# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0440 numbered 1 through 275 Created new target T0440 from T0440.a2m # command:CPU_time= 5.473 sec, elapsed time= 6.314 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2yxoA/T0440-2yxoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2yxoA expands to /projects/compbio/data/pdb/2yxo.pdb.gz 2yxoA:# T0440 read from 2yxoA/T0440-2yxoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxoA read from 2yxoA/T0440-2yxoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2yxoA to template set # found chain 2yxoA in template set T0440 1 :M 2yxoA 1 :M # choosing archetypes in rotamer library T0440 3 :RDGHTHTEFCPHGT 2yxoA 2 :VDSHVHTPLCGHAE T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPL 2yxoA 16 :GHPEAYLEEARAKGLKGVVFTDHSPM T0440 44 :SSE 2yxoA 46 :DPE T0440 61 :ASMAMSDLPYYFKKMNHIKKKY 2yxoA 49 :SRMRLEALPFYLLALERVRERA T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYG 2yxoA 71 :QDLYVGIGLEADFHPGTEGFLAQLLRRYP T0440 115 :TDDGVLSLHFLEGQGGFR 2yxoA 100 :FDYVIGSVHYLGAWPLDH T0440 142 :NEGIVQ 2yxoA 118 :PDHQEE T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMGHISLCQKFQQFFG 2yxoA 124 :YAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLFKPL 2yxoA 167 :EEALLELAEPALRAVAEAGLFLDVNTAGLRRPA T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYCQ 2yxoA 200 :KEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQA Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2yxoA/T0440-2yxoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2yxoA/T0440-2yxoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxoA read from 2yxoA/T0440-2yxoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yxoA in template set T0440 1 :M 2yxoA 1 :M T0440 3 :RDGHTHTEFC 2yxoA 2 :VDSHVHTPLC T0440 13 :PHGT 2yxoA 13 :HAEG T0440 19 :DVEEMVLKAIELDFDEYSIVEHAPL 2yxoA 17 :HPEAYLEEARAKGLKGVVFTDHSPM T0440 44 :SSEFMKN 2yxoA 43 :PWYDPES T0440 62 :SMAMSDLPYYFKKMNHIKKKYAS 2yxoA 50 :RMRLEALPFYLLALERVRERAQD T0440 86 :LLIHIGFEVDYLIGYEDFTRDFLNEYG 2yxoA 73 :LYVGIGLEADFHPGTEGFLAQLLRRYP T0440 115 :TDDGVLSLHFLEGQGGF 2yxoA 100 :FDYVIGSVHYLGAWPLD T0440 132 :RSIDFSAED 2yxoA 119 :DHQEEYAWR T0440 151 :GFEQAQLAYLEGVKQSIE 2yxoA 128 :DLKEVFRAYFQEVEKAAR T0440 171 :LGLFK 2yxoA 146 :SGLFH T0440 178 :RMGHISLCQ 2yxoA 151 :AIGHLDLPK T0440 188 :FQQFFGE 2yxoA 160 :KFGHRLP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLFKPL 2yxoA 167 :EEALLELAEPALRAVAEAGLFLDVNTAGLRRPA T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYCQ 2yxoA 200 :KEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQA Number of specific fragments extracted= 15 number of extra gaps= 0 total=26 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2yxoA/T0440-2yxoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2yxoA/T0440-2yxoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxoA read from 2yxoA/T0440-2yxoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yxoA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (2yxoA)M1 T0440 3 :RDGHTHTEFC 2yxoA 2 :VDSHVHTPLC T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 2yxoA 12 :GHAEGHPEAYLEEARAKGLKGVVFTDHSPMPPWYD T0440 59 :TTASMAMSDLPYYFKKMNHIKKKY 2yxoA 47 :PESRMRLEALPFYLLALERVRERA T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLN 2yxoA 71 :QDLYVGIGLEADFHPGTEGFLAQLLR T0440 112 :GPQTDDGVLSLHFLEGQGGFRSIDFSA 2yxoA 97 :RYPFDYVIGSVHYLGAWPLDHPDHQEE T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMGHISLCQKFQQFFG 2yxoA 124 :YAWRDLKEVFRAYFQEVEKAARSGLFHAIGHLDLPKKFGHRLP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLFKP 2yxoA 167 :EEALLELAEPALRAVAEAGLFLDVNTAGLRRP T0440 233 :CGETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYCQ 2yxoA 199 :AKEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQA Number of specific fragments extracted= 8 number of extra gaps= 0 total=34 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0440-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m65A expands to /projects/compbio/data/pdb/1m65.pdb.gz 1m65A:Skipped atom 249, because occupancy 0.5 <= existing 0.500 in 1m65A Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1m65A Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1m65A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1m65A # T0440 read from 1m65A/T0440-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0440-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m65A to template set # found chain 1m65A in template set Warning: unaligning (T0440)G227 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m65A)N172 Warning: unaligning (T0440)P238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m65A)N172 Warning: unaligning (T0440)H260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m65A)T195 Warning: unaligning (T0440)G261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0440 2 :KRDGHTHTEFCPHGT 1m65A 3 :PVDLHMHTVASTHAY T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPL 1m65A 18 :STLSDYIAQAKQKGIKLFAITDHGPD T0440 44 :SSEFMKNTA 1m65A 49 :HHWHFINMR T0440 53 :GDKEAVTTASMAMSDLP 1m65A 64 :DGVGILRGIEANIKNVD T0440 92 :FEVDY 1m65A 81 :GEIDC T0440 101 :EDFTRDF 1m65A 86 :SGKMFDS T0440 115 :TDDGVLSLHF 1m65A 93 :LDLIIAGFHE T0440 131 :FRSIDFS 1m65A 103 :PVFAPHD T0440 160 :LEGVKQSIEADLGLFKPRRMGHISL 1m65A 110 :KATNTQAMIATIASGNVHIISHPGN T0440 192 :FGEDTS 1m65A 135 :PKYEID T0440 207 :FRVILALVKKRDYELDFNTA 1m65A 141 :VKAVAEAAAKHQVALEINNS T0440 239 :PKKIVTLASELQIPFVYGSDS 1m65A 173 :CREVAAAVRDAGGWVALGSDS T0440 262 :VQDIG 1m65A 196 :AFTMG T0440 268 :GYSTYC 1m65A 201 :EFEECL Number of specific fragments extracted= 14 number of extra gaps= 1 total=48 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0440-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1m65A/T0440-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0440-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m65A in template set Warning: unaligning (T0440)G227 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m65A)N172 Warning: unaligning (T0440)P238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m65A)N172 Warning: unaligning (T0440)H260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m65A)T195 Warning: unaligning (T0440)G261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0440 1 :MKRDGHTHTEFC 1m65A 2 :YPVDLHMHTVAS T0440 13 :PHGT 1m65A 15 :HAYS T0440 19 :DVEEMVLKAIELDFDEYSIVEHAPL 1m65A 19 :TLSDYIAQAKQKGIKLFAITDHGPD T0440 44 :SSEFMK 1m65A 47 :APHHWH T0440 62 :SMAMSDLPYYF 1m65A 53 :FINMRIWPRVV T0440 84 :SDLLIHIGFEVDYLIG 1m65A 64 :DGVGILRGIEANIKNV T0440 100 :YEDFTRD 1m65A 86 :SGKMFDS T0440 115 :TDDGVLSLHF 1m65A 93 :LDLIIAGFHE T0440 133 :SIDFSA 1m65A 103 :PVFAPH T0440 151 :GF 1m65A 109 :DK T0440 157 :LAYLEGVKQSIE 1m65A 111 :ATNTQAMIATIA T0440 171 :LGLFK 1m65A 123 :SGNVH T0440 178 :RMGHIS 1m65A 128 :IISHPG T0440 189 :QQFFGED 1m65A 134 :NPKYEID T0440 207 :FRVILALVKKRDYELDFNTA 1m65A 141 :VKAVAEAAAKHQVALEINNS T0440 239 :PKKIVTLASELQIPFVYGSDS 1m65A 173 :CREVAAAVRDAGGWVALGSDS T0440 262 :VQDIG 1m65A 196 :AFTMG T0440 268 :GYSTYCQ 1m65A 201 :EFEECLK Number of specific fragments extracted= 18 number of extra gaps= 1 total=66 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0440-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1m65A/T0440-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0440-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m65A in template set Warning: unaligning (T0440)G227 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m65A)N172 Warning: unaligning (T0440)P238 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m65A)N172 Warning: unaligning (T0440)H260 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m65A)T195 Warning: unaligning (T0440)G261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0440 2 :KRDGHTHTEFC 1m65A 3 :PVDLHMHTVAS T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEFMKN 1m65A 14 :THAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHH T0440 60 :TASMAMSDLP 1m65A 51 :WHFINMRIWP T0440 84 :SDLLIHIGFEVDYLIG 1m65A 64 :DGVGILRGIEANIKNV T0440 100 :YEDFTRDF 1m65A 85 :CSGKMFDS T0440 115 :TDDGVLSLH 1m65A 93 :LDLIIAGFH T0440 128 :QGGFRSIDF 1m65A 102 :EPVFAPHDK T0440 161 :EGVKQSIEADLGLFKPRRMGHISL 1m65A 111 :ATNTQAMIATIASGNVHIISHPGN T0440 190 :QFFGED 1m65A 135 :PKYEID T0440 207 :FRVILALVKKRDYELDFNTA 1m65A 141 :VKAVAEAAAKHQVALEINNS T0440 239 :PKKIVTLASELQIPFVYGSDS 1m65A 173 :CREVAAAVRDAGGWVALGSDS T0440 262 :VQDIG 1m65A 196 :AFTMG T0440 268 :GYSTYCQ 1m65A 201 :EFEECLK Number of specific fragments extracted= 13 number of extra gaps= 1 total=79 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2anuA/T0440-2anuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2anuA expands to /projects/compbio/data/pdb/2anu.pdb.gz 2anuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 2anuA/T0440-2anuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anuA read from 2anuA/T0440-2anuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2anuA to template set # found chain 2anuA in template set Warning: unaligning (T0440)H40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2anuA)I46 Warning: unaligning (T0440)A41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2anuA)I46 Warning: unaligning (T0440)M63 because of BadResidue code BAD_PEPTIDE in next template residue (2anuA)T99 Warning: unaligning (T0440)A64 because of BadResidue code BAD_PEPTIDE at template residue (2anuA)T99 Warning: unaligning (T0440)Q186 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2anuA)L151 Warning: unaligning (T0440)F192 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2anuA)L151 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2anuA)N173 Warning: unaligning (T0440)T225 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2anuA)N173 T0440 1 :M 2anuA 6 :E T0440 2 :KRDGHTHTEFC 2anuA 9 :LCDFHVHTNMS T0440 14 :HGT 2anuA 20 :DGH T0440 18 :DDVEEMVLKAIELDFDEYSIVE 2anuA 23 :LPLGEVVDLFGKHGVDVVSITD T0440 42 :PL 2anuA 73 :YL T0440 44 :SSEFMKNTAG 2anuA 77 :LWREQKRAWE T0440 54 :DKEAVTTAS 2anuA 89 :GMILIPGVE T0440 65 :MSD 2anuA 100 :NNT T0440 84 :SDLLIHIGFEVDYLI 2anuA 103 :DLYHIVAVDVKEYVD T0440 110 :EYG 2anuA 118 :PSL T0440 162 :GVKQSIEADLGLFKPRRMGHISLC 2anuA 121 :PVEEIVEKLKEQNALVIAAHPDRK T0440 193 :G 2anuA 152 :S T0440 194 :EDTSD 2anuA 160 :ERFKD T0440 217 :RDYELDF 2anuA 165 :TFDAWEI T0440 226 :AG 2anuA 174 :RD T0440 234 :GETY 2anuA 176 :DLFN T0440 245 :LASELQIPFVYGSDSHGVQDIG 2anuA 180 :SVGVKKYRYVANSDFHELWHVY Number of specific fragments extracted= 17 number of extra gaps= 3 total=96 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2anuA/T0440-2anuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2anuA/T0440-2anuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anuA read from 2anuA/T0440-2anuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2anuA in template set Warning: unaligning (T0440)H40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2anuA)I46 Warning: unaligning (T0440)A41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2anuA)I46 Warning: unaligning (T0440)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2anuA)T99 Warning: unaligning (T0440)E126 because of BadResidue code BAD_PEPTIDE at template residue (2anuA)T99 Warning: unaligning (T0440)F191 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2anuA)L151 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2anuA)N173 Warning: unaligning (T0440)T225 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2anuA)N173 T0440 2 :KRDGHTHTEFCPHGT 2anuA 9 :LCDFHVHTNMSDGHL T0440 19 :DVEEMVLKAIELDFDEYSIVE 2anuA 24 :PLGEVVDLFGKHGVDVVSITD T0440 42 :P 2anuA 47 :V T0440 44 :SSEFMK 2anuA 48 :DRRTLE T0440 62 :SMAMSDLPYYFKK 2anuA 54 :QRKRNGEPLGAIT T0440 77 :H 2anuA 67 :E T0440 83 :AS 2anuA 68 :DK T0440 97 :LIGYEDFTRDFLNEYGPQTDDGVLSLHF 2anuA 70 :FQDYLKRLWREQKRAWEEYGMILIPGVE T0440 127 :GQGGF 2anuA 100 :NNTDL T0440 132 :RSIDFSA 2anuA 114 :EYVDPSL T0440 151 :GFEQAQLAYLE 2anuA 121 :PVEEIVEKLKE T0440 171 :LGLFK 2anuA 132 :QNALV T0440 178 :RMGHIS 2anuA 137 :IAAHPD T0440 189 :QQ 2anuA 143 :RK T0440 198 :DFSEE 2anuA 154 :YLWAN T0440 214 :VKKRDYELDF 2anuA 162 :FKDTFDAWEI T0440 226 :AGLFKP 2anuA 174 :RDDLFN T0440 245 :LASELQIPFVYGSDSHGVQ 2anuA 180 :SVGVKKYRYVANSDFHELW Number of specific fragments extracted= 18 number of extra gaps= 3 total=114 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2anuA/T0440-2anuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2anuA/T0440-2anuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2anuA read from 2anuA/T0440-2anuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2anuA in template set Warning: unaligning (T0440)H40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2anuA)I46 Warning: unaligning (T0440)A41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2anuA)I46 Warning: unaligning (T0440)V94 because of BadResidue code BAD_PEPTIDE in next template residue (2anuA)T99 Warning: unaligning (T0440)D95 because of BadResidue code BAD_PEPTIDE at template residue (2anuA)T99 Warning: unaligning (T0440)K230 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2anuA)L151 Warning: unaligning (T0440)Y237 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2anuA)L151 T0440 3 :RDGHTHTEFC 2anuA 10 :CDFHVHTNMS T0440 15 :GTHDDVEEMVLKAIELDFDEYSIVE 2anuA 20 :DGHLPLGEVVDLFGKHGVDVVSITD T0440 42 :PLSSEF 2anuA 47 :VDRRTL T0440 52 :AGDKEAV 2anuA 53 :EQRKRNG T0440 59 :TTASMAMSDLPYYFKKMNHIKKKYAS 2anuA 61 :PLGAITEDKFQDYLKRLWREQKRAWE T0440 85 :DLLIHIGFE 2anuA 89 :GMILIPGVE T0440 96 :YLIG 2anuA 100 :NNTD T0440 121 :SLHFLEGQGGF 2anuA 106 :HIVAVDVKEYV T0440 133 :SID 2anuA 117 :DPS T0440 196 :TS 2anuA 120 :LP T0440 207 :FRVILALVKKRDYELDFNTAGLF 2anuA 122 :VEEIVEKLKEQNALVIAAHPDRK T0440 238 :PPKKIV 2anuA 152 :SWYLWA T0440 244 :TLASELQIPFVYGSDSHGVQDIG 2anuA 179 :NSVGVKKYRYVANSDFHELWHVY T0440 267 :RGYSTYCQ 2anuA 211 :KNIEAIKE Number of specific fragments extracted= 14 number of extra gaps= 2 total=128 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnhA/T0440-2hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hnhA expands to /projects/compbio/data/pdb/2hnh.pdb.gz 2hnhA:Skipped atom 2290, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2292, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2296, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2300, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2302, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2304, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2306, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2308, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2310, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2576, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2580, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2584, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2586, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2588, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2651, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2653, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2655, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2657, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 2659, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3020, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3024, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3026, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3028, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3030, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3032, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3235, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3237, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3239, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3241, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3243, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 3245, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4037, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4041, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4043, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4045, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4047, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 4049, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5198, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5202, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5204, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5206, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5208, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5210, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5212, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5720, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5724, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5726, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5728, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 5730, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6034, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6038, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6040, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6042, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6044, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6046, because occupancy 0.500 <= existing 0.500 in 2hnhA Skipped atom 6048, because occupancy 0.500 <= existing 0.500 in 2hnhA # T0440 read from 2hnhA/T0440-2hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnhA read from 2hnhA/T0440-2hnhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hnhA to template set # found chain 2hnhA in template set Warning: unaligning (T0440)M63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N71 Warning: unaligning (T0440)A64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N71 Warning: unaligning (T0440)L86 because of BadResidue code BAD_PEPTIDE in next template residue (2hnhA)T85 Warning: unaligning (T0440)L87 because of BadResidue code BAD_PEPTIDE at template residue (2hnhA)T85 Warning: unaligning (T0440)F148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N125 Warning: unaligning (T0440)L173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N125 Warning: unaligning (T0440)M179 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)S132 Warning: unaligning (T0440)G180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)S132 Warning: unaligning (T0440)C185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)D138 Warning: unaligning (T0440)Q186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)D138 T0440 1 :M 2hnhA 4 :P T0440 2 :KRDGHTHTEFCP 2hnhA 6 :FVHLRVHSDYSM T0440 14 :HGT 2hnhA 19 :DGL T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPL 2hnhA 22 :AKTAPLVKKAAALGMPALAITDFTNL T0440 44 :SSEFMKNTAG 2hnhA 50 :LVKFYGAGHG T0440 54 :DKEAVTTAS 2hnhA 61 :GIKPIVGAD T0440 65 :MSD 2hnhA 72 :VQC T0440 80 :KKYAS 2hnhA 75 :DLLGD T0440 85 :D 2hnhA 83 :H T0440 88 :IHIGFEVDYLIGYEDFTRDFLNEYGPQTDDGV 2hnhA 86 :VLAANNTGYQNLTLLISKAYQRGYGAAGPIID T0440 134 :I 2hnhA 118 :R T0440 143 :EGIVQ 2hnhA 119 :DWLIE T0440 174 :FKPRR 2hnhA 126 :EGLIL T0440 181 :HISL 2hnhA 133 :GGRM T0440 187 :KFQQFFGEDTSD 2hnhA 139 :VGRSLLRGNSAL T0440 207 :FRVILALVKKR 2hnhA 151 :VDECVAFYEEH T0440 218 :DY 2hnhA 164 :DR T0440 220 :ELDFNTAGLF 2hnhA 167 :FLELIRTGRP T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYST 2hnhA 177 :DEESYLHAAVELAEARGLPVVATNDVRFIDSSDFDAHE Number of specific fragments extracted= 19 number of extra gaps= 5 total=147 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnhA/T0440-2hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2hnhA/T0440-2hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnhA read from 2hnhA/T0440-2hnhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hnhA in template set Warning: unaligning (T0440)V94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N71 Warning: unaligning (T0440)D95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N71 Warning: unaligning (T0440)L120 because of BadResidue code BAD_PEPTIDE in next template residue (2hnhA)T85 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE at template residue (2hnhA)T85 Warning: unaligning (T0440)T196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)D138 Warning: unaligning (T0440)S197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)D138 T0440 1 :M 2hnhA 1 :M T0440 2 :KRDGHTHTEFC 2hnhA 6 :FVHLRVHSDYS T0440 13 :PHGT 2hnhA 19 :DGLA T0440 19 :DVEEMVLKAIELDFDEYSIVEHAPL 2hnhA 23 :KTAPLVKKAAALGMPALAITDFTNL T0440 44 :SSEFM 2hnhA 49 :GLVKF T0440 62 :SMAMSDLP 2hnhA 54 :YGAGHGAG T0440 86 :LLIHIGFE 2hnhA 62 :IKPIVGAD T0440 96 :YLIGYE 2hnhA 72 :VQCDLL T0440 109 :N 2hnhA 78 :G T0440 115 :TDDGV 2hnhA 79 :DELTH T0440 122 :LHF 2hnhA 86 :VLA T0440 151 :GFEQAQLAYLEGVKQSIE 2hnhA 89 :ANNTGYQNLTLLISKAYQ T0440 171 :LGLFKPRRM 2hnhA 107 :RGYGAAGPI T0440 182 :IS 2hnhA 116 :ID T0440 185 :CQK 2hnhA 118 :RDW T0440 192 :FGED 2hnhA 133 :GGRM T0440 198 :DFSEEVM 2hnhA 139 :VGRSLLR T0440 205 :EKFRVILALVKKR 2hnhA 149 :ALVDECVAFYEEH T0440 218 :DY 2hnhA 164 :DR T0440 220 :ELDFNTAGL 2hnhA 167 :FLELIRTGR T0440 235 :ETYP 2hnhA 176 :PDEE T0440 239 :PKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTY 2hnhA 182 :LHAAVELAEARGLPVVATNDVRFIDSSDFDAHEI Number of specific fragments extracted= 22 number of extra gaps= 3 total=169 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hnhA/T0440-2hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2hnhA/T0440-2hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hnhA read from 2hnhA/T0440-2hnhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hnhA in template set Warning: unaligning (T0440)V94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N71 Warning: unaligning (T0440)D95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N71 Warning: unaligning (T0440)D117 because of BadResidue code BAD_PEPTIDE in next template residue (2hnhA)T85 Warning: unaligning (T0440)G118 because of BadResidue code BAD_PEPTIDE at template residue (2hnhA)T85 Warning: unaligning (T0440)F188 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N125 Warning: unaligning (T0440)Q189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N125 T0440 2 :KRDGHTHTEFCPHGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEF 2hnhA 6 :FVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLV T0440 70 :YYFKKMNHI 2hnhA 52 :KFYGAGHGA T0440 85 :DLLIHIGFE 2hnhA 61 :GIKPIVGAD T0440 96 :YLIG 2hnhA 72 :VQCD T0440 112 :GPQTD 2hnhA 79 :DELTH T0440 119 :VLSL 2hnhA 86 :VLAA T0440 152 :F 2hnhA 90 :N T0440 157 :LAYLEGVKQSIEADLGLF 2hnhA 91 :NTGYQNLTLLISKAYQRG T0440 175 :KPRRM 2hnhA 113 :GPIID T0440 182 :ISLCQK 2hnhA 118 :RDWLIE T0440 190 :Q 2hnhA 126 :E T0440 191 :FFGED 2hnhA 145 :RGNSA T0440 206 :KFRVILALVKKR 2hnhA 150 :LVDECVAFYEEH T0440 218 :D 2hnhA 164 :D T0440 219 :YELDFNTAGLFKP 2hnhA 166 :YFLELIRTGRPDE T0440 238 :PPKKIVTLASELQIPFVYGSDSHGVQD 2hnhA 181 :YLHAAVELAEARGLPVVATNDVRFIDS Number of specific fragments extracted= 16 number of extra gaps= 3 total=185 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v77A/T0440-1v77A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v77A expands to /projects/compbio/data/pdb/1v77.pdb.gz 1v77A:# T0440 read from 1v77A/T0440-1v77A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v77A read from 1v77A/T0440-1v77A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v77A to template set # found chain 1v77A in template set T0440 21 :EEMVLKAIEL 1v77A 17 :KEAYELAKEW T0440 32 :FDEYSIVEHAP 1v77A 27 :FDEVVVSIKFN T0440 68 :LPYYFKKMNHIKKKYASDLLIHIG 1v77A 38 :EEVDKEKLREARKEYGKVAILLSN T0440 96 :YL 1v77A 62 :PK T0440 101 :EDFTRDFLNE 1v77A 64 :PSLVRDTVQK T0440 115 :TDDGVLSLHFL 1v77A 74 :FKSYLIYVESN T0440 159 :YLEGVKQSIE 1v77A 85 :DLRVIRYSIE T0440 174 :FKPRRMGHISL 1v77A 95 :KGVDAIISPWV T0440 190 :QFFGEDTSD 1v77A 106 :NRKDPGIDH T0440 209 :VILALVKKRDYELDFNTAGLFKPLC 1v77A 115 :VLAKLMVKKNVALGFSLRPLLYSNP T0440 239 :PKKIVTLASELQIPFVYGSDSHGVQDI 1v77A 149 :MMKAWKLVEKYKVRRFLTSSAQEKWDV Number of specific fragments extracted= 11 number of extra gaps= 0 total=196 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v77A/T0440-1v77A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1v77A/T0440-1v77A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v77A read from 1v77A/T0440-1v77A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v77A in template set T0440 21 :EEMVLKAIEL 1v77A 17 :KEAYELAKEW T0440 32 :FDEYSIVE 1v77A 27 :FDEVVVSI T0440 40 :HAPL 1v77A 36 :FNEE T0440 44 :SSEFMKNTAGDK 1v77A 41 :DKEKLREARKEY T0440 84 :SDLLIHIGFE 1v77A 53 :GKVAILLSNP T0440 100 :YEDFTRDFLNEYG 1v77A 63 :KPSLVRDTVQKFK T0440 115 :TDDGVLSLH 1v77A 76 :SYLIYVESN T0440 151 :GFEQA 1v77A 85 :DLRVI T0440 157 :LA 1v77A 90 :RY T0440 166 :SIE 1v77A 92 :SIE T0440 171 :LGL 1v77A 95 :KGV T0440 175 :K 1v77A 98 :D T0440 178 :RMGHIS 1v77A 99 :AIISPW T0440 189 :QQF 1v77A 105 :VNR T0440 194 :EDTS 1v77A 110 :PGID T0440 201 :EE 1v77A 114 :HV T0440 210 :ILALVKKRDYELDFNTAGLFKPLC 1v77A 116 :LAKLMVKKNVALGFSLRPLLYSNP T0440 239 :PKKIVTLASELQIPFVYGSDSHGVQDIG 1v77A 149 :MMKAWKLVEKYKVRRFLTSSAQEKWDVR Number of specific fragments extracted= 18 number of extra gaps= 0 total=214 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v77A/T0440-1v77A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1v77A/T0440-1v77A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v77A read from 1v77A/T0440-1v77A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v77A in template set T0440 21 :EEMVLKAIELDFDEYSIVEHAPLSSE 1v77A 17 :KEAYELAKEWFDEVVVSIKFNEEVDK T0440 73 :KKMNHIKKKYA 1v77A 43 :EKLREARKEYG T0440 87 :LIHIGFE 1v77A 54 :KVAILLS T0440 98 :IGYEDFTRDFLN 1v77A 61 :NPKPSLVRDTVQ T0440 112 :GPQTDDGVLSL 1v77A 73 :KFKSYLIYVES T0440 151 :GFEQAQLAYLE 1v77A 84 :NDLRVIRYSIE T0440 162 :G 1v77A 115 :V T0440 167 :IEADLGLFKPRRMGHISLCQKFQQ 1v77A 116 :LAKLMVKKNVALGFSLRPLLYSNP T0440 198 :DFSEEVMEKFRVILALVKKRDYELDFNTAGLFKP 1v77A 140 :YERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKW T0440 235 :ETYPPKKIVTLASELQIP 1v77A 174 :DVRYPRDLISLGVVIGME Number of specific fragments extracted= 10 number of extra gaps= 0 total=224 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0440-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j6oA expands to /projects/compbio/data/pdb/1j6o.pdb.gz 1j6oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 1j6oA/T0440-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0440-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j6oA to template set # found chain 1j6oA in template set Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0440 1 :M 1j6oA -2 :H T0440 2 :KRDGHTHTEFC 1j6oA 0 :MVDTHAHLHFH T0440 14 :HGT 1j6oA 11 :QFD T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAP 1j6oA 14 :DDRNAVISSFEENNIEFVVNVGVNL T0440 70 :YYFKKMNHIKKKY 1j6oA 39 :EDSKKSLDLSKTS T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDDGVL 1j6oA 52 :DRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAI T0440 123 :HFLEGQGGFRS 1j6oA 91 :TGLDFFRNISP T0440 156 :QLAYLEGVKQSIEADLGLFKPRRMGH 1j6oA 102 :AEVQKRVFVEQIELAGKLNLPLVVHI T0440 182 :ISLCQKFQQFFG 1j6oA 131 :YSEAYEILRTES T0440 194 :EDT 1j6oA 154 :SSD T0440 204 :MEKFRVILAL 1j6oA 157 :YEWAKKFIDL T0440 218 :DYELDFNTAGLF 1j6oA 167 :GFLLGIGGPVTY T0440 234 :GET 1j6oA 179 :PKN T0440 240 :KKIVTLASELQI 1j6oA 182 :EALREVVKRVGL T0440 252 :PFVYGSDSHGVQDIGRG 1j6oA 195 :YIVLETDCPFLPPQPFR Number of specific fragments extracted= 15 number of extra gaps= 1 total=239 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0440-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1j6oA/T0440-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0440-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6oA in template set Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0440 2 :KRDGHTHTE 1j6oA 0 :MVDTHAHLH T0440 12 :CPHGT 1j6oA 9 :FHQFD T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 1j6oA 14 :DDRNAVISSFEENNIEFVVNVGVNLEDSKKS T0440 62 :SMAMSDL 1j6oA 45 :LDLSKTS T0440 84 :SDLLIHIGF 1j6oA 52 :DRIFCSVGV T0440 93 :EVDYL 1j6oA 64 :DAKEV T0440 98 :IGYEDFTRDFLNE 1j6oA 70 :EDFIEHLEKFAKD T0440 115 :TDDGVL 1j6oA 83 :EKVVAI T0440 123 :HFLEGQ 1j6oA 91 :TGLDFF T0440 133 :SIDF 1j6oA 97 :RNIS T0440 151 :GFEQA 1j6oA 101 :PAEVQ T0440 157 :LAYLEGVKQSIEAD 1j6oA 106 :KRVFVEQIELAGKL T0440 172 :GLF 1j6oA 120 :NLP T0440 178 :RMGH 1j6oA 123 :LVVH T0440 182 :ISLCQK 1j6oA 135 :YEILRT T0440 189 :QQF 1j6oA 141 :ESL T0440 192 :FGED 1j6oA 153 :FSSD T0440 204 :MEKFRVILAL 1j6oA 157 :YEWAKKFIDL T0440 218 :DYELDF 1j6oA 167 :GFLLGI T0440 225 :TAGLFKPL 1j6oA 173 :GGPVTYPK T0440 239 :PKKIVTLASELQIP 1j6oA 181 :NEALREVVKRVGLE T0440 253 :FVYGSDSHGVQDIGRG 1j6oA 196 :IVLETDCPFLPPQPFR Number of specific fragments extracted= 22 number of extra gaps= 1 total=261 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0440-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1j6oA/T0440-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0440-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6oA in template set Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0440 34 :EYSIVEHAPLSSE 1j6oA 0 :MVDTHAHLHFHQF T0440 65 :MSDLPYYFKKM 1j6oA 13 :DDDRNAVISSF T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLN 1j6oA 24 :EENNIEFVVNVGVNLEDSKKSLDLSK T0440 112 :GPQTDDGVLSLHFLEGQG 1j6oA 50 :TSDRIFCSVGVHPHDAKE T0440 151 :GFEQ 1j6oA 68 :VPED T0440 163 :VKQSIEADLGLFKPRRM 1j6oA 72 :FIEHLEKFAKDEKVVAI T0440 182 :ISL 1j6oA 91 :TGL T0440 189 :QQFFGE 1j6oA 94 :DFFRNI T0440 198 :DFSEEVMEKFRVILALVKKRDYELDFNTAGLF 1j6oA 100 :SPAEVQKRVFVEQIELAGKLNLPLVVHIRDAY T0440 230 :KP 1j6oA 139 :RT T0440 233 :CG 1j6oA 141 :ES T0440 235 :ETYPPKKIVTLASELQIPFVYGS 1j6oA 152 :AFSSDYEWAKKFIDLGFLLGIGG T0440 263 :QDIGRGYSTYCQ 1j6oA 175 :PVTYPKNEALRE Number of specific fragments extracted= 13 number of extra gaps= 1 total=274 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gzxA/T0440-2gzxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gzxA expands to /projects/compbio/data/pdb/2gzx.pdb.gz 2gzxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 2gzxA/T0440-2gzxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzxA read from 2gzxA/T0440-2gzxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gzxA to template set # found chain 2gzxA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (2gzxA)L2 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (2gzxA)E92 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (2gzxA)E92 T0440 3 :RDGHTHTEFC 2gzxA 3 :IDTHVHLNDE T0440 14 :HGT 2gzxA 13 :QYD T0440 18 :DDVEEMVLKAIELDFDEYSIVEHA 2gzxA 16 :DDLSEVITRAREAGVDRMFVVGFN T0440 69 :PYYFKKMNHIKKKY 2gzxA 40 :KSTIERAMKLIDEY T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDDGVL 2gzxA 54 :DFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI T0440 123 :HFLEGQGGFRS 2gzxA 93 :MGLDYHWDKSP T0440 138 :A 2gzxA 104 :A T0440 157 :LAYLEGVKQSIEADLGLFKPRRMGHIS 2gzxA 105 :DVQKEVFRKQIALAKRLKLPIIIHNRE T0440 199 :F 2gzxA 132 :A T0440 207 :FRVILALVKKR 2gzxA 133 :TQDCIDILLEE T0440 218 :DYEL 2gzxA 170 :NFYI T0440 224 :NTAGLFKP 2gzxA 174 :SLGGPVTF T0440 234 :GETY 2gzxA 182 :KNAK T0440 241 :KIVTLASELQI 2gzxA 186 :QPKEVAKHVSM T0440 252 :PFVYGSDSHGVQDIGR 2gzxA 198 :RLLVETDAPYLSPHPY Number of specific fragments extracted= 15 number of extra gaps= 1 total=289 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gzxA/T0440-2gzxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2gzxA/T0440-2gzxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzxA read from 2gzxA/T0440-2gzxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gzxA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (2gzxA)L2 Warning: unaligning (T0440)L120 because of BadResidue code BAD_PEPTIDE in next template residue (2gzxA)E92 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE at template residue (2gzxA)E92 T0440 3 :RDGHTHTE 2gzxA 3 :IDTHVHLN T0440 13 :PHGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 2gzxA 11 :DEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERA T0440 62 :SMAMSDL 2gzxA 47 :MKLIDEY T0440 84 :SDLLIHIGFEVDYLIGYE 2gzxA 54 :DFLYGIIGWHPVDAIDFT T0440 102 :DFTRDFLNEYGPQTDDGV 2gzxA 73 :EHLEWIESLAQHPKVIGI T0440 122 :LHFLEG 2gzxA 93 :MGLDYH T0440 171 :LGLFK 2gzxA 99 :WDKSP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGL 2gzxA 104 :ADVQKEVFRKQIALAKRLKLPIIIHNREA T0440 239 :PKKIVTLASELQ 2gzxA 133 :TQDCIDILLEEH T0440 251 :IPFVYG 2gzxA 148 :VGGIMH Number of specific fragments extracted= 10 number of extra gaps= 1 total=299 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gzxA/T0440-2gzxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2gzxA/T0440-2gzxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gzxA read from 2gzxA/T0440-2gzxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gzxA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (2gzxA)L2 Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (2gzxA)E92 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (2gzxA)E92 T0440 3 :RDGHTHTEF 2gzxA 3 :IDTHVHLND T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVE 2gzxA 12 :EQYDDDLSEVITRAREAGVDRMFVVG T0440 96 :YLIGYEDFTRDFLN 2gzxA 38 :FNKSTIERAMKLID T0440 112 :GPQTDDGVLSLHFL 2gzxA 52 :EYDFLYGIIGWHPV T0440 147 :QFYGGFE 2gzxA 66 :DAIDFTE T0440 162 :GVKQSIEADLGLFKPRRM 2gzxA 73 :EHLEWIESLAQHPKVIGI T0440 182 :ISL 2gzxA 93 :MGL T0440 190 :QFFGED 2gzxA 96 :DYHWDK T0440 198 :DFSEEVMEKFRVILALVKKRDYELDFNTAG 2gzxA 102 :SPADVQKEVFRKQIALAKRLKLPIIIHNRE T0440 238 :PPKKIVTLASELQ 2gzxA 132 :ATQDCIDILLEEH T0440 251 :IPFVY 2gzxA 148 :VGGIM Number of specific fragments extracted= 11 number of extra gaps= 1 total=310 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0440-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vflA expands to /projects/compbio/data/pdb/1vfl.pdb.gz 1vflA:# T0440 read from 1vflA/T0440-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0440-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vflA to template set # found chain 1vflA in template set T0440 2 :KRDGHTHT 1vflA 8 :KVELHVHL T0440 14 :HGT 1vflA 16 :DGA T0440 18 :DDVEEMVLKAIELDFD 1vflA 19 :IKPETILYYGKRRGIA T0440 41 :APL 1vflA 35 :LPA T0440 44 :SSEFMKNTA 1vflA 40 :PEELQNIIG T0440 57 :AVTTASMAMSD 1vflA 97 :VRYSPHLLANS T0440 70 :YYFKKMNHIKKKYASDLLIHIG 1vflA 129 :LVNQGLQEGERDFGVKVRSILC T0440 93 :EVDYLIGYEDFTRDFLNEYGPQ 1vflA 151 :CMRHQPSWSSEVVELCKKYREQ T0440 118 :GVLSLHFLEGQGGFRS 1vflA 173 :TVVAIDLAGDETIEGS T0440 134 :IDFSAEDYNEGIVQ 1vflA 191 :FPGHVQAYAEAVKS T0440 151 :GFEQAQ 1vflA 205 :GVHRTV T0440 165 :QSIEADLGLFKPRRMGHISLCQ 1vflA 219 :NVVKEAVDTLKTERLGHGYHTL T0440 195 :DTSDF 1vflA 241 :EDTTL T0440 211 :LALVKKRDYELDFNTA 1vflA 246 :YNRLRQENMHFEICPW T0440 227 :GLFKPLCG 1vflA 267 :GAWKPDTE T0440 237 :Y 1vflA 275 :H T0440 242 :IVTLASELQIPFVYGSD 1vflA 276 :AVIRFKNDQVNYSLNTD Number of specific fragments extracted= 17 number of extra gaps= 0 total=327 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0440-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1vflA/T0440-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0440-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vflA in template set T0440 3 :RDGHTHTEFC 1vflA 9 :VELHVHLDGA T0440 19 :DVEEMVLKAIELDFD 1vflA 20 :KPETILYYGKRRGIA T0440 41 :APL 1vflA 35 :LPA T0440 44 :SSEFMKNTAGDKE 1vflA 39 :TPEELQNIIGMDK T0440 62 :SMAMSDLPYYFKK 1vflA 113 :PWNQAEGDLTPDE T0440 75 :MNHIKKKY 1vflA 134 :LQEGERDF T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQT 1vflA 142 :GVKVRSILCCMRHQPSWSSEVVELCKKYREQT T0440 118 :GVLSLHF 1vflA 174 :VVAIDLA T0440 133 :SIDFSAEDY 1vflA 181 :GDETIEGSS T0440 151 :GFEQA 1vflA 190 :LFPGH T0440 157 :LAYLEGVKQ 1vflA 195 :VQAYAEAVK T0440 171 :LGLFKPRRMG 1vflA 204 :SGVHRTVHAG T0440 182 :ISLCQKFQQF 1vflA 218 :ANVVKEAVDT T0440 192 :FGEDTSDF 1vflA 238 :HTLEDTTL T0440 211 :LALVKKRDYELDFN 1vflA 246 :YNRLRQENMHFEIC T0440 227 :GLFKP 1vflA 267 :GAWKP T0440 234 :GETYPPKKIV 1vflA 272 :DTEHAVIRFK T0440 248 :ELQIPFVYGSD 1vflA 282 :NDQVNYSLNTD Number of specific fragments extracted= 18 number of extra gaps= 0 total=345 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0440-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1vflA/T0440-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0440-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vflA in template set T0440 20 :VEEMVLKAIELDFDEYSIVEH 1vflA 80 :AYEFVEMKAKDGVVYVEVRYS T0440 41 :APLSSEFMKNTAGDKEAV 1vflA 109 :VEPIPWNQAEGDLTPDEV T0440 68 :LPYYFKKMNHIKKKY 1vflA 127 :VSLVNQGLQEGERDF T0440 85 :DLLIHIGFEVDY 1vflA 142 :GVKVRSILCCMR T0440 97 :LIGYEDFTRDFLNE 1vflA 155 :QPSWSSEVVELCKK T0440 112 :GPQTDDGVLSL 1vflA 169 :YREQTVVAIDL T0440 123 :HFLEGQGGFRS 1vflA 181 :GDETIEGSSLF T0440 154 :QAQLAYLEGVKQS 1vflA 192 :PGHVQAYAEAVKS T0440 167 :IEADLGLFKPRRMGHISLCQ 1vflA 221 :VKEAVDTLKTERLGHGYHTL T0440 198 :DF 1vflA 241 :ED T0440 201 :EEV 1vflA 243 :TTL T0440 211 :LALVKKRDYELDFNTA 1vflA 246 :YNRLRQENMHFEICPW T0440 227 :GLFKP 1vflA 267 :GAWKP T0440 233 :CGET 1vflA 272 :DTEH T0440 242 :IVTLASELQIPFVYGSD 1vflA 276 :AVIRFKNDQVNYSLNTD Number of specific fragments extracted= 15 number of extra gaps= 0 total=360 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ob3A/T0440-2ob3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2ob3A/T0440-2ob3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ob3A read from 2ob3A/T0440-2ob3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ob3A in training set Warning: unaligning (T0440)T60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)T128 Warning: unaligning (T0440)A61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)T128 Warning: unaligning (T0440)A64 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)F132 Warning: unaligning (T0440)M65 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)F132 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ob3A)V170 Warning: unaligning (T0440)F124 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ob3A)V170 Warning: unaligning (T0440)K175 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)V196 Warning: unaligning (T0440)P176 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)V196 Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)H201 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)H201 Warning: unaligning (T0440)I182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)A203 Warning: unaligning (T0440)S183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)A203 T0440 5 :GHTHTEFCPH 2ob3A 54 :THEHICGSSA T0440 18 :DDVEE 2ob3A 74 :GSRKA T0440 23 :MVLKAIELDFDEYSIVEHAPL 2ob3A 86 :GLRRARAAGVRTIVDVSTFDI T0440 44 :SSEFMKNTAG 2ob3A 110 :VSLLAEVSRA T0440 54 :DKEAVT 2ob3A 121 :DVHIVA T0440 62 :SM 2ob3A 129 :GL T0440 66 :SDLP 2ob3A 133 :DPPL T0440 77 :HIKKKYASDL 2ob3A 137 :SMRLRSVEEL T0440 101 :EDFTRDFLNEYGPQTDDGVLS 2ob3A 147 :TQFFLREIQYGIEDTGIRAGI T0440 125 :LEGQ 2ob3A 171 :ATTG T0440 151 :GFEQAQLAYLEGVKQSIEAD 2ob3A 175 :KATPFQELVLKAAARASLAT T0440 177 :RRM 2ob3A 197 :PVT T0440 184 :LCQKF 2ob3A 204 :ASQRD T0440 207 :FRVILALVKKRDY 2ob3A 209 :GEQQAAIFESEGL T0440 220 :ELDFNTAGLFKP 2ob3A 225 :RVCIGHSDDTDD T0440 239 :PKKIVTLA 2ob3A 237 :LSYLTALA T0440 248 :ELQIPFVYGS 2ob3A 245 :ARGYLIGLDH Number of specific fragments extracted= 17 number of extra gaps= 4 total=377 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ob3A/T0440-2ob3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2ob3A/T0440-2ob3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ob3A read from 2ob3A/T0440-2ob3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ob3A in training set Warning: unaligning (T0440)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)T128 Warning: unaligning (T0440)F92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)T128 Warning: unaligning (T0440)D95 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)F132 Warning: unaligning (T0440)Y96 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)F132 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ob3A)V170 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ob3A)V170 Warning: unaligning (T0440)L173 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)V196 Warning: unaligning (T0440)F174 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)V196 Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)H201 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)H201 Warning: unaligning (T0440)I182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)A203 Warning: unaligning (T0440)S183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)A203 T0440 20 :VEEMVLKAIELDFDEYSIVEHAPL 2ob3A 83 :AVRGLRRARAAGVRTIVDVSTFDI T0440 44 :SSEFM 2ob3A 109 :DVSLL T0440 62 :SMAMSDLP 2ob3A 114 :AEVSRAAD T0440 86 :LLIHI 2ob3A 122 :VHIVA T0440 93 :EV 2ob3A 129 :GL T0440 97 :L 2ob3A 133 :D T0440 98 :IG 2ob3A 136 :LS T0440 100 :YEDFTRDFLNE 2ob3A 142 :SVEELTQFFLR T0440 111 :YGPQ 2ob3A 158 :IEDT T0440 115 :TDDGV 2ob3A 163 :IRAGI T0440 123 :HF 2ob3A 171 :AT T0440 126 :EGQ 2ob3A 173 :TGK T0440 151 :GFEQA 2ob3A 176 :ATPFQ T0440 157 :LAYLEGVKQSIEA 2ob3A 181 :ELVLKAAARASLA T0440 172 :G 2ob3A 194 :T T0440 175 :K 2ob3A 197 :P T0440 178 :RM 2ob3A 198 :VT T0440 192 :FGED 2ob3A 204 :ASQR T0440 206 :KFRVILALVKKRDY 2ob3A 208 :DGEQQAAIFESEGL T0440 220 :ELDFNTAGLFKP 2ob3A 225 :RVCIGHSDDTDD T0440 239 :PKKIVTLA 2ob3A 237 :LSYLTALA T0440 248 :ELQIPFVYGSDSHGVQDIG 2ob3A 245 :ARGYLIGLDHIPYSAIGLE T0440 268 :GYSTY 2ob3A 264 :DNASA Number of specific fragments extracted= 23 number of extra gaps= 4 total=400 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ob3A/T0440-2ob3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2ob3A/T0440-2ob3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ob3A read from 2ob3A/T0440-2ob3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ob3A in training set Warning: unaligning (T0440)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)T128 Warning: unaligning (T0440)F92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)T128 Warning: unaligning (T0440)L97 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)F132 Warning: unaligning (T0440)I98 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)F132 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ob3A)V170 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ob3A)V170 Warning: unaligning (T0440)K175 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)V196 Warning: unaligning (T0440)P176 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)V196 Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)H201 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)H201 Warning: unaligning (T0440)I182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ob3A)A203 Warning: unaligning (T0440)S183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ob3A)A203 T0440 20 :VEEMVLKAIELDFD 2ob3A 83 :AVRGLRRARAAGVR T0440 36 :SIVEHAPLSSEFM 2ob3A 97 :TIVDVSTFDIGRD T0440 72 :FKKMNHIKKKY 2ob3A 110 :VSLLAEVSRAA T0440 85 :DLLIHI 2ob3A 121 :DVHIVA T0440 95 :DY 2ob3A 129 :GL T0440 99 :G 2ob3A 133 :D T0440 100 :YEDFTRDFLNE 2ob3A 146 :LTQFFLREIQY T0440 112 :GPQTDDGV 2ob3A 160 :DTGIRAGI T0440 126 :EGQ 2ob3A 171 :ATT T0440 150 :GGFEQAQLAYLEGVKQSIEAD 2ob3A 174 :GKATPFQELVLKAAARASLAT T0440 177 :RRM 2ob3A 197 :PVT T0440 184 :LCQKFQQ 2ob3A 204 :ASQRDGE T0440 192 :FG 2ob3A 233 :DT T0440 198 :DFSEEVME 2ob3A 235 :DDLSYLTA T0440 214 :VKKRDYELDFNTAGLFKPLCG 2ob3A 243 :LAARGYLIGLDHIPYSAIGLE T0440 235 :ETYPPKKIVTLASE 2ob3A 273 :GIRSWQTRALLIKA T0440 249 :LQI 2ob3A 290 :QGY T0440 253 :FVYGSD 2ob3A 296 :ILVSND Number of specific fragments extracted= 18 number of extra gaps= 4 total=418 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0440-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zzmA expands to /projects/compbio/data/pdb/1zzm.pdb.gz 1zzmA:# T0440 read from 1zzmA/T0440-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0440-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zzmA to template set # found chain 1zzmA in template set Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 T0440 2 :KRDGHTHTEF 1zzmA 5 :FIDTHCHFDF T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVEHAP 1zzmA 15 :PPFSGDEEASLQRAAQAGVGKIIVPATEA T0440 70 :YYFKKMNHIKKKY 1zzmA 44 :ENFARVLALAENY T0440 84 :SDLLIHIGFEV 1zzmA 57 :QPLYAALGLHP T0440 95 :DYLIGYEDFTRDFLNEYG 1zzmA 72 :KHSDVSLEQLQQALERRP T0440 115 :TDDGVL 1zzmA 90 :AKVVAV T0440 123 :HFLEGQGGFRS 1zzmA 98 :IGLDLFGDDPQ T0440 156 :QLAYLEGVKQSIEADLGLFKPRRMGHISL 1zzmA 109 :FERQQWLLDEQLKLAKRYDLPVILHSRRT T0440 200 :SEEVMEKFRV 1zzmA 138 :HDKLAMHLKR T0440 210 :ILALVKKRDYELDFNTAGLF 1zzmA 165 :QAERFVQLGYKIGVGGTITY T0440 231 :PLCGE 1zzmA 185 :PRASK T0440 242 :IVTLASELQI 1zzmA 190 :TRDVIAKLPL T0440 252 :PFVYGSDSHGVQDIG 1zzmA 201 :SLLLETDAPDMPLNG Number of specific fragments extracted= 13 number of extra gaps= 1 total=431 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0440-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1zzmA/T0440-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0440-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0440)H123 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 T0440 1 :M 1zzmA 1 :M T0440 2 :KRDGHTH 1zzmA 5 :FIDTHCH T0440 11 :FCPHGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 1zzmA 12 :FDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARV T0440 62 :SMAMSDL 1zzmA 50 :LALAENY T0440 84 :SDLLIHIGFEVDYL 1zzmA 57 :QPLYAALGLHPGML T0440 98 :IGYEDFTRDFLNEY 1zzmA 75 :DVSLEQLQQALERR T0440 115 :TDDGVLS 1zzmA 89 :PAKVVAV T0440 124 :F 1zzmA 98 :I T0440 133 :SIDFSAE 1zzmA 99 :GLDLFGD T0440 173 :LFK 1zzmA 106 :DPQ T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGL 1zzmA 109 :FERQQWLLDEQLKLAKRYDLPVILHSRRT T0440 239 :PKKIVTLASELQIP 1zzmA 138 :HDKLAMHLKRHDLP T0440 253 :FVY 1zzmA 154 :GVV Number of specific fragments extracted= 13 number of extra gaps= 1 total=444 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0440-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1zzmA/T0440-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0440-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set Warning: unaligning (T0440)I182 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0440)S183 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 T0440 3 :RDGHTHTEF 1zzmA 6 :IDTHCHFDF T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVE 1zzmA 15 :PPFSGDEEASLQRAAQAGVGKIIVPA T0440 63 :MAMSDLPYYFKKMN 1zzmA 41 :TEAENFARVLALAE T0440 112 :GPQTDDGVLSLHFLEGQGGF 1zzmA 55 :NYQPLYAALGLHPGMLEKHS T0440 138 :A 1zzmA 75 :D T0440 162 :GVKQSIEADLGLFKPRRMGH 1zzmA 76 :VSLEQLQQALERRPAKVVAV T0440 184 :LCQKFQQ 1zzmA 98 :IGLDLFG T0440 195 :DT 1zzmA 105 :DD T0440 198 :DFSEEVMEKFRVILALVKKRDYELDFNTAGL 1zzmA 107 :PQFERQQWLLDEQLKLAKRYDLPVILHSRRT T0440 239 :PKKIVTLASELQI 1zzmA 138 :HDKLAMHLKRHDL T0440 252 :PFVY 1zzmA 153 :TGVV Number of specific fragments extracted= 11 number of extra gaps= 1 total=455 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ffiA/T0440-2ffiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ffiA expands to /projects/compbio/data/pdb/2ffi.pdb.gz 2ffiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 2ffiA/T0440-2ffiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ffiA read from 2ffiA/T0440-2ffiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ffiA to template set # found chain 2ffiA in template set T0440 2 :KRDGHTHTE 2ffiA 14 :AIDSHAHVF T0440 11 :FCP 2ffiA 33 :RYA T0440 14 :HGT 2ffiA 37 :NYD T0440 18 :DDVEEMVLKAIELDFDEYSI 2ffiA 40 :APLGDYLGQLRAHGFSHGVL T0440 63 :MAMSDLPYYFKKMNHIKKKYASDLL 2ffiA 60 :VQPSFLGTDNRYLLSALQTVPGQLR T0440 93 :EVDYLI 2ffiA 85 :GVVMLE T0440 99 :G 2ffiA 92 :D T0440 100 :YEDFTRDFL 2ffiA 94 :EQATLAEMA T0440 110 :EYG 2ffiA 103 :RLG T0440 115 :T 2ffiA 106 :V T0440 117 :DGVLSL 2ffiA 107 :RGVRLN T0440 128 :QGGFRSIDFSAEDYNEGIVQFYG 2ffiA 113 :LMGQDMPDLTGAQWRPLLERIGE T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMGHISLCQKF 2ffiA 137 :GWHVELHRQVADIPVLVRALQPYGLDIVIDHFGRPDAR T0440 195 :DTSDFSEEVMEKFRVILALVKKRDY 2ffiA 203 :RLQGSPEENLAFARQALCALEAHYG T0440 220 :ELDFNTAGLFKP 2ffiA 231 :LMWGSDWPHTQH T0440 234 :GETYPPKKIVTLASELQIP 2ffiA 243 :ESEVSFGSAVEQFEALGCS Number of specific fragments extracted= 16 number of extra gaps= 0 total=471 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ffiA/T0440-2ffiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2ffiA/T0440-2ffiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ffiA read from 2ffiA/T0440-2ffiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ffiA in template set T0440 1 :M 2ffiA 12 :L T0440 2 :KRDGHTHTE 2ffiA 14 :AIDSHAHVF T0440 11 :FCPHGT 2ffiA 35 :APNYDA T0440 19 :DVEEMVLKAIELDFDEYSIVEHAPL 2ffiA 41 :PLGDYLGQLRAHGFSHGVLVQPSFL T0440 44 :SSEFM 2ffiA 68 :DNRYL T0440 62 :S 2ffiA 73 :L T0440 77 :HIKKKYASDL 2ffiA 74 :SALQTVPGQL T0440 90 :IGFEVDYLIGYEDFTRDFLNE 2ffiA 84 :RGVVMLERDVEQATLAEMARL T0440 115 :TDDGVLSLHFLEGQGGFRS 2ffiA 105 :GVRGVRLNLMGQDMPDLTG T0440 139 :E 2ffiA 124 :A T0440 151 :GFEQAQLAYLE 2ffiA 125 :QWRPLLERIGE T0440 162 :GVKQSIEADLGLFKPRRMGHIS 2ffiA 148 :DIPVLVRALQPYGLDIVIDHFG T0440 192 :FGEDTSDFSEEVMEKFRVILALVKKRDY 2ffiA 200 :GIYRLQGSPEENLAFARQALCALEAHYG T0440 220 :ELDFNTAGL 2ffiA 231 :LMWGSDWPH T0440 230 :KPL 2ffiA 240 :TQH T0440 234 :GETYPPKKIVTLASELQIP 2ffiA 243 :ESEVSFGSAVEQFEALGCS Number of specific fragments extracted= 16 number of extra gaps= 0 total=487 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ffiA/T0440-2ffiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2ffiA/T0440-2ffiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ffiA read from 2ffiA/T0440-2ffiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ffiA in template set T0440 23 :MVLKAIELDFDEYSI 2ffiA 97 :TLAEMARLGVRGVRL T0440 42 :PLSSE 2ffiA 112 :NLMGQ T0440 59 :TTASMAMSDLPYYFKKMNHI 2ffiA 117 :DMPDLTGAQWRPLLERIGEQ T0440 85 :DLLI 2ffiA 137 :GWHV T0440 93 :EVDYLIGYEDFTRDFLN 2ffiA 141 :ELHRQVADIPVLVRALQ T0440 112 :GPQTDDGV 2ffiA 158 :PYGLDIVI T0440 124 :FLEGQGGFRSIDF 2ffiA 167 :HFGRPDARRGLGQ T0440 143 :EGIVQFYGGF 2ffiA 180 :PGFAELLTLS T0440 173 :LFKPRRMGHISL 2ffiA 190 :GRGKVWVKVSGI T0440 186 :QK 2ffiA 202 :YR T0440 192 :FG 2ffiA 204 :LQ T0440 198 :DFSEEVMEKFRVILALVKKRDY 2ffiA 206 :GSPEENLAFARQALCALEAHYG T0440 221 :LDFNTAGLFKP 2ffiA 231 :LMWGSDWPHTQ T0440 233 :CGETYPPKKIVTLASELQI 2ffiA 242 :HESEVSFGSAVEQFEALGC Number of specific fragments extracted= 14 number of extra gaps= 0 total=501 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vc7A/T0440-2vc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2vc7A expands to /projects/compbio/data/pdb/2vc7.pdb.gz 2vc7A:Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 484, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 485, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 486, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 487, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 488, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 489, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 490, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 491, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 492, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 493, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 494, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 592, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 593, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 594, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 596, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 598, because occupancy 0.300 <= existing 0.700 in 2vc7A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2vc7A Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 1239, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1240, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1241, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1242, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1243, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1244, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1245, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1246, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1247, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1343, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1344, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1345, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1346, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1347, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1348, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1349, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1350, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1369, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1370, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1371, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1372, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1373, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1374, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1375, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1376, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1377, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1395, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1399, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1400, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1402, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1487, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1488, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1489, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1490, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1491, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1492, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1493, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1494, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1560, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1561, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1562, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1563, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1564, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1565, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1566, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1567, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1568, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1569, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1570, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1826, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1827, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1828, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1829, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1830, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1831, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 1882, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1884, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1886, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1887, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1888, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1889, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1890, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1891, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 1892, because occupancy 0.500 <= existing 0.500 in 2vc7A Skipped atom 2011, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2012, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2013, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2014, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2015, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2016, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2017, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2018, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2019, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2483, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2484, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2485, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2486, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2487, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2488, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2489, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2490, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2491, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2492, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2493, because occupancy 0.480 <= existing 0.520 in 2vc7A Skipped atom 2603, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2604, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2605, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2606, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2607, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2608, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2609, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2610, because occupancy 0.400 <= existing 0.600 in 2vc7A Skipped atom 2611, because occupancy 0.400 <= existing 0.600 in 2vc7A # T0440 read from 2vc7A/T0440-2vc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vc7A read from 2vc7A/T0440-2vc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vc7A to template set # found chain 2vc7A in template set Warning: unaligning (T0440)L86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vc7A)I138 Warning: unaligning (T0440)F223 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2vc7A)D222 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2vc7A)D222 T0440 20 :VEEMVLKAIELDFDEYSIVEHAPL 2vc7A 49 :AVNEVKRAMQFGVKTIVDPTVMGL T0440 44 :SSEFMKNT 2vc7A 79 :MEKVVKAT T0440 54 :DKEAVTTASMAMSD 2vc7A 87 :GINLVAGTGIYIYI T0440 68 :LPYYFKKMNHIKKKYAS 2vc7A 107 :LNRSIDEIADLFIHDIK T0440 87 :LIHIGFEVDYLIGYEDFTRDFLNEYG 2vc7A 139 :AADEPGITKDVEKVIRAAAIANKETK T0440 115 :TDDGVLS 2vc7A 165 :VPIITHS T0440 126 :EGQG 2vc7A 172 :NAHN T0440 161 :EGVKQSIEADLGLFKP 2vc7A 176 :NTGLEQQRILTEEGVD T0440 177 :RRMGHISL 2vc7A 195 :ILIGHLGD T0440 193 :GED 2vc7A 203 :TDN T0440 204 :MEKFRVILA 2vc7A 206 :IDYIKKIAD T0440 217 :RDYELD 2vc7A 215 :KGSFIG T0440 225 :TAGL 2vc7A 223 :RYGL T0440 234 :GETYPPKKIVTLAS 2vc7A 227 :DLFLPVDKRNETTL T0440 248 :ELQI 2vc7A 244 :KDGY T0440 252 :PFVYGSDSHGV 2vc7A 250 :KIMISHDYCCT T0440 263 :QDIGRGY 2vc7A 264 :GTAKPEY Number of specific fragments extracted= 17 number of extra gaps= 1 total=518 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vc7A/T0440-2vc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2vc7A/T0440-2vc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vc7A read from 2vc7A/T0440-2vc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vc7A in template set Warning: unaligning (T0440)S121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vc7A)I138 Warning: unaligning (T0440)H123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vc7A)I138 Warning: unaligning (T0440)Y255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2vc7A)D222 Warning: unaligning (T0440)G256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2vc7A)D222 T0440 20 :VEEMVLKAIELDFDEYSIVEHAPL 2vc7A 49 :AVNEVKRAMQFGVKTIVDPTVMGL T0440 44 :SSEFM 2vc7A 75 :DIRFM T0440 62 :SMAMSDLP 2vc7A 80 :EKVVKATG T0440 86 :LLIHIGFEVDYLIG 2vc7A 88 :INLVAGTGIYIYID T0440 100 :YEDFTRDFLNEYGPQTDD 2vc7A 114 :IADLFIHDIKEGIQGTLN T0440 118 :GVL 2vc7A 133 :AGF T0440 124 :FLEGQ 2vc7A 139 :AADEP T0440 151 :GFEQAQLAYLEGVKQSIEA 2vc7A 144 :GITKDVEKVIRAAAIANKE T0440 172 :GLFK 2vc7A 163 :TKVP T0440 178 :RMGHIS 2vc7A 167 :IITHSN T0440 189 :QQF 2vc7A 173 :AHN T0440 194 :ED 2vc7A 176 :NT T0440 207 :FRVILALVKKRDY 2vc7A 178 :GLEQQRILTEEGV T0440 220 :ELDFNTAGL 2vc7A 194 :KILIGHLGD T0440 236 :TYPPKKIVTLA 2vc7A 203 :TDNIDYIKKIA T0440 248 :ELQIPFV 2vc7A 214 :DKGSFIG T0440 257 :SD 2vc7A 223 :RY Number of specific fragments extracted= 17 number of extra gaps= 1 total=535 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vc7A/T0440-2vc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2vc7A/T0440-2vc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vc7A read from 2vc7A/T0440-2vc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vc7A in template set Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vc7A)I138 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vc7A)I138 Warning: unaligning (T0440)F223 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2vc7A)D222 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2vc7A)D222 T0440 20 :VEEMVLKAIELDFDEYSIVEHAPLSSE 2vc7A 49 :AVNEVKRAMQFGVKTIVDPTVMGLGRD T0440 72 :FKKMNHIKKKY 2vc7A 76 :IRFMEKVVKAT T0440 85 :DLLIHIG 2vc7A 87 :GINLVAG T0440 94 :VDYLIG 2vc7A 94 :TGIYIY T0440 100 :YEDFTRDFLNE 2vc7A 114 :IADLFIHDIKE T0440 112 :GPQTDDGV 2vc7A 128 :GTLNKAGF T0440 125 :LEGQGGFRS 2vc7A 139 :AADEPGITK T0440 159 :YLEGVKQSIEADLGLFKPRRMGHIS 2vc7A 148 :DVEKVIRAAAIANKETKVPIITHSN T0440 184 :LCQKFQQ 2vc7A 177 :TGLEQQR T0440 195 :DTSDFSEEVME 2vc7A 201 :GDTDNIDYIKK T0440 214 :VKKRDYELD 2vc7A 212 :IADKGSFIG T0440 225 :TAGLFKP 2vc7A 223 :RYGLDLF T0440 237 :YPPKKIVTLASE 2vc7A 230 :LPVDKRNETTLR T0440 249 :LQI 2vc7A 245 :DGY T0440 252 :PFVYGSDS 2vc7A 250 :KIMISHDY Number of specific fragments extracted= 15 number of extra gaps= 1 total=550 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0440-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yixA expands to /projects/compbio/data/pdb/1yix.pdb.gz 1yixA:# T0440 read from 1yixA/T0440-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0440-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yixA to template set # found chain 1yixA in template set Warning: unaligning (T0440)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0440 2 :KRDGHTHT 1yixA 3 :LVDSHCHL T0440 10 :EFCP 1yixA 12 :GLDY T0440 14 :HGT 1yixA 17 :SLH T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPL 1yixA 20 :KDVDDVLAKAAARDVKFCLAVATTLP T0440 44 :SSEFMKNTAG 1yixA 47 :YLHMRDLVGE T0440 54 :DKEAVTT 1yixA 59 :NVVFSCG T0440 63 :MAMSDLP 1yixA 66 :VHPLNQN T0440 81 :KYAS 1yixA 73 :DPYD T0440 101 :EDFTRDFLNE 1yixA 77 :VEDLRRLAAE T0440 114 :QTDDGV 1yixA 87 :EGVVAL T0440 122 :LHF 1yixA 95 :TGL T0440 126 :EGQGG 1yixA 98 :DYYYT T0440 151 :GFE 1yixA 103 :PET T0440 156 :QLAYLEGVKQSIEADLGLFKPRRMGHI 1yixA 106 :KVRQQESFIHHIQIGRELNKPVIVHTR T0440 198 :DFSEEVMEKFRV 1yixA 133 :DARADTLAILRE T0440 210 :ILALVKKRDYELDFNTAGLF 1yixA 163 :TAGKLLDLGFYISFSGIVTF T0440 234 :GET 1yixA 183 :RNA T0440 240 :KKIVTLASELQI 1yixA 186 :EQLRDAARYVPL T0440 252 :PFVYGSDSHGVQDIGR 1yixA 199 :RLLVETDSPYLAPVPH Number of specific fragments extracted= 19 number of extra gaps= 1 total=569 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0440-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1yixA/T0440-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0440-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yixA in template set Warning: unaligning (T0440)I90 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0440)G91 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0440 3 :RDGHTHTEFCPHGT 1yixA 4 :VDSHCHLDGLDYES T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAP 1yixA 20 :KDVDDVLAKAAARDVKFCLAVATTL T0440 44 :SSEFMKNTAGDKE 1yixA 46 :SYLHMRDLVGERD T0440 61 :ASMAMSDLPYY 1yixA 64 :CGVHPLNQNDP T0440 73 :KKMNHIKKKY 1yixA 75 :YDVEDLRRLA T0440 83 :ASDLLIH 1yixA 86 :EEGVVAL T0440 92 :FEVDYL 1yixA 95 :TGLDYY T0440 98 :IGYEDFTRDFLNEY 1yixA 103 :PETKVRQQESFIHH T0440 211 :LALVKKRDYELDFNTAGL 1yixA 117 :IQIGRELNKPVIVHTRDA T0440 239 :PKKIVTLASELQIP 1yixA 135 :RADTLAILREEKVT T0440 253 :FVY 1yixA 152 :GVL Number of specific fragments extracted= 11 number of extra gaps= 1 total=580 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0440-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1yixA/T0440-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0440-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yixA in template set Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0440 1 :MKRDGHTHTE 1yixA 2 :FLVDSHCHLD T0440 11 :FCPHGTHDDVEEMVLKAIELDFDEYSIVE 1yixA 13 :LDYESLHKDVDDVLAKAAARDVKFCLAVA T0440 45 :S 1yixA 42 :T T0440 64 :A 1yixA 43 :T T0440 72 :FKKMNHIKKKYA 1yixA 44 :LPSYLHMRDLVG T0440 112 :GPQTDDGVLSLHFLEGQGGFRS 1yixA 56 :ERDNVVFSCGVHPLNQNDPYDV T0440 165 :QSIEADLGLFKPRRM 1yixA 78 :EDLRRLAAEEGVVAL T0440 182 :ISL 1yixA 95 :TGL T0440 192 :FGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTAG 1yixA 98 :DYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRD T0440 228 :LFKPLCG 1yixA 145 :EKVTDCG T0440 235 :ETYPPKKIVTLASELQIPFVYGS 1yixA 156 :CFTEDRETAGKLLDLGFYISFSG T0440 263 :QDIGRGYSTYC 1yixA 179 :IVTFRNAEQLR Number of specific fragments extracted= 12 number of extra gaps= 1 total=592 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qahA/T0440-2qahA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qahA expands to /projects/compbio/data/pdb/2qah.pdb.gz 2qahA:# T0440 read from 2qahA/T0440-2qahA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qahA read from 2qahA/T0440-2qahA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qahA to template set # found chain 2qahA in template set Warning: unaligning (T0440)D4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A30 Warning: unaligning (T0440)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)A30 Warning: unaligning (T0440)A64 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)D104 Warning: unaligning (T0440)M65 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)D104 Warning: unaligning (T0440)H77 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2qahA)L115 Warning: unaligning (T0440)I78 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2qahA)L115 Warning: unaligning (T0440)I98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A135 Warning: unaligning (T0440)G99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)A135 Warning: unaligning (T0440)Y100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)P136 Warning: unaligning (T0440)S259 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)P250 Warning: unaligning (T0440)H260 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)P250 T0440 1 :M 2qahA 25 :P T0440 2 :KR 2qahA 27 :AI T0440 6 :HTHTEFCP 2qahA 31 :HCHVFGPM T0440 14 :HGT 2qahA 40 :QFP T0440 17 :HDDVEEMVLKAIELDFDEYSIVEHAPL 2qahA 53 :DAGPDMLFALRDHLGFARNVIVQASCH T0440 44 :SSEFMKNTAG 2qahA 86 :TLDAIARAQG T0440 57 :AVTTASM 2qahA 96 :KARGIAV T0440 66 :SDLPY 2qahA 105 :PAIDE T0440 73 :KKMN 2qahA 110 :AELA T0440 79 :KKK 2qahA 116 :HEG T0440 85 :DLLIHIGFEVD 2qahA 119 :GMRGIRFNFLK T0440 96 :YL 2qahA 132 :VD T0440 101 :EDFTRDFLNEYGPQTD 2qahA 137 :KDKFLEVAGRLPAGWH T0440 120 :LSLHFLEGQ 2qahA 153 :VVIYFEADI T0440 163 :VKQSIEADLGLFKPRRMGHISLCQKFQQFFGEDTSD 2qahA 162 :LEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKA T0440 207 :FRVILAL 2qahA 198 :FRRLLDS T0440 219 :Y 2qahA 205 :R T0440 220 :ELDFNTAGLF 2qahA 207 :DIWFKATCPD T0440 230 :KPLCGETYP 2qahA 219 :DPAGPPWDD T0440 239 :PKKIVTLASELQIPFVYGSD 2qahA 229 :ARSVAPLVADYADRVIWGTD T0440 261 :GVQDIGR 2qahA 251 :HPNMQDA Number of specific fragments extracted= 21 number of extra gaps= 5 total=613 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qahA/T0440-2qahA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2qahA/T0440-2qahA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qahA read from 2qahA/T0440-2qahA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qahA in template set Warning: unaligning (T0440)D4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A30 Warning: unaligning (T0440)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)A30 Warning: unaligning (T0440)D95 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)D104 Warning: unaligning (T0440)Y96 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)D104 Warning: unaligning (T0440)D106 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2qahA)L115 Warning: unaligning (T0440)F107 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2qahA)L115 Warning: unaligning (T0440)D140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A135 Warning: unaligning (T0440)Y141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)A135 Warning: unaligning (T0440)G151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)P136 T0440 2 :KR 2qahA 27 :AI T0440 6 :HTHTEFCPHGT 2qahA 31 :HCHVFGPMAQF T0440 19 :DVEEMVLKAIELDFDEYSIVEHAPL 2qahA 55 :GPDMLFALRDHLGFARNVIVQASCH T0440 44 :SSEFM 2qahA 82 :DNAAT T0440 62 :SMAMSDLP 2qahA 87 :LDAIARAQ T0440 84 :SD 2qahA 95 :GK T0440 89 :HIGFEV 2qahA 97 :ARGIAV T0440 97 :LIGYEDFTR 2qahA 105 :PAIDEAELA T0440 108 :LNE 2qahA 116 :HEG T0440 115 :TDDGVLSLHFL 2qahA 119 :GMRGIRFNFLK T0440 136 :FSAE 2qahA 130 :RLVD T0440 152 :FEQA 2qahA 137 :KDKF T0440 164 :KQSIEADLGLFK 2qahA 141 :LEVAGRLPAGWH T0440 178 :RMGHIS 2qahA 153 :VVIYFE T0440 193 :GED 2qahA 159 :ADI T0440 207 :FRVILALVKKRDYELDFNTAGLFKPLC 2qahA 162 :LEELRPFMDAIPVPIVIDHMGRPDVRQ T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYCQ 2qahA 190 :PDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFAR Number of specific fragments extracted= 17 number of extra gaps= 4 total=630 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qahA/T0440-2qahA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2qahA/T0440-2qahA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qahA read from 2qahA/T0440-2qahA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qahA in template set Warning: unaligning (T0440)D4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A30 Warning: unaligning (T0440)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)A30 Warning: unaligning (T0440)G15 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)A47 Warning: unaligning (T0440)T16 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)A47 Warning: unaligning (T0440)D19 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)P51 Warning: unaligning (T0440)K80 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2qahA)L115 Warning: unaligning (T0440)K81 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2qahA)L115 Warning: unaligning (T0440)Y100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qahA)P136 Warning: unaligning (T0440)G227 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)P250 Warning: unaligning (T0440)L228 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)P250 T0440 3 :R 2qahA 28 :I T0440 6 :HTHTE 2qahA 31 :HCHVF T0440 11 :FC 2qahA 43 :FS T0440 14 :H 2qahA 45 :P T0440 17 :HD 2qahA 48 :KY T0440 20 :VEEMVLKA 2qahA 59 :LFALRDHL T0440 31 :DFDEYSIVE 2qahA 67 :GFARNVIVQ T0440 44 :SSEFMKNTAGDKEAVTT 2qahA 76 :ASCHGTDNAATLDAIAR T0440 64 :AMSD 2qahA 93 :AQGK T0440 76 :NHIK 2qahA 110 :AELA T0440 82 :YASD 2qahA 116 :HEGG T0440 89 :HIGFEVDYLIG 2qahA 120 :MRGIRFNFLKR T0440 101 :EDFTRDFLNEYGPQTDDGVLS 2qahA 137 :KDKFLEVAGRLPAGWHVVIYF T0440 137 :SAEDYNEGIVQFYGGFEQ 2qahA 158 :EADILEELRPFMDAIPVP T0440 162 :GVKQSIEADLGLFKPRRMGHISLCQKFQQFFG 2qahA 193 :ADMKAFRRLLDSREDIWFKATCPDRLDPAGPP T0440 200 :SEEVMEKFRVILAL 2qahA 225 :WDDFARSVAPLVAD T0440 217 :RDYEL 2qahA 240 :ADRVI T0440 223 :FNTA 2qahA 245 :WGTD T0440 229 :FKPLCGETYPPKKIVTLA 2qahA 251 :HPNMQDAIPDDGLVVDMI Number of specific fragments extracted= 19 number of extra gaps= 6 total=649 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i60A/T0440-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i60A expands to /projects/compbio/data/pdb/1i60.pdb.gz 1i60A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 1i60A/T0440-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0440-1i60A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i60A to template set # found chain 1i60A in template set T0440 12 :CPHGT 1i60A 9 :TTLEN T0440 18 :DDVEEMVLKAIELDFDEYSI 1i60A 14 :SNLKLDLELCEKHGYDYIEI T0440 64 :AMSD 1i60A 34 :RTMD T0440 74 :KMNHIKKKYA 1i60A 38 :KLPEYLKDHS T0440 101 :EDFTRDFLNEYG 1i60A 48 :LDDLAEYFQTHH T0440 117 :DGVLSLHFLEGQGG 1i60A 60 :IKPLALNALVFFNN T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMGHIS 1i60A 74 :RDEKGHNEIITEFKGMMETCKTLGVKYVVAVPL T0440 192 :FGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTAGLFKPL 1i60A 110 :QKIVKEEIKKSSVDVLTELSDIAEPYGVKIALEFVGHPQCT T0440 236 :TYPPKKIVTLASEL 1i60A 151 :VNTFEQAYEIVNTV T0440 250 :QIPFVYG 1i60A 168 :NVGLVLD Number of specific fragments extracted= 10 number of extra gaps= 0 total=659 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i60A/T0440-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1i60A/T0440-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0440-1i60A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i60A in template set T0440 8 :HTE 1i60A 6 :NEA T0440 12 :C 1i60A 9 :T T0440 13 :PHGT 1i60A 11 :LENS T0440 19 :DVEEMVLKAIELDFDEYSIV 1i60A 15 :NLKLDLELCEKHGYDYIEIR T0440 41 :AP 1i60A 36 :MD T0440 47 :FMKNTAGDKEAVTT 1i60A 38 :KLPEYLKDHSLDDL T0440 62 :SMAMSDLPYYF 1i60A 52 :AEYFQTHHIKP T0440 86 :LLIHIGFEVDYL 1i60A 63 :LALNALVFFNNR T0440 98 :IGYEDFTRDFLNEYGP 1i60A 76 :EKGHNEIITEFKGMME T0440 115 :TDDGVLSLHFLEGQGGF 1i60A 96 :LGVKYVVAVPLVTEQKI T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFK 1i60A 113 :VKEEIKKSSVDVLTELSDIAEPYGV T0440 178 :RMG 1i60A 138 :KIA T0440 191 :FFGEDTSDF 1i60A 141 :LEFVGHPQC T0440 200 :SEEVMEKFRVI 1i60A 154 :FEQAYEIVNTV T0440 218 :DYELDFN 1i60A 168 :NVGLVLD T0440 228 :LFKPLC 1i60A 191 :ADGKKI T0440 234 :GETYPPKKIVTLASELQIP 1i60A 222 :QGAIDLDAHLSALKEIGFS T0440 253 :FVYGS 1i60A 243 :VSVEL T0440 268 :GYSTYCQ 1i60A 248 :FRPEYYK Number of specific fragments extracted= 19 number of extra gaps= 0 total=678 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i60A/T0440-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1i60A/T0440-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i60A read from 1i60A/T0440-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i60A in template set T0440 19 :DVEEMVLKAIELDFDEYSIV 1i60A 15 :NLKLDLELCEKHGYDYIEIR T0440 65 :MSD 1i60A 35 :TMD T0440 78 :IKKKYASD 1i60A 38 :KLPEYLKD T0440 99 :GYEDFTRDFLN 1i60A 46 :HSLDDLAEYFQ T0440 112 :GPQTDDGVLSL 1i60A 57 :THHIKPLALNA T0440 125 :LEG 1i60A 68 :LVF T0440 148 :FYGGFEQAQLAYLEGVKQSIEADLGLFKPRRMGHIS 1i60A 71 :FNNRDEKGHNEIITEFKGMMETCKTLGVKYVVAVPL T0440 191 :FFGEDTS 1i60A 107 :VTEQKIV T0440 200 :SEEVMEKFRVILALVKKR 1i60A 114 :KEEIKKSSVDVLTELSDI T0440 218 :DYELDFNT 1i60A 136 :GVKIALEF T0440 228 :LFKP 1i60A 144 :VGHP T0440 233 :CGETYPPKKIVTLASE 1i60A 148 :QCTVNTFEQAYEIVNT T0440 249 :LQIPFVYG 1i60A 167 :DNVGLVLD Number of specific fragments extracted= 13 number of extra gaps= 0 total=691 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0440-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xwyA expands to /projects/compbio/data/pdb/1xwy.pdb.gz 1xwyA:# T0440 read from 1xwyA/T0440-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0440-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xwyA to template set # found chain 1xwyA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0440 3 :RDGHTHTEFC 1xwyA 2 :FDIGVNLTSS T0440 14 :HGT 1xwyA 12 :QFA T0440 18 :DDVEEMVLKAIELDFDEYSIVEH 1xwyA 15 :KDRDDVVACAFDAGVNGLLITGT T0440 67 :DL 1xwyA 38 :NL T0440 70 :YYFKKMNHIKKKY 1xwyA 40 :RESQQAQKLARQY T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDDGVL 1xwyA 53 :SSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAI T0440 123 :HFLEGQGGFRS 1xwyA 92 :CGLDFNRNFST T0440 138 :A 1xwyA 103 :P T0440 157 :LAYLEGVKQSIEADLGLFKPRRMGHISLCQKFQQFFGEDTSDF 1xwyA 104 :EEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKL T0440 200 :SE 1xwyA 158 :RE T0440 210 :ILALVKKRDYELDF 1xwyA 160 :EMQACVAHGIYIGI T0440 225 :TAGLFKP 1xwyA 174 :TGWVCDE T0440 234 :GETY 1xwyA 181 :RRGL T0440 241 :KIVTLASELQI 1xwyA 185 :ELRELLPLIPA T0440 252 :PFVYGSDSHGVQDI 1xwyA 197 :KLLIETDAPYLLPR Number of specific fragments extracted= 15 number of extra gaps= 1 total=706 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0440-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1xwyA/T0440-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0440-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwyA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0440 3 :RDGHTHTE 1xwyA 2 :FDIGVNLT T0440 13 :PHGTHDDVEEMVLKAIELDFDEYSIVE 1xwyA 10 :SSQFAKDRDDVVACAFDAGVNGLLITG T0440 44 :SSEFMKNT 1xwyA 38 :NLRESQQA T0440 62 :SMAMSDL 1xwyA 46 :QKLARQY T0440 84 :SDLLIHIGFEV 1xwyA 53 :SSCWSTAGVHP T0440 95 :DYL 1xwyA 67 :SQW T0440 98 :IGYEDFTRDFLNE 1xwyA 71 :AATEEAIIELAAQ T0440 115 :TDDGVL 1xwyA 84 :PEVVAI T0440 123 :HFLEGQ 1xwyA 92 :CGLDFN T0440 171 :LGLFK 1xwyA 98 :RNFST T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLF 1xwyA 103 :PEEQERAFVAQLRIAADLNMPVFMHCRDAH T0440 230 :KPLC 1xwyA 140 :EPWL T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIG 1xwyA 152 :HCFTGTREEMQACVAHGIYIGITGWVCDERRGL T0440 268 :GYSTYCQ 1xwyA 185 :ELRELLP Number of specific fragments extracted= 14 number of extra gaps= 1 total=720 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0440-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 1xwyA/T0440-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0440-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwyA in template set Warning: unaligning (T0440)K2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0440)G180 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0440)H181 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0440 3 :RDGHTHTEF 1xwyA 2 :FDIGVNLTS T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVE 1xwyA 11 :SQFAKDRDDVVACAFDAGVNGLLITG T0440 63 :MAMSDLPYYFKKMNH 1xwyA 37 :TNLRESQQAQKLARQ T0440 113 :PQTDDGVLSLHF 1xwyA 52 :YSSCWSTAGVHP T0440 146 :VQFYGGFEQ 1xwyA 64 :HDSSQWQAA T0440 163 :VKQSIEADLGLFKPRRM 1xwyA 73 :TEEAIIELAAQPEVVAI T0440 182 :ISL 1xwyA 92 :CGL T0440 191 :FFGEDT 1xwyA 95 :DFNRNF T0440 198 :DFSEEVMEKFRVILALVKKRDYELDFNTAGLF 1xwyA 101 :STPEEQERAFVAQLRIAADLNMPVFMHCRDAH T0440 230 :KPLCG 1xwyA 140 :EPWLD T0440 235 :ETYPPKKIVTLASELQIPFVYGS 1xwyA 153 :CFTGTREEMQACVAHGIYIGITG T0440 262 :VQDIGRGYSTYCQ 1xwyA 176 :WVCDERRGLELRE Number of specific fragments extracted= 12 number of extra gaps= 1 total=732 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0440-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gokA expands to /projects/compbio/data/pdb/2gok.pdb.gz 2gokA:# T0440 read from 2gokA/T0440-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0440-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gokA to template set # found chain 2gokA in template set T0440 2 :KRDGHTHTEFCP 2gokA 82 :LIDCHTHLVFGG T0440 18 :DDVEE 2gokA 128 :LSDEV T0440 23 :MVLKAIELDF 2gokA 140 :RLDTLLSEGV T0440 35 :YSIVEHAPL 2gokA 150 :STIEIKSGY T0440 44 :SSEFMKNTAGDKEAVTTASMAMSDL 2gokA 168 :MLRVARRLETLRPVRIVTSYLAAHA T0440 69 :PYYFKKMNHIK 2gokA 195 :ADYKGRNADYI T0440 101 :EDFTRDFLNEYGPQTDDGVLSLHFLEGQGG 2gokA 206 :TDVVLPGLEKAHAEGLADAVDGFCEGIAFS T0440 160 :LEGVKQSIEADLGLFKPRRM 2gokA 236 :VKEIDRVFAAAQQRGLPVKL T0440 180 :G 2gokA 257 :A T0440 182 :ISLCQKFQQF 2gokA 263 :LGGAELAASY T0440 194 :EDTSD 2gokA 281 :EYLDE T0440 209 :VILALVKKRDYELDFNTAGLFKPLCGETYPPKKIVTL 2gokA 286 :TGAKALAKAGTVAVLLPGAFYALREKQLPPVQALRDA T0440 250 :QIPFVYGSDS 2gokA 323 :GAEIALATDC Number of specific fragments extracted= 13 number of extra gaps= 0 total=745 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0440-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2gokA/T0440-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0440-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gokA in template set T0440 19 :DVEEMVLKA 2gokA 129 :SDEVLVAQA T0440 45 :SEFMKNTAGD 2gokA 138 :LPRLDTLLSE T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDDGVLSLHFLEGQGG 2gokA 148 :GVSTIEIKSGYGLDIETELKMLRVARRLETLRPVRIVTSYLAAHATP T0440 138 :AE 2gokA 195 :AD T0440 148 :FYGGFEQAQLA 2gokA 197 :YKGRNADYITD T0440 159 :YLEGVKQSIE 2gokA 209 :VLPGLEKAHA T0440 171 :LGLFK 2gokA 219 :EGLAD T0440 178 :RMGHIS 2gokA 224 :AVDGFC T0440 188 :FQQFFG 2gokA 230 :EGIAFS T0440 204 :MEKFRVILALVKKRDY 2gokA 236 :VKEIDRVFAAAQQRGL T0440 220 :ELDFNTAGLFK 2gokA 254 :KLHAEQLSNLG T0440 242 :IVTLASELQIPFVYGS 2gokA 265 :GAELAASYNALSADHL Number of specific fragments extracted= 12 number of extra gaps= 0 total=757 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0440-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2gokA/T0440-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0440-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gokA in template set T0440 3 :RDGHTHTEFC 2gokA 83 :IDCHTHLVFG T0440 14 :HGTHDDVEE 2gokA 93 :GNRAMEFEM T0440 28 :IELDF 2gokA 102 :RLNGA T0440 44 :SSEFMKNTAGDKEAV 2gokA 107 :TYEEIAKAGGGIVSS T0440 60 :TASMAMSDLPYYFKKMNHIKKKYASDL 2gokA 122 :VRDTRALSDEVLVAQALPRLDTLLSEG T0440 88 :IHIGFEVDYLIGYEDFTRDFLN 2gokA 149 :VSTIEIKSGYGLDIETELKMLR T0440 110 :EYGPQTDDGVL 2gokA 177 :TLRPVRIVTSY T0440 125 :LEGQGGFRSID 2gokA 188 :LAAHATPADYK T0440 153 :EQAQLAYLEGVKQSIEADLGLFKPRRM 2gokA 199 :GRNADYITDVVLPGLEKAHAEGLADAV T0440 188 :FQQFFGEDTS 2gokA 226 :DGFCEGIAFS T0440 204 :MEKFRVILALVKKRDYELDFNTAGLFKP 2gokA 236 :VKEIDRVFAAAQQRGLPVKLHAEQLSNL T0440 234 :G 2gokA 264 :G T0440 235 :ETYPPKKIVTLASELQIPFVY 2gokA 280 :LEYLDETGAKALAKAGTVAVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=770 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pajA/T0440-2pajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pajA expands to /projects/compbio/data/pdb/2paj.pdb.gz 2pajA:# T0440 read from 2pajA/T0440-2pajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pajA read from 2pajA/T0440-2pajA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pajA to template set # found chain 2pajA in template set Warning: unaligning (T0440)S183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pajA)G264 T0440 10 :EFCP 2pajA 140 :VYYP T0440 14 :HGT 2pajA 145 :MPF T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAP 2pajA 148 :DSSAILFEEAEKLGLRFVLLRGGAT T0440 65 :MSDLP 2pajA 173 :QTRQL T0440 79 :KKKYASD 2pajA 178 :EADLPTA T0440 92 :FEVDYLIGYEDFTRDFLNEYG 2pajA 185 :LRPETLDAYVADIERLAARYH T0440 113 :PQTDDGVLSLHFLEGQGGFRS 2pajA 207 :ASPRAMRRVVMAPTTVLYSIS T0440 160 :LEGVKQSIEADLGLF 2pajA 228 :PREMRETAAVARRLG T0440 176 :PRRMGHI 2pajA 243 :LRMHSHL T0440 211 :LALVKKRDY 2pajA 268 :VAFCGEHDW T0440 220 :ELDFNTA 2pajA 280 :DVWYAHL T0440 236 :TYPPKKIVTLASELQIPFVY 2pajA 287 :VKVDADEIALLAQTGTGVAH Number of specific fragments extracted= 12 number of extra gaps= 0 total=782 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pajA/T0440-2pajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2pajA/T0440-2pajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pajA read from 2pajA/T0440-2pajA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pajA in template set Warning: unaligning (T0440)T16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pajA)F106 Warning: unaligning (T0440)A41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pajA)F106 Warning: unaligning (T0440)A226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pajA)G264 T0440 3 :RDGHTHTEFC 2pajA 73 :VNTHHHLFQS T0440 13 :PHG 2pajA 85 :KGE T0440 42 :PL 2pajA 107 :RA T0440 44 :SSEFMKNTA 2pajA 111 :DERRFRLAA T0440 62 :SMAMS 2pajA 120 :RIGLI T0440 77 :H 2pajA 125 :E T0440 81 :KYASDLLIHIGFEVDYLIGYE 2pajA 126 :LARSGCATVADHNYVYYPGMP T0440 102 :DFTRDFLNE 2pajA 151 :AILFEEAEK T0440 115 :TDDGVLSLHFL 2pajA 160 :LGLRFVLLRGG T0440 126 :EGQGGFRSIDFSA 2pajA 176 :QLEADLPTALRPE T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMG 2pajA 189 :TLDAYVADIERLAARYHDASPRAMRRVVMA T0440 185 :CQKFQQFFG 2pajA 219 :PTTVLYSIS T0440 204 :MEKFRVILALVKKRDYELDFNT 2pajA 228 :PREMRETAAVARRLGLRMHSHL T0440 234 :GETYPPKKIVTLASELQIPFVY 2pajA 285 :HLVKVDADEIALLAQTGTGVAH Number of specific fragments extracted= 14 number of extra gaps= 0 total=796 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pajA/T0440-2pajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2pajA/T0440-2pajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pajA read from 2pajA/T0440-2pajA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pajA in template set Warning: unaligning (T0440)S183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pajA)G264 Warning: unaligning (T0440)S197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pajA)G264 T0440 8 :HT 2pajA 141 :YY T0440 13 :PHGTHDDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 2pajA 143 :PGMPFDSSAILFEEAEKLGLRFVLLRGGATQTRQLE T0440 57 :AVTTASMAMSDLPYYFKKMNHIKKKY 2pajA 179 :ADLPTALRPETLDAYVADIERLAARY T0440 97 :LI 2pajA 205 :HD T0440 111 :YGPQTDDGVLSL 2pajA 207 :ASPRAMRRVVMA T0440 125 :LEGQGGFRS 2pajA 219 :PTTVLYSIS T0440 157 :LAYLEGVKQSIEA 2pajA 228 :PREMRETAAVARR T0440 174 :FKPRRMGHI 2pajA 241 :LGLRMHSHL T0440 198 :DFS 2pajA 265 :KSP T0440 211 :LALVKKRD 2pajA 268 :VAFCGEHD T0440 219 :YELDF 2pajA 280 :DVWYA T0440 234 :GETYPPKKIVTLASELQIPFVY 2pajA 285 :HLVKVDADEIALLAQTGTGVAH Number of specific fragments extracted= 12 number of extra gaps= 0 total=808 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pgfA/T0440-2pgfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pgfA expands to /projects/compbio/data/pdb/2pgf.pdb.gz 2pgfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 185, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 187, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 189, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 191, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 193, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 195, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 197, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 199, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 201, because occupancy 0.300 <= existing 0.700 in 2pgfA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1143, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1147, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1293, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1295, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1297, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1299, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1301, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1303, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 1305, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1460, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1466, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1468, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1470, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1472, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2863, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2865, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2867, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2869, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2871, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2873, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2875, because occupancy 0.400 <= existing 0.600 in 2pgfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2877, because occupancy 0.400 <= existing 0.600 in 2pgfA Skipped atom 2952, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2954, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2956, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2958, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2960, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2962, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2964, because occupancy 0.500 <= existing 0.500 in 2pgfA Skipped atom 2966, because occupancy 0.500 <= existing 0.500 in 2pgfA # T0440 read from 2pgfA/T0440-2pgfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pgfA read from 2pgfA/T0440-2pgfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pgfA to template set # found chain 2pgfA in template set T0440 2 :KRDGHTHT 2pgfA 38 :KCELHCHL T0440 14 :HGT 2pgfA 46 :DLC T0440 18 :DDVEEMVLKAIELDF 2pgfA 49 :FSADFFVSCIRKYNL T0440 41 :A 2pgfA 64 :Q T0440 44 :SSEFMKNTA 2pgfA 69 :DEEVLDYYL T0440 58 :VTTASMAM 2pgfA 121 :VVLMEFRY T0440 66 :SDLP 2pgfA 135 :FKYN T0440 70 :YYFKKMNHIKKKYAS 2pgfA 147 :AIVKGIKEVVELLDH T0440 85 :DLLIHIGFEVDYLIGYEDFTRDFLNEYG 2pgfA 164 :HVALMCIGDTGHEAANIKASADFCLKHK T0440 117 :DGVLSLHFLEG 2pgfA 192 :ADFVGFDHGGH T0440 131 :FRSIDFSAEDYNEGIVQ 2pgfA 203 :EVDLKEYKEIFDYVRES T0440 151 :GFEQ 2pgfA 220 :GVPL T0440 165 :QSIEADLGLFKPRRMGHISLCQK 2pgfA 237 :NTLYSAIQVLKVERIGHGIRVAE T0440 207 :FRVILALVKKRDYELDFN 2pgfA 260 :SQELIDMVKEKNILLEVC T0440 226 :AGLFKPLCGET 2pgfA 284 :LKNAKSMDTHP T0440 243 :VTLASELQIPFVYGSD 2pgfA 295 :IRQLYDAGVKVSVNSD Number of specific fragments extracted= 16 number of extra gaps= 0 total=824 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pgfA/T0440-2pgfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2pgfA/T0440-2pgfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pgfA read from 2pgfA/T0440-2pgfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pgfA in template set T0440 2 :KRDGHTHTEFC 2pgfA 38 :KCELHCHLDLC T0440 19 :DVEEMVLKAIELDF 2pgfA 50 :SADFFVSCIRKYNL T0440 41 :APL 2pgfA 64 :QPN T0440 44 :SSEFMKNTAGDKE 2pgfA 68 :SDEEVLDYYLFAK T0440 68 :LPYYFKKMNHIKKKYASD 2pgfA 81 :GGKSLGEFVEKAIKVADI T0440 94 :VDYLIGYEDFTRDFLNEYGPQTDDGVLSLHF 2pgfA 99 :FHDYEVIEDLAKHAVFNKYKEGVVLMEFRYS T0440 142 :NEGIVQFYG 2pgfA 130 :PTFVAFKYN T0440 151 :GFEQAQLAYLEGVKQSIEA 2pgfA 140 :DIELIHQAIVKGIKEVVEL T0440 171 :LGLFKPRRMGHIS 2pgfA 159 :LDHKIHVALMCIG T0440 189 :QQFFGEDT 2pgfA 172 :DTGHEAAN T0440 207 :FRVILALVKKRD 2pgfA 180 :IKASADFCLKHK T0440 219 :Y 2pgfA 194 :F T0440 220 :ELDFNTAG 2pgfA 196 :GFDHGGHE T0440 234 :GETYPPKKIVTLASELQIPFVYGSDS 2pgfA 204 :VDLKEYKEIFDYVRESGVPLSVHAGE Number of specific fragments extracted= 14 number of extra gaps= 0 total=838 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pgfA/T0440-2pgfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2pgfA/T0440-2pgfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pgfA read from 2pgfA/T0440-2pgfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pgfA in template set T0440 20 :VEEMVLKAIELDFDEYSIVEH 2pgfA 109 :AKHAVFNKYKEGVVLMEFRYS T0440 45 :SEFM 2pgfA 131 :TFVA T0440 59 :TTASMAMSD 2pgfA 135 :FKYNLDIEL T0440 68 :LPYYFKKMNHIKKKYASDLLIHIGFEVDYLIG 2pgfA 145 :HQAIVKGIKEVVELLDHKIHVALMCIGDTGHE T0440 100 :YEDFTRDFLNEYGPQTDDGVLSL 2pgfA 179 :NIKASADFCLKHKADFVGFDHGG T0440 130 :GFRSIDFSAEDYNEGIV 2pgfA 202 :HEVDLKEYKEIFDYVRE T0440 149 :YGGF 2pgfA 219 :SGVP T0440 165 :QSIEADLGLFKPRRMGHISLCQ 2pgfA 237 :NTLYSAIQVLKVERIGHGIRVA T0440 192 :F 2pgfA 259 :E T0440 200 :SEE 2pgfA 260 :SQE T0440 210 :ILALVKKRDYELDFNT 2pgfA 263 :LIDMVKEKNILLEVCP T0440 226 :AGLFKPLCG 2pgfA 280 :SNVLLKNAK T0440 235 :ETYPPKKIV 2pgfA 291 :DTHPIRQLY T0440 248 :ELQIPFVYGSD 2pgfA 300 :DAGVKVSVNSD Number of specific fragments extracted= 14 number of extra gaps= 0 total=852 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnyA/T0440-3cnyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cnyA expands to /projects/compbio/data/pdb/3cny.pdb.gz 3cnyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 61, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 3cnyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1482, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 3cnyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1804, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 3cnyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2122, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 2126, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 3cnyA Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 3cnyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 3cnyA/T0440-3cnyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnyA read from 3cnyA/T0440-3cnyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cnyA to template set # found chain 3cnyA in template set T0440 1 :MKRDGHTHTEFC 3cnyA 9 :IKWGIAPIGWRN T0440 13 :PHGTHDDVEEMVLKAIELDFDEY 3cnyA 25 :SIGKDNNLQQLLSDIVVAGFQGT T0440 63 :MAMSDLP 3cnyA 48 :EVGGFFP T0440 84 :S 3cnyA 55 :G T0440 101 :EDFTRDFLNEYG 3cnyA 56 :PEKLNYELKLRN T0440 115 :TDDGVLSLHF 3cnyA 68 :LEIAGQWFSS T0440 135 :DFSAEDYNEG 3cnyA 78 :YIIRDGIEKA T0440 160 :LEGVKQSIEADLGLFKPRRMGHISL 3cnyA 88 :SEAFEKHCQYLKAINAPVAVVSEQT T0440 189 :QQFFGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTAG 3cnyA 124 :FKDKPYFTDKEWDEVCKGLNHYGEIAAKYGLKVAYHHHM T0440 234 :GET 3cnyA 163 :GTG T0440 237 :YPPKKIVTLASEL 3cnyA 167 :QTKEETDRLMANT T0440 250 :QIPFVYG 3cnyA 183 :LVGLLYD Number of specific fragments extracted= 12 number of extra gaps= 0 total=864 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnyA/T0440-3cnyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 3cnyA/T0440-3cnyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnyA read from 3cnyA/T0440-3cnyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnyA in template set T0440 13 :PHGT 3cnyA 27 :GKDN T0440 19 :DVEEMVLKAIELDFDEY 3cnyA 31 :NLQQLLSDIVVAGFQGT T0440 93 :EVDYLIGYEDFTRDFLNEYG 3cnyA 48 :EVGGFFPGPEKLNYELKLRN T0440 115 :TDDGVLSLHF 3cnyA 68 :LEIAGQWFSS T0440 127 :G 3cnyA 78 :Y T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRMGHIS 3cnyA 79 :IIRDGIEKASEAFEKHCQYLKAINAPVAVVSEQ T0440 189 :QQF 3cnyA 112 :TYT T0440 192 :FGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTAG 3cnyA 127 :KPYFTDKEWDEVCKGLNHYGEIAAKYGLKVAYHHHM T0440 234 :GETY 3cnyA 163 :GTGI T0440 238 :PPKKIVTLAS 3cnyA 168 :TKEETDRLMA T0440 249 :L 3cnyA 178 :N T0440 250 :QIPFVYG 3cnyA 183 :LVGLLYD Number of specific fragments extracted= 12 number of extra gaps= 0 total=876 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cnyA/T0440-3cnyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 3cnyA/T0440-3cnyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnyA read from 3cnyA/T0440-3cnyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnyA in template set T0440 63 :MAMSDLPYYFKKMNHI 3cnyA 27 :GKDNNLQQLLSDIVVA T0440 85 :DLL 3cnyA 43 :GFQ T0440 91 :GFEVDYLIGYEDFTRDFLNEYGPQTDDGVLSL 3cnyA 46 :GTEVGGFFPGPEKLNYELKLRNLEIAGQWFSS T0440 150 :GGFEQAQLAYLEGVKQSIEADLGLFKPRRMGHISL 3cnyA 78 :YIIRDGIEKASEAFEKHCQYLKAINAPVAVVSEQT T0440 191 :FFGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTA 3cnyA 126 :DKPYFTDKEWDEVCKGLNHYGEIAAKYGLKVAYHHH T0440 233 :CGETYPPKKIVTLASEL 3cnyA 162 :MGTGIQTKEETDRLMAN T0440 250 :QIPFVYG 3cnyA 183 :LVGLLYD Number of specific fragments extracted= 7 number of extra gaps= 0 total=883 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2icsA/T0440-2icsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2icsA expands to /projects/compbio/data/pdb/2ics.pdb.gz 2icsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0440 read from 2icsA/T0440-2icsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2icsA read from 2icsA/T0440-2icsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2icsA to template set # found chain 2icsA in template set Warning: unaligning (T0440)I88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2icsA)I153 Warning: unaligning (T0440)H89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2icsA)I153 Warning: unaligning (T0440)G91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2icsA)A155 T0440 2 :KRDGHTHTEF 2icsA 56 :WIDDHVHCFE T0440 14 :HGTH 2icsA 66 :KMAL T0440 18 :DDVEEM 2icsA 72 :DYPDEI T0440 30 :LDFDEYSIVEHAPL 2icsA 81 :KGVTTVIDAGTTGA T0440 44 :SSEFMKNTAG 2icsA 97 :IHEFYDLAQQ T0440 54 :DKEAVTTASMAMSD 2icsA 108 :KTNVFGLVNISKWG T0440 68 :LP 2icsA 129 :AD T0440 72 :FKKMNHIKKKYASDLL 2icsA 136 :ASLVKKAIQELPDFVV T0440 92 :FEVD 2icsA 156 :RMSR T0440 96 :YLIGYEDFTRDFLNEYG 2icsA 165 :NGITPLELAKQIQQENQ T0440 117 :DGVLSLHFLEGQGG 2icsA 182 :EIPLMVHIGSAPPH T0440 163 :VKQSIEA 2icsA 196 :LDEILAL T0440 173 :LFKPRRMGHISL 2icsA 203 :MEKGDVLTHCFN T0440 194 :EDTSDFSEE 2icsA 223 :QATDKIKDF T0440 207 :FRVILA 2icsA 232 :AWQAYN T0440 217 :RDYELDFNTAG 2icsA 238 :KGVVFDIGHGT T0440 236 :TYPPKKIVTLASELQI 2icsA 249 :DSFNFHVAETALREGM T0440 252 :PFVYGSDS 2icsA 266 :AASISTDI Number of specific fragments extracted= 18 number of extra gaps= 1 total=901 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2icsA/T0440-2icsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2icsA/T0440-2icsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2icsA read from 2icsA/T0440-2icsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2icsA in template set Warning: unaligning (T0440)D117 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2icsA)I153 Warning: unaligning (T0440)G118 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2icsA)I153 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2icsA)A155 T0440 3 :RDGHTHT 2icsA 57 :IDDHVHC T0440 10 :EFC 2icsA 65 :EKM T0440 13 :PHGT 2icsA 69 :LYYD T0440 19 :DVEEM 2icsA 73 :YPDEI T0440 31 :DFDEYSIVEHAPL 2icsA 82 :GVTTVIDAGTTGA T0440 44 :SSEFM 2icsA 96 :NIHEF T0440 62 :SMAMSDLPYY 2icsA 101 :YDLAQQAKTN T0440 86 :LLIHIGFEV 2icsA 111 :VFGLVNISK T0440 95 :DYL 2icsA 126 :DEL T0440 100 :YEDFTRDFLNEYGPQTD 2icsA 135 :QASLVKKAIQELPDFVV T0440 121 :SLH 2icsA 156 :RMS T0440 143 :EGIVQFYGG 2icsA 159 :RTVIGDNGI T0440 158 :AYLEGVKQSIEADLGLF 2icsA 168 :TPLELAKQIQQENQEIP T0440 178 :RMGHIS 2icsA 185 :LMVHIG T0440 191 :FFGED 2icsA 191 :SAPPH T0440 207 :FRVILAL 2icsA 196 :LDEILAL T0440 217 :RDYELDFNTAGLFKPLC 2icsA 203 :MEKGDVLTHCFNGKENG T0440 234 :GETYPPKKIVTLA 2icsA 224 :ATDKIKDFAWQAY T0440 248 :ELQIPFVYGSDS 2icsA 237 :NKGVVFDIGHGT T0440 260 :HGVQD 2icsA 250 :SFNFH Number of specific fragments extracted= 20 number of extra gaps= 1 total=921 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2icsA/T0440-2icsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0440 read from 2icsA/T0440-2icsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2icsA read from 2icsA/T0440-2icsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2icsA in template set Warning: unaligning (T0440)G118 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2icsA)I153 Warning: unaligning (T0440)V119 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2icsA)I153 Warning: unaligning (T0440)S121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2icsA)A155 T0440 4 :DGHTHTEFCPHGTHDDVEEM 2icsA 58 :DDHVHCFEKMALYYDYPDEI T0440 32 :F 2icsA 83 :V T0440 34 :EYSIVEHAPLSSE 2icsA 84 :TTVIDAGTTGAEN T0440 75 :MNHIKKKY 2icsA 97 :IHEFYDLA T0440 84 :SDLLIHIGFEVDYLIG 2icsA 105 :QQAKTNVFGLVNISKW T0440 100 :YEDFTRDFLNE 2icsA 135 :QASLVKKAIQE T0440 112 :GPQTDD 2icsA 146 :LPDFVV T0440 122 :LHF 2icsA 156 :RMS T0440 146 :VQFYGGFEQ 2icsA 159 :RTVIGDNGI T0440 162 :GVKQSIEADLGLF 2icsA 168 :TPLELAKQIQQEN T0440 175 :KPRRMGHIS 2icsA 182 :EIPLMVHIG T0440 193 :GEDTS 2icsA 191 :SAPPH T0440 207 :FRVILAL 2icsA 196 :LDEILAL T0440 217 :RDYELD 2icsA 205 :KGDVLT T0440 224 :NTAGLFKP 2icsA 211 :HCFNGKEN T0440 232 :LCGE 2icsA 224 :ATDK T0440 238 :PPKKIVT 2icsA 228 :IKDFAWQ T0440 246 :ASELQIPFVYGS 2icsA 235 :AYNKGVVFDIGH Number of specific fragments extracted= 18 number of extra gaps= 1 total=939 Will force an alignment to be made, even if fragment is small Number of alignments=63 # command:CPU_time= 21.263 sec, elapsed time= 22.944 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 63 Adding 6048 constraints to all_contacts Done adding distance constraints # command:CPU_time= 21.366 sec, elapsed time= 23.056 sec. # command:Reading probabilities from T0440.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 33.112 Optimizing... Probability sum: -492.171, CN propb: -492.171 weights: 0.193 constraints: 1035 # command:CPU_time= 284.291 sec, elapsed time= 286.292 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 1035 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 1035 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 5013 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 5013 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 284.391 sec, elapsed time= 286.449 sec. # command: