parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0356/ # command:# Making conformation for sequence T0356 numbered 1 through 505 Created new target T0356 from T0356.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0356/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0356//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0356/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0356//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0356/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0356/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0356/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e9rA expands to /projects/compbio/data/pdb/1e9r.pdb.gz 1e9rA:# T0356 read from 1e9rA/merged-good-all-a2m # 1e9rA read from 1e9rA/merged-good-all-a2m # adding 1e9rA to template set # found chain 1e9rA in template set T0356 28 :PVDPHLEITEIADRTLR 1e9rA 133 :GTGKSVLLRELAYTGLL # choosing archetypes in rotamer library T0356 393 :MYTKFVIVCDDD 1e9rA 150 :RGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTP 1e9rA 163 :MLSKFGRDKDIILNPYDQ T0356 435 :IDYLDFASPVSG 1e9rA 185 :WSFFNEIRNDYD T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1e9rA read from 1e9rA/merged-good-all-a2m # found chain 1e9rA in template set T0356 341 :VPILQKQFPE 1e9rA 96 :GGKLKRMTRE T0356 351 :IVDFYLPPEGCSYRLAV 1e9rA 112 :VAGVPMPRDAEPRHLLV T0356 374 :YAGHAKRVMMGVWSFLRQFMYTKFVIVCDDD 1e9rA 131 :ATGTGKSVLLRELAYTGLLRGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTPIDY 1e9rA 163 :MLSKFGRDKDIILNPYDQRTK T0356 438 :LDFASPVSG 1e9rA 185 :WSFFNEIRN T0356 460 :PGETQR 1e9rA 194 :DYDWQR T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 7 number of extra gaps= 0 total=12 Number of alignments=2 # 1e9rA read from 1e9rA/merged-good-all-a2m # found chain 1e9rA in template set T0356 313 :EDAIYHSTYTGRPPDEP 1e9rA 106 :KAKQVTVAGVPMPRDAE T0356 349 :PEIVDFYLPPEGC 1e9rA 123 :PRHLLVNGATGTG T0356 375 :AGHAKRVMMGVWS 1e9rA 137 :SVLLRELAYTGLL T0356 393 :MYTKFVIVCDDD 1e9rA 150 :RGDRMVIVDPNG T0356 417 :ITTRMDPARDTVLVENTPIDYLDFASPVSG 1e9rA 163 :MLSKFGRDKDIILNPYDQRTKGWSFFNEIR T0356 470 :PIKKDPDVVAHID 1e9rA 206 :PRGKTDEAEEWAS Number of specific fragments extracted= 6 number of extra gaps= 0 total=18 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fcr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0356 read from 2fcr/merged-good-all-a2m # 2fcr read from 2fcr/merged-good-all-a2m # found chain 2fcr in training set Warning: unaligning (T0356)E213 because of BadResidue code BAD_PEPTIDE in next template residue (2fcr)D84 Warning: unaligning (T0356)R214 because of BadResidue code BAD_PEPTIDE at template residue (2fcr)D84 T0356 50 :LLFE 2fcr 4 :IFFS T0356 78 :GQEDV 2fcr 8 :TSTGN T0356 85 :LREVGKLLA 2fcr 13 :TTEVADFIG T0356 109 :DKLPQF 2fcr 22 :KTLGAK T0356 119 :NMPTKRLR 2fcr 28 :ADAPIDVD T0356 137 :GDDVDLNRIPI 2fcr 38 :TDPQALKDYDL T0356 160 :TWGLTVTRGPHKERQNL 2fcr 49 :LFLGAPTWNTGADTERS T0356 196 :HRGGALDYQE 2fcr 66 :GTSWDEFLYD T0356 208 :A 2fcr 76 :K T0356 215 :FPVSVALGAD 2fcr 85 :LPVAIFGLGD T0356 234 :PVPDTL 2fcr 97 :GYPDNF T0356 240 :SEYAFAGLLRGTKTEVV 2fcr 105 :AIEEIHDCFAKQGAKPV T0356 275 :GYIEQ 2fcr 122 :GFSNP T0356 284 :PEGPYGDHTGYYNEV 2fcr 127 :DDYDYEESKSVRDGK T0356 315 :AIYHSTYTGRPPDEPA 2fcr 143 :LGLPLDMVNDQIPMEK T0356 336 :LNEVFVPILQKQ 2fcr 159 :RVAGWVEAVVSE Number of specific fragments extracted= 16 number of extra gaps= 1 total=34 Number of alignments=4 # 2fcr read from 2fcr/merged-good-all-a2m # found chain 2fcr in training set T0356 30 :DPHLEITEIADRTLRAGGPALLFENPKGYSM 2fcr 101 :NFCDAIEEIHDCFAKQGAKPVGFSNPDDYDY T0356 62 :VLCNLFGT 2fcr 145 :LPLDMVND T0356 79 :QEDV 2fcr 153 :QIPM T0356 83 :SALREVGK 2fcr 158 :KRVAGWVE T0356 91 :LLAF 2fcr 167 :VVSE Number of specific fragments extracted= 5 number of extra gaps= 0 total=39 Number of alignments=5 # 2fcr read from 2fcr/merged-good-all-a2m # found chain 2fcr in training set T0356 100 :PPKGFRDLFDKLPQFKQVLNMPTKRLRGA 2fcr 9 :STGNTTEVADFIGKTLGAKADAPIDVDDV T0356 137 :GDDVDLNRIP 2fcr 38 :TDPQALKDYD T0356 217 :V 2fcr 48 :L T0356 219 :VALG 2fcr 49 :LFLG T0356 256 :VKCISNDLEVP 2fcr 53 :APTWNTGADTE T0356 321 :YTGR 2fcr 64 :RSGT T0356 339 :VFVPILQKQFPEI 2fcr 68 :SWDEFLYDKLPEV T0356 393 :MYTKFVIVC 2fcr 85 :LPVAIFGLG T0356 402 :DDDVNARDWNDVIWAITTR 2fcr 98 :YPDNFCDAIEEIHDCFAKQ T0356 421 :MDPAR 2fcr 124 :SNPDD T0356 435 :IDYLDFASPVSGLGSKMGLDATNKWPGE 2fcr 129 :YDYEESKSVRDGKFLGLPLDMVNDQIPM T0356 474 :DPDVVAHIDAIWDELA 2fcr 157 :EKRVAGWVEAVVSETG Number of specific fragments extracted= 12 number of extra gaps= 0 total=51 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vheA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vheA expands to /projects/compbio/data/pdb/1vhe.pdb.gz 1vheA:Skipped atom 28, because occupancy 0.4 <= existing 0.600 in 1vheA Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 1vheA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 1vheA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 244, because occupancy 0.350 <= existing 0.650 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1294, because occupancy 0.500 <= existing 0.500 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2469, because occupancy 0.350 <= existing 0.650 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2471, because occupancy 0.350 <= existing 0.650 in 1vheA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2473, because occupancy 0.350 <= existing 0.650 in 1vheA Skipped atom 2760, because occupancy 0.350 <= existing 0.650 in 1vheA # T0356 read from 1vheA/merged-good-all-a2m # 1vheA read from 1vheA/merged-good-all-a2m # adding 1vheA to template set # found chain 1vheA in template set Warning: unaligning (T0356)P329 because of BadResidue code BAD_PEPTIDE in next template residue (1vheA)N183 Warning: unaligning (T0356)A330 because of BadResidue code BAD_PEPTIDE at template residue (1vheA)N183 T0356 79 :QE 1vheA 4 :LD T0356 83 :SALREVGKLLA 1vheA 6 :ETLTMLKDLTD T0356 97 :EPEPPKGFRDLFDKLPQFKQVLNMPTKRLRGAPC 1vheA 17 :AKGIPGNEREVRQVMKSYIEPFADEVTTDRLGSL T0356 163 :LTVTRGPHKERQ 1vheA 51 :IAKKTGAENGPK T0356 175 :NLGIYRQQLIGKNKLIMRWLSH 1vheA 71 :EVGFMVTQITDKGFIRFQTVGG T0356 208 :AAHPGER 1vheA 96 :QVMLAQR T0356 269 :AEIV 1vheA 103 :VTIV T0356 273 :LEGYI 1vheA 112 :ITGVI T0356 278 :EQGETAPE 1vheA 120 :PPHILSPE T0356 290 :DHTGYYNEVDSFPV 1vheA 164 :HFEFTVMNNEKFLL T0356 320 :T 1vheA 178 :A T0356 326 :PDE 1vheA 179 :KAW T0356 331 :VLGVALNEVFVPILQKQ 1vheA 184 :RIGCAIAIDVLRNLQNT T0356 348 :FP 1vheA 202 :HP T0356 351 :IVDFYLPPEGCSY 1vheA 206 :VYGVGTVQEEVGL T0356 376 :GHAKRVMMGV 1vheA 219 :RGAKTAAHTI T0356 394 :YTKFVIVCD 1vheA 229 :QPDIAFGVD T0356 427 :TVLVENTPIDYLDFASPVSGLGSKMG 1vheA 238 :VGIAGDTPGISEKEAQSKMGKGPQII T0356 471 :IKKDPDVVAHIDAIWDELAIF 1vheA 269 :MVSHKGLRDAVVATAEEAGIP Number of specific fragments extracted= 19 number of extra gaps= 1 total=70 Number of alignments=7 # 1vheA read from 1vheA/merged-good-all-a2m # found chain 1vheA in template set Warning: unaligning (T0356)P329 because of BadResidue code BAD_PEPTIDE in next template residue (1vheA)N183 Warning: unaligning (T0356)A330 because of BadResidue code BAD_PEPTIDE at template residue (1vheA)N183 T0356 80 :E 1vheA 5 :D T0356 83 :SALREVGKLLA 1vheA 6 :ETLTMLKDLTD T0356 97 :EPEPPKGFRDLFDKLPQFKQVLNMPTKRLR 1vheA 17 :AKGIPGNEREVRQVMKSYIEPFADEVTTDR T0356 161 :WGLTVTR 1vheA 47 :LGSLIAK T0356 168 :G 1vheA 55 :T T0356 169 :PHKERQ 1vheA 57 :AENGPK T0356 175 :NLGIYRQQLIGKNKLIMRWLSH 1vheA 71 :EVGFMVTQITDKGFIRFQTVGG T0356 263 :LE 1vheA 93 :WW T0356 267 :ASAEIVLEG 1vheA 99 :LAQRVTIVT T0356 288 :YGDHTGYYN 1vheA 109 :KGEITGVIG T0356 297 :EVDSF 1vheA 120 :PPHIL T0356 302 :PVFTVT 1vheA 138 :MFIDIG T0356 312 :REDAIYHSTYTGRPPDE 1vheA 157 :PGDMIVPHFEFTVMNNE T0356 331 :VLGVALNEVFVPILQKQ 1vheA 184 :RIGCAIAIDVLRNLQNT T0356 348 :FP 1vheA 202 :HP T0356 351 :IVDFYLPPEGCSYR 1vheA 206 :VYGVGTVQEEVGLR T0356 377 :HAKRVMMGV 1vheA 220 :GAKTAAHTI T0356 394 :YTKFVIVCD 1vheA 229 :QPDIAFGVD T0356 427 :TVLVENTPIDYLDFASPVSGLGSKMG 1vheA 238 :VGIAGDTPGISEKEAQSKMGKGPQII T0356 454 :DAT 1vheA 266 :DAS T0356 471 :IKKDPDVVAHIDAIWDELAIF 1vheA 269 :MVSHKGLRDAVVATAEEAGIP Number of specific fragments extracted= 21 number of extra gaps= 1 total=91 Number of alignments=8 # 1vheA read from 1vheA/merged-good-all-a2m # found chain 1vheA in template set Warning: unaligning (T0356)E80 because first residue in template chain is (1vheA)K3 Warning: unaligning (T0356)P329 because of BadResidue code BAD_PEPTIDE in next template residue (1vheA)N183 Warning: unaligning (T0356)A330 because of BadResidue code BAD_PEPTIDE at template residue (1vheA)N183 T0356 81 :DVSALREVGKLLAF 1vheA 4 :LDETLTMLKDLTDA T0356 98 :PEPPKGFRDLFDKLPQFKQVLNMPTKRLRGA 1vheA 18 :KGIPGNEREVRQVMKSYIEPFADEVTTDRLG T0356 161 :WGLTVTRGPHKE 1vheA 49 :SLIAKKTGAENG T0356 173 :RQNLGIYRQQLIGKNKLIMRWLSHRGGA 1vheA 69 :LDEVGFMVTQITDKGFIRFQTVGGWWAQ T0356 247 :LLRGTKTEVV 1vheA 97 :VMLAQRVTIV T0356 273 :LEGYI 1vheA 112 :ITGVI T0356 278 :EQGETAPEGP 1vheA 120 :PPHILSPEAR T0356 288 :YGD 1vheA 164 :HFE T0356 293 :GYYNEVDSFPVF 1vheA 167 :FTVMNNEKFLLA T0356 326 :PDE 1vheA 179 :KAW T0356 331 :VLGVALNEVFVPILQKQFPE 1vheA 184 :RIGCAIAIDVLRNLQNTDHP T0356 351 :IVDFYLPPEGCSY 1vheA 206 :VYGVGTVQEEVGL T0356 376 :GHAKRVMMGV 1vheA 219 :RGAKTAAHTI T0356 394 :YTKFVIVC 1vheA 229 :QPDIAFGV T0356 426 :DTVLVENTPIDYLDFASPVSGLGSKMG 1vheA 237 :DVGIAGDTPGISEKEAQSKMGKGPQII T0356 471 :IKKDPDVVAHIDAIWDELAI 1vheA 269 :MVSHKGLRDAVVATAEEAGI Number of specific fragments extracted= 16 number of extra gaps= 1 total=107 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0356 read from 1q7zA/merged-good-all-a2m # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0356 6 :YNDLRDFLTLLEQQG 1q7zA 125 :YENFRETVEIMVEEG T0356 29 :VDPHLEITEIADRTLRA 1q7zA 148 :FSDILELKAAVLAAREV T0356 46 :GGPALLFENP 1q7zA 167 :DVFLIAHMTF T0356 56 :KG 1q7zA 179 :KG T0356 58 :YSMPVLC 1q7zA 198 :LDIDALG T0356 65 :NLFGTPKRVA 1q7zA 206 :NCSLGPEEIL T0356 83 :SALREVGK 1q7zA 216 :PIFQELSQ T0356 158 :LITWGLTVTRGPHKERQ 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 185 :GKNKLI 1q7zA 241 :ENGKTV T0356 194 :LSHRGGALDYQEWCAAH 1q7zA 249 :LKPHDFAVHIDSYYELG T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 224 :DPAT 1q7zA 276 :TPEH T0356 241 :EYAFAGLLRGTKTEVVKCIS 1q7zA 280 :VKLFRKVLGNRKPLQRKKKR T0356 262 :DLEVPAS 1q7zA 300 :IFAVSSP T0356 307 :THITQREDAIYHSTYT 1q7zA 307 :SKLVTFDHFVVIGERI T0356 324 :RPPDEPAVLGVAL 1q7zA 323 :NPAGRKKLWAEMQ T0356 337 :NEVFVPILQKQFP 1q7zA 339 :EEIVIKEAKTQVE T0356 350 :EIVDFYLPPEGCS 1q7zA 355 :EVLDVNFGIESQI T0356 374 :YAGHAKRVMMGVWSFLRQF 1q7zA 368 :DVRYVEKIVQTLPYVSNVP T0356 398 :VIV 1q7zA 387 :LSL T0356 406 :NARDWNDVIWAITTRM 1q7zA 390 :DIQNVDLTERALRAYP T0356 426 :DTVLVENTPID 1q7zA 406 :GRSLFNSAKVD T0356 447 :LGSKMGLDATNK 1q7zA 430 :YGGTLIVLLMGK T0356 469 :RPIKKDP 1q7zA 442 :DVPKSFE T0356 476 :DVVAHIDAIWDELAIFN 1q7zA 452 :EYFEKALKILERHDFSD Number of specific fragments extracted= 25 number of extra gaps= 0 total=132 Number of alignments=10 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0356 9 :LRDFLTLLE 1q7zA 121 :FEEFYENFR T0356 37 :EIADRTLRAGGPALLFENP 1q7zA 130 :ETVEIMVEEGVDGIIFETF T0356 57 :GYSMPVLCNLFG 1q7zA 165 :SRDVFLIAHMTF T0356 69 :TPKRVAMGM 1q7zA 187 :DPANFAITF T0356 85 :LREVGKLLAF 1q7zA 211 :PEEILPIFQE T0356 114 :FKQ 1q7zA 221 :LSQ T0356 158 :LITWGLTVTRGPHKERQ 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 185 :GKNK 1q7zA 241 :ENGK T0356 194 :LSHRGGALDYQEWCAA 1q7zA 249 :LKPHDFAVHIDSYYEL T0356 212 :G 1q7zA 265 :G T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 224 :DPATI 1q7zA 276 :TPEHV T0356 242 :YAFAGLLRGTKTEVVKCIS 1q7zA 281 :KLFRKVLGNRKPLQRKKKR T0356 262 :DLEVPAS 1q7zA 300 :IFAVSSP T0356 307 :THITQREDAIYHSTYTG 1q7zA 307 :SKLVTFDHFVVIGERIN T0356 325 :PPDEPAVLGVAL 1q7zA 324 :PAGRKKLWAEMQ T0356 337 :NEVFVPILQKQ 1q7zA 339 :EEIVIKEAKTQ T0356 348 :FPEIVDFYLPPEGCSY 1q7zA 353 :GAEVLDVNFGIESQID T0356 375 :AGHAKRVMMGVWSFLRQF 1q7zA 369 :VRYVEKIVQTLPYVSNVP T0356 399 :IVCD 1q7zA 387 :LSLD T0356 407 :ARDWNDVIWAITTRM 1q7zA 391 :IQNVDLTERALRAYP T0356 426 :DTVLVENTPID 1q7zA 406 :GRSLFNSAKVD T0356 448 :GSKMGLDATN 1q7zA 431 :GGTLIVLLMG T0356 468 :GRPIKKDPDVVA 1q7zA 441 :KDVPKSFEERKE T0356 480 :HIDAIWDELAIFN 1q7zA 456 :KALKILERHDFSD Number of specific fragments extracted= 25 number of extra gaps= 0 total=157 Number of alignments=11 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0356 7 :NDLRDFLTLLEQQG 1q7zA 126 :ENFRETVEIMVEEG T0356 28 :PVDPHLEITEIADRTLR 1q7zA 147 :TFSDILELKAAVLAARE T0356 45 :AGGPALLFENP 1q7zA 166 :RDVFLIAHMTF T0356 56 :KGY 1q7zA 179 :KGR T0356 59 :SMPVL 1q7zA 199 :DIDAL T0356 64 :CNLFGTPKRVA 1q7zA 205 :INCSLGPEEIL T0356 83 :SALREVGK 1q7zA 216 :PIFQELSQ T0356 117 :VLNMPTKRLRGAPCQQK 1q7zA 224 :YTDKFLVVEPNAGKPIV T0356 170 :HKERQNL 1q7zA 241 :ENGKTVY T0356 194 :LSHRGGALDYQEWCAAH 1q7zA 249 :LKPHDFAVHIDSYYELG T0356 217 :VSVALGA 1q7zA 266 :VNIFGGC T0356 237 :DTLSEYAFAGLLRGTKTEVVKCISN 1q7zA 276 :TPEHVKLFRKVLGNRKPLQRKKKRI T0356 263 :LEVPASAEIV 1q7zA 301 :FAVSSPSKLV T0356 276 :YI 1q7zA 311 :TF T0356 313 :EDA 1q7zA 313 :DHF T0356 316 :IYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPE 1q7zA 318 :IGERINPAGRKKLWAEMQKGNEEIVIKEAKTQVEK T0356 351 :IVDFYLPPEGCS 1q7zA 356 :VLDVNFGIESQI T0356 374 :YAGHAKRVMMGVWSFLR 1q7zA 368 :DVRYVEKIVQTLPYVSN T0356 395 :TKFVIVC 1q7zA 385 :VPLSLDI T0356 409 :DWNDVIWAITT 1q7zA 393 :NVDLTERALRA T0356 433 :TPIDYLDFASPVSG 1q7zA 404 :YPGRSLFNSAKVDE T0356 447 :LGSKMGLDATNK 1q7zA 430 :YGGTLIVLLMGK T0356 469 :RPIKKDPDVVAHIDAIWDELAIFNNGK 1q7zA 442 :DVPKSFEERKEYFEKALKILERHDFSD Number of specific fragments extracted= 23 number of extra gaps= 0 total=180 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1innA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1innA expands to /projects/compbio/data/pdb/1inn.pdb.gz 1innA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0356 read from 1innA/merged-good-all-a2m # 1innA read from 1innA/merged-good-all-a2m # adding 1innA to template set # found chain 1innA in template set T0356 290 :DHTGYYNEVDSFPVFTVTHITQ 1innA 8 :ESFDLDHTKVKAPYVRLAGVKT T0356 312 :REDAIYHSTYTGRPPDE 1innA 32 :KGDQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLPPEGC 1innA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPMGCRT T0356 365 :LAVVTIKKQY 1innA 85 :GMYMAVIGEP T0356 375 :AGHAKRVMMGVWSFLRQF 1innA 96 :EQGVMKAFEAALKDTAGH T0356 402 :DDD 1innA 114 :DQP T0356 430 :VENTP 1innA 117 :IPGVS T0356 460 :PGE 1innA 122 :ELE T0356 467 :WGRPIKKD 1innA 125 :CGNYRDHD T0356 475 :PDVVAHIDAIWDE 1innA 134 :AAARQHARDVLDQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=190 Number of alignments=13 # 1innA read from 1innA/merged-good-all-a2m # found chain 1innA in template set Warning: unaligning (T0356)L498 because last residue in template chain is (1innA)L156 T0356 296 :NEVDSFPVFTVTHITQRED 1innA 14 :HTKVKAPYVRLAGVKTTPK T0356 315 :AIYHSTYTGRPPDE 1innA 35 :QISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAV 1innA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPMGCRTGMYMAV T0356 371 :KKQYAGHAKRVMMGVWSFLRQF 1innA 92 :GEPDEQGVMKAFEAALKDTAGH T0356 402 :DDD 1innA 114 :DQP T0356 430 :VENTP 1innA 117 :IPGVS T0356 460 :PGET 1innA 122 :ELEC T0356 468 :GRPIKKD 1innA 126 :GNYRDHD T0356 475 :PDVVAHIDAIWDE 1innA 134 :AAARQHARDVLDQ T0356 489 :AIFNNGKSA 1innA 147 :GLKVQETIL Number of specific fragments extracted= 10 number of extra gaps= 0 total=200 Number of alignments=14 # 1innA read from 1innA/merged-good-all-a2m # found chain 1innA in template set T0356 290 :DHTGYYNEVDSFPVFTVTHITQRE 1innA 8 :ESFDLDHTKVKAPYVRLAGVKTTP T0356 314 :DAIYHSTYTGRPPDE 1innA 34 :DQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAV 1innA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPMGCRTGMYMAV T0356 370 :IKKQYAGHAKRVMMGVWSFLRQ 1innA 91 :IGEPDEQGVMKAFEAALKDTAG T0356 435 :IDYLDFASPVSGLG 1innA 113 :HDQPIPGVSELECG T0356 460 :PGETQ 1innA 127 :NYRDH T0356 473 :KDPDVVAHIDAIWDE 1innA 132 :DLAAARQHARDVLDQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=207 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ejeA expands to /projects/compbio/data/pdb/1eje.pdb.gz 1ejeA:# T0356 read from 1ejeA/merged-good-all-a2m # 1ejeA read from 1ejeA/merged-good-all-a2m # adding 1ejeA to template set # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0356)Q181 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0356 162 :GLTVTRG 1ejeA 30 :VMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 182 :QLI 1ejeA 49 :TMP T0356 185 :GKNKLIMRWLSHRGGALDYQE 1ejeA 55 :DPPVVAFASAPDHHTARNIES T0356 208 :AA 1ejeA 76 :TH T0356 216 :PVSVALGAD 1ejeA 78 :EFVINITPA T0356 225 :PATILGAVTPVPDTLSEYAFA 1ejeA 89 :IERMWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPV 1ejeA 137 :RMFEVGDHNL T0356 304 :FTVTHITQREDAI 1ejeA 149 :GSVVSASVRSGAV Number of specific fragments extracted= 10 number of extra gaps= 1 total=217 Number of alignments=16 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 Warning: unaligning (T0356)Q181 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ejeA)F48 T0356 162 :GLTVTRG 1ejeA 30 :VMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 182 :QLI 1ejeA 49 :TMP T0356 185 :GKNKLIMRWLSHRGGALDYQEW 1ejeA 55 :DPPVVAFASAPDHHTARNIEST T0356 216 :PVSVALGA 1ejeA 78 :EFVINITP T0356 225 :PATILGAVTPVPDTLSEYAFA 1ejeA 89 :IERMWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPV 1ejeA 137 :RMFEVGDHNL T0356 304 :FTVTHITQREDAI 1ejeA 149 :GSVVSASVRSGAV Number of specific fragments extracted= 9 number of extra gaps= 1 total=226 Number of alignments=17 # 1ejeA read from 1ejeA/merged-good-all-a2m # found chain 1ejeA in template set Warning: unaligning (T0356)R180 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ejeA)F48 T0356 161 :WGLTVTRG 1ejeA 29 :TVMVTTVD T0356 170 :HKERQNLGIY 1ejeA 37 :EEGNINAAPF T0356 181 :QQLIG 1ejeA 49 :TMPVS T0356 186 :KNKLIMRWLSHRGGALDYQEW 1ejeA 56 :PPVVAFASAPDHHTARNIEST T0356 216 :PVSVALGADPAT 1ejeA 78 :EFVINITPADII T0356 228 :ILGAVTPVPDTLSEYAFA 1ejeA 92 :MWVTARDIPAGENELEAA T0356 252 :KTEVVKCISNDLEVPASAEIVLEGYIE 1ejeA 110 :GLAWTSSRRVKPPRIVEAPGHLECELL T0356 294 :YYNEVDSFPVFT 1ejeA 137 :RMFEVGDHNLIT T0356 306 :VTHITQREDAI 1ejeA 151 :VVSASVRSGAV Number of specific fragments extracted= 9 number of extra gaps= 1 total=235 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iyeA expands to /projects/compbio/data/pdb/1iye.pdb.gz 1iyeA:# T0356 read from 1iyeA/merged-good-all-a2m # 1iyeA read from 1iyeA/merged-good-all-a2m # adding 1iyeA to template set # found chain 1iyeA in template set T0356 19 :QGELKR 1iyeA 11 :NGEMVR T0356 26 :TLPVDPHLEITE 1iyeA 19 :DAKVHVMSHALH T0356 45 :A 1iyeA 31 :Y T0356 48 :PALLFENP 1iyeA 32 :GTSVFEGI T0356 56 :KGY 1iyeA 46 :KGP T0356 62 :VLCN 1iyeA 49 :VVFR T0356 70 :PKRVA 1iyeA 53 :HREHM T0356 86 :REVGKLLAFLKE 1iyeA 58 :QRLHDSAKIYRF T0356 99 :EPPKGFRDLFDKLPQFKQVLNMPTK 1iyeA 70 :PVSQSIDELMEACRDVIRKNNLTSA T0356 134 :IVS 1iyeA 95 :YIR T0356 162 :GLTVTRGPHK 1iyeA 98 :PLIFVGDVGM T0356 188 :KLIMRWLSHRGGA 1iyeA 118 :DVIIAAFPWGAYL T0356 206 :WCAAH 1iyeA 134 :ALEQG T0356 215 :FPVSVA 1iyeA 139 :IDAMVS T0356 233 :TPVPDTL 1iyeA 148 :RAAPNTI T0356 240 :SEYAFAGLLRGTKTEVVKCI 1iyeA 166 :SSLLVGSEARRHGYQEGIAL T0356 290 :DHTGYYNEVDSFPVFTVT 1iyeA 186 :DVNGYISEGAGENLFEVK T0356 313 :EDAIYH 1iyeA 204 :DGVLFT T0356 325 :PPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEG 1iyeA 210 :PPFTSSALPGITRDAIIKLAKELGIEVREQVLSRES T0356 362 :SYRLAVV 1iyeA 249 :ADEVFMS T0356 375 :AGHAKRVMMGVWSFL 1iyeA 278 :GPVTKRIQQAFFGLF Number of specific fragments extracted= 21 number of extra gaps= 0 total=256 Number of alignments=19 # 1iyeA read from 1iyeA/merged-good-all-a2m # found chain 1iyeA in template set T0356 19 :QGELKRI 1iyeA 11 :NGEMVRW T0356 26 :TLPVDPHLEITE 1iyeA 19 :DAKVHVMSHALH T0356 47 :GPALLFENPKG 1iyeA 37 :EGIRCYDSHKG T0356 61 :PVLCNL 1iyeA 48 :PVVFRH T0356 71 :K 1iyeA 54 :R T0356 83 :SALREVGKLLAFLK 1iyeA 55 :EHMQRLHDSAKIYR T0356 98 :PEPPKGFRDLFDKLPQFKQVLNMPT 1iyeA 69 :FPVSQSIDELMEACRDVIRKNNLTS T0356 176 :LGIYRQQLIGKN 1iyeA 94 :AYIRPLIFVGDV T0356 188 :KLIMRWLSHRGGA 1iyeA 118 :DVIIAAFPWGAYL T0356 205 :EWCAAH 1iyeA 133 :EALEQG T0356 215 :FPVSVA 1iyeA 139 :IDAMVS T0356 233 :TPVPDTLS 1iyeA 148 :RAAPNTIP T0356 241 :EYAFAGLLRGTKTEVVKCI 1iyeA 167 :SLLVGSEARRHGYQEGIAL T0356 290 :DHTGYYNEVDSFPVFTV 1iyeA 186 :DVNGYISEGAGENLFEV T0356 312 :REDAIYH 1iyeA 203 :KDGVLFT T0356 325 :PPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSY 1iyeA 210 :PPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLYL T0356 364 :RLA 1iyeA 253 :FMS T0356 367 :VVTIKK 1iyeA 261 :ITPVRS T0356 373 :QYAGHAKRVMMGVWSFLRQ 1iyeA 276 :RCGPVTKRIQQAFFGLFTG Number of specific fragments extracted= 19 number of extra gaps= 0 total=275 Number of alignments=20 # 1iyeA read from 1iyeA/merged-good-all-a2m # found chain 1iyeA in template set T0356 62 :VLC 1iyeA 49 :VVF T0356 81 :DVSALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMP 1iyeA 52 :RHREHMQRLHDSAKIYRFPVSQSIDELMEACRDVIRKNNLT T0356 156 :APLIT 1iyeA 93 :SAYIR T0356 162 :GLTVTRGPHK 1iyeA 98 :PLIFVGDVGM T0356 188 :KLIMRWLSHRGGA 1iyeA 118 :DVIIAAFPWGAYL T0356 207 :CAAHP 1iyeA 133 :EALEQ T0356 215 :FPVSVA 1iyeA 139 :IDAMVS T0356 233 :TPVPD 1iyeA 148 :RAAPN T0356 239 :LSEYAFAGLLRGTKTEVVKCI 1iyeA 165 :LSSLLVGSEARRHGYQEGIAL T0356 290 :DHTGYYNEVDSFPVFTV 1iyeA 186 :DVNGYISEGAGENLFEV T0356 312 :REDAIYH 1iyeA 203 :KDGVLFT T0356 325 :PPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPE 1iyeA 210 :PPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE T0356 360 :GCSYRLA 1iyeA 249 :ADEVFMS T0356 368 :VTIK 1iyeA 262 :TPVR T0356 372 :KQYAGHAKRVMMGVW 1iyeA 275 :GRCGPVTKRIQQAFF T0356 390 :RQF 1iyeA 290 :GLF Number of specific fragments extracted= 16 number of extra gaps= 0 total=291 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zczA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zczA expands to /projects/compbio/data/pdb/1zcz.pdb.gz 1zczA:Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2592, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2594, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2596, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2933, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2935, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2937, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2939, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 2941, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 3302, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 3304, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 3306, because occupancy 0.500 <= existing 0.500 in 1zczA Skipped atom 3308, because occupancy 0.500 <= existing 0.500 in 1zczA # T0356 read from 1zczA/merged-good-all-a2m # 1zczA read from 1zczA/merged-good-all-a2m # adding 1zczA to template set # found chain 1zczA in template set Warning: unaligning (T0356)G78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zczA)I126 Warning: unaligning (T0356)Q79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zczA)I126 Warning: unaligning (T0356)Y363 because of BadResidue code BAD_PEPTIDE in next template residue (1zczA)N356 Warning: unaligning (T0356)R364 because of BadResidue code BAD_PEPTIDE at template residue (1zczA)N356 T0356 35 :ITEIADRTLRA 1zczA 97 :GVALLRAAAKN T0356 46 :GG 1zczA 109 :KK T0356 64 :CNLFGTPKRVAMGM 1zczA 111 :VKPAFDMETLKLAI T0356 80 :EDVSALREVGKLLAF 1zczA 127 :DDEETRKYLAGMTFA T0356 104 :FRDLFDK 1zczA 142 :FTSVYDS T0356 114 :FKQV 1zczA 149 :IRAN T0356 119 :NMPTKRLRG 1zczA 166 :DLQLRYGEN T0356 128 :APCQQKIVSGDDVD 1zczA 184 :KPAFEILHEGKTIS T0356 144 :RIP 1zczA 213 :NLP T0356 160 :TWGLTVTR 1zczA 216 :RMGAVVVK T0356 172 :ERQNL 1zczA 224 :HQSPC T0356 192 :RWLSHRGGALDYQEWCAAHPGE 1zczA 229 :GAAIGEDKVEIVKKAIEADDES T0356 214 :RFPVSVA 1zczA 273 :YLEVIVA T0356 237 :DTLS 1zczA 280 :PSFT T0356 242 :YAFAGLLRGTKTEVVKCISNDLEV 1zczA 284 :QEAIEVLSKKKVRLLKPGDYASWA T0356 293 :GYYNEVD 1zczA 308 :GKMAFGS T0356 304 :F 1zczA 315 :L T0356 308 :HITQREDA 1zczA 316 :VLSERKYP T0356 318 :HSTYTGRPPDEPAVLGVALNEVFVP 1zczA 327 :FELVVGEPLSEKELEDLEFAYRVVE T0356 360 :GCS 1zczA 352 :GAK T0356 365 :LAVVTIKKQ 1zczA 357 :AVLIAKDGV T0356 375 :AGHAKRVMMGVWSFLRQFMYTK 1zczA 373 :QPSRKRAAWIATVMAGEKAKGA T0356 398 :VIVCDDDV 1zczA 395 :VAASDAFF T0356 408 :RDWNDVIWAITTR 1zczA 403 :PFPDSLEILAQAG T0356 449 :SK 1zczA 416 :VK T0356 452 :GLDATNKWPG 1zczA 418 :AVVAPLGSIR T0356 474 :DPDVVAHIDAI 1zczA 428 :DEEVIEKAREL Number of specific fragments extracted= 27 number of extra gaps= 2 total=318 Number of alignments=22 # 1zczA read from 1zczA/merged-good-all-a2m # found chain 1zczA in template set Warning: unaligning (T0356)G78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zczA)I126 Warning: unaligning (T0356)Q79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zczA)I126 Warning: unaligning (T0356)S362 because of BadResidue code BAD_PEPTIDE in next template residue (1zczA)N356 Warning: unaligning (T0356)Y363 because of BadResidue code BAD_PEPTIDE at template residue (1zczA)N356 T0356 34 :EITEIADRTLRA 1zczA 96 :GGVALLRAAAKN T0356 46 :G 1zczA 110 :K T0356 64 :CNLFGTPKRVAMGM 1zczA 111 :VKPAFDMETLKLAI T0356 80 :EDVSALREVGKLLAF 1zczA 127 :DDEETRKYLAGMTFA T0356 107 :LFDKLPQFKQVL 1zczA 142 :FTSVYDSIRANQ T0356 119 :NMPTKRLRG 1zczA 166 :DLQLRYGEN T0356 128 :APCQQKIVSGDDVD 1zczA 184 :KPAFEILHEGKTIS T0356 144 :RIPI 1zczA 213 :NLPR T0356 161 :WGLTVTR 1zczA 217 :MGAVVVK T0356 172 :ERQNLGI 1zczA 224 :HQSPCGA T0356 194 :LSHRGGALDYQEWCAAHPG 1zczA 231 :AIGEDKVEIVKKAIEADDE T0356 214 :RFPVSVA 1zczA 273 :YLEVIVA T0356 237 :DTLS 1zczA 280 :PSFT T0356 242 :YAFAGLLRGTKTEVVKCISNDLEV 1zczA 284 :QEAIEVLSKKKVRLLKPGDYASWA T0356 278 :EQG 1zczA 311 :AFG T0356 281 :ETAPEGPY 1zczA 320 :RKYPEGNF T0356 319 :STYTGRPPDEPAVLGVALNEVFVPILQ 1zczA 328 :ELVVGEPLSEKELEDLEFAYRVVEGAK T0356 364 :RLAV 1zczA 357 :AVLI T0356 368 :VTIKKQYAG 1zczA 367 :VGIGSGQPS T0356 378 :AKRVMMGVWSFLRQFMYTK 1zczA 376 :RKRAAWIATVMAGEKAKGA T0356 398 :VIVCDDD 1zczA 395 :VAASDAF T0356 407 :ARDWNDVIWAITTRMD 1zczA 402 :FPFPDSLEILAQAGVK T0356 452 :GLDA 1zczA 418 :AVVA T0356 468 :GRPIKKDPDVVAHIDAI 1zczA 422 :PLGSIRDEEVIEKAREL Number of specific fragments extracted= 24 number of extra gaps= 2 total=342 Number of alignments=23 # 1zczA read from 1zczA/merged-good-all-a2m # found chain 1zczA in template set Warning: unaligning (T0356)G78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zczA)I126 Warning: unaligning (T0356)Q79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zczA)I126 Warning: unaligning (T0356)G360 because of BadResidue code BAD_PEPTIDE in next template residue (1zczA)N356 Warning: unaligning (T0356)C361 because of BadResidue code BAD_PEPTIDE at template residue (1zczA)N356 T0356 35 :ITEIADRTLR 1zczA 97 :GVALLRAAAK T0356 45 :AG 1zczA 108 :WK T0356 64 :CNLFGTPKRVAMGM 1zczA 111 :VKPAFDMETLKLAI T0356 80 :EDVSALREVGKLLAF 1zczA 127 :DDEETRKYLAGMTFA T0356 104 :FRDLFDK 1zczA 142 :FTSVYDS T0356 114 :FKQVL 1zczA 149 :IRANQ T0356 119 :NMPTKRLR 1zczA 166 :DLQLRYGE T0356 127 :GAPCQQKIVSGDDVDL 1zczA 183 :GKPAFEILHEGKTISF T0356 144 :RIPI 1zczA 213 :NLPR T0356 161 :WGLTVTR 1zczA 217 :MGAVVVK T0356 172 :ERQNLGIY 1zczA 224 :HQSPCGAA T0356 195 :SHRGGALDYQEWCAAHPG 1zczA 232 :IGEDKVEIVKKAIEADDE T0356 213 :ERFPVSVA 1zczA 272 :KYLEVIVA T0356 242 :YAFAGLLRGTKTEVVKCIS 1zczA 284 :QEAIEVLSKKKVRLLKPGD T0356 288 :YGDHTGYYNEVD 1zczA 303 :YASWAGKMAFGS T0356 304 :FTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFV 1zczA 315 :LVLSERKYPEGNFELVVGEPLSEKELEDLEFAYRVVEG T0356 359 :E 1zczA 354 :K T0356 362 :SYRLA 1zczA 357 :AVLIA T0356 368 :VTIKKQYAG 1zczA 367 :VGIGSGQPS T0356 378 :AKRVMMGVWSFLRQFMY 1zczA 376 :RKRAAWIATVMAGEKAK T0356 397 :FVIVCDDDVN 1zczA 394 :AVAASDAFFP T0356 409 :DWNDVIWAITTRMD 1zczA 404 :FPDSLEILAQAGVK T0356 452 :GLDATNKWP 1zczA 418 :AVVAPLGSI T0356 473 :KDPDVVAHIDAI 1zczA 427 :RDEEVIEKAREL Number of specific fragments extracted= 24 number of extra gaps= 2 total=366 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f5gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f5gA expands to /projects/compbio/data/pdb/2f5g.pdb.gz 2f5gA:# T0356 read from 2f5gA/merged-good-all-a2m # 2f5gA read from 2f5gA/merged-good-all-a2m # adding 2f5gA to template set # found chain 2f5gA in template set T0356 303 :VFTVTH 2f5gA 14 :NYHFVW T0356 321 :YTGRPPDE 2f5gA 20 :IPKHRRNT T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLPPE 2f5gA 29 :VNEIAEYTKEVLKSIAEELGCEIIALEVMPD T0356 363 :YRLAVVTIKKQY 2f5gA 60 :HIHLFVNCPPRY T0356 375 :AGHAKRVMMGVWSFLRQF 2f5gA 78 :NYFKGKSARLILKKFPQL T0356 446 :GLG 2f5gA 96 :NKG T0356 457 :NKWPGE 2f5gA 99 :KLWTRS T0356 465 :REWGRPIKKDPDVVAHIDAIWDE 2f5gA 105 :YFVATAGNVSSEVIKKYIEEQWR Number of specific fragments extracted= 8 number of extra gaps= 0 total=374 Number of alignments=25 # 2f5gA read from 2f5gA/merged-good-all-a2m # found chain 2f5gA in template set T0356 305 :TVT 2f5gA 16 :HFV T0356 319 :S 2f5gA 19 :W T0356 321 :YTGRPPDE 2f5gA 20 :IPKHRRNT T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLPP 2f5gA 29 :VNEIAEYTKEVLKSIAEELGCEIIALEVMP T0356 362 :SYRLAVVTIKKQY 2f5gA 59 :DHIHLFVNCPPRY T0356 375 :AGHAKR 2f5gA 73 :PSYLAN T0356 381 :VMMGVWSFLRQF 2f5gA 84 :SARLILKKFPQL T0356 446 :GLG 2f5gA 96 :NKG T0356 457 :NKWPGETQR 2f5gA 99 :KLWTRSYFV T0356 468 :GRPIKKDPDVVAHIDAIWDE 2f5gA 108 :ATAGNVSSEVIKKYIEEQWR Number of specific fragments extracted= 10 number of extra gaps= 0 total=384 Number of alignments=26 # 2f5gA read from 2f5gA/merged-good-all-a2m # found chain 2f5gA in template set T0356 320 :TYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPE 2f5gA 20 :IPKHRRNTLVNEIAEYTKEVLKSIAEELGCEIIALEVMPD T0356 363 :YRLAVVTIKKQY 2f5gA 60 :HIHLFVNCPPRY T0356 375 :AGHAKRVMM 2f5gA 73 :PSYLANYFK T0356 411 :NDVIWAITTRMD 2f5gA 82 :GKSARLILKKFP T0356 424 :A 2f5gA 94 :Q T0356 442 :SPVSG 2f5gA 95 :LNKGK T0356 459 :W 2f5gA 100 :L T0356 461 :GETQREWGRPIKKDPDVVAHI 2f5gA 101 :WTRSYFVATAGNVSSEVIKKY T0356 482 :DAIWDE 2f5gA 123 :EEQWRK Number of specific fragments extracted= 9 number of extra gaps= 0 total=393 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0356 read from 1wqaA/merged-good-all-a2m # 1wqaA read from 1wqaA/merged-good-all-a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0356 8 :DLRDF 1wqaA 56 :MLKEA T0356 13 :LTLLEQQG 1wqaA 62 :ISGLLSVG T0356 21 :ELKRITL 1wqaA 71 :DVIDVGI T0356 33 :LEITEIADRTLRAGGPALLFENPKGYS 1wqaA 78 :APTPAVQWATKHFNADGGAVITASHNP T0356 62 :VLCNLFG 1wqaA 108 :NGIKLLE T0356 75 :MGMGQED 1wqaA 116 :NGMGLKK T0356 83 :SALREVGKLLAF 1wqaA 123 :EREAIVEELFFK T0356 96 :KEPEPPKG 1wqaA 135 :EDFDRAKW T0356 119 :NMPTKR 1wqaA 145 :IGEVRR T0356 197 :RGGALDYQEWCAA 1wqaA 151 :EDIIKPYIEAIKS T0356 214 :RFPVSVALGADPAT 1wqaA 174 :KPFVVVDTSNGAGS T0356 239 :LSEYAFAGLL 1wqaA 188 :LTLPYLLREL T0356 250 :GTKTEVVKCI 1wqaA 198 :GCKVITVNAQ T0356 261 :NDLEVPA 1wqaA 208 :PDGYFPA T0356 291 :HTG 1wqaA 215 :RNP T0356 324 :RPPDEP 1wqaA 218 :EPNEEN T0356 337 :NEVFVPILQKQ 1wqaA 224 :LKEFMEIVKAL T0356 352 :VDFYLPPEGCSYRLAV 1wqaA 238 :FGVAQDGDADRAVFID T0356 371 :KKQYAGHAKRVMMGVWSFLRQFMYTK 1wqaA 255 :NGRFIQGDKTFALVADAVLKEKGGGL T0356 399 :IVCDDDVN 1wqaA 281 :LVTTVATS T0356 410 :WND 1wqaA 291 :LDD T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVENTPIDYLDFASPVSG 1wqaA 319 :NNGTIGGEENGGVIFPEHVLGRDG T0356 458 :KWPGETQREWGRPIKKD 1wqaA 366 :ELPKYYQIKTKRHVEGD T0356 475 :PDVVAHIDAIWDELAI 1wqaA 384 :HAIVNKVAEMARERGY Number of specific fragments extracted= 25 number of extra gaps= 0 total=418 Number of alignments=28 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0356 28 :PVDPHLEIT 1wqaA 17 :KITPEFAMK T0356 37 :EIADRTLRAGG 1wqaA 29 :AFGTLLKREGR T0356 59 :SMPVLCNLFGT 1wqaA 41 :KPLVVVGRDTR T0356 80 :EDVSAL 1wqaA 52 :VSGEML T0356 86 :REVGKLLAFLK 1wqaA 59 :EALISGLLSVG T0356 110 :KLPQFKQVLN 1wqaA 82 :AVQWATKHFN T0356 160 :TWGLTVTRGPHK 1wqaA 92 :ADGGAVITASHN T0356 185 :GKNKLIMRWLSHRGGA 1wqaA 104 :PPEYNGIKLLEPNGMG T0356 201 :LDYQEWCAA 1wqaA 126 :AIVEELFFK T0356 212 :GE 1wqaA 135 :ED T0356 214 :RFPVSVALGAD 1wqaA 174 :KPFVVVDTSNG T0356 241 :EYAFAGLLRGTKTEVVKCIS 1wqaA 189 :TLPYLLRELGCKVITVNAQP T0356 285 :EGP 1wqaA 209 :DGY T0356 321 :YTGRPPDEPA 1wqaA 212 :FPARNPEPNE T0356 336 :LNEVFVPILQKQ 1wqaA 223 :NLKEFMEIVKAL T0356 352 :VDFYLPPEGCSYRLAV 1wqaA 238 :FGVAQDGDADRAVFID T0356 371 :KKQY 1wqaA 255 :NGRF T0356 375 :AGHAKRVMMGVWSFLRQF 1wqaA 262 :DKTFALVADAVLKEKGGG T0356 398 :VIVCDDDVN 1wqaA 280 :LLVTTVATS T0356 412 :D 1wqaA 293 :D T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVENTPIDYLDFASP 1wqaA 319 :NNGTIGGEENGGVIFPEHVLG T0356 458 :KWPGETQREWGRPIKKD 1wqaA 366 :ELPKYYQIKTKRHVEGD T0356 475 :PDVVAHIDAIWDELAI 1wqaA 384 :HAIVNKVAEMARERGY Number of specific fragments extracted= 24 number of extra gaps= 0 total=442 Number of alignments=29 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0356 22 :LKRITLPVDPHLEI 1wqaA 11 :RGIANEKITPEFAM T0356 36 :TEIADRTLRAGGPALLF 1wqaA 28 :MAFGTLLKREGRKKPLV T0356 61 :PVLCNLFGTPKRVA 1wqaA 45 :VVGRDTRVSGEMLK T0356 86 :REVGKLLAFLK 1wqaA 59 :EALISGLLSVG T0356 123 :KRLRGAPCQQK 1wqaA 73 :IDVGIAPTPAV T0356 147 :IMTCWPEDAAPLITWG 1wqaA 86 :ATKHFNADGGAVITAS T0356 169 :P 1wqaA 102 :H T0356 184 :IGKNKLIMRWLSHRGGA 1wqaA 103 :NPPEYNGIKLLEPNGMG T0356 201 :LDYQEWCA 1wqaA 126 :AIVEELFF T0356 214 :RFPVSVALGADPATILG 1wqaA 174 :KPFVVVDTSNGAGSLTL T0356 242 :YAFAGLLR 1wqaA 191 :PYLLRELG T0356 253 :TEVVKCISN 1wqaA 199 :CKVITVNAQ T0356 262 :DLEVPAS 1wqaA 209 :DGYFPAR T0356 299 :D 1wqaA 216 :N T0356 323 :GRPPDEP 1wqaA 217 :PEPNEEN T0356 337 :NEVFVPILQKQ 1wqaA 224 :LKEFMEIVKAL T0356 350 :EIVDFYLPPEGCSYRLAV 1wqaA 235 :GADFGVAQDGDADRAVFI T0356 373 :QY 1wqaA 257 :RF T0356 376 :GHAKRVMMGVWSFLRQ 1wqaA 260 :QGDKTFALVADAVLKE T0356 393 :MYTKFVIVC 1wqaA 276 :KGGGLLVTT T0356 413 :VIWAITT 1wqaA 312 :VARALYE T0356 423 :PARDTVLVEN 1wqaA 319 :NNGTIGGEEN T0356 435 :IDYLDFASPVSG 1wqaA 329 :GGVIFPEHVLGR T0356 462 :ETQREWGRPIKKDPDVVAHIDAIWDELAIFNN 1wqaA 368 :PKYYQIKTKRHVEGDRHAIVNKVAEMARERGY Number of specific fragments extracted= 24 number of extra gaps= 0 total=466 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aisB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aisB expands to /projects/compbio/data/pdb/1ais.pdb.gz 1aisB:# T0356 read from 1aisB/merged-good-all-a2m # 1aisB read from 1aisB/merged-good-all-a2m # adding 1aisB to template set # found chain 1aisB in template set T0356 7 :NDLRDFLTLLEQQG 1aisB 1131 :EEAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 45 :AG 1aisB 1166 :LK T0356 66 :LFGTPKRVAMGMGQED 1aisB 1168 :VPRTLDEIADIARVDK T0356 83 :SALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMP 1aisB 1184 :KEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS T0356 197 :RGGALDYQEWCAA 1aisB 1223 :EKVRRRAIEILDE T0356 210 :HPGE 1aisB 1238 :KRGL T0356 222 :GADPATILGAV 1aisB 1244 :GKSPAGLVAAA T0356 242 :YAFAGLLRGTKTE 1aisB 1255 :LYIASLLEGEKRT Number of specific fragments extracted= 9 number of extra gaps= 0 total=475 Number of alignments=31 # 1aisB read from 1aisB/merged-good-all-a2m # found chain 1aisB in template set T0356 7 :NDLRDFLTLLEQQG 1aisB 1131 :EEAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 45 :AGG 1aisB 1166 :LKV T0356 67 :FGTPKRVAMGMGQEDVSALREVGKLLAFLK 1aisB 1169 :PRTLDEIADIARVDKKEIGRSYRFIARNLN T0356 98 :PEPPKGFRDLFDKLPQFKQVLNMPTK 1aisB 1199 :LTPKKLFVKPTDYVNKFADELGLSEK T0356 196 :HRGGALDYQEWCAA 1aisB 1226 :RRRAIEILDEAYKR T0356 212 :G 1aisB 1240 :G T0356 222 :GADPATILGAV 1aisB 1244 :GKSPAGLVAAA T0356 242 :YAFAGLLRGTKTE 1aisB 1255 :LYIASLLEGEKRT Number of specific fragments extracted= 9 number of extra gaps= 0 total=484 Number of alignments=32 # 1aisB read from 1aisB/merged-good-all-a2m # found chain 1aisB in template set T0356 8 :DLRDFLTLLEQQG 1aisB 1132 :EAARLYREAVRKG T0356 28 :PVDPHLEITEIADRTLR 1aisB 1148 :GRSIESVMAACVYAACR T0356 46 :GG 1aisB 1167 :KV T0356 67 :FGTPKRVAMGMGQED 1aisB 1169 :PRTLDEIADIARVDK T0356 83 :SALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMP 1aisB 1184 :KEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS T0356 132 :QKIV 1aisB 1223 :EKVR T0356 197 :RGGALDYQ 1aisB 1227 :RRAIEILD T0356 207 :CAAHPGE 1aisB 1235 :EAYKRGL T0356 222 :GADPATILGA 1aisB 1244 :GKSPAGLVAA T0356 241 :EYAFAGLLRGTKTE 1aisB 1254 :ALYIASLLEGEKRT Number of specific fragments extracted= 10 number of extra gaps= 0 total=494 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o2dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0356 read from 1o2dA/merged-good-all-a2m # 1o2dA read from 1o2dA/merged-good-all-a2m # found chain 1o2dA in training set Warning: unaligning (T0356)G323 because of BadResidue code BAD_PEPTIDE in next template residue (1o2dA)G139 Warning: unaligning (T0356)R324 because of BadResidue code BAD_PEPTIDE at template residue (1o2dA)G139 T0356 107 :LFDKLPQFKQVLNMPTKRLRG 1o2dA 45 :SLDDLKKLLDETEISYEIFDE T0356 135 :V 1o2dA 66 :V T0356 195 :SHRGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 67 :EENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLRGTKT 1o2dA 103 :KAVAVLLKEKDL T0356 264 :EV 1o2dA 115 :SV T0356 293 :GYYNEVD 1o2dA 118 :DLYDREK T0356 315 :AIYHSTYT 1o2dA 130 :PVVEIPTT T0356 325 :PPDE 1o2dA 140 :TGSE T0356 329 :PAVL 1o2dA 146 :PYSI T0356 348 :FPE 1o2dA 152 :DPE T0356 351 :IVDFYLPPEGCSYR 1o2dA 165 :PVYAFLDPRYTYSM T0356 374 :YAGHAKRVMMGVWSFL 1o2dA 179 :SDELTLSTGVDALSHA T0356 413 :VIWAITTRM 1o2dA 195 :VEGYLSRKS T0356 474 :DPDVVAHIDAIWDELAIF 1o2dA 204 :TPPSDALAIEAMKIIHRN Number of specific fragments extracted= 14 number of extra gaps= 1 total=508 Number of alignments=34 # 1o2dA read from 1o2dA/merged-good-all-a2m # found chain 1o2dA in training set Warning: unaligning (T0356)G286 because of BadResidue code BAD_PEPTIDE at template residue (1o2dA)G139 T0356 55 :PKGYSMPVLCNLFGT 1o2dA 24 :IDLLGKRALVVTGKS T0356 78 :GQEDVSALREVGKLLAFLK 1o2dA 39 :SSKKNGSLDDLKKLLDETE T0356 120 :MPTKRLRG 1o2dA 58 :ISYEIFDE T0356 130 :CQ 1o2dA 66 :VE T0356 138 :D 1o2dA 68 :E T0356 197 :RGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 69 :NPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLRGTKTEV 1o2dA 103 :KAVAVLLKEKDLSV T0356 278 :EQGETAPE 1o2dA 121 :DREKVKHW T0356 287 :PYGDHTGYY 1o2dA 140 :TGSEVTPYS T0356 309 :ITQREDAIYHSTYTGRP 1o2dA 149 :ILTDPEGNKRGCTLMFP T0356 352 :VDFYLPPEGCSYR 1o2dA 166 :VYAFLDPRYTYSM T0356 374 :YAGHAKRVMMGVWSF 1o2dA 179 :SDELTLSTGVDALSH T0356 412 :DVIWAITTRM 1o2dA 194 :AVEGYLSRKS T0356 474 :DPDVVAHIDAIWDEL 1o2dA 204 :TPPSDALAIEAMKII Number of specific fragments extracted= 14 number of extra gaps= 1 total=522 Number of alignments=35 # 1o2dA read from 1o2dA/merged-good-all-a2m # found chain 1o2dA in training set T0356 106 :DLFDKLPQFKQVLNMPTKRLRG 1o2dA 44 :GSLDDLKKLLDETEISYEIFDE T0356 194 :LSHRGGALDYQEWCAAHPGERFPVSVALGADPATILG 1o2dA 66 :VEENPSFDNVMKAVERYRNDSFDFVVGLGGGSPMDFA T0356 242 :YAFAGLLR 1o2dA 103 :KAVAVLLK T0356 260 :SNDLEV 1o2dA 111 :EKDLSV T0356 278 :EQGETAPEGP 1o2dA 121 :DREKVKHWLP T0356 288 :YGDHTGYY 1o2dA 141 :GSEVTPYS T0356 296 :NEVDSF 1o2dA 152 :DPEGNK T0356 351 :IVDFYLPPEGC 1o2dA 165 :PVYAFLDPRYT T0356 375 :AGHAKRVMMGVWSF 1o2dA 180 :DELTLSTGVDALSH T0356 412 :DVIWAITTRM 1o2dA 194 :AVEGYLSRKS T0356 474 :DPDVVAHIDAIWDEL 1o2dA 204 :TPPSDALAIEAMKII Number of specific fragments extracted= 11 number of extra gaps= 0 total=533 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nz9A/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/T0356/1nz9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0356/1nz9A/merged-good-all-a2m.gz for input Trying 1nz9A/merged-good-all-a2m Error: Couldn't open file 1nz9A/merged-good-all-a2m or 1nz9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sviA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sviA expands to /projects/compbio/data/pdb/1svi.pdb.gz 1sviA:# T0356 read from 1sviA/merged-good-all-a2m # 1sviA read from 1sviA/merged-good-all-a2m # adding 1sviA to template set # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 212 :GERFPVSVALG 1sviA 20 :EGGLPEIALAG T0356 236 :PDTLSEYAFAGLLRG 1sviA 31 :RSNVGKSSFINSLIN T0356 303 :VFTVTHI 1sviA 61 :TLNFYII T0356 313 :EDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYL 1sviA 68 :NDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQ T0356 367 :VVTIKKQYAGHAKRVMMGVWS 1sviA 112 :IVDLRHAPSNDDVQMYEFLKY T0356 392 :FMYTKFVIVCD 1sviA 133 :YGIPVIVIATK T0356 403 :DDVNARDWNDVIWAITT 1sviA 145 :DKIPKGKWDKHAKVVRQ T0356 420 :RMDPARDTVLVEN 1sviA 164 :NIDPEDELILFSS T0356 444 :VSGLG 1sviA 177 :ETKKG T0356 478 :VAHIDAIWDEL 1sviA 182 :KDEAWGAIKKM Number of specific fragments extracted= 10 number of extra gaps= 0 total=543 Number of alignments=37 # 1sviA read from 1sviA/merged-good-all-a2m # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 214 :RFPVSVALG 1sviA 22 :GLPEIALAG T0356 236 :PDTLSEYAFAGLLRG 1sviA 31 :RSNVGKSSFINSLIN T0356 303 :VFTVTHI 1sviA 61 :TLNFYII T0356 313 :EDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYL 1sviA 68 :NDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQ T0356 367 :VVTIKKQYAGHAKRVMMGVWS 1sviA 112 :IVDLRHAPSNDDVQMYEFLKY T0356 392 :FMYTKFVIVCD 1sviA 133 :YGIPVIVIATK T0356 403 :DDVNARDWNDVIWAITT 1sviA 145 :DKIPKGKWDKHAKVVRQ T0356 420 :RMDPARDTVLVEN 1sviA 164 :NIDPEDELILFSS T0356 444 :VSGLG 1sviA 177 :ETKKG T0356 450 :K 1sviA 182 :K T0356 475 :PDVVAHIDAIW 1sviA 183 :DEAWGAIKKMI Number of specific fragments extracted= 11 number of extra gaps= 0 total=554 Number of alignments=38 # 1sviA read from 1sviA/merged-good-all-a2m # found chain 1sviA in template set Warning: unaligning (T0356)T251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0356)P302 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0356 212 :GERFPVSVALGA 1sviA 20 :EGGLPEIALAGR T0356 237 :DTLSEYAFAGLLRG 1sviA 32 :SNVGKSSFINSLIN T0356 303 :VFTV 1sviA 61 :TLNF T0356 310 :TQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLP 1sviA 65 :YIINDELHFVDVPGYGFAKVSKSEREAWGRMIETYITTREELKAVVQI T0356 368 :VTIKKQYAGHAKRVMMGVWSF 1sviA 113 :VDLRHAPSNDDVQMYEFLKYY T0356 393 :MYTKFVIVCDDD 1sviA 134 :GIPVIVIATKAD T0356 405 :VNARDWNDVIWAI 1sviA 147 :IPKGKWDKHAKVV T0356 418 :TTRMDPARDTVLVEN 1sviA 162 :TLNIDPEDELILFSS T0356 442 :SPV 1sviA 177 :ETK T0356 475 :PDVVAHIDAIW 1sviA 183 :DEAWGAIKKMI Number of specific fragments extracted= 10 number of extra gaps= 0 total=564 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u0vA/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/T0356/1u0vA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0356/1u0vA/merged-good-all-a2m.gz for input Trying 1u0vA/merged-good-all-a2m Error: Couldn't open file 1u0vA/merged-good-all-a2m or 1u0vA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pvvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pvvA expands to /projects/compbio/data/pdb/1pvv.pdb.gz 1pvvA:# T0356 read from 1pvvA/merged-good-all-a2m # 1pvvA read from 1pvvA/merged-good-all-a2m # adding 1pvvA to template set # found chain 1pvvA in template set Warning: unaligning (T0356)T320 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)R107 Warning: unaligning (T0356)Y321 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)R107 Warning: unaligning (T0356)T322 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V108 Warning: unaligning (T0356)Y394 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)V155 Warning: unaligning (T0356)T395 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V155 Warning: unaligning (T0356)R469 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)G188 Warning: unaligning (T0356)P470 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)G188 T0356 91 :LL 1pvvA 26 :TA T0356 201 :LDYQEWCAA 1pvvA 28 :KMFKIWQKI T0356 212 :GER 1pvvA 37 :GKP T0356 215 :FPVSVALGA 1pvvA 46 :KTLAMIFQK T0356 236 :PDT 1pvvA 55 :PST T0356 241 :EYAFAGLLRGTKTEVVKCISNDLE 1pvvA 62 :SFEVAMAHLGGHALYLNAQDLQLR T0356 279 :QGET 1pvvA 86 :RGET T0356 312 :REDAIYHS 1pvvA 98 :SRYVDAIM T0356 323 :GR 1pvvA 109 :YD T0356 329 :PAV 1pvvA 111 :HKD T0356 341 :VPILQKQFP 1pvvA 114 :VEDLAKYAT T0356 350 :EIVDFYLPP 1pvvA 124 :PVINGLSDF T0356 373 :QYAGHAKRVMMGVWSFLRQFM 1pvvA 133 :SHPCQALADYMTIWEKKGTIK T0356 396 :K 1pvvA 156 :K T0356 398 :VIVCDDD 1pvvA 157 :VVYVGDG T0356 410 :WNDVIWAITT 1pvvA 167 :AHSLMIAGTK T0356 447 :LGSKMGLDA 1pvvA 177 :LGADVVVAT T0356 468 :G 1pvvA 186 :P T0356 471 :IKKDPDVVAHIDAIWDELAI 1pvvA 189 :YEPDEKVIKWAEQNAAESGG Number of specific fragments extracted= 19 number of extra gaps= 3 total=583 Number of alignments=40 # 1pvvA read from 1pvvA/merged-good-all-a2m # found chain 1pvvA in template set Warning: unaligning (T0356)H318 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)R107 Warning: unaligning (T0356)S319 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)R107 Warning: unaligning (T0356)P325 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V108 Warning: unaligning (T0356)Y394 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)V155 Warning: unaligning (T0356)T395 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V155 Warning: unaligning (T0356)R469 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)G188 Warning: unaligning (T0356)P470 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)G188 T0356 200 :ALDYQEWCAA 1pvvA 27 :AKMFKIWQKI T0356 212 :GER 1pvvA 37 :GKP T0356 215 :FPVSVALGA 1pvvA 46 :KTLAMIFQK T0356 238 :TLS 1pvvA 55 :PST T0356 241 :EYAFAGLLRGTKTEVVKCISNDLE 1pvvA 62 :SFEVAMAHLGGHALYLNAQDLQLR T0356 279 :QGET 1pvvA 86 :RGET T0356 312 :RE 1pvvA 98 :SR T0356 314 :DAIY 1pvvA 102 :DAIM T0356 326 :PDEPAV 1pvvA 109 :YDHKDV T0356 342 :PILQKQFP 1pvvA 115 :EDLAKYAT T0356 350 :EIVDFYLPP 1pvvA 124 :PVINGLSDF T0356 373 :QYAGHAKRVMMGVWSFLRQFM 1pvvA 133 :SHPCQALADYMTIWEKKGTIK T0356 396 :KFVIVCDDD 1pvvA 156 :KVVYVGDGN T0356 410 :WNDVIWAITT 1pvvA 167 :AHSLMIAGTK T0356 447 :LGSKMGLDA 1pvvA 177 :LGADVVVAT T0356 468 :G 1pvvA 186 :P T0356 471 :IKKDPDVVAHIDAIWDELAI 1pvvA 189 :YEPDEKVIKWAEQNAAESGG Number of specific fragments extracted= 17 number of extra gaps= 3 total=600 Number of alignments=41 # 1pvvA read from 1pvvA/merged-good-all-a2m # found chain 1pvvA in template set Warning: unaligning (T0356)L239 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)V61 Warning: unaligning (T0356)S240 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V61 Warning: unaligning (T0356)H318 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)R107 Warning: unaligning (T0356)S319 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)R107 Warning: unaligning (T0356)T320 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V108 Warning: unaligning (T0356)Y394 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)V155 Warning: unaligning (T0356)T395 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)V155 Warning: unaligning (T0356)R469 because of BadResidue code BAD_PEPTIDE in next template residue (1pvvA)G188 Warning: unaligning (T0356)P470 because of BadResidue code BAD_PEPTIDE at template residue (1pvvA)G188 T0356 87 :EVGKLLAF 1pvvA 22 :TILETAKM T0356 203 :Y 1pvvA 30 :F T0356 206 :WCAAHPGER 1pvvA 31 :KIWQKIGKP T0356 215 :FPVSVALGA 1pvvA 46 :KTLAMIFQK T0356 234 :PVPDT 1pvvA 55 :PSTRT T0356 241 :EYAFAGLLRGTKTEVVKCISNDL 1pvvA 62 :SFEVAMAHLGGHALYLNAQDLQL T0356 278 :EQGETAP 1pvvA 85 :RRGETIA T0356 314 :DAIY 1pvvA 102 :DAIM T0356 326 :PDE 1pvvA 109 :YDH T0356 339 :VFVPILQKQFPE 1pvvA 112 :KDVEDLAKYATV T0356 351 :IVDFY 1pvvA 125 :VINGL T0356 357 :P 1pvvA 130 :S T0356 371 :KKQYAGHAKRVMMGVWSFLRQFM 1pvvA 131 :DFSHPCQALADYMTIWEKKGTIK T0356 396 :KFVIVCDDD 1pvvA 156 :KVVYVGDGN T0356 410 :WNDVIWAITT 1pvvA 167 :AHSLMIAGTK T0356 447 :LGSKMGLD 1pvvA 177 :LGADVVVA T0356 467 :WG 1pvvA 185 :TP T0356 471 :IKKDPDVVAHIDAIWDELA 1pvvA 189 :YEPDEKVIKWAEQNAAESG Number of specific fragments extracted= 18 number of extra gaps= 4 total=618 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w1wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w1wA expands to /projects/compbio/data/pdb/1w1w.pdb.gz 1w1wA:# T0356 read from 1w1wA/merged-good-all-a2m # 1w1wA read from 1w1wA/merged-good-all-a2m # adding 1w1wA to template set # found chain 1w1wA in template set Warning: unaligning (T0356)Q79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)L62 Warning: unaligning (T0356)P101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)L62 Warning: unaligning (T0356)K123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)P89 Warning: unaligning (T0356)R173 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)P89 Warning: unaligning (T0356)F348 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)G1095 Warning: unaligning (T0356)C361 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)G1095 Warning: unaligning (T0356)A366 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)K1113 Warning: unaligning (T0356)D474 because last residue in template chain is (1w1wA)Y1223 T0356 25 :ITLPV 1w1wA 19 :TKVGF T0356 45 :AGGPALLFENPKGY 1w1wA 24 :GESNFTSIIGPNGS T0356 68 :GTPKRVAMGMG 1w1wA 41 :NMMDAISFVLG T0356 102 :KGF 1w1wA 63 :KDL T0356 120 :MPT 1w1wA 66 :IYR T0356 174 :QNLGIYRQQLIGKN 1w1wA 90 :QSAYVKAFYQKGNK T0356 188 :KLIMRWLSHRG 1w1wA 106 :ELMRIISRNGD T0356 199 :GALDYQEWCAAHP 1w1wA 127 :SYKDYSIFLENEN T0356 212 :GE 1w1wA 152 :GD T0356 333 :GVALNEVFVPILQKQ 1w1wA 1068 :FDYVSDHLDAIYREL T0356 362 :SYRL 1w1wA 1096 :NASL T0356 375 :AGHAKRVMMGVWSFLRQFMYTKFVIV 1w1wA 1131 :GGEKTVAALALLFAINSYQPSPFFVL T0356 401 :CDDDVNARDWNDVIWAITTRMDPARDTVLVEN 1w1wA 1159 :VDAALDITNVQRIAAYIRRHRNPDLQFIVISL T0356 444 :V 1w1wA 1191 :K T0356 447 :LGSKMGLDATNKWPGETQREWGRPIKK 1w1wA 1196 :EKSDALVGVYRQQQENSSKIITLDLSN Number of specific fragments extracted= 15 number of extra gaps= 0 total=633 Number of alignments=43 # 1w1wA read from 1w1wA/merged-good-all-a2m # found chain 1w1wA in template set Warning: unaligning (T0356)Q79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)L62 Warning: unaligning (T0356)P101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)L62 Warning: unaligning (T0356)K123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)P89 Warning: unaligning (T0356)Q174 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)P89 Warning: unaligning (T0356)F348 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)G1095 Warning: unaligning (T0356)P357 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1w1wA)K1113 Warning: unaligning (T0356)T369 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1w1wA)K1113 Warning: unaligning (T0356)D474 because last residue in template chain is (1w1wA)Y1223 T0356 24 :RITLPV 1w1wA 18 :VTKVGF T0356 45 :AGGPALLFENPKGY 1w1wA 24 :GESNFTSIIGPNGS T0356 69 :TPKRVAMGMG 1w1wA 42 :MMDAISFVLG T0356 102 :KGF 1w1wA 63 :KDL T0356 120 :MPT 1w1wA 66 :IYR T0356 175 :NLGIYRQQLIGKN 1w1wA 90 :QSAYVKAFYQKGN T0356 188 :KLIMRWLSHRG 1w1wA 106 :ELMRIISRNGD T0356 200 :ALDYQEWCAAHP 1w1wA 128 :YKDYSIFLENEN T0356 212 :GE 1w1wA 152 :GD T0356 333 :GVALNEVFVPILQKQ 1w1wA 1068 :FDYVSDHLDAIYREL T0356 353 :DFYL 1w1wA 1096 :NASL T0356 370 :IKK 1w1wA 1114 :YHA T0356 373 :QYAGHAKRVMMGVWSFLRQFMYTKFVIVCD 1w1wA 1128 :YLSGGEKTVAALALLFAINSYQPSPFFVLD T0356 403 :DDVNARDWNDVIWAITTRMDPARDTVLV 1w1wA 1161 :AALDITNVQRIAAYIRRHRNPDLQFIVI T0356 447 :LGSKMGLDATNKWPGETQREWGRPIKK 1w1wA 1196 :EKSDALVGVYRQQQENSSKIITLDLSN Number of specific fragments extracted= 15 number of extra gaps= 0 total=648 Number of alignments=44 # 1w1wA read from 1w1wA/merged-good-all-a2m # found chain 1w1wA in template set T0356 375 :AGHAKRVMMGVWSFLRQFMYTKFVIV 1w1wA 1131 :GGEKTVAALALLFAINSYQPSPFFVL T0356 401 :CDDDVNARDWNDVIWAITTRMDPARDTVLVEN 1w1wA 1159 :VDAALDITNVQRIAAYIRRHRNPDLQFIVISL Number of specific fragments extracted= 2 number of extra gaps= 0 total=650 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jwxA/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/T0356/1jwxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0356/1jwxA/merged-good-all-a2m.gz for input Trying 1jwxA/merged-good-all-a2m Error: Couldn't open file 1jwxA/merged-good-all-a2m or 1jwxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2u1a/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2u1a expands to /projects/compbio/data/pdb/2u1a.pdb.gz 2u1a:Warning: there is no chain 2u1a will retry with 2u1aA # T0356 read from 2u1a/merged-good-all-a2m # 2u1a read from 2u1a/merged-good-all-a2m # adding 2u1a to template set # found chain 2u1a in template set T0356 312 :REDAIYHSTYTGRPPDE 2u1a 8 :SENPPNHILFLTNLPEE T0356 337 :NEVFVPILQK 2u1a 27 :ELMLSMLFNQ T0356 348 :FPEIVDFYLPPEGC 2u1a 37 :FPGFKEVRLVPGRH T0356 364 :RLAVVTIK 2u1a 51 :DIAFVEFD T0356 374 :YAGHAKRVMM 2u1a 59 :NEVQAGAARD Number of specific fragments extracted= 5 number of extra gaps= 0 total=655 Number of alignments=46 # 2u1a read from 2u1a/merged-good-all-a2m # found chain 2u1a in template set T0356 312 :REDAIYHSTYTGRPPDE 2u1a 8 :SENPPNHILFLTNLPEE T0356 337 :NEVFVPIL 2u1a 27 :ELMLSMLF T0356 346 :KQFPEIVDFYLPPEG 2u1a 35 :NQFPGFKEVRLVPGR T0356 363 :YRLAVVTI 2u1a 50 :HDIAFVEF T0356 373 :QYAGHAKRVMMG 2u1a 58 :DNEVQAGAARDA Number of specific fragments extracted= 5 number of extra gaps= 0 total=660 Number of alignments=47 # 2u1a read from 2u1a/merged-good-all-a2m # found chain 2u1a in template set T0356 313 :EDAIYHSTYTGRPPDEP 2u1a 9 :ENPPNHILFLTNLPEET T0356 337 :NEVFVPILQKQFPEIVDFYLPPEGC 2u1a 26 :NELMLSMLFNQFPGFKEVRLVPGRH T0356 364 :RLAVVTIK 2u1a 51 :DIAFVEFD T0356 374 :YAGHAKRVMM 2u1a 59 :NEVQAGAARD Number of specific fragments extracted= 4 number of extra gaps= 0 total=664 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjeA expands to /projects/compbio/data/pdb/1vje.pdb.gz 1vjeA:# T0356 read from 1vjeA/merged-good-all-a2m # 1vjeA read from 1vjeA/merged-good-all-a2m # adding 1vjeA to template set # found chain 1vjeA in template set Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 T0356 291 :HTGYYNEVDSFPVFTVTHITQR 1vjeA 9 :SFDLDHTKVKAPYVRLAGVKTT T0356 313 :EDAIYHSTYTGRPPDE 1vjeA 33 :GDQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :C 1vjeA 84 :T T0356 365 :LAVVTIKKQY 1vjeA 85 :GMYMAVIGEP T0356 375 :AGHAKRVMMGVWSFLRQF 1vjeA 96 :EQGVMKAFEAALKDTAGH T0356 402 :DD 1vjeA 114 :DQ T0356 430 :VENTP 1vjeA 117 :IPGVS T0356 444 :VSGL 1vjeA 122 :ELEC T0356 468 :GRPIKKD 1vjeA 126 :GNYRDHD T0356 475 :PDVVAHIDAIWDE 1vjeA 134 :AAARQHARDVLDQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=675 Number of alignments=49 # 1vjeA read from 1vjeA/merged-good-all-a2m # found chain 1vjeA in template set Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 Warning: unaligning (T0356)L498 because last residue in template chain is (1vjeA)L156 T0356 297 :EVDSFPVFTVTHITQRED 1vjeA 15 :TKVKAPYVRLAGVKTTPK T0356 315 :AIYHSTYTGRPPDE 1vjeA 35 :QISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :CSYRLAV 1vjeA 84 :TGMYMAV T0356 371 :KKQYAGHAKRVMMGVWSFLRQFM 1vjeA 92 :GEPDEQGVMKAFEAALKDTAGHD T0356 403 :DD 1vjeA 115 :QP T0356 430 :VENTP 1vjeA 117 :IPGVS T0356 461 :GETQREWG 1vjeA 122 :ELECGNYR T0356 472 :KKD 1vjeA 130 :DHD T0356 475 :PDVVAHIDAIWDE 1vjeA 134 :AAARQHARDVLDQ T0356 489 :AIFNNGKSA 1vjeA 147 :GLKVQETIL Number of specific fragments extracted= 11 number of extra gaps= 0 total=686 Number of alignments=50 # 1vjeA read from 1vjeA/merged-good-all-a2m # found chain 1vjeA in template set Warning: unaligning (T0356)D290 because first residue in template chain is (1vjeA)E8 Warning: unaligning (T0356)P358 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vjeA)R83 Warning: unaligning (T0356)G360 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vjeA)R83 T0356 291 :HTGYYNEVDSFPVFTVTHITQRE 1vjeA 9 :SFDLDHTKVKAPYVRLAGVKTTP T0356 314 :DAIYHSTYTGRPPDE 1vjeA 34 :DQISKYDLRFLQPNQ T0356 329 :PAVLGVALNEVFVPILQKQFPEIVDFYLP 1vjeA 52 :DPAAIHTLEHLLAGYMRDHLEGVVDVSPM T0356 361 :CSYRLAV 1vjeA 84 :TGMYMAV T0356 370 :IKKQYAGHAKRVMMGVWSFLRQ 1vjeA 91 :IGEPDEQGVMKAFEAALKDTAG T0356 421 :MDP 1vjeA 113 :HDQ T0356 438 :LDFASPVSGLG 1vjeA 116 :PIPGVSELECG T0356 460 :PGETQ 1vjeA 127 :NYRDH T0356 473 :KDPDVVAHIDAIWDE 1vjeA 132 :DLAAARQHARDVLDQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=695 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dbbA expands to /projects/compbio/data/pdb/2dbb.pdb.gz 2dbbA:# T0356 read from 2dbbA/merged-good-all-a2m # 2dbbA read from 2dbbA/merged-good-all-a2m # adding 2dbbA to template set # found chain 2dbbA in template set T0356 7 :NDLRDFLTLLEQ 2dbbA 9 :RVDMQLVKILSE T0356 19 :QG 2dbbA 22 :SR T0356 68 :GTPKRVAMGMGQED 2dbbA 24 :LTYRELADILNTTR T0356 83 :SALREVGK 2dbbA 38 :QRIARRID T0356 113 :QFKQV 2dbbA 46 :KLKKL T0356 119 :NM 2dbbA 51 :GI T0356 130 :CQQKIVSG 2dbbA 53 :IRKFTIIP T0356 141 :DLNR 2dbbA 61 :DIDK T0356 172 :ER 2dbbA 66 :GY T0356 187 :NKLIMRWLSHR 2dbbA 68 :MYAIVLIKSKV T0356 200 :ALDYQEWCAAHPGE 2dbbA 79 :PSDADKVISEISDI T0356 252 :K 2dbbA 93 :E T0356 302 :PVFTVTHITQREDAIYHSTYTGR 2dbbA 94 :YVKSVEKGVGRYNIIVRLLLPKD T0356 334 :VALNEVFVPILQKQFPEIVDFY 2dbbA 117 :IKDAENLISEFLQRIKNAENVE Number of specific fragments extracted= 14 number of extra gaps= 0 total=709 Number of alignments=52 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set T0356 7 :NDLRDFLTLLEQQ 2dbbA 9 :RVDMQLVKILSEN T0356 45 :AG 2dbbA 22 :SR T0356 68 :GTPKRVAMGMGQEDVSALREVGKLLAF 2dbbA 24 :LTYRELADILNTTRQRIARRIDKLKKL T0356 119 :NM 2dbbA 51 :GI T0356 130 :CQQKIVS 2dbbA 53 :IRKFTII T0356 167 :RGPHK 2dbbA 60 :PDIDK T0356 172 :ERQ 2dbbA 66 :GYM T0356 188 :KLIMRWLSH 2dbbA 69 :YAIVLIKSK T0356 199 :GALDYQEWCAAHPGE 2dbbA 78 :VPSDADKVISEISDI T0356 290 :DHTGYYNEVDSFPVFTVTHITQRE 2dbbA 93 :EYVKSVEKGVGRYNIIVRLLLPKD T0356 334 :VALNEVFVPILQKQFPEIVDFY 2dbbA 117 :IKDAENLISEFLQRIKNAENVE Number of specific fragments extracted= 11 number of extra gaps= 0 total=720 Number of alignments=53 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set T0356 10 :RDFLTLLEQ 2dbbA 12 :MQLVKILSE T0356 20 :G 2dbbA 22 :S T0356 46 :G 2dbbA 23 :R T0356 68 :GTPKRVAMGMGQED 2dbbA 24 :LTYRELADILNTTR T0356 83 :SALREVGKLLAFLK 2dbbA 38 :QRIARRIDKLKKLG T0356 129 :PCQQKIVSGDDVDL 2dbbA 52 :IIRKFTIIPDIDKL T0356 172 :ER 2dbbA 66 :GY T0356 187 :NKLIMRWLSHRGGALDYQ 2dbbA 68 :MYAIVLIKSKVPSDADKV T0356 207 :CAAHPGER 2dbbA 86 :ISEISDIE T0356 291 :H 2dbbA 94 :Y T0356 303 :VFTVTHITQREDAIYHSTYTGR 2dbbA 95 :VKSVEKGVGRYNIIVRLLLPKD T0356 334 :VALNEVFVPILQKQFPEIVDFY 2dbbA 117 :IKDAENLISEFLQRIKNAENVE Number of specific fragments extracted= 12 number of extra gaps= 0 total=732 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6jA expands to /projects/compbio/data/pdb/1o6j.pdb.gz 1o6jA:Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1o6jA # T0356 read from 1o6jA/merged-good-all-a2m # 1o6jA read from 1o6jA/merged-good-all-a2m # adding 1o6jA to template set # found chain 1o6jA in template set T0356 358 :PEGCSYRLAVVTIKKQY 1o6jA 40 :PSLAGKTVFFYFSASWC T0356 375 :AGHAKRVMMGVWS 1o6jA 60 :RAFTPQLIDFYKA T0356 389 :LRQFMYTK 1o6jA 73 :HAEKKNFE T0356 398 :VIVCDDD 1o6jA 81 :VMLISWD T0356 408 :RDWNDVIWAIT 1o6jA 88 :ESAEDFKDYYA T0356 432 :NTPIDYLDFAS 1o6jA 99 :KMPWLALPFED Number of specific fragments extracted= 6 number of extra gaps= 0 total=738 Number of alignments=55 # 1o6jA read from 1o6jA/merged-good-all-a2m # found chain 1o6jA in template set T0356 342 :PILQKQFPEIVDFYL 1o6jA 17 :SGLKKFFPYSTNVLK T0356 357 :PPEGCSYRLAVVTIKKQYAG 1o6jA 39 :LPSLAGKTVFFYFSASWCPP T0356 377 :HAKRVMMGVWSF 1o6jA 62 :FTPQLIDFYKAH T0356 390 :RQFMYTKFVIVC 1o6jA 74 :AEKKNFEVMLIS T0356 402 :DD 1o6jA 87 :DE T0356 409 :DWNDVIWAIT 1o6jA 89 :SAEDFKDYYA T0356 432 :NTPIDYLDFAS 1o6jA 99 :KMPWLALPFED T0356 478 :VAHIDAIWDELAIFNNGKSALEH 1o6jA 110 :RKGMEFLTTGFDVKSIPTLVGVE Number of specific fragments extracted= 8 number of extra gaps= 0 total=746 Number of alignments=56 # 1o6jA read from 1o6jA/merged-good-all-a2m # found chain 1o6jA in template set T0356 5 :KYNDLRDFLTLLEQ 1o6jA 55 :WCPPCRAFTPQLID T0356 38 :IADRT 1o6jA 69 :FYKAH T0356 55 :PKGYSMPVLCNLF 1o6jA 74 :AEKKNFEVMLISW T0356 79 :QEDVSALREVGK 1o6jA 87 :DESAEDFKDYYA T0356 94 :FLKEPEPPKGFRDLFDKLPQFKQVLNM 1o6jA 99 :KMPWLALPFEDRKGMEFLTTGFDVKSI T0356 161 :WGLTVTRGPHKERQ 1o6jA 126 :PTLVGVEADSGNII Number of specific fragments extracted= 6 number of extra gaps= 0 total=752 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0356 read from 2fbiA/merged-good-all-a2m # 2fbiA read from 2fbiA/merged-good-all-a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0356)K56 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0356)G57 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0356 4 :MKYNDLRDFLTLLEQQGELKRITLP 2fbiA 60 :ILRPSMTGVLARLERDGIVRRWKAP T0356 58 :YS 2fbiA 87 :QR T0356 61 :PVLCNLF 2fbiA 89 :RVYVNLT T0356 71 :KRVAMGM 2fbiA 96 :EKGQQCF T0356 82 :VSALREVGKLLAF 2fbiA 106 :SGDMEKNYQRIQE T0356 100 :PPKGFRDLFDKLPQFKQ 2fbiA 121 :GEEKLAQLLELLNELKK Number of specific fragments extracted= 6 number of extra gaps= 1 total=758 Number of alignments=58 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set T0356 6 :YNDLRDFLTLLEQQGELKRITLP 2fbiA 62 :RPSMTGVLARLERDGIVRRWKAP T0356 63 :LCNL 2fbiA 91 :YVNL T0356 70 :PKRVAMGM 2fbiA 95 :TEKGQQCF T0356 82 :VSALREV 2fbiA 106 :SGDMEKN T0356 89 :GKLLAFL 2fbiA 114 :QRIQERF T0356 100 :PPKGFRDLFDKLPQFKQ 2fbiA 121 :GEEKLAQLLELLNELKK Number of specific fragments extracted= 6 number of extra gaps= 0 total=764 Number of alignments=59 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0356)K56 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0356)G57 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0356 5 :KYNDLRDFLTLLEQQGELKRITLP 2fbiA 61 :LRPSMTGVLARLERDGIVRRWKAP T0356 58 :YSMPVL 2fbiA 87 :QRRVYV T0356 65 :NL 2fbiA 93 :NL T0356 70 :PKRVAMGM 2fbiA 95 :TEKGQQCF T0356 80 :EDVSALREVGKLLAFLKE 2fbiA 104 :SMSGDMEKNYQRIQERFG T0356 101 :PKGFRDLFDKLPQFKQV 2fbiA 122 :EEKLAQLLELLNELKKI Number of specific fragments extracted= 6 number of extra gaps= 1 total=770 Number of alignments=60 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 60 Done printing distance constraints # command: