1i1nA 58 :ISAPHMHAYALELLF T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1i1nA 75 :LHEGAKALDVGSGSGILTACFARMVG T0295 44 :KVITIDIDSRMISEVKKRCL 1i1nA 104 :KVIGIDHIKELVDDSVNNVR T0295 64 :YE 1i1nA 131 :SS T0295 68 :NNLEVYEGDAIK 1i1nA 133 :GRVQLVVGDGRM T0295 81 :VFPK 1i1nA 145 :GYAE T0295 85 :FDVCTANIPYKISSPL 1i1nA 152 :YDAIHVGAAAPVVPQA T0295 107 :HRPLFKCAVLMFQKE 1i1nA 168 :LIDQLKPGGRLILPV T0295 128 :ANVGD 1i1nA 183 :GPAGG T0295 136 :SRLTINVKL 1i1nA 188 :NQMLEQYDK T0295 146 :CKVTKVCNVNRSS 1i1nA 202 :IKMKPLMGVIYVP T0295 180 :LTNFDE 1i1nA 215 :LTDKEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=23 Number of alignments=2 # 1i1nA read from 1i1nA/merged-good-all-a2m # found chain 1i1nA in training set T0295 3 :LKNPGILDKIIYAAK 1i1nA 58 :ISAPHMHAYALELLF T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 1i1nA 75 :LHEGAKALDVGSGSGILTACFARM T0295 42 :AKKVITIDIDSRMISEVKKRCLY 1i1nA 102 :TGKVIGIDHIKELVDDSVNNVRK T0295 65 :EG 1i1nA 131 :SS T0295 68 :NNLEVYEGDAIKTVFPK 1i1nA 133 :GRVQLVVGDGRMGYAEE T0295 85 :FDVCTANIPYKISSPLIFKLIS 1i1nA 152 :YDAIHVGAAAPVVPQALIDQLK T0295 127 :LANVGDS 1i1nA 182 :VGPAGGN T0295 139 :TINVKLF 1i1nA 189 :QMLEQYD T0295 146 :CKVTKVC 1i1nA 202 :IKMKPLM Number of specific fragments extracted= 9 number of extra gaps= 0 total=32 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f3lA expands to /projects/compbio/data/pdb/1f3l.pdb.gz 1f3lA:# T0295 read from 1f3lA/merged-good-all-a2m # 1f3lA read from 1f3lA/merged-good-all-a2m # adding 1f3lA to template set # found chain 1f3lA in template set T0295 2 :LLKNPGILDKIIYAAK 1f3lA 230 :MLKDKVRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 1f3lA 250 :IFKDKVVLDVGCGTGILSMFAAKA T0295 42 :AKKVITIDIDS 1f3lA 275 :AKKVIAVDQSE T0295 54 :MISEVKKRCLYEGY 1f3lA 286 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIK 1f3lA 301 :DTIVLIKGKIEE T0295 80 :TVFPKFDVCTANIPYKISS 1f3lA 315 :LPVEKVDVIISEWMGYFLL T0295 99 :PLIFKLIS 1f3lA 339 :DSVLYAKS T0295 109 :PLFKCAVLMFQ 1f3lA 347 :KYLAKGGSVYP T0295 138 :LTINVKLFCK 1f3lA 358 :DICTISLVAV T0295 209 :AVLNMLEHNYKNWCTLNKQVPVN 1f3lA 368 :SDVSKHADRIAFWDDVYGFNMSC Number of specific fragments extracted= 10 number of extra gaps= 0 total=42 Number of alignments=4 # 1f3lA read from 1f3lA/merged-good-all-a2m # found chain 1f3lA in template set T0295 4 :KNPGILDKIIYAAK 1f3lA 232 :KDKVRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1f3lA 250 :IFKDKVVLDVGCGTGILSMFAAKAGA T0295 44 :KVITIDIDS 1f3lA 277 :KVIAVDQSE T0295 54 :MISEVKKRCLYEGY 1f3lA 286 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIKTVFPK 1f3lA 301 :DTIVLIKGKIEEVSLPV T0295 85 :FDVCTAN 1f3lA 320 :VDVIISE T0295 92 :IPYKISSP 1f3lA 328 :MGYFLLFE T0295 100 :LIFKLISH 1f3lA 337 :MLDSVLYA T0295 108 :RPLFKCAVLMF 1f3lA 346 :SKYLAKGGSVY T0295 120 :K 1f3lA 357 :P T0295 166 :DSVIVKLIP 1f3lA 358 :DICTISLVA T0295 209 :AVLNMLEHNYKNWCTLNKQVPVN 1f3lA 368 :SDVSKHADRIAFWDDVYGFNMSC Number of specific fragments extracted= 12 number of extra gaps= 0 total=54 Number of alignments=5 # 1f3lA read from 1f3lA/merged-good-all-a2m # found chain 1f3lA in template set T0295 3 :LKNPGILDKIIYAAK 1f3lA 231 :LKDKVRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 1f3lA 250 :IFKDKVVLDVGCGTGILSMFAAKA T0295 42 :AKKVITIDIDS 1f3lA 275 :AKKVIAVDQSE T0295 54 :MISEVKKRCLYEGY 1f3lA 286 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIKTVF 1f3lA 301 :DTIVLIKGKIEEVSL T0295 83 :PKFDVCTANIPYKIS 1f3lA 318 :EKVDVIISEWMGYFL T0295 113 :CAVLMFQKEFAERMLANVGDSNYSRLTINVKLF 1f3lA 335 :ESMLDSVLYAKSKYLAKGGSVYPDICTISLVAV T0295 209 :AVLNMLEHNYKNWCTLNKQVPVN 1f3lA 368 :SDVSKHADRIAFWDDVYGFNMSC Number of specific fragments extracted= 8 number of extra gaps= 0 total=62 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b25A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b25A expands to /projects/compbio/data/pdb/2b25.pdb.gz 2b25A:# T0295 read from 2b25A/merged-good-all-a2m # 2b25A read from 2b25A/merged-good-all-a2m # adding 2b25A to template set # found chain 2b25A in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0295)N68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0295)N69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0295)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0295)T80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0295)V81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)T185 Warning: unaligning (T0295)C152 because of BadResidue code BAD_PEPTIDE in next template residue (2b25A)E244 Warning: unaligning (T0295)N153 because of BadResidue code BAD_PEPTIDE at template residue (2b25A)E244 Warning: unaligning (T0295)K175 because last residue in template chain is (2b25A)V329 T0295 4 :KNPGILDKIIYAAKIKSSDIVLE 2b25A 87 :TFPKDINMILSMMDINPGDTVLE T0295 29 :CGTGNLTVKLLPLA 2b25A 112 :SGSGGMSLFLSKAV T0295 43 :KKVITIDIDSRMISEVKKRCLYE 2b25A 129 :GRVISFEVRKDHHDLAKKNYKHW T0295 66 :GY 2b25A 162 :EW T0295 71 :EVYEGDAIK 2b25A 168 :DFIHKDISG T0295 85 :FDVCTANIPYKIS 2b25A 186 :FDAVALDMLNPHV T0295 103 :KLISHRPLFKCAVLMFQ 2b25A 199 :TLPVFYPHLKHGGVCAV T0295 120 :KEFAERMLANVGDSNYS 2b25A 220 :ITQVIELLDGIRTCELA T0295 146 :CKVTKV 2b25A 237 :LSCEKI T0295 154 :VNRSSF 2b25A 245 :VIVRDW T0295 160 :NPPPKVDSVIVKLIP 2b25A 314 :HWQPGHTAFLVKLRK Number of specific fragments extracted= 11 number of extra gaps= 4 total=73 Number of alignments=7 # 2b25A read from 2b25A/merged-good-all-a2m # found chain 2b25A in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0295)N68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0295)N69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0295)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0295)T80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0295)C152 because of BadResidue code BAD_PEPTIDE in next template residue (2b25A)E244 Warning: unaligning (T0295)N153 because of BadResidue code BAD_PEPTIDE at template residue (2b25A)E244 Warning: unaligning (T0295)K175 because last residue in template chain is (2b25A)V329 T0295 4 :KNPGILDKIIYAAKIKSSDIVLE 2b25A 87 :TFPKDINMILSMMDINPGDTVLE T0295 29 :CGTGNLTVKLLPLAK 2b25A 112 :SGSGGMSLFLSKAVG T0295 44 :KVITIDIDSRMISEVKKRCLYEG 2b25A 130 :RVISFEVRKDHHDLAKKNYKHWR T0295 67 :Y 2b25A 163 :W T0295 71 :EVYEGDAIK 2b25A 168 :DFIHKDISG T0295 85 :FDVCTANI 2b25A 186 :FDAVALDM T0295 98 :SPLIFKLISHRPLFKCAVLMFQ 2b25A 194 :LNPHVTLPVFYPHLKHGGVCAV T0295 120 :KEFAERMLANVGDSN 2b25A 220 :ITQVIELLDGIRTCE T0295 144 :LFCKVTKV 2b25A 235 :LALSCEKI T0295 154 :VNRSSFNPP 2b25A 245 :VIVRDWLVC T0295 163 :PKVDSVIVKLIP 2b25A 317 :PGHTAFLVKLRK Number of specific fragments extracted= 11 number of extra gaps= 4 total=84 Number of alignments=8 # 2b25A read from 2b25A/merged-good-all-a2m # found chain 2b25A in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)G111 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)G111 Warning: unaligning (T0295)N68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b25A)N166 Warning: unaligning (T0295)N69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)N166 Warning: unaligning (T0295)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b25A)V167 Warning: unaligning (T0295)T80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b25A)T185 Warning: unaligning (T0295)V81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b25A)T185 T0295 5 :NPGILDKIIYAAKIKSSDIVLE 2b25A 88 :FPKDINMILSMMDINPGDTVLE T0295 29 :CGTGNLTVKLLPL 2b25A 112 :SGSGGMSLFLSKA T0295 42 :AKKVITIDIDSRMISEVKKRCLY 2b25A 128 :QGRVISFEVRKDHHDLAKKNYKH T0295 65 :EGY 2b25A 161 :EEW T0295 71 :EVYEGDAIK 2b25A 168 :DFIHKDISG T0295 85 :FDVCTANI 2b25A 186 :FDAVALDM T0295 109 :PLFKCAVLMF 2b25A 194 :LNPHVTLPVF T0295 127 :LANV 2b25A 204 :YPHL T0295 164 :KVDSVIVKLI 2b25A 208 :KHGGVCAVYV T0295 181 :TNFDEWDNLLRICFS 2b25A 218 :VNITQVIELLDGIRT Number of specific fragments extracted= 10 number of extra gaps= 3 total=94 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ixkA expands to /projects/compbio/data/pdb/1ixk.pdb.gz 1ixkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1ixkA/merged-good-all-a2m # 1ixkA read from 1ixkA/merged-good-all-a2m # adding 1ixkA to template set # found chain 1ixkA in template set T0295 15 :AAKIKSSDIVLEIGCGTGNLTVKLLPLA 1ixkA 113 :ALDPKPGEIVADMAAAPGGKTSYLAQLM T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTV 1ixkA 144 :GVIYAFDVDENRLRETRLNLSRLGVLNVILFHSSSLHIG T0295 82 :FPK 1ixkA 184 :LNV T0295 85 :FDVCTANIPY 1ixkA 188 :FDKILLDAPC T0295 100 :LIFKLISHRPLFKCAVLMFQ 1ixkA 225 :QMRLLEKGLEVLKPGGILVY T0295 121 :EFAERMLANVG 1ixkA 256 :FVIQWALDNFD T0295 145 :FCKVTKVCNVNRSSF 1ixkA 269 :LLPLKYGEPALTNPF Number of specific fragments extracted= 7 number of extra gaps= 0 total=101 Number of alignments=10 # 1ixkA read from 1ixkA/merged-good-all-a2m # found chain 1ixkA in template set T0295 15 :AAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1ixkA 113 :ALDPKPGEIVADMAAAPGGKTSYLAQLMR T0295 44 :KVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKT 1ixkA 145 :VIYAFDVDENRLRETRLNLSRLGVLNVILFHSSSLHI T0295 81 :VFPK 1ixkA 183 :ELNV T0295 85 :FDVCTANIPY 1ixkA 188 :FDKILLDAPC T0295 99 :P 1ixkA 223 :G T0295 100 :LIFKLISHRPLFKCAVLMFQ 1ixkA 225 :QMRLLEKGLEVLKPGGILVY T0295 120 :KE 1ixkA 251 :PE T0295 122 :FAERMLANVG 1ixkA 257 :VIQWALDNFD T0295 145 :FCKVTKVCNVNRSSFNPP 1ixkA 269 :LLPLKYGEPALTNPFGIE T0295 163 :PKVDSVIVKL 1ixkA 305 :SGFFIAKIRK Number of specific fragments extracted= 10 number of extra gaps= 0 total=111 Number of alignments=11 # 1ixkA read from 1ixkA/merged-good-all-a2m # found chain 1ixkA in template set Warning: unaligning (T0295)T223 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ixkA)R213 Warning: unaligning (T0295)F232 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ixkA)R213 T0295 15 :AAKIKSSDIVLEIGCGTGNLTVKLLPL 1ixkA 113 :ALDPKPGEIVADMAAAPGGKTSYLAQL T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVF 1ixkA 143 :DGVIYAFDVDENRLRETRLNLSRLGVLNVILFHSSSLHIGE T0295 83 :P 1ixkA 185 :N T0295 85 :FDVCTANIPYKISSP 1ixkA 188 :FDKILLDAPCTGSGT T0295 111 :F 1ixkA 203 :I T0295 233 :PFKKYCLDVLEHLDMCEK 1ixkA 214 :TMDDIKFCQGLQMRLLEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=117 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8cA expands to /projects/compbio/data/pdb/1y8c.pdb.gz 1y8cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1y8cA/merged-good-all-a2m # 1y8cA read from 1y8cA/merged-good-all-a2m # adding 1y8cA to template set # found chain 1y8cA in template set T0295 6 :PGILDKIIYAA 1y8cA 22 :KKWSDFIIEKC T0295 17 :KIKSSD 1y8cA 36 :NLVFDD T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1y8cA 42 :YLDLACGTGNLTENLCPKFKNTWAVDLSQEMLSEAENKFRSQGLK T0295 70 :LEVYEGDAIKTVFPK 1y8cA 87 :PRLACQDISNLNINR T0295 85 :FDVCTAN 1y8cA 103 :FDLITCC T0295 92 :IPYKISS 1y8cA 111 :DSTNYII T0295 99 :PLIFKLISHRPLFKCAVLMFQ 1y8cA 121 :DLKKYFKAVSNHLKEGGVFIF T0295 120 :KEFAERMLANVGDSNYSRLT 1y8cA 143 :INSYYKLSQVLGNNDFNYDD T0295 140 :INVKLFCKVT 1y8cA 165 :VFYYWENQFE T0295 162 :PPKVDSVIVKLIPKESSF 1y8cA 175 :DDLVSMYISFFVRDGEFY T0295 180 :LTNFDEWDNLLRI 1y8cA 203 :AYKEEDIEKYLKH Number of specific fragments extracted= 11 number of extra gaps= 0 total=128 Number of alignments=13 # 1y8cA read from 1y8cA/merged-good-all-a2m # found chain 1y8cA in template set T0295 4 :KNPGILDKIIYAAK 1y8cA 20 :DYKKWSDFIIEKCV T0295 18 :IKSSD 1y8cA 37 :LVFDD T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1y8cA 42 :YLDLACGTGNLTENLCPKFKNTWAVDLSQEMLSEAENKFRSQGLK T0295 70 :LEVYEGDAIKTVFPK 1y8cA 87 :PRLACQDISNLNINR T0295 85 :FDVCTAN 1y8cA 103 :FDLITCC T0295 92 :IPYKISSP 1y8cA 111 :DSTNYIID T0295 100 :LIFKLISHRPLFKCAVLMFQ 1y8cA 122 :LKKYFKAVSNHLKEGGVFIF T0295 123 :AERMLANVGDSN 1y8cA 146 :YYKLSQVLGNND T0295 135 :YSRLTINVKLFCKVTK 1y8cA 160 :YDDDEVFYYWENQFED T0295 163 :PKVDSVIVKLIPKESSF 1y8cA 176 :DLVSMYISFFVRDGEFY T0295 180 :LTNFDEWDNLLRI 1y8cA 203 :AYKEEDIEKYLKH Number of specific fragments extracted= 11 number of extra gaps= 0 total=139 Number of alignments=14 # 1y8cA read from 1y8cA/merged-good-all-a2m # found chain 1y8cA in template set T0295 6 :PGILDKIIYAA 1y8cA 22 :KKWSDFIIEKC T0295 17 :KIKSSD 1y8cA 36 :NLVFDD T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1y8cA 42 :YLDLACGTGNLTENLCPKFKNTWAVDLSQEMLSEAENKFRSQGL T0295 69 :NLEVYEGDAIKTVFPK 1y8cA 86 :KPRLACQDISNLNINR T0295 85 :FDVCTANIP 1y8cA 103 :FDLITCCLD T0295 94 :YKISSPLIFKLIS 1y8cA 115 :YIIDSDDLKKYFK T0295 123 :AERMLANVGDSNYSRLT 1y8cA 146 :YYKLSQVLGNNDFNYDD T0295 140 :INVKL 1y8cA 165 :VFYYW T0295 145 :FCKVTKVCNVNRSSF 1y8cA 177 :LVSMYISFFVRDGEF T0295 181 :TNFDEWDNLLRI 1y8cA 204 :YKEEDIEKYLKH Number of specific fragments extracted= 10 number of extra gaps= 0 total=149 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uwvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uwvA expands to /projects/compbio/data/pdb/1uwv.pdb.gz 1uwvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1uwvA/merged-good-all-a2m # 1uwvA read from 1uwvA/merged-good-all-a2m # adding 1uwvA to template set # found chain 1uwvA in template set T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIK 1uwvA 272 :QKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEE T0295 80 :TVFPK 1uwvA 348 :TKQPW T0295 85 :FDVCTANIPYKISSPLIFKLIS 1uwvA 357 :FDKVLLDPARAGAAGVMQQIIK T0295 111 :FKCAVLMFQK 1uwvA 379 :LEPIRIVYVS T0295 181 :TNFDEWDNLLRICFS 1uwvA 389 :CNPATLARDSEALLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=154 Number of alignments=16 # 1uwvA read from 1uwvA/merged-good-all-a2m # found chain 1uwvA in template set T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIK 1uwvA 272 :QKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEE T0295 80 :T 1uwvA 347 :V T0295 81 :VFPK 1uwvA 349 :KQPW T0295 85 :FDVCTANIPYKISSPLIFKLISH 1uwvA 357 :FDKVLLDPARAGAAGVMQQIIKL T0295 112 :KCAVLM 1uwvA 380 :EPIRIV T0295 170 :VK 1uwvA 386 :YV T0295 180 :LTNFDEWDNLLRICFS 1uwvA 388 :SCNPATLARDSEALLK Number of specific fragments extracted= 7 number of extra gaps= 0 total=161 Number of alignments=17 # 1uwvA read from 1uwvA/merged-good-all-a2m # found chain 1uwvA in template set T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVF 1uwvA 272 :QKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVT T0295 83 :PKFDVCTANIPYKISSPLIFKLISHRPL 1uwvA 355 :NGFDKVLLDPARAGAAGVMQQIIKLEPI T0295 168 :VIVKL 1uwvA 383 :RIVYV T0295 181 :TNFDEWDNLLRICFS 1uwvA 389 :CNPATLARDSEALLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=165 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o54A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1o54A/merged-good-all-a2m # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0295)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o54A)V84 Warning: unaligning (T0295)K4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o54A)V84 Warning: unaligning (T0295)I27 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 Warning: unaligning (T0295)S178 because last residue in template chain is (1o54A)E263 T0295 5 :NPGILDKIIYAAKIKSSDIVLE 1o54A 85 :YPKDSSFIAMMLDVKEGDRIID T0295 29 :CGTGNLTVKLLPLA 1o54A 109 :VGSGAMCAVLARAV T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1o54A 126 :GKVFAYEKREEFAKLAESNLTKWGL T0295 68 :NNLEVYEGDAIK 1o54A 152 :ERVTIKVRDISE T0295 80 :TVFPKFDVCTAN 1o54A 165 :FDEKDVDALFLD T0295 97 :SS 1o54A 177 :VP T0295 99 :PLIFKLISH 1o54A 182 :NYIDKCWEA T0295 111 :FKCAVLMFQ 1o54A 191 :LKGGGRFAT T0295 120 :KEFAERMLANVGDSNYSRLTIN 1o54A 204 :TNQVQETLKKLQELPFIRIEVW T0295 151 :VCNVNRSSF 1o54A 231 :PYKPVPERL T0295 160 :NPPPKVDSVIVKLIPKES 1o54A 245 :MVAHTAYMIFATKVCRRE Number of specific fragments extracted= 11 number of extra gaps= 2 total=176 Number of alignments=19 # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0295)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o54A)V84 Warning: unaligning (T0295)K4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o54A)V84 Warning: unaligning (T0295)I27 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 Warning: unaligning (T0295)S178 because last residue in template chain is (1o54A)E263 T0295 5 :NPGILDKIIYAAKIKSSDIVLE 1o54A 85 :YPKDSSFIAMMLDVKEGDRIID T0295 29 :CGTGNLTVKLLPLAK 1o54A 109 :VGSGAMCAVLARAVG T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1o54A 127 :KVFAYEKREEFAKLAESNLTKWGL T0295 68 :NNLEVYEGDAIK 1o54A 152 :ERVTIKVRDISE T0295 80 :TVFPKFDVCTANIPYK 1o54A 165 :FDEKDVDALFLDVPDP T0295 98 :SPLIFKLISH 1o54A 181 :WNYIDKCWEA T0295 111 :FKCAVLMFQ 1o54A 191 :LKGGGRFAT T0295 120 :KEFAERMLANVGDS 1o54A 204 :TNQVQETLKKLQEL T0295 136 :SRLTINVK 1o54A 218 :PFIRIEVW T0295 147 :KVTKVCNVNRSSFNPP 1o54A 227 :SLFRPYKPVPERLRPV T0295 163 :PKVDSVIVKLIPKES 1o54A 248 :HTAYMIFATKVCRRE Number of specific fragments extracted= 11 number of extra gaps= 2 total=187 Number of alignments=20 # 1o54A read from 1o54A/merged-good-all-a2m # found chain 1o54A in training set Warning: unaligning (T0295)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o54A)V84 Warning: unaligning (T0295)K4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o54A)V84 Warning: unaligning (T0295)I27 because of BadResidue code BAD_PEPTIDE in next template residue (1o54A)G108 Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE at template residue (1o54A)G108 T0295 5 :NPGILDKIIYAAKIKSSDIVLE 1o54A 85 :YPKDSSFIAMMLDVKEGDRIID T0295 29 :CGTGNLTVKLLPLA 1o54A 109 :VGSGAMCAVLARAV T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1o54A 126 :GKVFAYEKREEFAKLAESNLTKWGL T0295 68 :NNLEVYEGDAIK 1o54A 152 :ERVTIKVRDISE T0295 80 :TVFPKFDVCTANIPYK 1o54A 165 :FDEKDVDALFLDVPDP T0295 98 :SPLIFKLISH 1o54A 181 :WNYIDKCWEA T0295 163 :PKVDSVIVKLIPK 1o54A 191 :LKGGGRFATVCPT T0295 183 :FDEWDNLLRICFS 1o54A 204 :TNQVQETLKKLQE Number of specific fragments extracted= 8 number of extra gaps= 2 total=195 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i9gA expands to /projects/compbio/data/pdb/1i9g.pdb.gz 1i9gA:# T0295 read from 1i9gA/merged-good-all-a2m # 1i9gA read from 1i9gA/merged-good-all-a2m # adding 1i9gA to template set # found chain 1i9gA in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 Warning: unaligning (T0295)F179 because last residue in template chain is (1i9gA)A267 T0295 4 :KNPGILDKIIYAAKIKSSDIVLE 1i9gA 83 :IYPKDAAQIVHEGDIFPGARVLE T0295 29 :CGTGNLTVKLLPLA 1i9gA 108 :AGSGALTLSLLRAV T0295 43 :KKVITIDIDSRMISEVKKRCLYE 1i9gA 125 :GQVISYEQRADHAEHARRNVSGC T0295 66 :GYNNLEVYEGDAIKTVFPK 1i9gA 151 :PPDNWRLVVSDLADSELPD T0295 85 :FDVCTANIPYK 1i9gA 172 :VDRAVLDMLAP T0295 98 :SPLIFKLISH 1i9gA 183 :WEVLDAVSRL T0295 111 :FKCAVLMFQ 1i9gA 193 :LVAGGVLMV T0295 120 :KEFAERMLANVGD 1i9gA 206 :VTQLSRIVEALRA T0295 133 :SNYSRLTIN 1i9gA 220 :QCWTEPRAW T0295 144 :LFCKVTKVCNVNRSSFNPP 1i9gA 233 :RGWNVVGLAVRPQHSMRGH T0295 164 :KVDSVIVKLIPKESS 1i9gA 252 :TAFLVATRRLAPGAV Number of specific fragments extracted= 11 number of extra gaps= 1 total=206 Number of alignments=22 # 1i9gA read from 1i9gA/merged-good-all-a2m # found chain 1i9gA in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 Warning: unaligning (T0295)N182 because last residue in template chain is (1i9gA)A267 T0295 2 :LLKNPGILDKIIYAAKIKSSDIVLE 1i9gA 81 :QVIYPKDAAQIVHEGDIFPGARVLE T0295 29 :CGTGNLTVKLLPLAK 1i9gA 108 :AGSGALTLSLLRAVG T0295 44 :KVITIDIDSRMISEVKKRCLYE 1i9gA 126 :QVISYEQRADHAEHARRNVSGC T0295 66 :GY 1i9gA 150 :QP T0295 68 :NNLEVYEGDAIKTVFPK 1i9gA 153 :DNWRLVVSDLADSELPD T0295 85 :FDVCTANIPYK 1i9gA 172 :VDRAVLDMLAP T0295 98 :SPLIFKLISH 1i9gA 183 :WEVLDAVSRL T0295 111 :FKCAVLMFQ 1i9gA 193 :LVAGGVLMV T0295 120 :KEFAERMLANVGDSN 1i9gA 206 :VTQLSRIVEALRAKQ T0295 135 :YSRLTINVK 1i9gA 222 :WTEPRAWET T0295 144 :LFCKVTKVCNVNRSSFNPPP 1i9gA 233 :RGWNVVGLAVRPQHSMRGHT T0295 168 :VIVKLIPKESSFLT 1i9gA 253 :AFLVATRRLAPGAV Number of specific fragments extracted= 12 number of extra gaps= 1 total=218 Number of alignments=23 # 1i9gA read from 1i9gA/merged-good-all-a2m # found chain 1i9gA in template set Warning: unaligning (T0295)I27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i9gA)G107 Warning: unaligning (T0295)G28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i9gA)G107 T0295 4 :KNPGILDKIIYAAKIKSSDIVLE 1i9gA 83 :IYPKDAAQIVHEGDIFPGARVLE T0295 29 :CGTGNLTVKLLPL 1i9gA 108 :AGSGALTLSLLRA T0295 42 :AKKVITIDIDSRMISEVKKRCLY 1i9gA 124 :AGQVISYEQRADHAEHARRNVSG T0295 65 :EGYNNLEVYEGDAIKTVFPK 1i9gA 150 :QPPDNWRLVVSDLADSELPD T0295 85 :FDVCTANIPYKI 1i9gA 172 :VDRAVLDMLAPW T0295 97 :SSPLIFKLIS 1i9gA 185 :VLDAVSRLLV T0295 165 :VDSVIVKLI 1i9gA 195 :AGGVLMVYV T0295 181 :TNFDEWDNLLRICFSR 1i9gA 204 :ATVTQLSRIVEALRAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=226 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ercA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ercA expands to /projects/compbio/data/pdb/2erc.pdb.gz 2ercA:# T0295 read from 2ercA/merged-good-all-a2m # 2ercA read from 2ercA/merged-good-all-a2m # adding 2ercA to template set # found chain 2ercA in template set Warning: unaligning (T0295)S177 because of BadResidue code BAD_PEPTIDE in next template residue (2ercA)R182 Warning: unaligning (T0295)S178 because of BadResidue code BAD_PEPTIDE at template residue (2ercA)R182 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRC 2ercA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKL T0295 65 :EGYNNLEVYEGDAIKTVFPK 2ercA 73 :VDHDNFQVLNKDILQFKFPK T0295 85 :FDVCTANIPYKISSPLIFKLI 2ercA 95 :SYKIFGNIPYNISTDIIRKIV T0295 107 :HRPLFKCAVLMFQKEFAERML 2ercA 116 :FDSIADEIYLIVEYGFAKRLL T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKE 2ercA 137 :NTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKK T0295 179 :FLTNFDEWDNLLRICFSRKRK 2ercA 184 :SHKDKQKYNYFVMKWVNKEYK T0295 207 :RNAVLNMLEHNYKNWCTLN 2ercA 205 :KIFTKNQFNNSLKHAGIDD T0295 229 :PVNFPFKKYCLDVLEHLD 2ercA 224 :LNNISFEQFLSLFNSYKL Number of specific fragments extracted= 8 number of extra gaps= 1 total=234 Number of alignments=25 # 2ercA read from 2ercA/merged-good-all-a2m # found chain 2ercA in template set Warning: unaligning (T0295)S177 because of BadResidue code BAD_PEPTIDE at template residue (2ercA)R182 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCL 2ercA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLV T0295 66 :GYNNLEVYEGDAIKTVFPK 2ercA 74 :DHDNFQVLNKDILQFKFPK T0295 85 :F 2ercA 96 :Y T0295 87 :VCTANIPYKISSPLIFKLI 2ercA 97 :KIFGNIPYNISTDIIRKIV T0295 107 :HRPLFKCAVLMFQKEFAERML 2ercA 116 :FDSIADEIYLIVEYGFAKRLL T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKE 2ercA 137 :NTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKK T0295 178 :SFLTNFDEWDNLLRICFSRKRK 2ercA 183 :ISHKDKQKYNYFVMKWVNKEYK T0295 207 :RNAVLNMLEHNYKNWCTLNK 2ercA 205 :KIFTKNQFNNSLKHAGIDDL T0295 230 :VNFPFKKYCLDVLEHL 2ercA 225 :NNISFEQFLSLFNSYK Number of specific fragments extracted= 9 number of extra gaps= 1 total=243 Number of alignments=26 # 2ercA read from 2ercA/merged-good-all-a2m # found chain 2ercA in template set Warning: unaligning (T0295)S177 because of BadResidue code BAD_PEPTIDE in next template residue (2ercA)R182 Warning: unaligning (T0295)S178 because of BadResidue code BAD_PEPTIDE at template residue (2ercA)R182 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCL 2ercA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLV T0295 66 :GYNNLEVYEGDAIKTVFPK 2ercA 74 :DHDNFQVLNKDILQFKFPK T0295 85 :FDVCTANIPYKISSPLIFKLISH 2ercA 95 :SYKIFGNIPYNISTDIIRKIVFD T0295 109 :PLFKCAVLMFQKEFAERMLANVGD 2ercA 118 :SIADEIYLIVEYGFAKRLLNTKRS T0295 146 :CKVTKVCNVNRSSFNPPPKVDSVIVKLIPKE 2ercA 150 :VDISILSMVPREYFHPKPKVNSSLIRLNRKK T0295 179 :FL 2ercA 183 :IS T0295 181 :TNFDEWDNLLRICFSRKR 2ercA 186 :KDKQKYNYFVMKWVNKEY T0295 206 :KRNAVLNMLEHNYKNWCTLNK 2ercA 204 :KKIFTKNQFNNSLKHAGIDDL T0295 230 :VNFPFKKYCLDVLEHL 2ercA 225 :NNISFEQFLSLFNSYK Number of specific fragments extracted= 9 number of extra gaps= 1 total=252 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vl5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vl5A expands to /projects/compbio/data/pdb/1vl5.pdb.gz 1vl5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 535, because occupancy 0.5 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1vl5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1vl5A/merged-good-all-a2m # 1vl5A read from 1vl5A/merged-good-all-a2m # adding 1vl5A to template set # found chain 1vl5A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0295)I78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0295)K79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0295 9 :LDKIIYAAKIKSS 1vl5A 31 :LAKLMQIAALKGN T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDA 1vl5A 46 :VLDVATGGGHVANAFAPFVKKVVAFDLTEDILKVARAFIEGNGHQQVEYVQGDA T0295 80 :TVFPK 1vl5A 102 :MPFTD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQ 1vl5A 109 :FHIVTCRIAAHHFPNPASFVSEAYRVLKKGGQLLL T0295 169 :IVKLIPKE 1vl5A 144 :VDNSAPEN T0295 184 :DEWDNLLRICFSR 1vl5A 152 :DAFDVFYNYVEKE T0295 197 :KRKTLHAIFKRNAV 1vl5A 174 :KKSDWLKMLEEAGF T0295 211 :LNMLEHN 1vl5A 202 :EDWCDRM T0295 231 :NFPFKKYCLDVLEHLDM 1vl5A 209 :NVTTEKKQELSDFIKSK Number of specific fragments extracted= 9 number of extra gaps= 2 total=261 Number of alignments=28 # 1vl5A read from 1vl5A/merged-good-all-a2m # found chain 1vl5A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0295)I78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0295)K79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0295 9 :LDKIIYAAKIKSS 1vl5A 31 :LAKLMQIAALKGN T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDA 1vl5A 46 :VLDVATGGGHVANAFAPFVKKVVAFDLTEDILKVARAFIEGNGHQQVEYVQGDA T0295 80 :TVFPK 1vl5A 102 :MPFTD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQ 1vl5A 109 :FHIVTCRIAAHHFPNPASFVSEAYRVLKKGGQLLL T0295 169 :IVKLIPKE 1vl5A 144 :VDNSAPEN T0295 184 :DEWDNLLRICFSRK 1vl5A 152 :DAFDVFYNYVEKER T0295 207 :RNAVLNMLEHNYKNWCTLNKQ 1vl5A 171 :RAWKKSDWLKMLEEAGFELEE T0295 228 :VPVNFPFKKYCLD 1vl5A 195 :FHKTFIFEDWCDR T0295 253 :INLDENDFLKLLLEFNK 1vl5A 208 :MNVTTEKKQELSDFIKS Number of specific fragments extracted= 9 number of extra gaps= 2 total=270 Number of alignments=29 # 1vl5A read from 1vl5A/merged-good-all-a2m # found chain 1vl5A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vl5A)E45 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vl5A)E45 Warning: unaligning (T0295)I78 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vl5A)Q101 Warning: unaligning (T0295)K79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vl5A)Q101 T0295 9 :LDKIIYAAKIKSS 1vl5A 31 :LAKLMQIAALKGN T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDA 1vl5A 46 :VLDVATGGGHVANAFAPFVKKVVAFDLTEDILKVARAFIEGNGHQQVEYVQGDA T0295 80 :TVFPK 1vl5A 102 :MPFTD T0295 85 :FDVCTANIPYKISSPLIFK 1vl5A 109 :FHIVTCRIAAHHFPNPASF T0295 120 :KEFAERML 1vl5A 128 :VSEAYRVL T0295 164 :KVDSVIVKLIPKESSF 1vl5A 136 :KKGGQLLLVDNSAPEN T0295 184 :DEWDNLLRICFSRKRKT 1vl5A 152 :DAFDVFYNYVEKERDYS T0295 206 :KRNAVLNMLEHNYKNWCTLNK 1vl5A 170 :HRAWKKSDWLKMLEEAGFELE T0295 227 :QVPVNFPFKKYCLD 1vl5A 194 :CFHKTFIFEDWCDR T0295 253 :INLDENDFLKLLLEFN 1vl5A 208 :MNVTTEKKQELSDFIK Number of specific fragments extracted= 10 number of extra gaps= 2 total=280 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dusA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1dusA/merged-good-all-a2m # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNN 1dusA 42 :KGTKILVENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLDN T0295 70 :LEVYEGDAIK 1dusA 107 :IRVVHSDLYE T0295 81 :VFPK 1dusA 117 :NVKD T0295 85 :FDVCTANIPYKISSPLIFK 1dusA 123 :YNKIITNPPIRAGKEVLHR T0295 104 :LISHRPLFKCAVLMFQ 1dusA 143 :IEEGKELLKDNGEIWV T0295 120 :KEFAERMLANVGD 1dusA 167 :KSLAKYMKDVFGN T0295 137 :RLTINVK 1dusA 180 :VETVTIK T0295 144 :LFCKVT 1dusA 189 :YRVLKS Number of specific fragments extracted= 8 number of extra gaps= 0 total=288 Number of alignments=31 # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set Warning: unaligning (T0295)P174 because of BadResidue code BAD_PEPTIDE in next template residue (1dusA)T162 Warning: unaligning (T0295)K175 because of BadResidue code BAD_PEPTIDE at template residue (1dusA)T162 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1dusA 42 :KGTKILVENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNL T0295 68 :N 1dusA 106 :D T0295 70 :LEVYEGDAIK 1dusA 107 :IRVVHSDLYE T0295 81 :VFPK 1dusA 117 :NVKD T0295 85 :FDVCTANIPYKISSPLIFKL 1dusA 123 :YNKIITNPPIRAGKEVLHRI T0295 105 :ISHRPLFKCAVLMF 1dusA 144 :EEGKELLKDNGEIW T0295 171 :KLI 1dusA 158 :VVI T0295 176 :E 1dusA 163 :K T0295 196 :RKRKTLHAIFKRNAV 1dusA 164 :QGAKSLAKYMKDVFG Number of specific fragments extracted= 9 number of extra gaps= 1 total=297 Number of alignments=32 # 1dusA read from 1dusA/merged-good-all-a2m # found chain 1dusA in training set Warning: unaligning (T0295)P174 because of BadResidue code BAD_PEPTIDE in next template residue (1dusA)T162 Warning: unaligning (T0295)K175 because of BadResidue code BAD_PEPTIDE at template residue (1dusA)T162 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNN 1dusA 42 :KGTKILVENVVVDKDDDILDLGCGYGVIGIALADEVKSTTMADINRRAIKLAKENIKLNNLDN T0295 70 :LEVYEGDAIKTVFPK 1dusA 107 :IRVVHSDLYENVKDR T0295 85 :FDVCTANIPYKISSPLIFKLISH 1dusA 123 :YNKIITNPPIRAGKEVLHRIIEE T0295 119 :QKEF 1dusA 146 :GKEL T0295 127 :L 1dusA 150 :L T0295 164 :KVDSVIVKLI 1dusA 151 :KDNGEIWVVI T0295 176 :E 1dusA 163 :K T0295 196 :RKRKTLHAIFKRNAV 1dusA 164 :QGAKSLAKYMKDVFG Number of specific fragments extracted= 8 number of extra gaps= 1 total=305 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oriA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0295/1oriA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0295/1oriA/merged-good-all-a2m.gz for input Trying 1oriA/merged-good-all-a2m Error: Couldn't open file 1oriA/merged-good-all-a2m or 1oriA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fk8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fk8A expands to /projects/compbio/data/pdb/2fk8.pdb.gz 2fk8A:# T0295 read from 2fk8A/merged-good-all-a2m # 2fk8A read from 2fk8A/merged-good-all-a2m # adding 2fk8A to template set # found chain 2fk8A in template set Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0295)C29 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 Warning: unaligning (T0295)A209 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)S216 Warning: unaligning (T0295)V210 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)S216 T0295 7 :GILDKIIYAAKIKSSDIVLEI 2fk8A 60 :AKVDLNLDKLDLKPGMTLLDI T0295 30 :GTGNLTVKLLPLA 2fk8A 83 :GWGTTMRRAVERF T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYNN 2fk8A 97 :VNVIGLTLSKNQHARCEQVLASIDTNR T0295 70 :LEVYEGDAIKTV 2fk8A 125 :RQVLLQGWEDFA T0295 84 :K 2fk8A 137 :E T0295 85 :FDVCTANIPYKISS 2fk8A 139 :VDRIVSIEAFEHFG T0295 99 :PLIFKLISHRPLFKCAVLMFQ 2fk8A 155 :NYDDFFKRCFNIMPADGRMTV T0295 120 :KEF 2fk8A 184 :YEM T0295 128 :ANV 2fk8A 187 :AAR T0295 182 :NFDE 2fk8A 190 :GKKL T0295 186 :WDNLLRICFSR 2fk8A 197 :TARFIKFIVTE T0295 208 :N 2fk8A 214 :L T0295 211 :LNMLEHNYKNWCTLN 2fk8A 217 :TEMMVEHGEKAGFTV T0295 233 :P 2fk8A 232 :P T0295 234 :FKKYCLDVLEHLDMCEKRSI 2fk8A 238 :RPHYIKTLRIWGDTLQSNKD T0295 254 :NLDENDFLKLLLE 2fk8A 261 :EVTSEEVYNRYMK Number of specific fragments extracted= 16 number of extra gaps= 2 total=321 Number of alignments=34 # 2fk8A read from 2fk8A/merged-good-all-a2m # found chain 2fk8A in template set Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0295)C29 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 T0295 7 :GILDKIIYAAKIKSSDIVLEI 2fk8A 60 :AKVDLNLDKLDLKPGMTLLDI T0295 30 :GTGNLTVKLLPLAK 2fk8A 83 :GWGTTMRRAVERFD T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 2fk8A 98 :NVIGLTLSKNQHARCEQVLASIDT T0295 68 :NNLEVYEGDAIKTV 2fk8A 123 :RSRQVLLQGWEDFA T0295 83 :PKFDVCTANIPYKISSP 2fk8A 137 :EPVDRIVSIEAFEHFGH T0295 100 :LIFKLISHRPLFKCAVLM 2fk8A 156 :YDDFFKRCFNIMPADGRM T0295 168 :VIVKLIPKESSF 2fk8A 174 :TVQSSVSYHPYE T0295 180 :LTNFDEWDNLLRIC 2fk8A 188 :ARGKKLSFETARFI T0295 202 :HAIFKRNAV 2fk8A 202 :KFIVTEIFP T0295 211 :LNMLEHNYKNWCTLNKQ 2fk8A 217 :TEMMVEHGEKAGFTVPE T0295 234 :FKKYCLDVLEHLDMCEKRS 2fk8A 238 :RPHYIKTLRIWGDTLQSNK T0295 253 :INLDENDFLKLLLEF 2fk8A 260 :IEVTSEEVYNRYMKY Number of specific fragments extracted= 12 number of extra gaps= 1 total=333 Number of alignments=35 # 2fk8A read from 2fk8A/merged-good-all-a2m # found chain 2fk8A in template set Warning: unaligning (T0295)G28 because of BadResidue code BAD_PEPTIDE in next template residue (2fk8A)C82 Warning: unaligning (T0295)C29 because of BadResidue code BAD_PEPTIDE at template residue (2fk8A)C82 T0295 7 :GILDKIIYAAKIKSSDIVLEI 2fk8A 60 :AKVDLNLDKLDLKPGMTLLDI T0295 30 :GTGNLTVKLLPL 2fk8A 83 :GWGTTMRRAVER T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGYNN 2fk8A 96 :DVNVIGLTLSKNQHARCEQVLASIDTNR T0295 70 :LEVYEGDAIKTV 2fk8A 125 :RQVLLQGWEDFA T0295 83 :PKFDVCTANIPYKISS 2fk8A 137 :EPVDRIVSIEAFEHFG T0295 99 :PLIFKLISHRPL 2fk8A 158 :DFFKRCFNIMPA T0295 164 :KVDSVIVKLIPKESS 2fk8A 170 :DGRMTVQSSVSYHPY T0295 181 :TNFDEWDNLLRIC 2fk8A 189 :RGKKLSFETARFI T0295 202 :HAIFKRNAV 2fk8A 202 :KFIVTEIFP T0295 211 :LNMLEHNYKNWCTLNKQV 2fk8A 217 :TEMMVEHGEKAGFTVPEP T0295 234 :FKKYCLDVLEHLDMCEKRS 2fk8A 238 :RPHYIKTLRIWGDTLQSNK T0295 253 :INLDENDFLKLLLE 2fk8A 260 :IEVTSEEVYNRYMK Number of specific fragments extracted= 12 number of extra gaps= 1 total=345 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xvaA expands to /projects/compbio/data/pdb/1xva.pdb.gz 1xvaA:# T0295 read from 1xvaA/merged-good-all-a2m # 1xvaA read from 1xvaA/merged-good-all-a2m # adding 1xvaA to template set # found chain 1xvaA in template set Warning: unaligning (T0295)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0295)A42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0295)L116 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)L170 Warning: unaligning (T0295)M117 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)L170 Warning: unaligning (T0295)N129 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xvaA)P188 Warning: unaligning (T0295)V130 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xvaA)P188 Warning: unaligning (T0295)G131 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G189 Warning: unaligning (T0295)V154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)P225 Warning: unaligning (T0295)N155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)P225 Warning: unaligning (T0295)F159 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)D230 Warning: unaligning (T0295)N160 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)D230 Warning: unaligning (T0295)P161 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G231 T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLP 1xvaA 41 :TAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVE T0295 43 :KKVITIDIDSRMISEVKKRCLYEG 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRR T0295 68 :N 1xvaA 103 :K T0295 69 :NLEVYEGDAIK 1xvaA 109 :KWVIEEANWLT T0295 80 :TVFPK 1xvaA 124 :VPAGD T0295 85 :FDVCTAN 1xvaA 130 :FDAVICL T0295 92 :IPYKISS 1xvaA 138 :NSFAHLP T0295 99 :PLIFKLISHRPLFKCAV 1xvaA 152 :EHRLALKNIASMVRPGG T0295 118 :FQ 1xvaA 171 :VI T0295 120 :KEFAERMLA 1xvaA 178 :DYILSTGCA T0295 132 :DSNYSR 1xvaA 190 :KNIYYK T0295 139 :TINVK 1xvaA 201 :DITTS T0295 144 :LFCKVTKVCN 1xvaA 214 :HMVTLDYTVQ T0295 156 :RSS 1xvaA 226 :GAG T0295 162 :PPKVDSVIVKLIP 1xvaA 232 :APGFSKFRLSYYP T0295 181 :TNFDEWDNLLRICFSR 1xvaA 245 :HCLASFTELVQEAFGG Number of specific fragments extracted= 16 number of extra gaps= 5 total=361 Number of alignments=37 # 1xvaA read from 1xvaA/merged-good-all-a2m # found chain 1xvaA in template set Warning: unaligning (T0295)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0295)A42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0295)L116 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)L170 Warning: unaligning (T0295)M117 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)L170 Warning: unaligning (T0295)N129 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xvaA)P188 Warning: unaligning (T0295)V130 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xvaA)P188 Warning: unaligning (T0295)G131 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G189 Warning: unaligning (T0295)V154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)P225 Warning: unaligning (T0295)N155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)P225 Warning: unaligning (T0295)F159 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)D230 Warning: unaligning (T0295)N160 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)D230 Warning: unaligning (T0295)P161 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G231 T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLP 1xvaA 40 :RTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVE T0295 43 :KKVITIDIDSRMISEVKKRCLYEG 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRR T0295 68 :NNLEVYEGDAIKT 1xvaA 108 :DKWVIEEANWLTL T0295 81 :VFPK 1xvaA 125 :PAGD T0295 85 :FDVCTAN 1xvaA 130 :FDAVICL T0295 92 :IPYKIS 1xvaA 138 :NSFAHL T0295 98 :SPLIFKLISHRPLFKCAV 1xvaA 151 :SEHRLALKNIASMVRPGG T0295 118 :FQ 1xvaA 171 :VI T0295 123 :AERML 1xvaA 177 :YDYIL T0295 128 :A 1xvaA 186 :A T0295 132 :DSNYS 1xvaA 190 :KNIYY T0295 137 :R 1xvaA 202 :I T0295 139 :TINVK 1xvaA 203 :TTSVL T0295 144 :LFCKVTKVCN 1xvaA 214 :HMVTLDYTVQ T0295 156 :RSS 1xvaA 226 :GAG T0295 162 :PPKVDSVIVKLI 1xvaA 232 :APGFSKFRLSYY T0295 180 :LTNFDEWDNLLRICFSR 1xvaA 244 :PHCLASFTELVQEAFGG Number of specific fragments extracted= 17 number of extra gaps= 5 total=378 Number of alignments=38 # 1xvaA read from 1xvaA/merged-good-all-a2m # found chain 1xvaA in template set Warning: unaligning (T0295)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)G78 Warning: unaligning (T0295)A42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)G78 Warning: unaligning (T0295)N129 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xvaA)P188 Warning: unaligning (T0295)V130 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xvaA)P188 Warning: unaligning (T0295)G131 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G189 Warning: unaligning (T0295)V154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xvaA)P225 Warning: unaligning (T0295)N155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xvaA)P225 Warning: unaligning (T0295)F159 because of BadResidue code BAD_PEPTIDE in next template residue (1xvaA)D230 Warning: unaligning (T0295)N160 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)D230 Warning: unaligning (T0295)P161 because of BadResidue code BAD_PEPTIDE at template residue (1xvaA)G231 T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLP 1xvaA 41 :TAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVE T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1xvaA 79 :FSVTSVDASDKMLKYALKERWNRRK T0295 68 :NNLEVYEGDAIK 1xvaA 108 :DKWVIEEANWLT T0295 80 :TVFPK 1xvaA 124 :VPAGD T0295 85 :FDVCTANIPYKIS 1xvaA 130 :FDAVICLGNSFAH T0295 98 :SPLIFKLIS 1xvaA 154 :RLALKNIAS T0295 123 :AERML 1xvaA 177 :YDYIL T0295 128 :A 1xvaA 186 :A T0295 132 :DSNY 1xvaA 190 :KNIY T0295 137 :RLTINV 1xvaA 203 :TTSVLT T0295 143 :KLFCKVTKVCN 1xvaA 213 :AHMVTLDYTVQ T0295 156 :RSS 1xvaA 226 :GAG T0295 162 :PPKVDSVIVKL 1xvaA 232 :APGFSKFRLSY T0295 181 :TNFDEWDNLLRICFSRK 1xvaA 245 :HCLASFTELVQEAFGGR Number of specific fragments extracted= 14 number of extra gaps= 4 total=392 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ri5A expands to /projects/compbio/data/pdb/1ri5.pdb.gz 1ri5A:# T0295 read from 1ri5A/merged-good-all-a2m # 1ri5A read from 1ri5A/merged-good-all-a2m # adding 1ri5A to template set # found chain 1ri5A in template set T0295 8 :ILDKIIYAA 1ri5A 49 :ANNFIKACL T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPLA 1ri5A 61 :YTKRGDSVLDLGCGKGGDLLKYERAG T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1ri5A 88 :GEYYGVDIAEVSINDARVRARNMKR T0295 68 :NNLEVYEGDAIK 1ri5A 114 :FKVFFRAQDSYG T0295 80 :TVFPK 1ri5A 128 :MDLGK T0295 85 :FDVCTANIPYKISS 1ri5A 134 :FDVISSQFSFHYAF T0295 99 :PLIFK 1ri5A 151 :ESLDI T0295 104 :LISHRPLFKCAVLMFQ 1ri5A 157 :QRNIARHLRPGGYFIM T0295 120 :KEFAERMLANVG 1ri5A 177 :RDVILERYKQGR T0295 132 :DSNY 1ri5A 190 :SNDF T0295 144 :LFCKVTKVCNVNRSSFN 1ri5A 194 :YKIELEKMEDVPMESVR T0295 167 :S 1ri5A 211 :E T0295 170 :VKLIPKESS 1ri5A 212 :YRFTLLDSV T0295 179 :F 1ri5A 226 :Y T0295 208 :NAVLNMLEHNYKNWCTLN 1ri5A 227 :FVDFTRMVDGFKRLGLSL T0295 237 :YCLDVLEHLDMCEKRSINLDENDFLKLLLE 1ri5A 250 :FIDFYEDEGRRNPELSKKMGLGCLTREESE Number of specific fragments extracted= 16 number of extra gaps= 0 total=408 Number of alignments=40 # 1ri5A read from 1ri5A/merged-good-all-a2m # found chain 1ri5A in template set T0295 6 :PGILDKIIYAA 1ri5A 47 :RNANNFIKACL T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1ri5A 62 :TKRGDSVLDLGCGKGGDLLKYERAGI T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1ri5A 89 :EYYGVDIAEVSINDARVRARNMKR T0295 68 :NNLEVYEGDAIK 1ri5A 114 :FKVFFRAQDSYG T0295 80 :TVFPK 1ri5A 128 :MDLGK T0295 85 :FDVCTANIPYKIS 1ri5A 134 :FDVISSQFSFHYA T0295 98 :SPLIFKL 1ri5A 150 :SESLDIA T0295 105 :ISHRPLFKCAVLMFQ 1ri5A 158 :RNIARHLRPGGYFIM T0295 120 :KEFAERMLANVG 1ri5A 177 :RDVILERYKQGR T0295 133 :SNY 1ri5A 191 :NDF T0295 144 :LFCKVTKVCNVNRSSFN 1ri5A 194 :YKIELEKMEDVPMESVR T0295 169 :IVKLIPKESSF 1ri5A 211 :EYRFTLLDSVN T0295 208 :NAVLNMLEHNYKNWCTLN 1ri5A 227 :FVDFTRMVDGFKRLGLSL T0295 226 :KQ 1ri5A 246 :ER T0295 237 :YCLDVLEHLDMCEKRSINLDENDFLKLLLEF 1ri5A 250 :FIDFYEDEGRRNPELSKKMGLGCLTREESEV Number of specific fragments extracted= 15 number of extra gaps= 0 total=423 Number of alignments=41 # 1ri5A read from 1ri5A/merged-good-all-a2m # found chain 1ri5A in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1ri5A 51 :NFIKACLIRLYTKRGDSVLDLGCGKGGDLLKYERA T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 1ri5A 87 :IGEYYGVDIAEVSINDARVRARNMKR T0295 68 :NNLEVYEGDAIKTVF 1ri5A 114 :FKVFFRAQDSYGRHM T0295 83 :PK 1ri5A 131 :GK T0295 85 :FDVCTANIPYK 1ri5A 134 :FDVISSQFSFH T0295 96 :ISSPLIFKLISH 1ri5A 148 :STSESLDIAQRN T0295 127 :LANV 1ri5A 160 :IARH T0295 164 :KVDSVIVKLIPK 1ri5A 165 :RPGGYFIMTVPS T0295 198 :RKTLHAIFKRNAV 1ri5A 177 :RDVILERYKQGRM T0295 211 :LNMLEHNYKNWCTLN 1ri5A 230 :FTRMVDGFKRLGLSL T0295 237 :YCLDVLEHLDMCEKRSINLDENDFLKLLLE 1ri5A 250 :FIDFYEDEGRRNPELSKKMGLGCLTREESE Number of specific fragments extracted= 11 number of extra gaps= 0 total=434 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wznA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wznA expands to /projects/compbio/data/pdb/1wzn.pdb.gz 1wznA:# T0295 read from 1wznA/merged-good-all-a2m # 1wznA read from 1wznA/merged-good-all-a2m # adding 1wznA to template set # found chain 1wznA in template set Warning: unaligning (T0295)E121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wznA)G155 Warning: unaligning (T0295)D132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wznA)G155 T0295 6 :PGILDKIIYAAK 1wznA 24 :KAEIDFVEEIFK T0295 18 :IKSS 1wznA 38 :AKRE T0295 22 :DIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1wznA 43 :RRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLK T0295 70 :LEVYEGDAIKTVFPK 1wznA 90 :IEFLQGDVLEIAFKN T0295 85 :FDVCTAN 1wznA 106 :FDAVTMF T0295 92 :IPYKISS 1wznA 114 :STIMYFD T0295 99 :PLIFKLISHRPLFKCAVLMFQ 1wznA 123 :DLRKLFSKVAEALKPGGVFIT T0295 120 :K 1wznA 146 :P T0295 133 :SNYSRL 1wznA 156 :PVVWNE T0295 139 :TINVKLFCKVT 1wznA 167 :KLVIMDWREVE T0295 166 :DSVIVKLIPKESSF 1wznA 185 :FKRLVQILRPNGEV T0295 208 :NAVLNMLEHNYKNW 1wznA 209 :IYTPREVRLLAEKY Number of specific fragments extracted= 12 number of extra gaps= 0 total=446 Number of alignments=43 # 1wznA read from 1wznA/merged-good-all-a2m # found chain 1wznA in template set T0295 6 :PGILDKIIYAAK 1wznA 24 :KAEIDFVEEIFK T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1wznA 39 :KREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLK T0295 70 :LEVYEGDAIKTVFPK 1wznA 90 :IEFLQGDVLEIAFKN T0295 85 :FDVCTAN 1wznA 106 :FDAVTMF T0295 92 :IPYKISSP 1wznA 114 :STIMYFDE T0295 100 :LIFKLISHRPLFKCAVLMFQ 1wznA 124 :LRKLFSKVAEALKPGGVFIT T0295 137 :RLTINVKLFCKVTK 1wznA 165 :EEKLVIMDWREVEP T0295 163 :PKVDSV 1wznA 179 :AVQKLR T0295 169 :IVKLIPKESSF 1wznA 188 :LVQILRPNGEV T0295 180 :LTNFDEWDNLL 1wznA 209 :IYTPREVRLLA Number of specific fragments extracted= 10 number of extra gaps= 0 total=456 Number of alignments=44 # 1wznA read from 1wznA/merged-good-all-a2m # found chain 1wznA in template set Warning: unaligning (T0295)D132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wznA)G155 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1wznA 28 :DFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNL T0295 69 :NLEVYEGDAIKTVFPK 1wznA 89 :KIEFLQGDVLEIAFKN T0295 85 :FDVCTANIPY 1wznA 106 :FDAVTMFFST T0295 95 :KISSPLIFKLIS 1wznA 118 :YFDEEDLRKLFS T0295 133 :SNYSR 1wznA 156 :PVVWN T0295 138 :LTINVKLFCKVT 1wznA 166 :EKLVIMDWREVE T0295 150 :KVCN 1wznA 183 :LRFK T0295 168 :VIVKLIPKESS 1wznA 187 :RLVQILRPNGE T0295 208 :NAVLNMLEHNYKNW 1wznA 209 :IYTPREVRLLAEKY Number of specific fragments extracted= 9 number of extra gaps= 0 total=465 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kp9B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kp9B expands to /projects/compbio/data/pdb/1kp9.pdb.gz 1kp9B:# T0295 read from 1kp9B/merged-good-all-a2m # 1kp9B read from 1kp9B/merged-good-all-a2m # adding 1kp9B to template set # found chain 1kp9B in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1kp9B 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEKY T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1kp9B 88 :VNVVGLTLSKNQANHVQQLVANSEN T0295 69 :N 1kp9B 114 :R T0295 70 :LEVYEGDAIKTV 1kp9B 116 :KRVLLAGWEQFD T0295 84 :K 1kp9B 128 :E T0295 85 :FDVCTANIPYKISS 1kp9B 130 :VDRIVSIGAFEHFG T0295 99 :PLIFKLISHRPLFKCAVLMFQ 1kp9B 146 :RYDAFFSLAHRLLPADGVMLL T0295 170 :VKLIPKESS 1kp9B 167 :HTITGLHPK T0295 179 :FLTNFDEWDNL 1kp9B 182 :LPMSFTFARFL T0295 202 :HAIFKRNAV 1kp9B 193 :KFIVTEIFP T0295 211 :LNMLEHNYKNWCTLNKQ 1kp9B 208 :IPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSIN 1kp9B 229 :QPHYAKTLDLWSAALQANKGQ T0295 255 :LDENDFLKLLLE 1kp9B 253 :LQSEEVYERYMK Number of specific fragments extracted= 13 number of extra gaps= 0 total=478 Number of alignments=46 # 1kp9B read from 1kp9B/merged-good-all-a2m # found chain 1kp9B in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1kp9B 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEKYD T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1kp9B 89 :NVVGLTLSKNQANHVQQLVANSEN T0295 68 :NNLEVYEGDAIKTV 1kp9B 114 :RSKRVLLAGWEQFD T0295 83 :PKFDVCTANIPYKIS 1kp9B 128 :EPVDRIVSIGAFEHF T0295 98 :SP 1kp9B 144 :HE T0295 100 :LIFKLISHRPLFKCAVLM 1kp9B 147 :YDAFFSLAHRLLPADGVM T0295 168 :VIVKLIPKESSF 1kp9B 165 :LLHTITGLHPKE T0295 180 :LTNFDEWDN 1kp9B 183 :PMSFTFARF T0295 201 :LHAIFKRNAV 1kp9B 192 :LKFIVTEIFP T0295 211 :LNMLEHNYKNWCTLNKQ 1kp9B 208 :IPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSIN 1kp9B 229 :QPHYAKTLDLWSAALQANKGQ T0295 255 :LDENDFLKLLLEF 1kp9B 253 :LQSEEVYERYMKY Number of specific fragments extracted= 12 number of extra gaps= 0 total=490 Number of alignments=47 # 1kp9B read from 1kp9B/merged-good-all-a2m # found chain 1kp9B in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1kp9B 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEK T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 1kp9B 87 :DVNVVGLTLSKNQANHVQQLVANSEN T0295 68 :N 1kp9B 114 :R T0295 70 :LEVYEGDAIKTVFP 1kp9B 116 :KRVLLAGWEQFDEP T0295 85 :FDVCTANIPYK 1kp9B 130 :VDRIVSIGAFE T0295 110 :LFKCAVLMFQKEFAERMLA 1kp9B 141 :HFGHERYDAFFSLAHRLLP T0295 163 :PKVDSVIVKLIPKESS 1kp9B 160 :ADGVMLLHTITGLHPK T0295 179 :FLTNFDEWDNLLRI 1kp9B 182 :LPMSFTFARFLKFI T0295 205 :FKRNAV 1kp9B 196 :VTEIFP T0295 211 :LNMLEHNYKNWCTLNKQ 1kp9B 208 :IPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSINLDENDFLKLLLEF 1kp9B 232 :YAKTLDLWSAALQANKGQAIALQSEEVYERYMKY Number of specific fragments extracted= 11 number of extra gaps= 0 total=501 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1im8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1im8A expands to /projects/compbio/data/pdb/1im8.pdb.gz 1im8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1im8A/merged-good-all-a2m # 1im8A read from 1im8A/merged-good-all-a2m # adding 1im8A to template set # found chain 1im8A in template set T0295 6 :PGILDKIIYAAK 1im8A 39 :SNIITAIGMLAE T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLA 1im8A 53 :VTADSNVYDLGCSRGAATLSARRNI T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1im8A 82 :VKIIGIDNSQPMVERCRQHIAAYHS T0295 68 :N 1im8A 109 :P T0295 70 :LEVYEGDAIKTVFPKFDVCTANIPYKISS 1im8A 110 :VEILCNDIRHVEIKNASMVILNFTLQFLP T0295 99 :PLIFKLISHRPLFKCAVLMFQKEF 1im8A 141 :DRIALLTKIYEGLNPNGVLVLSEK T0295 178 :SFLTNFDEWDNLLRICFSR 1im8A 165 :FRFEDTKINHLLIDLHHQF T0295 197 :KRKTLHAIFKRN 1im8A 194 :VSQKRTALENVM T0295 209 :AVLNMLEHNYKNWCT 1im8A 208 :DSIETHKVRLKNVGF Number of specific fragments extracted= 9 number of extra gaps= 0 total=510 Number of alignments=49 # 1im8A read from 1im8A/merged-good-all-a2m # found chain 1im8A in template set Warning: unaligning (T0295)L2 because first residue in template chain is (1im8A)F17 T0295 3 :LKNPGILDK 1im8A 18 :IFDENVAEV T0295 12 :IIYAAK 1im8A 41 :IITAIG T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1im8A 53 :VTADSNVYDLGCSRGAATLSARRNIN T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1im8A 83 :KIIGIDNSQPMVERCRQHIAAYHS T0295 68 :N 1im8A 109 :P T0295 70 :LEVYEGDAIKTVFPKFDVCTANIPYKISSP 1im8A 110 :VEILCNDIRHVEIKNASMVILNFTLQFLPP T0295 100 :LIFKLISHRPLFKCAVLMFQ 1im8A 142 :RIALLTKIYEGLNPNGVLVL T0295 177 :SSFLTNFDEWDNLLRICFSRKR 1im8A 164 :KFRFEDTKINHLLIDLHHQFKR T0295 211 :LNMLEHNYKNWC 1im8A 195 :SQKRTALENVMR T0295 254 :NLDENDFLKLLLEFN 1im8A 207 :TDSIETHKVRLKNVG Number of specific fragments extracted= 10 number of extra gaps= 0 total=520 Number of alignments=50 # 1im8A read from 1im8A/merged-good-all-a2m # found chain 1im8A in template set T0295 6 :PGILDKIIYAAK 1im8A 39 :SNIITAIGMLAE T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 1im8A 53 :VTADSNVYDLGCSRGAATLSARRN T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 1im8A 81 :NVKIIGIDNSQPMVERCRQHIAAYHS T0295 68 :NNLEVYEGDAIKTVFPKFDVCTANIPYKISSP 1im8A 108 :IPVEILCNDIRHVEIKNASMVILNFTLQFLPP T0295 100 :LIFKLISH 1im8A 145 :LLTKIYEG T0295 130 :V 1im8A 153 :L T0295 166 :DSVIVKLIPKESSFLTNFDEWDNLLRICFSR 1im8A 156 :NGVLVLSEKFRFEDTKINHLLIDLHHQFKRA T0295 197 :KRKTLHAIFKRNAVLNMLEHNYKNWCT 1im8A 196 :QKRTALENVMRTDSIETHKVRLKNVGF Number of specific fragments extracted= 8 number of extra gaps= 0 total=528 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1dl5A/merged-good-all-a2m # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1dl5A 59 :SQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVV T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1dl5A 101 :GLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEF T0295 85 :FDVCTANIPYKISSPLIFK 1dl5A 145 :YDVIFVTVGVDEVPETWFT T0295 110 :LFKCAVLMFQK 1dl5A 164 :QLKEGGRVIVP T0295 130 :VGDSNYSRLTINVK 1dl5A 175 :INLKLSRRQPAFLF T0295 144 :LFCKVTKVCNV 1dl5A 195 :LVGNYKLETRF T0295 155 :NRSSF 1dl5A 209 :GGNLG T0295 160 :NPPPKVDSV 1dl5A 224 :REFPFNREI T0295 179 :FLTNFDEWDNLLRICFSR 1dl5A 233 :LLVRSHIFVELVDLLTRR T0295 197 :KRKTLHAIFKRN 1dl5A 279 :DAPEIENLLTQW T0295 215 :EHN 1dl5A 291 :ESC T0295 225 :NKQVPVNF 1dl5A 294 :GYRSFEYL Number of specific fragments extracted= 12 number of extra gaps= 0 total=540 Number of alignments=52 # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0295 3 :LKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1dl5A 58 :SSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVG T0295 44 :KVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIK 1dl5A 102 :LVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYY T0295 81 :VFPK 1dl5A 138 :GVPE T0295 85 :FDVCTANIPYKISSPLIFKL 1dl5A 145 :YDVIFVTVGVDEVPETWFTQ T0295 111 :FKCAVLMFQK 1dl5A 165 :LKEGGRVIVP T0295 130 :VGDSNYSRLTINVK 1dl5A 175 :INLKLSRRQPAFLF T0295 144 :LFCKVTKVCNV 1dl5A 195 :LVGNYKLETRF T0295 155 :NRS 1dl5A 209 :GGN T0295 158 :SFNPP 1dl5A 222 :LLREF T0295 163 :PKVDSV 1dl5A 263 :PNGVVE T0295 169 :IVKLIPK 1dl5A 273 :RMRIYGD T0295 183 :FDEWDNLLRICFS 1dl5A 280 :APEIENLLTQWES T0295 224 :LNKQVPVNF 1dl5A 293 :CGYRSFEYL Number of specific fragments extracted= 13 number of extra gaps= 0 total=553 Number of alignments=53 # 1dl5A read from 1dl5A/merged-good-all-a2m # found chain 1dl5A in training set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1dl5A 59 :SQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRV T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1dl5A 100 :KGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEF T0295 85 :FDVCTANIPYKISSPLIFKLIS 1dl5A 145 :YDVIFVTVGVDEVPETWFTQLK T0295 133 :SNYSRLTINV 1dl5A 181 :RRQPAFLFKK T0295 143 :KLFCKVTKVCNV 1dl5A 194 :YLVGNYKLETRF T0295 251 :RSINLDENDFLKLLLEFNKKGIHF 1dl5A 206 :ITAGGNLGNLLERNRKLLREFPFN Number of specific fragments extracted= 6 number of extra gaps= 0 total=559 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1or8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0295/1or8A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0295/1or8A/merged-good-all-a2m.gz for input Trying 1or8A/merged-good-all-a2m Error: Couldn't open file 1or8A/merged-good-all-a2m or 1or8A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qzzA expands to /projects/compbio/data/pdb/1qzz.pdb.gz 1qzzA:# T0295 read from 1qzzA/merged-good-all-a2m # 1qzzA read from 1qzzA/merged-good-all-a2m # adding 1qzzA to template set # found chain 1qzzA in template set Warning: unaligning (T0295)P174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)A296 Warning: unaligning (T0295)K175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qzzA)A296 T0295 10 :DKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1qzzA 172 :EAPADAYDWSAVRHVLDVGGGNGGMLAAIALRA T0295 43 :KKVITIDID 1qzzA 207 :LRGTLVELA T0295 53 :RMISEVKKRCLYEGY 1qzzA 216 :GPAERARRRFADAGL T0295 68 :NNLEVYEGDAIK 1qzzA 232 :DRVTVAEGDFFK T0295 81 :VFPK 1qzzA 244 :PLPV T0295 85 :FDVCTANIPYKISSP 1qzzA 249 :ADVVLLSFVLLNWSD T0295 100 :LIF 1qzzA 266 :ALT T0295 104 :LISHRPLFKCAVLMFQKE 1qzzA 270 :LRGCVRALEPGGRLLVLD T0295 176 :E 1qzzA 297 :D T0295 184 :DEWDNLLRICFSR 1qzzA 298 :RFFSTLLDLRMLT T0295 209 :AVLNMLEHNYKNWCT 1qzzA 317 :RTRDEVVDLAGSAGL Number of specific fragments extracted= 11 number of extra gaps= 1 total=570 Number of alignments=55 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set T0295 10 :DKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1qzzA 172 :EAPADAYDWSAVRHVLDVGGGNGGMLAAIALRAP T0295 44 :KVITIDIDS 1qzzA 208 :RGTLVELAG T0295 54 :MISEVKKRCLYEGY 1qzzA 217 :PAERARRRFADAGL T0295 68 :NNLEVYEGDAIK 1qzzA 232 :DRVTVAEGDFFK T0295 81 :VFPK 1qzzA 244 :PLPV T0295 85 :FDVCTANIPYKISSP 1qzzA 249 :ADVVLLSFVLLNWSD T0295 100 :LIFKLISHRPLFKCAVLMFQ 1qzzA 266 :ALTILRGCVRALEPGGRLLV T0295 122 :FAERMLANVG 1qzzA 321 :EVVDLAGSAG T0295 146 :CKVTKVCNVNRSSFN 1qzzA 331 :LALASERTSGSTTLP T0295 165 :VDSVIVKLIPK 1qzzA 346 :FDFSILEFTAV Number of specific fragments extracted= 10 number of extra gaps= 0 total=580 Number of alignments=56 # 1qzzA read from 1qzzA/merged-good-all-a2m # found chain 1qzzA in template set Warning: unaligning (T0295)P174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)A296 Warning: unaligning (T0295)K175 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qzzA)A296 T0295 10 :DKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1qzzA 172 :EAPADAYDWSAVRHVLDVGGGNGGMLAAIALR T0295 42 :AKKVITIDI 1qzzA 206 :HLRGTLVEL T0295 52 :SRMISEVKKRCLYEGY 1qzzA 215 :AGPAERARRRFADAGL T0295 68 :NNLEVYEGDAIKTVFPKFDVCTANIPYK 1qzzA 232 :DRVTVAEGDFFKPLPVTADVVLLSFVLL T0295 96 :ISSPLIFKLISH 1qzzA 261 :WSDEDALTILRG T0295 123 :AERML 1qzzA 273 :CVRAL T0295 164 :KVDSVIVKLI 1qzzA 278 :EPGGRLLVLD T0295 176 :E 1qzzA 297 :D T0295 184 :DEWDNLLRICFSR 1qzzA 298 :RFFSTLLDLRMLT T0295 205 :FKRN 1qzzA 311 :FMGG T0295 211 :LNMLEHNYKNWCT 1qzzA 319 :RDEVVDLAGSAGL Number of specific fragments extracted= 11 number of extra gaps= 1 total=591 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufkA expands to /projects/compbio/data/pdb/1ufk.pdb.gz 1ufkA:# T0295 read from 1ufkA/merged-good-all-a2m # 1ufkA read from 1ufkA/merged-good-all-a2m # adding 1ufkA to template set # found chain 1ufkA in template set T0295 7 :GILDKIIYAAK 1ufkA 105 :ETTRLALKALA T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1ufkA 118 :LRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVR T0295 70 :LEVYEGDAIK 1ufkA 169 :PRFLEGSLEA T0295 80 :TVFPKFDVCTANIP 1ufkA 180 :LPFGPFDLLVANLY T0295 98 :SPLIFKLIS 1ufkA 194 :AELHAALAP T0295 107 :HRPLFKCAVLMFQ 1ufkA 204 :YREALVPGGRALL T0295 120 :KEFAERMLANVG 1ufkA 224 :APLVREAMAGAG T0295 135 :YSRLTINVK 1ufkA 236 :FRPLEEAAE T0295 144 :LFC 1ufkA 250 :LAY Number of specific fragments extracted= 9 number of extra gaps= 0 total=600 Number of alignments=58 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set T0295 6 :PGILDKIIYAAK 1ufkA 104 :HETTRLALKALA T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1ufkA 118 :LRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVR T0295 70 :LEVYEGDAIK 1ufkA 169 :PRFLEGSLEA T0295 80 :TVFPKFDVCTANIP 1ufkA 180 :LPFGPFDLLVANLY T0295 98 :SPLIFKL 1ufkA 194 :AELHAAL T0295 105 :ISHRPLFKCAVLMFQ 1ufkA 202 :PRYREALVPGGRALL T0295 120 :KEFAERMLANVG 1ufkA 224 :APLVREAMAGAG T0295 135 :YSRLTINVK 1ufkA 236 :FRPLEEAAE T0295 144 :L 1ufkA 250 :L Number of specific fragments extracted= 9 number of extra gaps= 0 total=609 Number of alignments=59 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set T0295 7 :GILDKIIYAAK 1ufkA 105 :ETTRLALKALA T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEG 1ufkA 118 :LRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNG T0295 68 :NNLEVYEGDAIKTVF 1ufkA 167 :VRPRFLEGSLEAALP T0295 84 :K 1ufkA 182 :F T0295 85 :FDVCTANI 1ufkA 185 :FDLLVANL T0295 97 :SSPLIFKLISH 1ufkA 193 :YAELHAALAPR T0295 123 :AERML 1ufkA 204 :YREAL T0295 162 :PPKVDSVIVKLIPKE 1ufkA 209 :VPGGRALLTGILKDR T0295 211 :LNMLEHNYKNWCT 1ufkA 224 :APLVREAMAGAGF Number of specific fragments extracted= 9 number of extra gaps= 0 total=618 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aqjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aqjA expands to /projects/compbio/data/pdb/1aqj.pdb.gz 1aqjA:# T0295 read from 1aqjA/merged-good-all-a2m # 1aqjA read from 1aqjA/merged-good-all-a2m # adding 1aqjA to template set # found chain 1aqjA in template set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1aqjA 23 :TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAH T0295 43 :KKVITIDIDSR 1aqjA 65 :YRFVGVEIDPK T0295 66 :GY 1aqjA 76 :AL T0295 68 :NNLEVYEGDAIKTVFPK 1aqjA 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPY 1aqjA 99 :FDLILGNPPY T0295 97 :SSPLIFKLISHRPLFKCAVLMFQ 1aqjA 140 :YNLYGAFLEKAVRLLKPGGVLVF T0295 120 :KEFAERMLAN 1aqjA 175 :ALLREFLARE T0295 131 :GDSNYSRLTINVK 1aqjA 197 :PQKKVSAVVIRFQ T0295 144 :LFCKVTK 1aqjA 216 :SLWDTQE T0295 161 :PPPKVDSVIVKLIPK 1aqjA 223 :SESGFTPILWAEYPH T0295 176 :ESSFLTNFDEWDNLL 1aqjA 240 :GEIIRFETEETRKLE Number of specific fragments extracted= 11 number of extra gaps= 0 total=629 Number of alignments=61 # 1aqjA read from 1aqjA/merged-good-all-a2m # found chain 1aqjA in template set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1aqjA 23 :TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHG T0295 44 :KVITIDIDSR 1aqjA 66 :RFVGVEIDPK T0295 66 :GY 1aqjA 78 :DL T0295 68 :NNLEVYEGDAIKTVFPK 1aqjA 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPY 1aqjA 99 :FDLILGNPPY T0295 95 :KISSPLIFKLISHRPLFKCAVLMFQ 1aqjA 138 :GKYNLYGAFLEKAVRLLKPGGVLVF T0295 120 :KEFAERMLAN 1aqjA 175 :ALLREFLARE T0295 130 :VGDSNYSRLTINVK 1aqjA 196 :FPQKKVSAVVIRFQ T0295 144 :LFCKVTKVCNVNRSSFNPP 1aqjA 225 :SGFTPILWAEYPHWEGEII Number of specific fragments extracted= 9 number of extra gaps= 0 total=638 Number of alignments=62 # 1aqjA read from 1aqjA/merged-good-all-a2m # found chain 1aqjA in template set Warning: unaligning (T0295)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1aqjA)A124 T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1aqjA 24 :PPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREA T0295 42 :AKKVITIDIDSR 1aqjA 64 :GYRFVGVEIDPK T0295 66 :GY 1aqjA 76 :AL T0295 68 :NNLEVYEGDAIKTVFPK 1aqjA 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPYKI 1aqjA 99 :FDLILGNPPYGI T0295 107 :HRPLFKCAVLMFQKEF 1aqjA 136 :WKGKYNLYGAFLEKAV T0295 125 :RML 1aqjA 152 :RLL T0295 148 :VTKVCNVNRSSF 1aqjA 158 :GVLVFVVPATWL T0295 160 :NPPPKVDSVIVKLIPKE 1aqjA 196 :FPQKKVSAVVIRFQKSG Number of specific fragments extracted= 9 number of extra gaps= 0 total=647 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ex4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ex4A expands to /projects/compbio/data/pdb/2ex4.pdb.gz 2ex4A:# T0295 read from 2ex4A/merged-good-all-a2m # 2ex4A read from 2ex4A/merged-good-all-a2m # adding 2ex4A to template set # found chain 2ex4A in template set Warning: unaligning (T0295)K19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ex4A)K60 T0295 6 :PGILDKIIYAAK 2ex4A 39 :SIDINSSRKFLQ T0295 18 :I 2ex4A 53 :L T0295 22 :DIVLEIGCGTGNLTVKLL 2ex4A 64 :SCALDCGAGIGRITKRLL T0295 40 :PLAKKVITIDIDSRMISEVKKRCLYEG 2ex4A 83 :PLFREVDMVDITEDFLVQAKTYLGEEG T0295 68 :NNLE 2ex4A 110 :KRVR T0295 72 :VYEGDAIKTVFPK 2ex4A 115 :YFCCGLQDFTPEP T0295 85 :FDVCTANIPYKISSP 2ex4A 130 :YDVIWIQWVIGHLTD T0295 100 :LIF 2ex4A 147 :LAE T0295 104 :LISHRPLFKCAVLMFQK 2ex4A 151 :LRRCKGSLRPNGIIVIK T0295 121 :EFAERMLANVGDS 2ex4A 189 :DVVRRIICSAGLS T0295 145 :FCKVTKVCNVNRSSF 2ex4A 202 :LLAEERQENLPDEIY T0295 164 :KVDSVIV 2ex4A 217 :HVYSFAL Number of specific fragments extracted= 12 number of extra gaps= 0 total=659 Number of alignments=64 # 2ex4A read from 2ex4A/merged-good-all-a2m # found chain 2ex4A in template set Warning: unaligning (T0295)K19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ex4A)K60 T0295 6 :PGILDKIIYAAK 2ex4A 39 :SIDINSSRKFLQ T0295 18 :I 2ex4A 53 :L T0295 22 :DIVLEIGCGTGNLTVKLL 2ex4A 64 :SCALDCGAGIGRITKRLL T0295 40 :PLAKKVITIDIDSRMISEVKKRCLYEG 2ex4A 83 :PLFREVDMVDITEDFLVQAKTYLGEEG T0295 68 :NNL 2ex4A 110 :KRV T0295 71 :EVYEGDAIKTVFPK 2ex4A 114 :NYFCCGLQDFTPEP T0295 85 :FDVCTANIPYKISSP 2ex4A 130 :YDVIWIQWVIGHLTD T0295 100 :LIFKLISHRPLFKCAVLM 2ex4A 147 :LAEFLRRCKGSLRPNGII T0295 118 :FQKEFAERMLANVG 2ex4A 186 :RDLDVVRRIICSAG T0295 132 :D 2ex4A 201 :S T0295 137 :RL 2ex4A 202 :LL T0295 147 :KVTKVCNVNRSSF 2ex4A 204 :AEERQENLPDEIY T0295 164 :KVDSVIV 2ex4A 217 :HVYSFAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=672 Number of alignments=65 # 2ex4A read from 2ex4A/merged-good-all-a2m # found chain 2ex4A in template set Warning: unaligning (T0295)K19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ex4A)K60 T0295 6 :PGILDKIIYAAK 2ex4A 39 :SIDINSSRKFLQ T0295 18 :I 2ex4A 53 :L T0295 22 :DIVLEIGCGTGNLTVKLL 2ex4A 64 :SCALDCGAGIGRITKRLL T0295 40 :PLAKKVITIDIDSRMISEVKKRCLYEG 2ex4A 83 :PLFREVDMVDITEDFLVQAKTYLGEEG T0295 68 :NNLE 2ex4A 110 :KRVR T0295 72 :VYEGDAIKTVFPK 2ex4A 115 :YFCCGLQDFTPEP T0295 85 :FDVCTANIPYKISSPLIF 2ex4A 130 :YDVIWIQWVIGHLTDQHL T0295 120 :KEFAERMLANVGD 2ex4A 148 :AEFLRRCKGSLRP T0295 166 :DSVIVKLIPKESSFL 2ex4A 161 :NGIIVIKDNMAQEGV T0295 211 :LNMLEHNYKNWCTL 2ex4A 188 :LDVVRRIICSAGLS Number of specific fragments extracted= 10 number of extra gaps= 0 total=682 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m6yA expands to /projects/compbio/data/pdb/1m6y.pdb.gz 1m6yA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 1m6yA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 1m6yA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1m6yA/merged-good-all-a2m # 1m6yA read from 1m6yA/merged-good-all-a2m # adding 1m6yA to template set # found chain 1m6yA in template set T0295 9 :LDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1m6yA 13 :VREVIEFLKPEDEKIILDCTVGEGGHSRAILEHC T0295 43 :KKVITIDIDSRMISEVKKRCLYEG 1m6yA 49 :CRIIGIDVDSEVLRIAEEKLKEFS T0295 68 :NNLEVYEGDAIK 1m6yA 73 :DRVSLFKVSYRE T0295 80 :TVFPKFDVCTANIPY 1m6yA 92 :LGIEKVDGILMDLGV T0295 98 :SPLIFKLISHR 1m6yA 136 :VTAQKVLNELP T0295 120 :KEFAERMLANVGD 1m6yA 147 :EEELARIIFEYGE T0295 133 :SNY 1m6yA 161 :KRF T0295 186 :WDNLLRICFSR 1m6yA 164 :ARRIARKIVEN T0295 197 :KRKTLHAIFKRNAVLNMLEHN 1m6yA 179 :TTLDLVKAVREALPSYEIRRR T0295 231 :NFP 1m6yA 200 :KRH T0295 234 :FKKYCLDVLEHLDMCE 1m6yA 205 :TKTFQAIRIYVNRELE T0295 260 :FLKLLLEFNKKGIH 1m6yA 221 :NLKEFLKKAEDLLN Number of specific fragments extracted= 12 number of extra gaps= 0 total=694 Number of alignments=67 # 1m6yA read from 1m6yA/merged-good-all-a2m # found chain 1m6yA in template set T0295 9 :LDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1m6yA 13 :VREVIEFLKPEDEKIILDCTVGEGGHSRAILEHCP T0295 44 :KVITIDIDSRMISEVKKRCLYEG 1m6yA 50 :RIIGIDVDSEVLRIAEEKLKEFS T0295 68 :NNLEVYEGDAIKT 1m6yA 73 :DRVSLFKVSYREA T0295 81 :VFPKFDVCTANIPY 1m6yA 93 :GIEKVDGILMDLGV T0295 98 :SPLIFKLIS 1m6yA 165 :RRIARKIVE T0295 177 :SSFLTNFDEWDNLLRIC 1m6yA 174 :NRPLNTTLDLVKAVREA T0295 195 :SRKR 1m6yA 195 :EIRR T0295 199 :KTLHAIFKRNAV 1m6yA 205 :TKTFQAIRIYVN T0295 211 :LNMLEHNYKNW 1m6yA 219 :LENLKEFLKKA T0295 235 :KKYCLDVLEHLDMCE 1m6yA 246 :SLEDRIVKETFRNSK T0295 250 :KRSINLDENDFLK 1m6yA 267 :EKPVRPSEEEIRE Number of specific fragments extracted= 11 number of extra gaps= 0 total=705 Number of alignments=68 # 1m6yA read from 1m6yA/merged-good-all-a2m # found chain 1m6yA in template set T0295 9 :LDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1m6yA 13 :VREVIEFLKPEDEKIILDCTVGEGGHSRAILEH T0295 42 :AKKVITIDIDSRMISEVKKRCLYEG 1m6yA 48 :GCRIIGIDVDSEVLRIAEEKLKEFS T0295 68 :NNLEVYEGDAIKTVF 1m6yA 73 :DRVSLFKVSYREADF T0295 83 :PKFDVCTANIPYK 1m6yA 95 :EKVDGILMDLGVS T0295 102 :FKLIS 1m6yA 108 :TYQLK T0295 109 :PLFKCAVLMFQ 1m6yA 133 :ESEVTAQKVLN T0295 120 :KEFAERMLANVGDSN 1m6yA 147 :EEELARIIFEYGEEK T0295 184 :DEWDNLLRICFSRK 1m6yA 162 :RFARRIARKIVENR T0295 198 :RKTLHAIFKRNAV 1m6yA 180 :TLDLVKAVREALP T0295 211 :LNMLEHNYKNWC 1m6yA 219 :LENLKEFLKKAE Number of specific fragments extracted= 10 number of extra gaps= 0 total=715 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ne2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1ne2A/merged-good-all-a2m # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0295)L2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)Y27 Warning: unaligning (T0295)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 Warning: unaligning (T0295)F159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)R182 T0295 3 :LKNPGILDKIIYAA 1ne2A 28 :PTDASTAAYFLIEI T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPL 1ne2A 45 :GNIGGRSVIDAGTGNGILACGSYLL T0295 42 :AKKVITIDIDSRMISEVKKRC 1ne2A 71 :AESVTAFDIDPDAIETAKRNC T0295 68 :NNLEVYEGDAIKTV 1ne2A 92 :GGVNFMVADVSEIS T0295 83 :PKFDVCTANIP 1ne2A 106 :GKYDTWIMNPP T0295 99 :PLIFKLISH 1ne2A 127 :AFIDKAFET T0295 113 :CAVLMFQ 1ne2A 136 :SMWIYSI T0295 120 :KEFAERMLANV 1ne2A 148 :RDFLRREFSAR T0295 146 :CKVTKVCNV 1ne2A 159 :GDVFREEKV T0295 156 :RSS 1ne2A 172 :PRI T0295 163 :PKVDSVIVKLIPKE 1ne2A 183 :ARIEAVIFGVRNHS Number of specific fragments extracted= 11 number of extra gaps= 1 total=726 Number of alignments=70 # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0295)L2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)Y27 Warning: unaligning (T0295)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 Warning: unaligning (T0295)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ne2A)D125 T0295 3 :LKNPGILDKIIYAA 1ne2A 28 :PTDASTAAYFLIEI T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPLAK 1ne2A 45 :GNIGGRSVIDAGTGNGILACGSYLLGA T0295 44 :KVITIDIDSRMISEVKKRC 1ne2A 73 :SVTAFDIDPDAIETAKRNC T0295 68 :NNLEVYEGDAIKTV 1ne2A 92 :GGVNFMVADVSEIS T0295 83 :PKFDVCTANIP 1ne2A 106 :GKYDTWIMNPP T0295 98 :SPLIFKLISH 1ne2A 126 :RAFIDKAFET T0295 115 :VLMFQ 1ne2A 136 :SMWIY T0295 120 :KEFAERMLA 1ne2A 148 :RDFLRREFS T0295 140 :INVKLFCKVTKVCNVNR 1ne2A 157 :ARGDVFREEKVYITVPR T0295 163 :PKVDSVIVKLIPK 1ne2A 183 :ARIEAVIFGVRNH Number of specific fragments extracted= 10 number of extra gaps= 0 total=736 Number of alignments=71 # 1ne2A read from 1ne2A/merged-good-all-a2m # found chain 1ne2A in training set Warning: unaligning (T0295)Y94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ne2A)D125 T0295 5 :NPGILDKIIYAA 1ne2A 30 :DASTAAYFLIEI T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPL 1ne2A 45 :GNIGGRSVIDAGTGNGILACGSYLL T0295 42 :AKKVITIDIDSRMISEVKKR 1ne2A 71 :AESVTAFDIDPDAIETAKRN T0295 67 :YNNLEVYEGDAIKTV 1ne2A 91 :CGGVNFMVADVSEIS T0295 83 :PKFDVCTANIP 1ne2A 106 :GKYDTWIMNPP T0295 98 :SPLIFKLIS 1ne2A 126 :RAFIDKAFE T0295 107 :H 1ne2A 147 :A T0295 120 :KEFAERMLANV 1ne2A 148 :RDFLRREFSAR Number of specific fragments extracted= 8 number of extra gaps= 0 total=744 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2avnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2avnA expands to /projects/compbio/data/pdb/2avn.pdb.gz 2avnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2avnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2avnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1901, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1905, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1911, because occupancy 0.500 <= existing 0.500 in 2avnA Skipped atom 1913, because occupancy 0.500 <= existing 0.500 in 2avnA # T0295 read from 2avnA/merged-good-all-a2m # 2avnA read from 2avnA/merged-good-all-a2m # adding 2avnA to template set # found chain 2avnA in template set Warning: unaligning (T0295)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0295)M117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 T0295 7 :GILDKIIYAA 2avnA 26 :KLYHRLIGSF T0295 17 :K 2avnA 37 :E T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKR 2avnA 40 :LKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEMLEVAREK T0295 66 :GYNNL 2avnA 84 :GVKNV T0295 73 :YEGDAIKTVFPK 2avnA 89 :VEAKAEDLPFPS T0295 85 :FDVCTAN 2avnA 103 :FEAVLAL T0295 92 :IPYKISSPLIFKLISHRPLFKCAV 2avnA 111 :DVLSYVENKDKAFSEIRRVLVPDG T0295 118 :FQ 2avnA 137 :IA T0295 120 :KEFAERMLANVGDSNY 2avnA 144 :YTFLQQMIEKDAWDQI T0295 136 :SRLTIN 2avnA 166 :QTTSVG T0295 150 :KVCN 2avnA 175 :FSFN T0295 154 :VNRSSFNPPPKVDSVIVKLIPKESS 2avnA 182 :FKPEDLDSLEGFETVDIRGIGVMEY T0295 210 :VLNMLEH 2avnA 207 :PDERISE T0295 233 :PFKKYCLDVLEHLDMCEK 2avnA 214 :REETIFRLEQELSRDRNI Number of specific fragments extracted= 14 number of extra gaps= 1 total=758 Number of alignments=73 # 2avnA read from 2avnA/merged-good-all-a2m # found chain 2avnA in template set Warning: unaligning (T0295)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0295)M117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 T0295 7 :GILDKIIYAA 2avnA 26 :KLYHRLIGSF T0295 17 :K 2avnA 37 :E T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKR 2avnA 40 :LKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEMLEVAREK T0295 66 :GYNNL 2avnA 84 :GVKNV T0295 73 :YEGDAIKTVFPK 2avnA 89 :VEAKAEDLPFPS T0295 85 :FDVCTAN 2avnA 103 :FEAVLAL T0295 92 :IPYKISSPLIFKLISHRPLFKCAV 2avnA 111 :DVLSYVENKDKAFSEIRRVLVPDG T0295 118 :FQKEFAERMLANVGDSNYSRL 2avnA 142 :NFYTFLQQMIEKDAWDQITRF T0295 139 :TINVKLFCKVTKVCN 2avnA 164 :KTQTTSVGTTLFSFN T0295 154 :VNRSSFNPPPKVDSVIVKLIPKESSF 2avnA 182 :FKPEDLDSLEGFETVDIRGIGVMEYP T0295 211 :LNMLEH 2avnA 208 :DERISE T0295 233 :PFKKYCLDVLEHLDMCEK 2avnA 214 :REETIFRLEQELSRDRNI Number of specific fragments extracted= 12 number of extra gaps= 1 total=770 Number of alignments=74 # 2avnA read from 2avnA/merged-good-all-a2m # found chain 2avnA in template set Warning: unaligning (T0295)V168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2avnA)L136 Warning: unaligning (T0295)I169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2avnA)L136 T0295 7 :GILDKIIYAA 2avnA 30 :RLIGSFLEEY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKR 2avnA 40 :LKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEMLEVAREK T0295 66 :GYNNL 2avnA 84 :GVKNV T0295 73 :YEGDAIKTVFPK 2avnA 89 :VEAKAEDLPFPS T0295 85 :FDVCTANIP 2avnA 103 :FEAVLALGD T0295 101 :IFKLISH 2avnA 112 :VLSYVEN T0295 116 :LMFQKEFAERMLA 2avnA 119 :KDKAFSEIRRVLV T0295 166 :DS 2avnA 133 :DG T0295 170 :VKLIPK 2avnA 137 :IATVDN T0295 186 :WDNLLRICFSRKRKTLHAIFKRNAV 2avnA 143 :FYTFLQQMIEKDAWDQITRFLKTQT T0295 211 :LNMLEH 2avnA 208 :DERISE T0295 233 :PFKKYCLDVLEHLDMCEKRS 2avnA 214 :REETIFRLEQELSRDRNIIW Number of specific fragments extracted= 12 number of extra gaps= 1 total=782 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xtpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xtpA expands to /projects/compbio/data/pdb/1xtp.pdb.gz 1xtpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1724, because occupancy 0.350 <= existing 0.650 in 1xtpA Skipped atom 1726, because occupancy 0.350 <= existing 0.650 in 1xtpA Skipped atom 1728, because occupancy 0.350 <= existing 0.650 in 1xtpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1xtpA/merged-good-all-a2m # 1xtpA read from 1xtpA/merged-good-all-a2m # adding 1xtpA to template set # found chain 1xtpA in template set Warning: unaligning (T0295)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xtpA)I193 Warning: unaligning (T0295)M117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xtpA)I193 T0295 6 :PGILDKIIYAAKIKSS 1xtpA 76 :DVDIEGSRNFIASLPG T0295 22 :DIVLEIGCGTGNLTVK 1xtpA 95 :SRALDCGAGIGRITKN T0295 38 :LLPLAKKVITIDIDSRMISEVKKRCL 1xtpA 112 :LTKLYATTDLLEPVKHMLEEAKRELA T0295 66 :GYN 1xtpA 138 :GMP T0295 70 :L 1xtpA 141 :V T0295 71 :EVYEGDAIKTVFPK 1xtpA 143 :KFILASMETATLPP T0295 85 :FDVCTANIPYKISS 1xtpA 159 :YDLIVIQWTAIYLT T0295 99 :PLIFKLISHRPLFKCAV 1xtpA 175 :DFVKFFKHCQQALTPNG T0295 118 :FQK 1xtpA 194 :FFK T0295 121 :EFAERMLANVGDS 1xtpA 219 :IHYKRLFNESGVR T0295 145 :FCKVTKVCNVNRSSFN 1xtpA 232 :VVKEAFQEEWPTDLFP T0295 165 :V 1xtpA 248 :L T0295 168 :VIVK 1xtpA 249 :KMYA Number of specific fragments extracted= 13 number of extra gaps= 1 total=795 Number of alignments=76 # 1xtpA read from 1xtpA/merged-good-all-a2m # found chain 1xtpA in template set Warning: unaligning (T0295)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xtpA)I193 Warning: unaligning (T0295)M117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xtpA)I193 T0295 6 :PGILDKIIYAAKIKSS 1xtpA 76 :DVDIEGSRNFIASLPG T0295 22 :DIVLEIGCGTGNLTV 1xtpA 95 :SRALDCGAGIGRITK T0295 37 :KLLPLAKKVITIDIDSRMISEVKKRCL 1xtpA 111 :LLTKLYATTDLLEPVKHMLEEAKRELA T0295 66 :GYN 1xtpA 138 :GMP T0295 70 :L 1xtpA 141 :V T0295 71 :EVYEGDAIKTVFPK 1xtpA 143 :KFILASMETATLPP T0295 85 :FDVCTANIPYKISSP 1xtpA 159 :YDLIVIQWTAIYLTD T0295 100 :LIFKLISHRPLFKCAV 1xtpA 176 :FVKFFKHCQQALTPNG T0295 118 :FQKE 1xtpA 194 :FFKE T0295 122 :FAERMLANVG 1xtpA 220 :HYKRLFNESG T0295 132 :D 1xtpA 231 :R T0295 148 :VTKVCNV 1xtpA 232 :VVKEAFQ T0295 155 :NRSSFNP 1xtpA 241 :WPTDLFP T0295 167 :SVIVK 1xtpA 248 :LKMYA Number of specific fragments extracted= 14 number of extra gaps= 1 total=809 Number of alignments=77 # 1xtpA read from 1xtpA/merged-good-all-a2m # found chain 1xtpA in template set T0295 6 :PGILDKIIYAAKIKSS 1xtpA 76 :DVDIEGSRNFIASLPG T0295 22 :DIVLEIGCGTGNLTV 1xtpA 95 :SRALDCGAGIGRITK T0295 37 :KLLPLAKKVITIDIDSRMISEVKKRCL 1xtpA 111 :LLTKLYATTDLLEPVKHMLEEAKRELA T0295 66 :GYNNLEVYEGDAIKTVFPK 1xtpA 138 :GMPVGKFILASMETATLPP T0295 85 :FDVCTANIPYKISS 1xtpA 159 :YDLIVIQWTAIYLT T0295 183 :FDEWDNLLRICFS 1xtpA 173 :DADFVKFFKHCQQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=815 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nv8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nv8A expands to /projects/compbio/data/pdb/1nv8.pdb.gz 1nv8A:Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1786, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1788, because occupancy 0.500 <= existing 0.500 in 1nv8A Skipped atom 1790, because occupancy 0.500 <= existing 0.500 in 1nv8A # T0295 read from 1nv8A/merged-good-all-a2m # 1nv8A read from 1nv8A/merged-good-all-a2m # adding 1nv8A to template set # found chain 1nv8A in template set Warning: unaligning (T0295)K95 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)D224 Warning: unaligning (T0295)I96 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)D224 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1nv8A 107 :EELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFS T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1nv8A 145 :AIVFATDVSSKAVEIARKNAERHGV T0295 68 :NNLEVYEGDAIK 1nv8A 171 :DRFFVRKGEFLE T0295 81 :VFPK 1nv8A 183 :PFKE T0295 85 :FDVCTANIPY 1nv8A 191 :IEMILSNPPY T0295 97 :SSPLIFKLISHRPL 1nv8A 225 :GLDFYREFFGRYDT T0295 113 :CAVLMFQ 1nv8A 239 :SGKIVLM T0295 120 :KEFAERML 1nv8A 252 :VEELKKIV T0295 133 :SNYSRLT 1nv8A 260 :SDTVFLK T0295 154 :VNRS 1nv8A 267 :DSAG T0295 164 :KVDSVIV 1nv8A 271 :KYRFLLL Number of specific fragments extracted= 11 number of extra gaps= 1 total=826 Number of alignments=79 # 1nv8A read from 1nv8A/merged-good-all-a2m # found chain 1nv8A in template set Warning: unaligning (T0295)K95 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)D224 Warning: unaligning (T0295)I96 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)D224 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1nv8A 107 :EELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSD T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1nv8A 146 :IVFATDVSSKAVEIARKNAERHGV T0295 68 :NNLEVYEGDAIK 1nv8A 171 :DRFFVRKGEFLE T0295 81 :VFPK 1nv8A 183 :PFKE T0295 85 :FDVCTANIPY 1nv8A 191 :IEMILSNPPY T0295 97 :SSPLIFKLISHRPLFKCAVLM 1nv8A 225 :GLDFYREFFGRYDTSGKIVLM T0295 120 :KEFAERMLANV 1nv8A 252 :VEELKKIVSDT Number of specific fragments extracted= 7 number of extra gaps= 1 total=833 Number of alignments=80 # 1nv8A read from 1nv8A/merged-good-all-a2m # found chain 1nv8A in template set Warning: unaligning (T0295)I96 because of BadResidue code BAD_PEPTIDE in next template residue (1nv8A)S203 Warning: unaligning (T0295)S97 because of BadResidue code BAD_PEPTIDE at template residue (1nv8A)S203 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1nv8A 107 :EELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFS T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1nv8A 145 :AIVFATDVSSKAVEIARKNAERHGV T0295 68 :NNLEVYEGDAIKTVFPK 1nv8A 171 :DRFFVRKGEFLEPFKEK T0295 85 :FDVCTANIPYK 1nv8A 191 :IEMILSNPPYV T0295 98 :S 1nv8A 204 :S T0295 106 :SHRPLFKCAVLMFQK 1nv8A 205 :AHLPKDVLFEPPEAL T0295 121 :EFAERMLANVGDSNY 1nv8A 227 :DFYREFFGRYDTSGK T0295 211 :LNMLEHNYKN 1nv8A 252 :VEELKKIVSD Number of specific fragments extracted= 8 number of extra gaps= 1 total=841 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1dA expands to /projects/compbio/data/pdb/1h1d.pdb.gz 1h1dA:# T0295 read from 1h1dA/merged-good-all-a2m # 1h1dA read from 1h1dA/merged-good-all-a2m # adding 1h1dA to template set # found chain 1h1dA in template set Warning: unaligning (T0295)E176 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1dA)S216 Warning: unaligning (T0295)S177 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h1dA)S216 T0295 2 :LLKN 1h1dA 38 :WAMN T0295 6 :PGILDKIIYAAKI 1h1dA 47 :GQIMDAVIREYSP T0295 22 :DIVLEIGCGTGNLTVKLLPLA 1h1dA 60 :SLVLELGAYCGYSAVRMARLL T0295 43 :KKVITIDIDSRMISEVKKRCLYEGY 1h1dA 84 :ARLLTMEMNPDYAAITQQMLNFAGL T0295 68 :NNLEVYEGDAIK 1h1dA 110 :DKVTILNGASQD T0295 81 :VFPKFDVCTANIPYKISSPLIFKLISH 1h1dA 131 :DVDTLDMVFLDHWKDRYLPDTLLLEKC T0295 109 :PLFKCAVLMFQ 1h1dA 158 :GLLRKGTVLLA T0295 120 :KEFAERML 1h1dA 177 :PDFLAYVR T0295 131 :GDSNYSRLTINVK 1h1dA 185 :GSSSFECTHYSSY T0295 162 :PPKVDSVIVKLIPK 1h1dA 201 :MKVVDGLEKAIYQG Number of specific fragments extracted= 10 number of extra gaps= 1 total=851 Number of alignments=82 # 1h1dA read from 1h1dA/merged-good-all-a2m # found chain 1h1dA in template set Warning: unaligning (T0295)E176 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1dA)S216 Warning: unaligning (T0295)S177 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h1dA)S216 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1h1dA 44 :DAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQ T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1h1dA 85 :RLLTMEMNPDYAAITQQMLNFAGL T0295 68 :NNLEVYEGDAIKT 1h1dA 110 :DKVTILNGASQDL T0295 81 :VFPKFDVCTANIPYKISSPLIFKLISH 1h1dA 131 :DVDTLDMVFLDHWKDRYLPDTLLLEKC T0295 109 :PLFKCAVLMFQ 1h1dA 158 :GLLRKGTVLLA T0295 120 :KEFAERMLAN 1h1dA 177 :PDFLAYVRGS T0295 133 :SNYSRLTINVK 1h1dA 187 :SSFECTHYSSY T0295 162 :PPKVDSVIVKLIPK 1h1dA 201 :MKVVDGLEKAIYQG Number of specific fragments extracted= 8 number of extra gaps= 1 total=859 Number of alignments=83 # 1h1dA read from 1h1dA/merged-good-all-a2m # found chain 1h1dA in template set T0295 7 :GILDKIIYAAKI 1h1dA 48 :QIMDAVIREYSP T0295 22 :DIVLEIGCGTGNLTVKLLPL 1h1dA 60 :SLVLELGAYCGYSAVRMARL T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 1h1dA 83 :GARLLTMEMNPDYAAITQQMLNFAGL T0295 68 :NNLEVYEGDAIKTVF 1h1dA 110 :DKVTILNGASQDLIP T0295 83 :PKFDVCTANIPYKISSPLIFKLISHR 1h1dA 133 :DTLDMVFLDHWKDRYLPDTLLLEKCG T0295 129 :NVGD 1h1dA 161 :RKGT T0295 169 :IVKLI 1h1dA 165 :VLLAD T0295 235 :KKYCLDVLE 1h1dA 177 :PDFLAYVRG Number of specific fragments extracted= 8 number of extra gaps= 0 total=867 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kpgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kpgA expands to /projects/compbio/data/pdb/1kpg.pdb.gz 1kpgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1kpgA/merged-good-all-a2m # 1kpgA read from 1kpgA/merged-good-all-a2m # adding 1kpgA to template set # found chain 1kpgA in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1kpgA 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEKY T0295 43 :KKVITIDIDSRMISEVKKRCL 1kpgA 88 :VNVVGLTLSKNQANHVQQLVA T0295 66 :GYNN 1kpgA 109 :NSEN T0295 70 :LEVYEGDAIKTV 1kpgA 116 :KRVLLAGWEQFD T0295 84 :K 1kpgA 128 :E T0295 85 :FDVCTANIPYKISS 1kpgA 130 :VDRIVSIGAFEHFG T0295 99 :PLIFKLISH 1kpgA 145 :ERYDAFFSL T0295 108 :RPLFKCAVLMF 1kpgA 155 :HRLLPADGVML T0295 169 :IVKLIPKE 1kpgA 166 :LHTITGLH T0295 177 :SSFLTNFDEWDNLLRICFSR 1kpgA 179 :ERGLPMSFTFARFLKFIVTE T0295 208 :NAVLNMLEHNYKNWCTLNKQ 1kpgA 205 :LPSIPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSI 1kpgA 229 :QPHYAKTLDLWSAALQANKG T0295 254 :NLDENDFLKLLLE 1kpgA 252 :ALQSEEVYERYMK Number of specific fragments extracted= 13 number of extra gaps= 0 total=880 Number of alignments=85 # 1kpgA read from 1kpgA/merged-good-all-a2m # found chain 1kpgA in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1kpgA 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEKYD T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1kpgA 89 :NVVGLTLSKNQANHVQQLVANSEN T0295 68 :N 1kpgA 115 :S T0295 70 :LEVYEGDAIKTV 1kpgA 116 :KRVLLAGWEQFD T0295 83 :PKFDVCTANIPYKISSP 1kpgA 128 :EPVDRIVSIGAFEHFGH T0295 100 :LIFKLISH 1kpgA 146 :RYDAFFSL T0295 123 :AERML 1kpgA 154 :AHRLL T0295 162 :PPKVDSVIVKLIPKE 1kpgA 159 :PADGVMLLHTITGLH T0295 177 :SSFLTNFDEWDNLLRICFSR 1kpgA 179 :ERGLPMSFTFARFLKFIVTE T0295 208 :NAV 1kpgA 199 :IFP T0295 211 :LNMLEHNYKNWCTLNKQ 1kpgA 208 :IPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSIN 1kpgA 229 :QPHYAKTLDLWSAALQANKGQ T0295 255 :LDENDFLKLLLEF 1kpgA 253 :LQSEEVYERYMKY Number of specific fragments extracted= 13 number of extra gaps= 0 total=893 Number of alignments=86 # 1kpgA read from 1kpgA/merged-good-all-a2m # found chain 1kpgA in template set T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1kpgA 51 :AKIDLALGKLGLQPGMTLLDVGCGWGATMMRAVEK T0295 42 :AKKVITIDIDSRMISEVKKRCL 1kpgA 87 :DVNVVGLTLSKNQANHVQQLVA T0295 66 :GYNN 1kpgA 109 :NSEN T0295 70 :LEVYEGDAIKTVF 1kpgA 116 :KRVLLAGWEQFDE T0295 84 :KFDVCTANIPYKISS 1kpgA 129 :PVDRIVSIGAFEHFG T0295 109 :PLF 1kpgA 144 :HER T0295 116 :LMFQKEFAERML 1kpgA 147 :YDAFFSLAHRLL T0295 129 :NVG 1kpgA 159 :PAD T0295 165 :VDSVIVKLIPKE 1kpgA 162 :GVMLLHTITGLH T0295 177 :SSFLTNFDEWDNLLRICFSR 1kpgA 179 :ERGLPMSFTFARFLKFIVTE T0295 208 :NAV 1kpgA 199 :IFP T0295 211 :LNMLEHNYKNWCTLNKQ 1kpgA 208 :IPMVQECASANGFTVTR T0295 234 :FKKYCLDVLEHLDMCEKRSINLDENDFLKLLLEF 1kpgA 232 :YAKTLDLWSAALQANKGQAIALQSEEVYERYMKY Number of specific fragments extracted= 13 number of extra gaps= 0 total=906 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d2gA expands to /projects/compbio/data/pdb/1d2g.pdb.gz 1d2gA:# T0295 read from 1d2gA/merged-good-all-a2m # 1d2gA read from 1d2gA/merged-good-all-a2m # adding 1d2gA to template set # found chain 1d2gA in template set Warning: unaligning (T0295)V154 because of BadResidue code BAD_PEPTIDE in next template residue (1d2gA)P225 Warning: unaligning (T0295)N155 because of BadResidue code BAD_PEPTIDE at template residue (1d2gA)P225 T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEG 1d2gA 41 :TAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRR T0295 69 :NLEVYEGDAIK 1d2gA 109 :KWVIEEANWLT T0295 80 :TVFPK 1d2gA 124 :VPAGD T0295 85 :FDVCTAN 1d2gA 130 :FDAVICL T0295 92 :IPYKISS 1d2gA 138 :NSFAHLP T0295 99 :PLIFKLISHRPLFKCAVLMFQ 1d2gA 152 :EHRLALKNIASMVRPGGLLVI T0295 120 :KEFAERMLANVGDSNYSR 1d2gA 178 :DYILSTGCAPPGKNIYYK T0295 138 :LTINVK 1d2gA 204 :TSVLTV T0295 144 :LFCKVTKVCN 1d2gA 214 :HMVTLDYTVQ T0295 156 :RSSFNPPPKVDSVIVKLIP 1d2gA 226 :GAGRDGAPGFSKFRLSYYP T0295 181 :TNFDEWDNLLRICFSRK 1d2gA 245 :HCLASFTELVQEAFGGR Number of specific fragments extracted= 11 number of extra gaps= 1 total=917 Number of alignments=88 # 1d2gA read from 1d2gA/merged-good-all-a2m # found chain 1d2gA in template set Warning: unaligning (T0295)V154 because of BadResidue code BAD_PEPTIDE in next template residue (1d2gA)P225 Warning: unaligning (T0295)N155 because of BadResidue code BAD_PEPTIDE at template residue (1d2gA)P225 T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEG 1d2gA 40 :RTAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRR T0295 68 :NNLEVYEGDAIKT 1d2gA 108 :DKWVIEEANWLTL T0295 81 :VFPK 1d2gA 125 :PAGD T0295 85 :FDVCTAN 1d2gA 130 :FDAVICL T0295 92 :IPYKISS 1d2gA 138 :NSFAHLP T0295 99 :PLIFKLISHRPLFKCAVLMFQ 1d2gA 152 :EHRLALKNIASMVRPGGLLVI T0295 123 :AERML 1d2gA 177 :YDYIL T0295 128 :ANVGDSNYS 1d2gA 186 :APPGKNIYY T0295 137 :RLTINVK 1d2gA 203 :TTSVLTV T0295 144 :LFCKVTKVCN 1d2gA 214 :HMVTLDYTVQ T0295 156 :RSSFNPPPKVDSVIVKLI 1d2gA 226 :GAGRDGAPGFSKFRLSYY T0295 180 :LTNFDEWDNLLRICFS 1d2gA 244 :PHCLASFTELVQEAFG Number of specific fragments extracted= 12 number of extra gaps= 1 total=929 Number of alignments=89 # 1d2gA read from 1d2gA/merged-good-all-a2m # found chain 1d2gA in template set Warning: unaligning (T0295)V154 because of BadResidue code BAD_PEPTIDE in next template residue (1d2gA)P225 Warning: unaligning (T0295)N155 because of BadResidue code BAD_PEPTIDE at template residue (1d2gA)P225 T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1d2gA 41 :TAEYKAWLLGLLRQHGCHRVLDVACGTGVDSIMLVEEGFSVTSVDASDKMLKYALKERWNRRK T0295 68 :NNLEVYEGDAIK 1d2gA 108 :DKWVIEEANWLT T0295 80 :TVFPK 1d2gA 124 :VPAGD T0295 85 :FDVCTANI 1d2gA 130 :FDAVICLG T0295 94 :YKIS 1d2gA 138 :NSFA T0295 98 :SPLIFKLIS 1d2gA 154 :RLALKNIAS T0295 128 :ANVGDSNY 1d2gA 186 :APPGKNIY T0295 136 :SRLTI 1d2gA 205 :SVLTV T0295 143 :KLFCKVTKVCN 1d2gA 213 :AHMVTLDYTVQ T0295 156 :RSSFNPPPKVDSVI 1d2gA 226 :GAGRDGAPGFSKFR T0295 181 :TNFDEWDNLLRICFSRK 1d2gA 245 :HCLASFTELVQEAFGGR Number of specific fragments extracted= 11 number of extra gaps= 1 total=940 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1sqgA/merged-good-all-a2m # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0295 12 :IIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1sqgA 238 :CMTWLAPQNGEHILDLCAAPGGKTTHILEVA T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYN 1sqgA 271 :AQVVAVDIDEQRLSRVYDNLKRLGMK T0295 70 :LEVYEGDAIKTV 1sqgA 297 :ATVKQGDGRYPS T0295 83 :PK 1sqgA 312 :GE T0295 85 :FDVCTANIPY 1sqgA 316 :FDRILLDAPC T0295 96 :ISSPLIFK 1sqgA 345 :DIPELAQL T0295 104 :LISHRPLFKCAVLMFQ 1sqgA 357 :LDAIWPHLKTGGTLVY T0295 120 :KEFAERMLANVGDSNY 1sqgA 383 :SLQIKAFLQRTADAEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=948 Number of alignments=91 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0295 12 :IIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1sqgA 238 :CMTWLAPQNGEHILDLCAAPGGKTTHILEVAP T0295 44 :KVITIDIDSRMISEVKKRCLYEGYN 1sqgA 272 :QVVAVDIDEQRLSRVYDNLKRLGMK T0295 70 :LEVYEGDAIKT 1sqgA 297 :ATVKQGDGRYP T0295 81 :V 1sqgA 312 :G T0295 83 :PK 1sqgA 313 :EQ T0295 85 :FDVCTANIPY 1sqgA 316 :FDRILLDAPC T0295 95 :KISSPLIFKLISH 1sqgA 344 :RDIPELAQLQSEI T0295 108 :RPLFKCAVLM 1sqgA 361 :WPHLKTGGTL T0295 120 :KE 1sqgA 379 :PE T0295 122 :FAERMLANVGD 1sqgA 385 :QIKAFLQRTAD T0295 146 :CKV 1sqgA 396 :AEL T0295 156 :RSSFNPP 1sqgA 399 :CETGTPE T0295 163 :PKVDSVIVKLI 1sqgA 417 :EGDGFFYAKLI Number of specific fragments extracted= 13 number of extra gaps= 0 total=961 Number of alignments=92 # 1sqgA read from 1sqgA/merged-good-all-a2m # found chain 1sqgA in training set T0295 12 :IIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1sqgA 238 :CMTWLAPQNGEHILDLCAAPGGKTTHILEV T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 1sqgA 270 :EAQVVAVDIDEQRLSRVYDNLKRLGM T0295 69 :NLEVYEGDAIKT 1sqgA 296 :KATVKQGDGRYP T0295 83 :PK 1sqgA 313 :EQ T0295 85 :FDVCTANIPYKIS 1sqgA 316 :FDRILLDAPCSAT T0295 98 :SPLIF 1sqgA 334 :HPDIK T0295 126 :MLANVGD 1sqgA 339 :WLRRDRD T0295 234 :FKKYCLDVLEHLDMCEK 1sqgA 346 :IPELAQLQSEILDAIWP Number of specific fragments extracted= 8 number of extra gaps= 0 total=969 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1orhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0295/1orhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0295/1orhA/merged-good-all-a2m.gz for input Trying 1orhA/merged-good-all-a2m Error: Couldn't open file 1orhA/merged-good-all-a2m or 1orhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ve3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ve3A expands to /projects/compbio/data/pdb/1ve3.pdb.gz 1ve3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1ve3A/merged-good-all-a2m # 1ve3A read from 1ve3A/merged-good-all-a2m # adding 1ve3A to template set # found chain 1ve3A in template set Warning: unaligning (T0295)D132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ve3A)I164 Warning: unaligning (T0295)R137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ve3A)I164 Warning: unaligning (T0295)V148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ve3A)S186 T0295 3 :LKNPGILDKIIYAAK 1ve3A 16 :INSQEYRSRIETLEP T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYN 1ve3A 36 :MKKRGKVLDLACGVGGFSFLLEDYGFEVVGVDISEDMIRKAREYAKSRESN T0295 70 :LEVYEGDAIKTVFPK 1ve3A 87 :VEFIVGDARKLSFED T0295 85 :FDVCTANIPYKISSPLIFK 1ve3A 104 :FDYVIFIDSIVHFEPLELN T0295 104 :LISHRPLFKCAVLMFQ 1ve3A 125 :FKEVRRVLKPSGKFIM T0295 120 :KEFAER 1ve3A 143 :TDLREL T0295 127 :LANVG 1ve3A 149 :LPRLK T0295 138 :LTINVK 1ve3A 165 :SKVIPD T0295 144 :LFCK 1ve3A 176 :VVIE T0295 150 :KVCNVN 1ve3A 187 :FRVRFN T0295 208 :NAVLNMLEHNYKNW 1ve3A 193 :VWGKTGVELLAKLY Number of specific fragments extracted= 11 number of extra gaps= 0 total=980 Number of alignments=94 # 1ve3A read from 1ve3A/merged-good-all-a2m # found chain 1ve3A in template set T0295 5 :NPGILDKIIYAAK 1ve3A 18 :SQEYRSRIETLEP T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1ve3A 36 :MKKRGKVLDLACGVGGFSFLLEDYGFEVVGVDISEDMIRKAREYAKSRES T0295 69 :NLEVYEGDAIKTVFPK 1ve3A 86 :NVEFIVGDARKLSFED T0295 85 :FDVCTANIPYKISSP 1ve3A 104 :FDYVIFIDSIVHFEP T0295 100 :LIFKL 1ve3A 120 :ELNQV T0295 105 :ISHRPLFKC 1ve3A 126 :KEVRRVLKP T0295 114 :AVLMFQKE 1ve3A 137 :KFIMYFTD T0295 211 :LNMLEHNYKN 1ve3A 196 :KTGVELLAKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=988 Number of alignments=95 # 1ve3A read from 1ve3A/merged-good-all-a2m # found chain 1ve3A in template set Warning: unaligning (T0295)V210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ve3A)I164 T0295 6 :PGILDKIIYAAK 1ve3A 22 :RSRIETLEPLLM T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEG 1ve3A 36 :MKKRGKVLDLACGVGGFSFLLEDYGFEVVGVDISEDMIRKAREYAKSRE T0295 68 :NNLEVYEGDAIKTVFPK 1ve3A 85 :SNVEFIVGDARKLSFED T0295 85 :FDVCTANIPYKISSPL 1ve3A 104 :FDYVIFIDSIVHFEPL T0295 115 :VLMFQKEFAERML 1ve3A 120 :ELNQVFKEVRRVL T0295 164 :KVDSVIVKLIPK 1ve3A 133 :KPSGKFIMYFTD T0295 201 :LHAIFKRNA 1ve3A 145 :LRELLPRLK T0295 211 :LNMLEHNYKN 1ve3A 196 :KTGVELLAKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=996 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gh1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gh1A expands to /projects/compbio/data/pdb/2gh1.pdb.gz 2gh1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 2gh1A/merged-good-all-a2m # 2gh1A read from 2gh1A/merged-good-all-a2m # adding 2gh1A to template set # found chain 2gh1A in template set T0295 5 :NPGILDKIIY 2gh1A 23 :NDDYVSFLVN T0295 15 :AAKIKSSDIVLEIGCGTGNLTVKLLPLA 2gh1A 34 :VWKITKPVHIVDYGCGYGYLGLVLMPLL T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYN 2gh1A 65 :SKYTGIDSGETLLAEARELFRLLPYD T0295 70 :LEVYEGDAIKTVFPK 2gh1A 91 :SEFLEGDATEIELND T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQ 2gh1A 107 :YDIAICHAFLLHMTTPETMLQKMIHSVKKGGKIIC T0295 120 :KEFAERM 2gh1A 144 :PHWISNM T0295 133 :SN 2gh1A 151 :AS T0295 172 :LIPKESS 2gh1A 153 :YLLDGEK T0295 179 :FLTNFDEWDNLLRICFSR 2gh1A 162 :EFIQLGVLQKLFESDTQR T0295 197 :KRKTLHAIFKRN 2gh1A 221 :DKNDLYQSLKEE T0295 209 :AVLNMLEHNYKN 2gh1A 239 :GDKQQFVERLIA T0295 230 :VNFPFK 2gh1A 251 :RGLTYD T0295 236 :KYCLDVLEHLDMCEK 2gh1A 260 :AQYEAELRFFKALHL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1009 Number of alignments=97 # 2gh1A read from 2gh1A/merged-good-all-a2m # found chain 2gh1A in template set T0295 4 :KNPGILDKIIYAA 2gh1A 22 :YNDDYVSFLVNTV T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPLAK 2gh1A 36 :KITKPVHIVDYGCGYGYLGLVLMPLLP T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 2gh1A 66 :KYTGIDSGETLLAEARELFRLLPY T0295 69 :NLEVYEGDAIKTVFPK 2gh1A 90 :DSEFLEGDATEIELND T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLM 2gh1A 107 :YDIAICHAFLLHMTTPETMLQKMIHSVKKGGKI T0295 118 :FQKE 2gh1A 164 :IQLG T0295 122 :FAERMLANVG 2gh1A 189 :KIPIYLSELG T0295 144 :LFCKV 2gh1A 202 :IECRV T0295 149 :TKVCNVNRSSFN 2gh1A 208 :DKVNFLDSNMHH T0295 196 :RKRKTLHAIFKRN 2gh1A 220 :NDKNDLYQSLKEE T0295 209 :AVLNMLEHNYKNWCT 2gh1A 239 :GDKQQFVERLIARGL T0295 233 :PFK 2gh1A 254 :TYD T0295 236 :KYCLDVLEHLDMCE 2gh1A 260 :AQYEAELRFFKALH Number of specific fragments extracted= 13 number of extra gaps= 0 total=1022 Number of alignments=98 # 2gh1A read from 2gh1A/merged-good-all-a2m # found chain 2gh1A in template set T0295 5 :NPGILDKIIY 2gh1A 23 :NDDYVSFLVN T0295 15 :AAKIKSSDIVLEIGCGTGNLTVKLLPL 2gh1A 34 :VWKITKPVHIVDYGCGYGYLGLVLMPL T0295 42 :AKKVITIDIDSRMISEVKKRCLYEG 2gh1A 64 :GSKYTGIDSGETLLAEARELFRLLP T0295 68 :NNLEVYEGDAIKTVFPK 2gh1A 89 :YDSEFLEGDATEIELND T0295 85 :FDVCTANIPYKISS 2gh1A 107 :YDIAICHAFLLHMT T0295 99 :PLIFKLISH 2gh1A 124 :TMLQKMIHS T0295 130 :V 2gh1A 133 :V T0295 164 :KVDSVIVKLIPK 2gh1A 134 :KKGGKIICFEPH T0295 176 :ESSFL 2gh1A 157 :GEKQS T0295 181 :TNFDEWDNLLRICFSRKRK 2gh1A 164 :IQLGVLQKLFESDTQRNGK T0295 200 :TLHAIFKRNAV 2gh1A 189 :KIPIYLSELGV T0295 211 :LNMLEHNYKNWCTLNKQV 2gh1A 222 :KNDLYQSLKEEGIAGDPG T0295 233 :PFKKYCLDVL 2gh1A 240 :DKQQFVERLI T0295 252 :SINLDENDFLKLLLE 2gh1A 250 :ARGLTYDNALAQYEA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1036 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vlmA expands to /projects/compbio/data/pdb/1vlm.pdb.gz 1vlmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 1vlmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1vlmA/merged-good-all-a2m # 1vlmA read from 1vlmA/merged-good-all-a2m # adding 1vlmA to template set # found chain 1vlmA in template set Warning: unaligning (T0295)D132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 Warning: unaligning (T0295)N134 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vlmA)V146 Warning: unaligning (T0295)A209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)S155 Warning: unaligning (T0295)V210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)S155 T0295 9 :LDKIIYAA 1vlmA 26 :ELQAVKCL T0295 19 :KSSDIVLEIGCGTGNLTVKL 1vlmA 34 :LPEGRGVEIGVGTGRFAVPL T0295 46 :ITIDIDSRMISEVKKR 1vlmA 57 :IGVEPSERMAEIARKR T0295 68 :N 1vlmA 73 :G T0295 70 :LEVYEGDAIKTVFPK 1vlmA 74 :VFVLKGTAENLPLKD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQ 1vlmA 91 :FDFALMVTTICFVDDPERALKEAYRILKKGGYLIV T0295 120 :KEFAERMLANVG 1vlmA 132 :SFLGREYEKNKE T0295 135 :YS 1vlmA 147 :FY T0295 176 :ESSF 1vlmA 149 :KNAR T0295 208 :N 1vlmA 153 :F T0295 211 :LNMLEHNYKNWCTL 1vlmA 156 :TEELMDLMRKAGFE Number of specific fragments extracted= 11 number of extra gaps= 1 total=1047 Number of alignments=100 # 1vlmA read from 1vlmA/merged-good-all-a2m # found chain 1vlmA in template set Warning: unaligning (T0295)D132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 Warning: unaligning (T0295)N134 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vlmA)V146 Warning: unaligning (T0295)V142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)S155 Warning: unaligning (T0295)K143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)S155 T0295 9 :LDKIIYAA 1vlmA 26 :ELQAVKCL T0295 19 :KSSDIVLEIGCGTGNLTVKL 1vlmA 34 :LPEGRGVEIGVGTGRFAVPL T0295 46 :ITIDIDSRMISEVKKR 1vlmA 57 :IGVEPSERMAEIARKR T0295 68 :N 1vlmA 73 :G T0295 70 :LEVYEGDAIKTVFPK 1vlmA 74 :VFVLKGTAENLPLKD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLM 1vlmA 91 :FDFALMVTTICFVDDPERALKEAYRILKKGGYL T0295 123 :AERMLANVG 1vlmA 135 :GREYEKNKE T0295 135 :YSRLTIN 1vlmA 147 :FYKNARF T0295 144 :LFCKVTKVCNVNRSSFNPP 1vlmA 169 :EEFKVVQTLFKHPSELSEI T0295 163 :PKVDSVIVKLI 1vlmA 195 :GEGAFVVIRGT Number of specific fragments extracted= 10 number of extra gaps= 1 total=1057 Number of alignments=101 # 1vlmA read from 1vlmA/merged-good-all-a2m # found chain 1vlmA in template set Warning: unaligning (T0295)I173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlmA)V128 Warning: unaligning (T0295)P174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlmA)V128 Warning: unaligning (T0295)V210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vlmA)V146 T0295 8 :ILDKIIYAA 1vlmA 25 :SELQAVKCL T0295 20 :SSDIVLEIGCGTGNLTVKL 1vlmA 35 :PEGRGVEIGVGTGRFAVPL T0295 46 :ITIDIDSRMISEVKKR 1vlmA 57 :IGVEPSERMAEIARKR T0295 66 :G 1vlmA 73 :G T0295 70 :LEVYEGDAIKTVFPK 1vlmA 74 :VFVLKGTAENLPLKD T0295 85 :FDVCTANIPYKISSPLIF 1vlmA 91 :FDFALMVTTICFVDDPER T0295 119 :QKEFAERML 1vlmA 109 :ALKEAYRIL T0295 164 :KVDSVIVKL 1vlmA 118 :KKGGYLIVG T0295 175 :KESS 1vlmA 129 :DRES T0295 200 :TLHAIFKRNA 1vlmA 134 :LGREYEKNKE T0295 211 :LNMLEHNYKNWCTL 1vlmA 156 :TEELMDLMRKAGFE Number of specific fragments extracted= 11 number of extra gaps= 1 total=1068 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2as0A expands to /projects/compbio/data/pdb/2as0.pdb.gz 2as0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 2as0A/merged-good-all-a2m # 2as0A read from 2as0A/merged-good-all-a2m # adding 2as0A to template set # found chain 2as0A in template set T0295 11 :KIIYAAK 2as0A 206 :ENRLALE T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 2as0A 215 :VQPGDRVLDVFTYTGGFAIHAAIA T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 2as0A 240 :ADEVIGIDKSPRAIETAKENAKLNGV T0295 68 :NNLEVYEGDAIK 2as0A 267 :DRMKFIVGSAFE T0295 83 :PK 2as0A 287 :GE T0295 85 :FDVCTANIPYKISSP 2as0A 290 :FDIVVLDPPAFVQHE T0295 100 :LIFKLISH 2as0A 310 :GLRAYFNV T0295 108 :RPLFKCAVLMFQ 2as0A 322 :LNLVKDGGILVT T0295 229 :PVNFPFKKYCLDVLEHLDM 2as0A 337 :SQHVDLQMFKDMIIAAGAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1077 Number of alignments=103 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0295 11 :KIIYAAK 2as0A 206 :ENRLALE T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 2as0A 215 :VQPGDRVLDVFTYTGGFAIHAAIAGA T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 2as0A 242 :EVIGIDKSPRAIETAKENAKLNGV T0295 68 :NNLEVYEGDAIKT 2as0A 267 :DRMKFIVGSAFEE T0295 81 :V 2as0A 286 :K T0295 83 :PK 2as0A 287 :GE T0295 85 :FDVCTANIPYKISSP 2as0A 290 :FDIVVLDPPAFVQHE T0295 100 :LIFKLISH 2as0A 310 :GLRAYFNV T0295 108 :RPLFKCAVLM 2as0A 322 :LNLVKDGGIL T0295 118 :FQKEFAERMLANVG 2as0A 344 :MFKDMIIAAGAKAG T0295 149 :TKVCNVNRSSFNPP 2as0A 358 :KFLKMLEPYRTQAP T0295 163 :PKVDSVIVKLIPK 2as0A 383 :EYLKCLFLYVEDM Number of specific fragments extracted= 12 number of extra gaps= 0 total=1089 Number of alignments=104 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0295 12 :IIYAAK 2as0A 207 :NRLALE T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 2as0A 215 :VQPGDRVLDVFTYTGGFAIHAAIA T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGY 2as0A 240 :ADEVIGIDKSPRAIETAKENAKLNGV T0295 68 :NNLEVYEGDAIK 2as0A 267 :DRMKFIVGSAFE T0295 83 :PKFDVCTANIPYKISS 2as0A 288 :EKFDIVVLDPPAFVQH T0295 109 :PLFKCAVLMFQKEFAERMLANVGD 2as0A 304 :EKDLKAGLRAYFNVNFAGLNLVKD T0295 166 :DSVIVKLIPKE 2as0A 328 :GGILVTCSCSQ T0295 180 :LTNFDEWDNLLRICFS 2as0A 339 :HVDLQMFKDMIIAAGA Number of specific fragments extracted= 8 number of extra gaps= 0 total=1097 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l3iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l3iA expands to /projects/compbio/data/pdb/1l3i.pdb.gz 1l3iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1l3iA/merged-good-all-a2m # 1l3iA read from 1l3iA/merged-good-all-a2m # adding 1l3iA to template set # found chain 1l3iA in template set T0295 2 :LLKNP 1l3iA 7 :FIKNP T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1l3iA 20 :EVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGL T0295 68 :NNLEVYEGDAIK 1l3iA 82 :DNVTLMEGDAPE T0295 81 :VFPKFDVCTANIPYKISSPLIFKLIS 1l3iA 97 :KIPDIDIAVVGGSGGELQEILRIIKD T0295 110 :LFKCAVLMFQ 1l3iA 123 :KLKPGGRIIV T0295 120 :KEFAERMLANVGD 1l3iA 140 :KFEAMECLRDLGF T0295 136 :SRLT 1l3iA 153 :DVNI T0295 144 :LFCKVTKVCNVNRS 1l3iA 157 :TELNIARGRALDRG T0295 170 :VKLIPKES 1l3iA 171 :TMMVSRNP Number of specific fragments extracted= 9 number of extra gaps= 0 total=1106 Number of alignments=106 # 1l3iA read from 1l3iA/merged-good-all-a2m # found chain 1l3iA in template set T0295 3 :LKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1l3iA 16 :PTAMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGL T0295 68 :NNLEVYEGDAIKT 1l3iA 82 :DNVTLMEGDAPEA T0295 81 :VFPKFDVCTANIPYKISSPLIFKLI 1l3iA 97 :KIPDIDIAVVGGSGGELQEILRIIK T0295 109 :PLFKCAVLMFQ 1l3iA 122 :DKLKPGGRIIV T0295 120 :KE 1l3iA 141 :FE T0295 123 :AERMLANVG 1l3iA 143 :AMECLRDLG T0295 135 :YSRLTINVK 1l3iA 152 :FDVNITELN T0295 144 :LFCKVT 1l3iA 162 :ARGRAL T0295 150 :KVCNVNRSS 1l3iA 170 :GTMMVSRNP Number of specific fragments extracted= 9 number of extra gaps= 0 total=1115 Number of alignments=107 # 1l3iA read from 1l3iA/merged-good-all-a2m # found chain 1l3iA in template set T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1l3iA 18 :AMEVRCLIMCLAEPGKNDVAVDVGCGTGGVTLELAGRVRRVYAIDRNPEAISTTEMNLQRHGL T0295 68 :NNLEVYEGDAIKT 1l3iA 82 :DNVTLMEGDAPEA T0295 81 :VFPKFDVCTANIPYKISSPLIFKLISH 1l3iA 97 :KIPDIDIAVVGGSGGELQEILRIIKDK T0295 161 :PPPK 1l3iA 124 :LKPG T0295 167 :SVIVKLIPK 1l3iA 128 :GRIIVTAIL T0295 208 :NAVLNMLEHNYKNWCTLNK 1l3iA 137 :LETKFEAMECLRDLGFDVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=1121 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fytA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fytA expands to /projects/compbio/data/pdb/2fyt.pdb.gz 2fytA:Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 688, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2418, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2424, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2426, because occupancy 0.500 <= existing 0.500 in 2fytA Skipped atom 2428, because occupancy 0.500 <= existing 0.500 in 2fytA # T0295 read from 2fytA/merged-good-all-a2m # 2fytA read from 2fytA/merged-good-all-a2m # adding 2fytA to template set # found chain 2fytA in template set T0295 2 :LLKNPGILDKIIYAAK 2fytA 250 :MLKDKIRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 2fytA 270 :IFKDKVVLDVGCGTGILSMFAAKA T0295 42 :AKKVITIDIDS 2fytA 295 :AKKVLGVDQSE T0295 54 :MISEVKKRCLYEGY 2fytA 306 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIK 2fytA 321 :DTITLIKGKIEE T0295 80 :TVFPKFDVCTANIPYKISS 2fytA 335 :LPVEKVDVIISEWMGYFLL T0295 99 :PLIFKLIS 2fytA 359 :DSVLYAKN T0295 109 :PLFKCAVLMFQ 2fytA 367 :KYLAKGGSVYP T0295 136 :SRLTINVKLF 2fytA 378 :DICTISLVAV T0295 209 :AVLNMLEHNYKNWCTLNKQVPVN 2fytA 388 :SDVNKHADRIAFWDDVYGFKMSC Number of specific fragments extracted= 10 number of extra gaps= 0 total=1131 Number of alignments=109 # 2fytA read from 2fytA/merged-good-all-a2m # found chain 2fytA in template set Warning: unaligning (T0295)N153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fytA)V510 Warning: unaligning (T0295)V154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fytA)V510 T0295 4 :KNPGILDKIIYAAK 2fytA 252 :KDKIRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 2fytA 270 :IFKDKVVLDVGCGTGILSMFAAKAGA T0295 44 :KVITIDIDS 2fytA 297 :KVLGVDQSE T0295 54 :MISEVKKRCLYEGY 2fytA 306 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIKTVFPK 2fytA 321 :DTITLIKGKIEEVHLPV T0295 85 :FDVCTAN 2fytA 340 :VDVIISE T0295 92 :IPYKISSP 2fytA 348 :MGYFLLFE T0295 100 :LIFKLISHRPLFKCAVLMFQKE 2fytA 357 :MLDSVLYAKNKYLAKGGSVYPD T0295 135 :YSRLTINVK 2fytA 481 :HNRVVFSTG T0295 144 :LFCKVTKVC 2fytA 500 :TVFLLEKPF T0295 155 :NRS 2fytA 511 :KAG T0295 164 :KVDSVIVKLIPKESSF 2fytA 514 :EALKGKVTVHKNKKDP Number of specific fragments extracted= 12 number of extra gaps= 1 total=1143 Number of alignments=110 # 2fytA read from 2fytA/merged-good-all-a2m # found chain 2fytA in template set T0295 3 :LKNPGILDKIIYAAK 2fytA 251 :LKDKIRTESYRDFIY T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPL 2fytA 270 :IFKDKVVLDVGCGTGILSMFAAKA T0295 42 :AKKVITIDIDS 2fytA 295 :AKKVLGVDQSE T0295 54 :MISEVKKRCLYEGY 2fytA 306 :ILYQAMDIIRLNKL T0295 68 :NNLEVYEGDAIKTVF 2fytA 321 :DTITLIKGKIEEVHL T0295 83 :PKFDVCTANIPYKIS 2fytA 338 :EKVDVIISEWMGYFL T0295 112 :KCAVLMFQKEFAERMLANVGDSNYSRLTINVKLF 2fytA 354 :FESMLDSVLYAKNKYLAKGGSVYPDICTISLVAV T0295 209 :AVLNMLEHNYKNWCTLNKQVPVN 2fytA 388 :SDVNKHADRIAFWDDVYGFKMSC Number of specific fragments extracted= 8 number of extra gaps= 0 total=1151 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yb2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yb2A expands to /projects/compbio/data/pdb/1yb2.pdb.gz 1yb2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1yb2A/merged-good-all-a2m # 1yb2A read from 1yb2A/merged-good-all-a2m # adding 1yb2A to template set # found chain 1yb2A in template set Warning: unaligning (T0295)A16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yb2A)C86 Warning: unaligning (T0295)G66 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1yb2A)D140 T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPLA 1yb2A 87 :GLRPGMDILEVGVGSGNMSSYILYAL T0295 43 :KKVITIDIDSRMISEVKKRCLYE 1yb2A 116 :GTLTVVERDEDNLKKAMDNLSEF T0295 67 :YNNLEVYEGDAIKTVFPK 1yb2A 141 :IGNVRTSRSDIADFISDQ T0295 85 :FDVCTAN 1yb2A 160 :YDAVIAD T0295 92 :IPY 1yb2A 169 :DPW T0295 99 :PLIFKLIS 1yb2A 172 :NHVQKIAS T0295 110 :LFKCAVLMFQ 1yb2A 180 :MMKPGSVATF T0295 120 :KEFAERMLANVGDSNYSRLTI 1yb2A 194 :FDQSEKTVLSLSASGMHHLET T0295 145 :FCKVTKVCNVNRSSFNPP 1yb2A 215 :VELMKRRILVREGATRPA Number of specific fragments extracted= 9 number of extra gaps= 1 total=1160 Number of alignments=112 # 1yb2A read from 1yb2A/merged-good-all-a2m # found chain 1yb2A in template set Warning: unaligning (T0295)A16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yb2A)C86 Warning: unaligning (T0295)G66 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1yb2A)D140 T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPLAK 1yb2A 87 :GLRPGMDILEVGVGSGNMSSYILYALN T0295 44 :KVITIDIDSRMISEVKKRCLYE 1yb2A 117 :TLTVVERDEDNLKKAMDNLSEF T0295 67 :YNNLEVYEGDAIKTVFPK 1yb2A 141 :IGNVRTSRSDIADFISDQ T0295 85 :FDVCTANI 1yb2A 160 :YDAVIADI T0295 98 :SPLIFKLISHRPLFKCAVLMFQ 1yb2A 168 :PDPWNHVQKIASMMKPGSVATF T0295 120 :KEFAERMLANVGD 1yb2A 194 :FDQSEKTVLSLSA T0295 135 :YSRLTINVKLF 1yb2A 207 :SGMHHLETVEL T0295 148 :VTKVCNVNRSSFNPP 1yb2A 218 :MKRRILVREGATRPA T0295 163 :PKVDSVIVKLI 1yb2A 237 :THTAFITFAIK Number of specific fragments extracted= 9 number of extra gaps= 1 total=1169 Number of alignments=113 # 1yb2A read from 1yb2A/merged-good-all-a2m # found chain 1yb2A in template set Warning: unaligning (T0295)A16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yb2A)C86 Warning: unaligning (T0295)E65 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1yb2A)D140 Warning: unaligning (T0295)G66 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1yb2A)D140 T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPL 1yb2A 87 :GLRPGMDILEVGVGSGNMSSYILYA T0295 42 :AKKVITIDIDSRMISEVKKRCLY 1yb2A 115 :KGTLTVVERDEDNLKKAMDNLSE T0295 67 :YNNLEVYEGDAIKTVFPK 1yb2A 141 :IGNVRTSRSDIADFISDQ T0295 85 :FDVCTANIPYK 1yb2A 160 :YDAVIADIPDP T0295 98 :SPLIFKLISH 1yb2A 171 :WNHVQKIASM T0295 166 :DSVIVKLI 1yb2A 183 :PGSVATFY T0295 181 :TNFDEWDNLLRI 1yb2A 192 :PNFDQSEKTVLS Number of specific fragments extracted= 7 number of extra gaps= 1 total=1176 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xxlA expands to /projects/compbio/data/pdb/1xxl.pdb.gz 1xxlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1xxlA/merged-good-all-a2m # 1xxlA read from 1xxlA/merged-good-all-a2m # adding 1xxlA to template set # found chain 1xxlA in template set Warning: unaligning (T0295)N5 because first residue in template chain is (1xxlA)H-3 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1xxlA -2 :HHSLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQKEFA 1xxlA 79 :FDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLLVDHY T0295 180 :LTNFDEWDNLLRICFSRKRKT 1xxlA 118 :APEDPVLDEFVNHLNRLRDPS T0295 208 :NAVLNMLEHNYKNWCTLNKQ 1xxlA 142 :ESSLSEWQAMFSANQLAYQD T0295 228 :VPVNFPFKKYCLDV 1xxlA 165 :WNLPIQYDSWIKRG T0295 254 :NLDENDFLKLLLE 1xxlA 179 :GTPADREKQIITH Number of specific fragments extracted= 6 number of extra gaps= 0 total=1182 Number of alignments=115 # 1xxlA read from 1xxlA/merged-good-all-a2m # found chain 1xxlA in template set Warning: unaligning (T0295)N5 because first residue in template chain is (1xxlA)H-3 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1xxlA -2 :HHSLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPD T0295 85 :FDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQ 1xxlA 79 :FDIITCRYAAHHFSDVRKAVREVARVLKQDGRFLL T0295 120 :KEFAERMLANVGDSNYSRLTINVK 1xxlA 125 :DEFVNHLNRLRDPSHVRESSLSEW T0295 144 :LFCKVTKVCNVNRS 1xxlA 157 :LAYQDIQKWNLPIQ T0295 186 :WDNLLRICF 1xxlA 171 :YDSWIKRGG T0295 195 :SRKRKTLHAIFKRN 1xxlA 182 :ADREKQIITHLNHA T0295 211 :LNMLEHN 1xxlA 196 :SDEARDT Number of specific fragments extracted= 7 number of extra gaps= 0 total=1189 Number of alignments=116 # 1xxlA read from 1xxlA/merged-good-all-a2m # found chain 1xxlA in template set Warning: unaligning (T0295)N5 because first residue in template chain is (1xxlA)H-3 T0295 6 :PGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1xxlA -2 :HHSLGLMIKTAECRAEHRVLDIGAGAGHTALAFSPYVQECIGVDATKEMVEVASSFAQEKGVENVRFQQGTAESLPFPD T0295 85 :FDVCTANIPYKISSPLIFKL 1xxlA 79 :FDIITCRYAAHHFSDVRKAV T0295 120 :KEFAERM 1xxlA 99 :REVARVL T0295 164 :KVDSVIVKLIPKESSFLTNFDEWDNLLRIC 1xxlA 106 :KQDGRFLLVDHYAPEDPVLDEFVNHLNRLR T0295 207 :RNAV 1xxlA 138 :SHVR T0295 211 :LNMLEHNYKNWCT 1xxlA 145 :LSEWQAMFSANQL T0295 224 :LNKQVPVNFPFKKYCLDV 1xxlA 161 :DIQKWNLPIQYDSWIKRG T0295 254 :NLDENDFLKLLLEFN 1xxlA 179 :GTPADREKQIITHLN Number of specific fragments extracted= 8 number of extra gaps= 0 total=1197 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jg1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0295 read from 1jg1A/merged-good-all-a2m # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1jg1A 75 :SAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIV T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1jg1A 115 :TDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPK T0295 85 :FDVCTANIPYKISSPL 1jg1A 159 :YDVIIVTAGAPKIPEP T0295 107 :HRPLFKCAVLMFQKEF 1jg1A 175 :LIEQLKIGGKLIIPVG T0295 133 :SNYSRLTINVKLF 1jg1A 191 :SYHLWQELLEVRK T0295 146 :CKVTKVCNVN 1jg1A 208 :IKIKNHGGVA T0295 159 :F 1jg1A 218 :F Number of specific fragments extracted= 7 number of extra gaps= 0 total=1204 Number of alignments=118 # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set T0295 3 :LKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1jg1A 74 :VSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVK T0295 44 :KVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIK 1jg1A 116 :DVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSK T0295 81 :VFPK 1jg1A 152 :GFPP T0295 85 :FDVCTANIPYKISSPLIF 1jg1A 159 :YDVIIVTAGAPKIPEPLI T0295 109 :PLFKCAVLMFQKE 1jg1A 177 :EQLKIGGKLIIPV T0295 131 :GDSNYSRLTINVK 1jg1A 190 :GSYHLWQELLEVR T0295 144 :LFCKVTKVCNVNRSS 1jg1A 206 :DGIKIKNHGGVAFVP Number of specific fragments extracted= 7 number of extra gaps= 0 total=1211 Number of alignments=119 # 1jg1A read from 1jg1A/merged-good-all-a2m # found chain 1jg1A in training set T0295 3 :LKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1jg1A 74 :VSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEI T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGYNNLEVYEGDAIKTVFPK 1jg1A 114 :KTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPK T0295 85 :FDVCTANIPYKISSPLIFKLISH 1jg1A 159 :YDVIIVTAGAPKIPEPLIEQLKI T0295 147 :KVTKVCNVNRSSFN 1jg1A 182 :GGKLIIPVGSYHLW T0295 165 :VDSVIVKLIPK 1jg1A 196 :QELLEVRKTKD Number of specific fragments extracted= 5 number of extra gaps= 0 total=1216 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qyrA expands to /projects/compbio/data/pdb/1qyr.pdb.gz 1qyrA:# T0295 read from 1qyrA/merged-good-all-a2m # 1qyrA read from 1qyrA/merged-good-all-a2m # adding 1qyrA to template set # found chain 1qyrA in template set Warning: unaligning (T0295)R108 because of BadResidue code BAD_PEPTIDE in next template residue (1qyrA)D131 Warning: unaligning (T0295)P109 because of BadResidue code BAD_PEPTIDE at template residue (1qyrA)D131 Warning: unaligning (T0295)C146 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qyrA)N169 Warning: unaligning (T0295)K147 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qyrA)N169 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVK 1qyrA 18 :NFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQ T0295 68 :NNLEVYEGDAIKTVF 1qyrA 83 :PKLTIYQQDAMTFNF T0295 83 :PKFDVCTANIPYKISSPLIFKLISH 1qyrA 105 :GQPLRVFGNLPYNISTPLMFHLFSY T0295 110 :LFKCAVLMFQKEFAERMLANVGDSNYSRLTINVKLF 1qyrA 132 :AIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYY T0295 148 :VTKVCNVNRSSFNPPPKVDSVIVKLIPKESS 1qyrA 170 :VIPVLEVPPSAFTPPPKVDSAVVRLVPHATM T0295 179 :FLTNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNMLEHN 1qyrA 203 :PVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGM T0295 222 :CTLNKQVPVNFPFKKYCLDVLEHLDM 1qyrA 242 :GIDPAMRAENISVAQYCQMANYLAEN Number of specific fragments extracted= 7 number of extra gaps= 2 total=1223 Number of alignments=121 # 1qyrA read from 1qyrA/merged-good-all-a2m # found chain 1qyrA in template set Warning: unaligning (T0295)R108 because of BadResidue code BAD_PEPTIDE in next template residue (1qyrA)D131 Warning: unaligning (T0295)P109 because of BadResidue code BAD_PEPTIDE at template residue (1qyrA)D131 Warning: unaligning (T0295)C146 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qyrA)N169 Warning: unaligning (T0295)K147 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qyrA)N169 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVK 1qyrA 18 :NFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQ T0295 68 :NNLEVYEGDAIKTVF 1qyrA 83 :PKLTIYQQDAMTFNF T0295 83 :PKFDVCTANIPYKISSPLIFKLISH 1qyrA 105 :GQPLRVFGNLPYNISTPLMFHLFSY T0295 110 :LFKCAVLMFQKEFAERMLANVGDSNYSRLTINVKLF 1qyrA 132 :AIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYY T0295 148 :VTKVCNVNRSSFNPPPKVDSVIVKLIPKE 1qyrA 170 :VIPVLEVPPSAFTPPPKVDSAVVRLVPHA T0295 177 :SSFLTNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNM 1qyrA 201 :PHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEV T0295 218 :YKNWCTLNKQVPVNFPFKKYCLDVLEHLDM 1qyrA 238 :LTGMGIDPAMRAENISVAQYCQMANYLAEN Number of specific fragments extracted= 7 number of extra gaps= 2 total=1230 Number of alignments=122 # 1qyrA read from 1qyrA/merged-good-all-a2m # found chain 1qyrA in template set Warning: unaligning (T0295)R108 because of BadResidue code BAD_PEPTIDE in next template residue (1qyrA)D131 Warning: unaligning (T0295)P109 because of BadResidue code BAD_PEPTIDE at template residue (1qyrA)D131 Warning: unaligning (T0295)C146 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qyrA)N169 Warning: unaligning (T0295)K147 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qyrA)N169 T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVK 1qyrA 18 :NFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQ T0295 66 :GY 1qyrA 77 :TH T0295 68 :NNLEVYEGDAIKTVF 1qyrA 83 :PKLTIYQQDAMTFNF T0295 83 :PKFDVCTANIPYKISSPLIFKLISH 1qyrA 105 :GQPLRVFGNLPYNISTPLMFHLFSY T0295 110 :LFKCAVLMFQKEFAERMLANVGDSNYS 1qyrA 132 :AIADMHFMLQKEVVNRLVAGPNSKAYG T0295 148 :VTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFL 1qyrA 170 :VIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPH T0295 181 :TNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNMLEH 1qyrA 205 :KDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTG T0295 221 :WCTLNKQVPVNFPFKKYCLDVLEHLDM 1qyrA 241 :MGIDPAMRAENISVAQYCQMANYLAEN Number of specific fragments extracted= 8 number of extra gaps= 2 total=1238 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g6q2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g6q2 expands to /projects/compbio/data/pdb/1g6q.pdb.gz 1g6q2:# T0295 read from 1g6q2/merged-good-all-a2m # 1g6q2 read from 1g6q2/merged-good-all-a2m # adding 1g6q2 to template set # found chain 1g6q2 in template set Warning: unaligning (T0295)S20 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0295)S21 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 T0295 7 :GILDKIIYAAKIK 1g6q2 45 :SYRNAIIQNKDLF T0295 22 :DIVLEIGCGTGNLTVKLLPL 1g6q2 60 :KIVLDVGCGTGILSMFAAKH T0295 42 :AKKVITIDIDS 1g6q2 81 :AKHVIGVDMSS T0295 54 :MISEVKKRCLYEGY 1g6q2 92 :IIEMAKELVELNGF T0295 68 :NNLEVYEGDAIKTVFPK 1g6q2 107 :DKITLLRGKLEDVHLPF T0295 85 :FDVCTANIPYKISS 1g6q2 126 :VDIIISEWMGYFLL T0295 99 :PLIFKLI 1g6q2 145 :DTVLYAR T0295 108 :RPLFKCAVLMF 1g6q2 152 :DHYLVEGGLIF T0295 135 :YSRLTINVKLF 1g6q2 163 :PDKCSIHLAGL T0295 209 :AVLNMLEHNYKNWCTLNKQ 1g6q2 174 :EDSQYKDEKLNYWQDVYGF T0295 256 :DENDFLKLLLEF 1g6q2 193 :DYSPFVPLVLHE T0295 268 :NKKGI 1g6q2 211 :ERNNV Number of specific fragments extracted= 12 number of extra gaps= 1 total=1250 Number of alignments=124 # 1g6q2 read from 1g6q2/merged-good-all-a2m # found chain 1g6q2 in template set Warning: unaligning (T0295)S20 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0295)S21 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 Warning: unaligning (T0295)S98 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)E141 Warning: unaligning (T0295)P99 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)E141 T0295 8 :ILDKIIYAAKIK 1g6q2 46 :YRNAIIQNKDLF T0295 22 :DIVLEIGCGTGNLTVKLLPLAK 1g6q2 60 :KIVLDVGCGTGILSMFAAKHGA T0295 44 :KVITIDIDS 1g6q2 83 :HVIGVDMSS T0295 54 :MISEVKKRCLYEGY 1g6q2 92 :IIEMAKELVELNGF T0295 68 :NNLEVYEGDAIKTVFPK 1g6q2 107 :DKITLLRGKLEDVHLPF T0295 85 :FDVCTAN 1g6q2 126 :VDIIISE T0295 92 :IPYKIS 1g6q2 134 :MGYFLL T0295 100 :LIFKLISHRPLFKCAVLMFQKE 1g6q2 143 :MMDTVLYARDHYLVEGGLIFPD T0295 144 :LFCKVT 1g6q2 256 :TWFDIV T0295 156 :RSSFNPP 1g6q2 265 :PKGKRPV T0295 163 :PKVDSV 1g6q2 284 :WKQTIF T0295 169 :IVKLIPKESSF 1g6q2 306 :ELVCSPNEKNN Number of specific fragments extracted= 12 number of extra gaps= 2 total=1262 Number of alignments=125 # 1g6q2 read from 1g6q2/merged-good-all-a2m # found chain 1g6q2 in template set Warning: unaligning (T0295)S20 because of BadResidue code BAD_PEPTIDE in next template residue (1g6q2)D59 Warning: unaligning (T0295)S21 because of BadResidue code BAD_PEPTIDE at template residue (1g6q2)D59 T0295 7 :GILDKIIYAAK 1g6q2 44 :LSYRNAIIQNK T0295 18 :IK 1g6q2 56 :LF T0295 22 :DIVLEIGCGTGNLTVKLLPL 1g6q2 60 :KIVLDVGCGTGILSMFAAKH T0295 42 :AKKVITIDIDS 1g6q2 81 :AKHVIGVDMSS T0295 54 :MISEVKKRCLYEGY 1g6q2 92 :IIEMAKELVELNGF T0295 68 :NNLEVYEGDAIKTVFPK 1g6q2 107 :DKITLLRGKLEDVHLPF T0295 85 :FDVCTANIPYK 1g6q2 126 :VDIIISEWMGY T0295 96 :ISSPLIFKLIS 1g6q2 142 :SMMDTVLYARD T0295 135 :YSRLTINVKLF 1g6q2 163 :PDKCSIHLAGL T0295 209 :AVLNMLEHNYKNWCTLNKQVPV 1g6q2 174 :EDSQYKDEKLNYWQDVYGFDYS Number of specific fragments extracted= 10 number of extra gaps= 1 total=1272 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g38A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g38A expands to /projects/compbio/data/pdb/1g38.pdb.gz 1g38A:# T0295 read from 1g38A/merged-good-all-a2m # 1g38A read from 1g38A/merged-good-all-a2m # adding 1g38A to template set # found chain 1g38A in template set T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1g38A 24 :PPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAH T0295 43 :KKVITIDIDSRM 1g38A 65 :YRFVGVEIDPKA T0295 65 :EGY 1g38A 77 :LDL T0295 68 :NNLEVYEGDAIKTVFPK 1g38A 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPY 1g38A 99 :FDLILGNPPY T0295 95 :KISSPLIFKLISHRPL 1g38A 120 :HVFKAVKDLYKKAFST T0295 111 :FKCAVLMFQ 1g38A 154 :LKPGGVLVF T0295 121 :EFAER 1g38A 176 :LLREF T0295 127 :LANV 1g38A 181 :LARE T0295 131 :GDSNYSRLTINVK 1g38A 197 :PQKKVSAVVIRFQ T0295 144 :LFCKVTKV 1g38A 216 :SLWDTQES T0295 162 :PPKVDSVIVKLIPK 1g38A 224 :ESGFTPILWAEYPH T0295 176 :ESSFLTNFDEWDNLL 1g38A 240 :GEIIRFETEETRKLE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1285 Number of alignments=127 # 1g38A read from 1g38A/merged-good-all-a2m # found chain 1g38A in template set T0295 4 :KNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1g38A 23 :TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHG T0295 44 :KVITIDIDSR 1g38A 66 :RFVGVEIDPK T0295 66 :GY 1g38A 78 :DL T0295 68 :NNLEVYEGDAIKTVFPK 1g38A 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPY 1g38A 99 :FDLILGNPPY T0295 95 :KISSPLIFKLISHRPLFKC 1g38A 120 :HVFKAVKDLYKKAFSTWKG T0295 114 :AVLM 1g38A 157 :GGVL T0295 123 :AERMLAN 1g38A 177 :LREFLAR T0295 130 :VGDSNYSRLTINVK 1g38A 196 :FPQKKVSAVVIRFQ T0295 144 :LFCKVTKVCNVNRSSFNPP 1g38A 225 :SGFTPILWAEYPHWEGEII T0295 163 :PKVDS 1g38A 362 :EGVRL T0295 210 :VLNMLEHNYKN 1g38A 367 :DPSSLVQWLNS T0295 235 :KKYCLDVLEHL 1g38A 378 :EAMQKHVRTLY Number of specific fragments extracted= 13 number of extra gaps= 0 total=1298 Number of alignments=128 # 1g38A read from 1g38A/merged-good-all-a2m # found chain 1g38A in template set T0295 5 :NPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1g38A 24 :PPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREA T0295 42 :AKKVITIDIDSR 1g38A 64 :GYRFVGVEIDPK T0295 66 :GY 1g38A 78 :DL T0295 68 :NNLEVYEGDAIKTVFPK 1g38A 81 :PWAEGILADFLLWEPGE T0295 85 :FDVCTANIPYK 1g38A 99 :FDLILGNPPYG T0295 96 :ISSPLIFKLISHRPLFKC 1g38A 121 :VFKAVKDLYKKAFSTWKG T0295 114 :AVLMFQKEFAERMLAN 1g38A 141 :NLYGAFLEKAVRLLKP T0295 147 :KVTKVCNVNRSSF 1g38A 157 :GGVLVFVVPATWL T0295 160 :NPPPKVDSVIVKLIPKES 1g38A 196 :FPQKKVSAVVIRFQKSGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1307 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i4wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i4wA expands to /projects/compbio/data/pdb/1i4w.pdb.gz 1i4wA:# T0295 read from 1i4wA/merged-good-all-a2m # 1i4wA read from 1i4wA/merged-good-all-a2m # adding 1i4wA to template set # found chain 1i4wA in template set T0295 2 :LLKNPGILDKIIYAAKIK 1i4wA 22 :YLWNPTVYNKIFDKLDLT T0295 20 :SSDIVLEIGCGTGNLTVKLLPLA 1i4wA 46 :EELKVLDLYPGVGIQSAIFYNKY T0295 43 :KKVITIDIDSRMISEVKKRCL 1i4wA 71 :RQYSLLEKRSSLYKFLNAKFE T0295 66 :GYN 1i4wA 92 :GSP T0295 70 :LEVYEGDAIK 1i4wA 95 :LQILKRDPYD T0295 86 :DVCTANIPYKISSPLIFKLIS 1i4wA 132 :FLTVANVTGEGSEGLIMQWLS T0295 107 :HRPLFKCAVLMFQ 1i4wA 160 :LYRFGKVKMLLWM T0295 120 :KEFAERMLANVGDSNYSRLTINVKLFCKVTKVCNVNRSSF 1i4wA 174 :STTARKLLARPGMHSRSKCSVVREAFTDTKLIAISDANEL T0295 160 :NPPPKVDSVIVKLIPKE 1i4wA 235 :WPTKGKPIALVEMDPID T0295 179 :FLTNFDEWDNLLRICFSR 1i4wA 252 :FDFDVDNWDYVTRHLMIL T0295 197 :KRKTLHAIFKRNAV 1i4wA 281 :LGHGGQQYFNSRIT T0295 211 :LNM 1i4wA 296 :KDL T0295 225 :NKQVPVNFPFKKYCLDVLEHLDMCE 1i4wA 299 :LKKCPIDLTNDEFIYLTKLFMEWPF Number of specific fragments extracted= 13 number of extra gaps= 0 total=1320 Number of alignments=130 # 1i4wA read from 1i4wA/merged-good-all-a2m # found chain 1i4wA in template set T0295 2 :LLKNPGILDKIIYAAK 1i4wA 22 :YLWNPTVYNKIFDKLD T0295 20 :SSDIVLEIGCGTGNLTVKLLPLAK 1i4wA 46 :EELKVLDLYPGVGIQSAIFYNKYC T0295 44 :KVITIDIDSRMISEVKKRCLY 1i4wA 72 :QYSLLEKRSSLYKFLNAKFEG T0295 68 :NNLEVYEGDAIKT 1i4wA 93 :SPLQILKRDPYDW T0295 83 :PK 1i4wA 126 :DH T0295 85 :F 1i4wA 132 :F T0295 87 :VCTANIPY 1i4wA 133 :LTVANVTG T0295 95 :KISSPLIFKLISHRPLFKCAVLMFQ 1i4wA 145 :GLIMQWLSCIGNKNWLYRFGKVKML T0295 120 :KEFAERMLANVGDSNYSRLTINVKLFCKVTKVCNVNRS 1i4wA 174 :STTARKLLARPGMHSRSKCSVVREAFTDTKLIAISDAN T0295 158 :SFNPPPKVDSVIVKLIPK 1i4wA 233 :EIWPTKGKPIALVEMDPI T0295 178 :SFLTNFDEWDNLLRICFSRKR 1i4wA 251 :DFDFDVDNWDYVTRHLMILKR T0295 211 :LNMLEHNYKNWCTLNKQ 1i4wA 282 :GHGGQQYFNSRITDKDL T0295 228 :VPVNFPFKKYCLDVLEHLDM 1i4wA 302 :CPIDLTNDEFIYLTKLFMEW Number of specific fragments extracted= 13 number of extra gaps= 0 total=1333 Number of alignments=131 # 1i4wA read from 1i4wA/merged-good-all-a2m # found chain 1i4wA in template set Warning: unaligning (T0295)R251 because last residue in template chain is (1i4wA)P325 T0295 2 :LLKNPGILDKIIYAAKIK 1i4wA 22 :YLWNPTVYNKIFDKLDLT T0295 20 :SSDIVLEIGCGTGNLTVKLLPL 1i4wA 46 :EELKVLDLYPGVGIQSAIFYNK T0295 42 :AKKVITIDIDSRMISEVKKRCL 1i4wA 70 :PRQYSLLEKRSSLYKFLNAKFE T0295 66 :G 1i4wA 92 :G T0295 68 :NNLEVYEGDAIK 1i4wA 93 :SPLQILKRDPYD T0295 88 :CTANIPYKISSPLIFKLIS 1i4wA 134 :TVANVTGEGSEGLIMQWLS T0295 107 :HRPLFKCAVLMFQKEFAERMLANVGDSNYS 1i4wA 161 :YRFGKVKMLLWMPSTTARKLLARPGMHSRS T0295 146 :CKVTKVCNVNRSSF 1i4wA 200 :TDTKLIAISDANEL T0295 160 :NPPPKVDSVIVKLIPKESS 1i4wA 235 :WPTKGKPIALVEMDPIDFD T0295 181 :TNFDEWDNLLRICFSRKRKTLHAIFKRN 1i4wA 254 :FDVDNWDYVTRHLMILKRTPLNTVMDSL T0295 210 :V 1i4wA 283 :H T0295 215 :EHNYKNWCTLN 1i4wA 286 :QQYFNSRITDK T0295 226 :KQVPVNFPFKKYCLDVLEHLDMCEK 1i4wA 300 :KKCPIDLTNDEFIYLTKLFMEWPFK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1346 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yub/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yub expands to /projects/compbio/data/pdb/1yub.pdb.gz 1yub:Warning: there is no chain 1yub will retry with 1yubA # T0295 read from 1yub/merged-good-all-a2m # 1yub read from 1yub/merged-good-all-a2m # adding 1yub to template set # found chain 1yub in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDS 1yub 10 :NFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDS T0295 64 :YEGY 1yub 70 :KLKL T0295 68 :NNLEVYEGDAIKTVFPK 1yub 75 :TRVTLIHQDILQFQFPN T0295 85 :FDVCTANIPYKISSPLIFKLISHRP 1yub 94 :RYKIVGNIPYHLSTQIIKKVVFESR T0295 111 :FKCAVLMFQKEFAERMLANV 1yub 119 :ASDIYLIVEEGFYKRTLDIH T0295 136 :SR 1yub 139 :RT T0295 145 :FCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESS 1yub 148 :QVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTD T0295 179 :FLTNFDEWDNLLRICFSRKRKTL 1yub 183 :PDKYWKLYTYFVSKWVNREYRQL T0295 209 :AVLNMLEHNYKNWCTLN 1yub 206 :FTKNQFHQAMKHAKVNN T0295 229 :PVNFPFKKYCLDVLEHLDMC 1yub 223 :LSTITYEQVLSIFNSYLLFN Number of specific fragments extracted= 10 number of extra gaps= 0 total=1356 Number of alignments=133 # 1yub read from 1yub/merged-good-all-a2m # found chain 1yub in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDS 1yub 10 :NFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDS T0295 64 :YEGY 1yub 70 :KLKL T0295 68 :NNLEVYEGDAIKTVFPK 1yub 75 :TRVTLIHQDILQFQFPN T0295 85 :FDVCTANIPYKISSPLIFKLISHR 1yub 94 :RYKIVGNIPYHLSTQIIKKVVFES T0295 110 :LFKCAVLMFQKEFAERML 1yub 118 :RASDIYLIVEEGFYKRTL T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKE 1yub 136 :DIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHT T0295 177 :SSFLTNFDEWDNLLRICFSRKRKT 1yub 181 :DVPDKYWKLYTYFVSKWVNREYRQ T0295 208 :NAVLNMLEHNYKNWCTLN 1yub 205 :LFTKNQFHQAMKHAKVNN T0295 229 :PVNFPFKKYCLDVLEHLDM 1yub 223 :LSTITYEQVLSIFNSYLLF Number of specific fragments extracted= 9 number of extra gaps= 0 total=1365 Number of alignments=134 # 1yub read from 1yub/merged-good-all-a2m # found chain 1yub in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDID 1yub 10 :NFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELD T0295 64 :YEG 1yub 72 :KLN T0295 68 :NNLEVYEGDAIKTVFPK 1yub 75 :TRVTLIHQDILQFQFPN T0295 85 :FDVCTANIPYKISSPLIFKLISH 1yub 94 :RYKIVGNIPYHLSTQIIKKVVFE T0295 109 :PLFKCAVLMFQKEFAERMLANVGD 1yub 117 :SRASDIYLIVEEGFYKRTLDIHRT T0295 148 :VTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFL 1yub 151 :IQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVP T0295 181 :TNFDEWDNLLRICFSRKRKTL 1yub 185 :KYWKLYTYFVSKWVNREYRQL T0295 209 :AVLNMLEHNYKNWCTLN 1yub 206 :FTKNQFHQAMKHAKVNN T0295 229 :PVNFPFKKYCLDVLEHLDMC 1yub 223 :LSTITYEQVLSIFNSYLLFN Number of specific fragments extracted= 9 number of extra gaps= 0 total=1374 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qamA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qamA expands to /projects/compbio/data/pdb/1qam.pdb.gz 1qamA:# T0295 read from 1qamA/merged-good-all-a2m # 1qamA read from 1qamA/merged-good-all-a2m # adding 1qamA to template set # found chain 1qamA in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRC 1qamA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKL T0295 65 :EGYNNLEVYEGDAIKTVFPK 1qamA 73 :VDHDNFQVLNKDILQFKFPK T0295 85 :FDVCTANIPYKISSPLIFKLI 1qamA 95 :SYKIFGNIPYNISTDIIRKIV T0295 107 :HRPLFKCAVLMFQKEFAERML 1qamA 116 :FDSIADEIYLIVEYGFAKRLL T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESS 1qamA 137 :NTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSR T0295 179 :FLTNFDEWDNLLRICFSRKRK 1qamA 184 :SHKDKQKYNYFVMKWVNKEYK T0295 207 :RNAVLNMLEHNYKNWCTLN 1qamA 205 :KIFTKNQFNNSLKHAGIDD T0295 229 :PVNFPFKKYCLDVLEHLDM 1qamA 224 :LNNISFEQFLSLFNSYKLF Number of specific fragments extracted= 8 number of extra gaps= 0 total=1382 Number of alignments=136 # 1qamA read from 1qamA/merged-good-all-a2m # found chain 1qamA in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYE 1qamA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDH T0295 68 :NNLEVYEGDAIKTVFPK 1qamA 76 :DNFQVLNKDILQFKFPK T0295 85 :F 1qamA 96 :Y T0295 87 :VCTANIPYKISSPLIFKLI 1qamA 97 :KIFGNIPYNISTDIIRKIV T0295 107 :HRPLFKCAVLMFQKEFAERML 1qamA 116 :FDSIADEIYLIVEYGFAKRLL T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKE 1qamA 137 :NTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKK T0295 177 :SSFLTNFDEWDNLLRICFSRKR 1qamA 182 :RISHKDKQKYNYFVMKWVNKEY T0295 206 :KRNAVLNMLEHNYKNWCTLNK 1qamA 204 :KKIFTKNQFNNSLKHAGIDDL T0295 230 :VNFPFKKYCLDVLEHLDM 1qamA 225 :NNISFEQFLSLFNSYKLF Number of specific fragments extracted= 9 number of extra gaps= 0 total=1391 Number of alignments=137 # 1qamA read from 1qamA/merged-good-all-a2m # found chain 1qamA in template set T0295 1 :HLLKNPGILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCL 1qamA 11 :NFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLV T0295 66 :GYNNLEVYEGDAIKTVFPK 1qamA 74 :DHDNFQVLNKDILQFKFPK T0295 85 :FDVCTANIPYKISSPLIFKLISH 1qamA 95 :SYKIFGNIPYNISTDIIRKIVFD T0295 109 :PLFKCAVLMFQKEFAERMLANVGD 1qamA 118 :SIADEIYLIVEYGFAKRLLNTKRS T0295 146 :CKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFL 1qamA 150 :VDISILSMVPREYFHPKPKVNSSLIRLNRKKSRIS T0295 181 :TNFDEWDNLLRICFSRK 1qamA 186 :KDKQKYNYFVMKWVNKE T0295 205 :FKRNAVLNMLEHNYKNWCTLNK 1qamA 203 :YKKIFTKNQFNNSLKHAGIDDL T0295 230 :VNFPFKKYCLDVLEHLDM 1qamA 225 :NNISFEQFLSLFNSYKLF Number of specific fragments extracted= 8 number of extra gaps= 0 total=1399 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zq9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zq9A expands to /projects/compbio/data/pdb/1zq9.pdb.gz 1zq9A:# T0295 read from 1zq9A/merged-good-all-a2m # 1zq9A read from 1zq9A/merged-good-all-a2m # adding 1zq9A to template set # found chain 1zq9A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)V59 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)V59 Warning: unaligning (T0295)L70 because of BadResidue code BAD_PEPTIDE in next template residue (1zq9A)Q108 Warning: unaligning (T0295)E71 because of BadResidue code BAD_PEPTIDE at template residue (1zq9A)Q108 Warning: unaligning (T0295)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)G168 Warning: unaligning (T0295)G131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)G168 Warning: unaligning (T0295)D132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)D169 T0295 1 :HLLKNPGILDKIIYAAKIKSS 1zq9A 37 :HILKNPLIINSIIDKAALRPT T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1zq9A 60 :VLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPV T0295 68 :NN 1zq9A 105 :SK T0295 72 :VYEGDAIKTVFPKFDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQKEFAERMLAN 1zq9A 109 :VLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAK T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFLTNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNMLEHNYKNWC 1zq9A 170 :KLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHC T0295 223 :TLNKQVPVNFPFKKYCLDVLEHLDMCEKRSINLDENDFLKLLLEFNKKGIHFF 1zq9A 261 :VHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS Number of specific fragments extracted= 6 number of extra gaps= 3 total=1405 Number of alignments=139 # 1zq9A read from 1zq9A/merged-good-all-a2m # found chain 1zq9A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)V59 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)V59 Warning: unaligning (T0295)L70 because of BadResidue code BAD_PEPTIDE in next template residue (1zq9A)Q108 Warning: unaligning (T0295)E71 because of BadResidue code BAD_PEPTIDE at template residue (1zq9A)Q108 Warning: unaligning (T0295)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)G168 Warning: unaligning (T0295)G131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)G168 Warning: unaligning (T0295)D132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)D169 T0295 1 :HLLKNPGILDKIIYAAKIKSS 1zq9A 37 :HILKNPLIINSIIDKAALRPT T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1zq9A 60 :VLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPV T0295 68 :NN 1zq9A 105 :SK T0295 72 :VYEGDAIKTVFPKFDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQKEFAERMLAN 1zq9A 109 :VLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAK T0295 133 :SNYSRLTINVKLFCKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFLTNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNMLEHNYKNWC 1zq9A 170 :KLYCRLSINTQLLARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHC T0295 223 :TLNKQVPVNFPFKKYCLDVLEHLDMCEKRSINLDENDFLKLLLEFNKKGIHFF 1zq9A 261 :VHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHFS Number of specific fragments extracted= 6 number of extra gaps= 3 total=1411 Number of alignments=140 # 1zq9A read from 1zq9A/merged-good-all-a2m # found chain 1zq9A in template set Warning: unaligning (T0295)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)V59 Warning: unaligning (T0295)I23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)V59 Warning: unaligning (T0295)L70 because of BadResidue code BAD_PEPTIDE in next template residue (1zq9A)Q108 Warning: unaligning (T0295)E71 because of BadResidue code BAD_PEPTIDE at template residue (1zq9A)Q108 Warning: unaligning (T0295)V130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zq9A)G168 Warning: unaligning (T0295)G131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)G168 Warning: unaligning (T0295)D132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zq9A)D169 T0295 1 :HLLKNPGILDKIIYAAKIKSS 1zq9A 37 :HILKNPLIINSIIDKAALRPT T0295 24 :VLEIGCGTGNLTVKLLPLAKKVITIDIDSRMISEVKKRCLYEGY 1zq9A 60 :VLEVGPGTGNMTVKLLEKAKKVVACELDPRLVAELHKRVQGTPV T0295 68 :NN 1zq9A 105 :SK T0295 72 :VYEGDAIKTVFPKFDVCTANIPYKISSPLIFKLISHRPLFKCAVLMFQKEFAERMLAN 1zq9A 109 :VLVGDVLKTDLPFFDTCVANLPYQISSPFVFKLLLHRPFFRCAILMFQREFALRLVAK T0295 133 :SNYS 1zq9A 170 :KLYC T0295 146 :CKVTKVCNVNRSSFNPPPKVDSVIVKLIPKESSFLTNFDEWDNLLRICFSRKRKTLHAIFKRNAVLNMLEHNYKNWC 1zq9A 183 :ARVDHLMKVGKNNFRPPPKVESSVVRIEPKNPPPPINFQEWDGLVRITFVRKNKTLSAAFKSSAVQQLLEKNYRIHC T0295 223 :TLNKQVPVNFPFKKYCLDVLEHLDMCEKRSINLDENDFLKLLLEFNKKGIHF 1zq9A 261 :VHNIIIPEDFSIADKIQQILTSTGFSDKRARSMDIDDFIRLLHGFNAEGIHF Number of specific fragments extracted= 7 number of extra gaps= 3 total=1418 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kr5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kr5A expands to /projects/compbio/data/pdb/1kr5.pdb.gz 1kr5A:Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1kr5A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1kr5A # T0295 read from 1kr5A/merged-good-all-a2m # 1kr5A read from 1kr5A/merged-good-all-a2m # adding 1kr5A to template set # found chain 1kr5A in template set T0295 3 :LKNPGILDKIIYAAK 1kr5A 58 :ISAPHMHAYALELLF T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLA 1kr5A 75 :LHEGAKALDVGSGSGILTACFARMV T0295 43 :KKVITIDIDSRMISEVKKRCLYE 1kr5A 103 :GKVIGIDHIKELVDDSVNNVRKD T0295 66 :G 1kr5A 132 :S T0295 68 :NNLEVYEGDAIKTVFPK 1kr5A 133 :GRVQLVVGDGRMGYAEE T0295 85 :FDVCTANIPYKISSP 1kr5A 152 :YDAIHVGAAAPVVPQ T0295 106 :SHRPLFKCAVLMFQK 1kr5A 167 :ALIDQLKPGGRLILP T0295 127 :LANVGDS 1kr5A 182 :VGPAGGN T0295 140 :INVKLF 1kr5A 189 :QMLEQY T0295 146 :CKVTKVCNVN 1kr5A 202 :IKMKPLMGVI T0295 177 :SSFLTNFDEW 1kr5A 212 :YVPLTDKEKQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=1429 Number of alignments=142 # 1kr5A read from 1kr5A/merged-good-all-a2m # found chain 1kr5A in template set T0295 3 :LKNPGILDKIIYAAK 1kr5A 58 :ISAPHMHAYALELLF T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1kr5A 75 :LHEGAKALDVGSGSGILTACFARMVG T0295 44 :KVITIDIDSRMISEVKKRCL 1kr5A 104 :KVIGIDHIKELVDDSVNNVR T0295 64 :YE 1kr5A 131 :SS T0295 68 :NNLEVYEGDAIKTVFPK 1kr5A 133 :GRVQLVVGDGRMGYAEE T0295 85 :FDVCTANIPYKISSPL 1kr5A 152 :YDAIHVGAAAPVVPQA T0295 107 :HRPLFKCAVLMFQKE 1kr5A 168 :LIDQLKPGGRLILPV T0295 128 :A 1kr5A 183 :G T0295 133 :SNYSRLTINVKLF 1kr5A 184 :PAGGNQMLEQYDK T0295 146 :CKVTKVCNVNRSSF 1kr5A 202 :IKMKPLMGVIYVPL T0295 181 :TNFDE 1kr5A 216 :TDKEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=1440 Number of alignments=143 # 1kr5A read from 1kr5A/merged-good-all-a2m # found chain 1kr5A in template set T0295 3 :LKNPGILDKIIYAAK 1kr5A 58 :ISAPHMHAYALELLF T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLA 1kr5A 75 :LHEGAKALDVGSGSGILTACFARMV T0295 43 :KKVITIDIDSRMISEVKKRCLY 1kr5A 103 :GKVIGIDHIKELVDDSVNNVRK T0295 65 :EG 1kr5A 131 :SS T0295 68 :NNLEVYEGDAIKTVFPK 1kr5A 133 :GRVQLVVGDGRMGYAEE T0295 85 :FDVCTANIPYKISSPLIFKLIS 1kr5A 152 :YDAIHVGAAAPVVPQALIDQLK T0295 128 :ANVGDS 1kr5A 183 :GPAGGN T0295 140 :INVKLF 1kr5A 189 :QMLEQY T0295 146 :CKVTKVCNV 1kr5A 202 :IKMKPLMGV T0295 176 :ESSFLTNFDEW 1kr5A 211 :IYVPLTDKEKQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=1450 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l1eA expands to /projects/compbio/data/pdb/1l1e.pdb.gz 1l1eA:# T0295 read from 1l1eA/merged-good-all-a2m # 1l1eA read from 1l1eA/merged-good-all-a2m # adding 1l1eA to template set # found chain 1l1eA in template set Warning: unaligning (T0295)S178 because of BadResidue code BAD_PEPTIDE in next template residue (1l1eA)E179 Warning: unaligning (T0295)L180 because of BadResidue code BAD_PEPTIDE in next template residue (1l1eA)H186 Warning: unaligning (T0295)T181 because of BadResidue code BAD_PEPTIDE at template residue (1l1eA)H186 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLA 1l1eA 51 :AKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKY T0295 43 :KKVITIDIDSRMISEVKKRCLYEGYNN 1l1eA 88 :VNVVGLTLSENQAGHVQKMFDQMDTPR T0295 70 :LEVYEGDAIKTV 1l1eA 116 :RRVLLEGWEKFD T0295 84 :K 1l1eA 128 :E T0295 85 :FDVCTANIPYKISS 1l1eA 130 :VDRIVSIGAFEHFG T0295 99 :PLIFKLIS 1l1eA 145 :QRYHHFFE T0295 107 :HRPLFKCAVLMFQ 1l1eA 154 :THRTLPADGKMLL T0295 167 :SVIVKLIPKES 1l1eA 167 :HTIVRPTFKEG T0295 179 :F 1l1eA 184 :L T0295 182 :NFD 1l1eA 187 :ELV T0295 188 :NLLRICFSR 1l1eA 190 :HFTKFILAE T0295 208 :NAVLNMLEHNYKNWCTLNK 1l1eA 205 :LPSIPTVHEYAEKVGFRVT T0295 234 :FKKYCLDVLEHLDMCEKRSIN 1l1eA 229 :QLHYARTLDMWATALEANKDQ T0295 255 :LDENDFLKLLLE 1l1eA 253 :IQSQTVYDRYMK Number of specific fragments extracted= 14 number of extra gaps= 2 total=1464 Number of alignments=145 # 1l1eA read from 1l1eA/merged-good-all-a2m # found chain 1l1eA in template set Warning: unaligning (T0295)R156 because of BadResidue code BAD_PEPTIDE in next template residue (1l1eA)E179 Warning: unaligning (T0295)S157 because of BadResidue code BAD_PEPTIDE at template residue (1l1eA)E179 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPLAK 1l1eA 51 :AKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYD T0295 44 :KVITIDIDSRMISEVKKRCLYEGY 1l1eA 89 :NVVGLTLSENQAGHVQKMFDQMDT T0295 68 :NNLEVYEGDAIKTV 1l1eA 114 :RSRRVLLEGWEKFD T0295 83 :PKFDVCTANIPYKISSP 1l1eA 128 :EPVDRIVSIGAFEHFGH T0295 100 :LIFKLISH 1l1eA 146 :RYHHFFEV T0295 108 :RPLFKCAVLMFQ 1l1eA 155 :HRTLPADGKMLL T0295 145 :FCKVTKVCNVN 1l1eA 167 :HTIVRPTFKEG T0295 158 :SFNPP 1l1eA 180 :KGLTL T0295 163 :PKVDSVIVKLI 1l1eA 218 :VGFRVTAVQSL T0295 187 :DNLLRICFSRKRKTLHA 1l1eA 229 :QLHYARTLDMWATALEA T0295 204 :IFKRNAVLNML 1l1eA 249 :QAIAIQSQTVY T0295 235 :KKYCLDVLE 1l1eA 260 :DRYMKYLTG Number of specific fragments extracted= 12 number of extra gaps= 1 total=1476 Number of alignments=146 # 1l1eA read from 1l1eA/merged-good-all-a2m # found chain 1l1eA in template set Warning: unaligning (T0295)T181 because of BadResidue code BAD_PEPTIDE at template residue (1l1eA)H186 T0295 7 :GILDKIIYAAKIKSSDIVLEIGCGTGNLTVKLLPL 1l1eA 51 :AKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEK T0295 42 :AKKVITIDIDSRMISEVKKRCLYEGYNN 1l1eA 87 :DVNVVGLTLSENQAGHVQKMFDQMDTPR T0295 70 :LEVYEGDAIKTVF 1l1eA 116 :RRVLLEGWEKFDE T0295 84 :KFDVCTANIPY 1l1eA 129 :PVDRIVSIGAF T0295 109 :PLFKCAVLMFQKEFAERMLAN 1l1eA 140 :EHFGHQRYHHFFEVTHRTLPA T0295 164 :KVDSVIVKLIPKESSFL 1l1eA 161 :DGKMLLHTIVRPTFKEG T0295 182 :NFDEWDNLLRICF 1l1eA 187 :ELVHFTKFILAEI T0295 209 :AV 1l1eA 200 :FP T0295 211 :LNMLEHNYKNWCTLNK 1l1eA 208 :IPTVHEYAEKVGFRVT T0295 234 :FKKYCLDVLEHLDMCEKRSINLDENDFLKLLLE 1l1eA 236 :LDMWATALEANKDQAIAIQSQTVYDRYMKYLTG Number of specific fragments extracted= 10 number of extra gaps= 1 total=1486 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wy7A expands to /projects/compbio/data/pdb/1wy7.pdb.gz 1wy7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0295 read from 1wy7A/merged-good-all-a2m # 1wy7A read from 1wy7A/merged-good-all-a2m # adding 1wy7A to template set # found chain 1wy7A in template set Warning: unaligning (T0295)N155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy7A)H186 Warning: unaligning (T0295)P161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy7A)H186 Warning: unaligning (T0295)P162 because of BadResidue code BAD_PEPTIDE in next template residue (1wy7A)K188 Warning: unaligning (T0295)P163 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K188 Warning: unaligning (T0295)K164 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K189 T0295 2 :LLKNPGILDKIIYAA 1wy7A 28 :YRTPGNAASELLWLA T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPL 1wy7A 46 :GDIEGKVVADLGAGTGVLSYGALLL T0295 42 :AKKVITIDIDSRMISEVKKRCLYEG 1wy7A 72 :AKEVICVEVDKEAVDVLIENLGEFK T0295 68 :NNLEVYEGDAIKT 1wy7A 97 :GKFKVFIGDVSEF T0295 83 :PK 1wy7A 110 :NS T0295 85 :FDVCTANIPYKISS 1wy7A 113 :VDIVIMNPPFGSQR T0295 99 :PLIFKLISHRP 1wy7A 132 :PFLLKAFEISD T0295 116 :LMFQ 1wy7A 143 :VVYS T0295 120 :KEFAERMLANVG 1wy7A 155 :RRFIEKFSWEHG T0295 142 :VKLFCKVTKVCNV 1wy7A 167 :FVVTHRLTTKIEI T0295 165 :VDSVIVKL 1wy7A 190 :LERITVDI Number of specific fragments extracted= 11 number of extra gaps= 0 total=1497 Number of alignments=148 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set Warning: unaligning (T0295)N155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy7A)H186 Warning: unaligning (T0295)P161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy7A)H186 Warning: unaligning (T0295)P162 because of BadResidue code BAD_PEPTIDE in next template residue (1wy7A)K188 Warning: unaligning (T0295)P163 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K188 Warning: unaligning (T0295)K164 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K189 Warning: unaligning (T0295)E176 because last residue in template chain is (1wy7A)I204 T0295 2 :LLKNPGILDKIIYAA 1wy7A 28 :YRTPGNAASELLWLA T0295 18 :IKSSDIVLEIGCGTGNLTVKLLPLAK 1wy7A 47 :DIEGKVVADLGAGTGVLSYGALLLGA T0295 44 :KVITIDIDSRMISEVKKRCLYEG 1wy7A 74 :EVICVEVDKEAVDVLIENLGEFK T0295 68 :NNLEVYEGDAIKTV 1wy7A 97 :GKFKVFIGDVSEFN T0295 83 :PKFDVCTANIPY 1wy7A 111 :SRVDIVIMNPPF T0295 95 :KISSPLIFKLISHRPL 1wy7A 128 :HADRPFLLKAFEISDV T0295 115 :VLM 1wy7A 144 :VYS T0295 118 :FQKEF 1wy7A 150 :AKPEV T0295 123 :AERMLANVG 1wy7A 158 :IEKFSWEHG T0295 142 :VKLFCKVTKVCNV 1wy7A 167 :FVVTHRLTTKIEI T0295 165 :VDSV 1wy7A 190 :LERI T0295 169 :IVKLIPK 1wy7A 197 :IYRFSKV Number of specific fragments extracted= 12 number of extra gaps= 0 total=1509 Number of alignments=149 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set Warning: unaligning (T0295)N155 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wy7A)H186 Warning: unaligning (T0295)P161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wy7A)H186 Warning: unaligning (T0295)P162 because of BadResidue code BAD_PEPTIDE in next template residue (1wy7A)K188 Warning: unaligning (T0295)P163 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K188 Warning: unaligning (T0295)K164 because of BadResidue code BAD_PEPTIDE at template residue (1wy7A)K189 Warning: unaligning (T0295)E176 because last residue in template chain is (1wy7A)I204 T0295 5 :NPGILDKIIYAA 1wy7A 31 :PGNAASELLWLA T0295 17 :KIKSSDIVLEIGCGTGNLTVKLLPL 1wy7A 46 :GDIEGKVVADLGAGTGVLSYGALLL T0295 42 :AKKVITIDIDSRMISEVKKRCLYEG 1wy7A 72 :AKEVICVEVDKEAVDVLIENLGEFK T0295 68 :NNLEVYEGDAIKTV 1wy7A 97 :GKFKVFIGDVSEFN T0295 83 :PKFDVCTANIPYKIS 1wy7A 111 :SRVDIVIMNPPFGSQ T0295 98 :SPLIFKLISHR 1wy7A 131 :RPFLLKAFEIS T0295 117 :MFQKEFAERMLANVG 1wy7A 152 :PEVRRFIEKFSWEHG T0295 136 :SRLTINVK 1wy7A 167 :FVVTHRLT T0295 150 :KVCNV 1wy7A 175 :TKIEI T0295 165 :VD 1wy7A 190 :LE T0295 167 :SVIVKLIPK 1wy7A 195 :VDIYRFSKV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1520 Number of alignments=150 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 150 Adding 4632 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -498.8788, CN propb: -498.8788 weights: 0.2262 constraints: 818 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 818 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 818 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 3814 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 3814 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 4632 # command: