# 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= 6.445 sec, elapsed time= 7.202 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 :DDVEEMVLKAIELDFDEYSIVEH 2yxoA 16 :GHPEAYLEEARAKGLKGVVFTDH T0440 42 :PLSSE 2yxoA 39 :SPMPP T0440 53 :G 2yxoA 44 :W T0440 54 :DK 2yxoA 48 :ES T0440 62 :SMAMSDLPYYFKKMNHIKKKY 2yxoA 50 :RMRLEALPFYLLALERVRERA T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYG 2yxoA 71 :QDLYVGIGLEADFHPGTEGFLAQLLRRYP T0440 115 :TDDGVLSLHFLE 2yxoA 100 :FDYVIGSVHYLG T0440 127 :GQGGFRSIDF 2yxoA 113 :WPLDHPDHQE T0440 140 :DYNEG 2yxoA 123 :EYAWR T0440 151 :GFEQAQLAYLEGVKQSIE 2yxoA 128 :DLKEVFRAYFQEVEKAAR T0440 173 :LFKPRRMGHISLCQKFQQFFG 2yxoA 146 :SGLFHAIGHLDLPKKFGHRLP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLFKPL 2yxoA 167 :EEALLELAEPALRAVAEAGLFLDVNTAGLRRPA T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYC 2yxoA 200 :KEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=15 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 :TDDGVLSLHFLEGQGGFRSIDFSA 2yxoA 100 :FDYVIGSVHYLGAWPLDHPDHQEE T0440 139 :EDY 2yxoA 125 :AWR T0440 151 :GFEQAQLAYLEGVKQSIE 2yxoA 128 :DLKEVFRAYFQEVEKAAR T0440 171 :LGLFK 2yxoA 146 :SGLFH T0440 178 :RMGHISLCQKF 2yxoA 151 :AIGHLDLPKKF T0440 190 :QFFGE 2yxoA 162 :GHRLP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGLFKPL 2yxoA 167 :EEALLELAEPALRAVAEAGLFLDVNTAGLRRPA T0440 234 :GETYPPKKIVTLASELQIPFVYGSDSHGVQDIGRGYSTYCQ 2yxoA 200 :KEVYPAPALLRRARELGIGLVLGSDAHRPEEVGFAFPEVQA Number of specific fragments extracted= 15 number of extra gaps= 0 total=30 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=38 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 :DDVEEMVLKAIELDFDEYSIVEHAP 1m65A 18 :STLSDYIAQAKQKGIKLFAITDHGP T0440 43 :LSSEFMKNTAG 1m65A 48 :PHHWHFINMRI T0440 54 :DKEAVTTASMAMSDLPYYFKK 1m65A 65 :GVGILRGIEANIKNVDGEIDC T0440 97 :L 1m65A 86 :S T0440 102 :DFTRDF 1m65A 87 :GKMFDS T0440 115 :TDDGVLSLHFLE 1m65A 93 :LDLIIAGFHEPV T0440 133 :SI 1m65A 105 :FA T0440 153 :EQAQLAYLEGVKQSIE 1m65A 107 :PHDKATNTQAMIATIA T0440 173 :LFKPRRMGHISLCQ 1m65A 123 :SGNVHIISHPGNPK T0440 192 :FGED 1m65A 137 :YEID T0440 207 :FRVILALVKKRDYELDFNTA 1m65A 141 :VKAVAEAAAKHQVALEINNS T0440 239 :PKKIVTLASELQIPFVYGSDS 1m65A 173 :CREVAAAVRDAGGWVALGSDS T0440 262 :VQDIG 1m65A 196 :AFTMG T0440 268 :G 1m65A 201 :E Number of specific fragments extracted= 15 number of extra gaps= 1 total=53 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 :SMAMSDLPYY 1m65A 53 :FINMRIWPRV T0440 83 :ASDLLIHIGFEVDYLIG 1m65A 63 :VDGVGILRGIEANIKNV T0440 100 :YEDFTRD 1m65A 86 :SGKMFDS T0440 115 :TDDGVLSLHF 1m65A 93 :LDLIIAGFHE T0440 134 :IDFSAE 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 :VQDIGR 1m65A 196 :AFTMGE T0440 269 :Y 1m65A 202 :F Number of specific fragments extracted= 18 number of extra gaps= 1 total=71 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=84 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)L184 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 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 :PLSSEFMKNTAG 2anuA 72 :DYLKRLWREQKR T0440 54 :DKEAVTTAS 2anuA 89 :GMILIPGVE T0440 65 :MSD 2anuA 100 :NNT T0440 84 :SDLLIHIGFEVDY 2anuA 103 :DLYHIVAVDVKEY T0440 111 :YGPQTD 2anuA 116 :VDPSLP T0440 163 :VKQSIEADLGLFKPRRMGHI 2anuA 122 :VEEIVEKLKEQNALVIAAHP T0440 187 :KFQQFFGEDTS 2anuA 154 :YLWANMERFKD T0440 217 :RDYELDF 2anuA 165 :TFDAWEI T0440 226 :AGLF 2anuA 174 :RDDL T0440 234 :GE 2anuA 178 :FN T0440 245 :LASELQIPFVYGSDSHGVQDIG 2anuA 180 :SVGVKKYRYVANSDFHELWHVY Number of specific fragments extracted= 15 number of extra gaps= 3 total=99 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 :RSIDFSAED 2anuA 112 :VKEYVDPSL 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 196 :TSDFSEE 2anuA 152 :SWYLWAN 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=117 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 :PLSSEFM 2anuA 47 :VDRRTLE T0440 53 :GDKEAV 2anuA 54 :QRKRNG T0440 59 :TTASMAMSDLPYYFKKMNHIKKKYAS 2anuA 61 :PLGAITEDKFQDYLKRLWREQKRAWE T0440 85 :DLLIHIGFE 2anuA 89 :GMILIPGVE T0440 96 :YLIG 2anuA 100 :NNTD T0440 121 :SLHFLEGQG 2anuA 106 :HIVAVDVKE T0440 131 :FRSIDF 2anuA 115 :YVDPSL T0440 197 :S 2anuA 121 :P 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=131 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)K74 because of BadResidue code BAD_PEPTIDE in next template residue (2hnhA)T85 Warning: unaligning (T0440)M75 because of BadResidue code BAD_PEPTIDE at template residue (2hnhA)T85 T0440 1 :M 2hnhA 4 :P T0440 2 :KRDGHTHTEFCP 2hnhA 6 :FVHLRVHSDYSM T0440 14 :HGT 2hnhA 19 :DGL T0440 18 :DDVEEMVLKAIELDFDEYSIVEH 2hnhA 22 :AKTAPLVKKAAALGMPALAITDF T0440 42 :PLSSEFMKNTAG 2hnhA 45 :TNLCGLVKFYGA T0440 54 :DKEAVTTAS 2hnhA 61 :GIKPIVGAD T0440 65 :M 2hnhA 72 :V T0440 66 :SDLPYYFK 2hnhA 76 :LLGDELTH T0440 88 :IHIGFEVDYLIGYEDFTRDFLNEYGPQTDD 2hnhA 86 :VLAANNTGYQNLTLLISKAYQRGYGAAGPI T0440 118 :GVLSLHFL 2hnhA 166 :YFLELIRT T0440 151 :GFEQA 2hnhA 174 :GRPDE T0440 157 :LAYLEGVKQSIEA 2hnhA 179 :ESYLHAAVELAEA T0440 173 :LFKPRRM 2hnhA 192 :RGLPVVA T0440 180 :GH 2hnhA 202 :VR T0440 182 :ISLCQKF 2hnhA 207 :SSDFDAH T0440 189 :QQFFGEDTS 2hnhA 304 :LAFLFPDEE T0440 198 :DFSEEVMEKFRVILALVKKRDY 2hnhA 316 :KRRPEYDERLETELQVINQMGF T0440 228 :LF 2hnhA 341 :FL T0440 238 :PPKKIVTLASELQIP 2hnhA 343 :IVMEFIQWSKDNGVP Number of specific fragments extracted= 19 number of extra gaps= 2 total=150 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)I78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2hnhA)N71 Warning: unaligning (T0440)K79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2hnhA)N71 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 :SMAMSDLPYYFKKMNH 2hnhA 54 :YGAGHGAGIKPIVGAD T0440 80 :KKY 2hnhA 72 :VQC T0440 83 :ASDLL 2hnhA 163 :PDRYF T0440 90 :IGFEVDYLIG 2hnhA 168 :LELIRTGRPD T0440 100 :YEDFTRDFLNE 2hnhA 181 :YLHAAVELAEA T0440 115 :TDDGVLSLHFLEGQGGF 2hnhA 192 :RGLPVVATNDVRFIDSS T0440 132 :RSIDFSA 2hnhA 698 :SGYTLGG T0440 139 :EDYNEGIVQ 2hnhA 706 :DMLRRAMGK T0440 151 :GFEQA 2hnhA 716 :KPEEM T0440 157 :LAYLEGVKQSIEA 2hnhA 721 :AKQRSVFAEGAEK T0440 171 :LGLFKPRRMGHISLCQKFQQFFGEDTSDFSEEVM 2hnhA 734 :NGINAELAMKIFDLVEKFAGYGFNKSHSAAYALV T0440 234 :GETYPPKKIVTLASELQIPFV 2hnhA 792 :DNTEKVVGLVDECWRMGLKIL Number of specific fragments extracted= 17 number of extra gaps= 1 total=167 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 109 :N 2hnhA 78 :G 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= 17 number of extra gaps= 3 total=184 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 :LPYYFKKMNHIKKKY 1v77A 38 :EEVDKEKLREARKEY T0440 84 :SDLLIHI 1v77A 53 :GKVAILL T0440 94 :VDYL 1v77A 60 :SNPK T0440 101 :EDFTRDFLNEYG 1v77A 64 :PSLVRDTVQKFK T0440 115 :TDDGVLSLH 1v77A 76 :SYLIYVESN T0440 152 :F 1v77A 85 :D T0440 160 :LEGVKQSIE 1v77A 86 :LRVIRYSIE T0440 174 :FKPRRMGHIS 1v77A 95 :KGVDAIISPW T0440 192 :FGEDTSDFSEE 1v77A 105 :VNRKDPGIDHV T0440 210 :ILALVKKRDYELDFNTAGLFK 1v77A 116 :LAKLMVKKNVALGFSLRPLLY T0440 234 :GE 1v77A 137 :SN T0440 238 :PPKKIVTLASELQIPFVYGSDSHGVQDI 1v77A 148 :FMMKAWKLVEKYKVRRFLTSSAQEKWDV Number of specific fragments extracted= 14 number of extra gaps= 0 total=198 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 :SSEFMKNTAGDKE 1v77A 41 :DKEKLREARKEYG T0440 57 :AVTT 1v77A 63 :KPSL T0440 75 :MNHIKKKYASDLLIHI 1v77A 67 :VRDTVQKFKSYLIYVE T0440 98 :IGYEDFTRDFLN 1v77A 83 :SNDLRVIRYSIE T0440 115 :TDDGVLSLHFLEGQGGFR 1v77A 95 :KGVDAIISPWVNRKDPGI T0440 151 :G 1v77A 113 :D T0440 153 :EQAQLAYLEG 1v77A 114 :HVLAKLMVKK T0440 173 :LFK 1v77A 124 :NVA T0440 189 :QQFFGEDTSDFSEEVMEKFRVILALVKKRDYELDFNTAG 1v77A 131 :LRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSA T0440 229 :FKP 1v77A 170 :QEK T0440 234 :GETYPPKKIVTLASELQI 1v77A 173 :WDVRYPRDLISLGVVIGM Number of specific fragments extracted= 14 number of extra gaps= 0 total=212 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=222 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 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 :A 1vflA 35 :L T0440 42 :PLSSEFMKNTAG 1vflA 129 :LVNQGLQEGERD T0440 54 :DKEAVTTASMAMSD 1vflA 142 :GVKVRSILCCMRHQ T0440 69 :PYYFKKMNHIKKKYASDLLI 1vflA 156 :PSWSSEVVELCKKYREQTVV T0440 89 :HIGFEVDYLIGYEDFTRDFLN 1vflA 179 :LAGDETIEGSSLFPGHVQAYA T0440 110 :EYG 1vflA 203 :KSG T0440 115 :TDDGVLSLHF 1vflA 206 :VHRTVHAGEV T0440 152 :FEQ 1vflA 216 :GSA T0440 161 :EGVKQSIE 1vflA 219 :NVVKEAVD T0440 173 :LFKPRRMGHISLCQK 1vflA 227 :TLKTERLGHGYHTLE T0440 200 :SEE 1vflA 242 :DTT T0440 210 :ILALVKKRDYELDFNTA 1vflA 245 :LYNRLRQENMHFEICPW T0440 227 :GLFKPLCGE 1vflA 267 :GAWKPDTEH T0440 242 :IVTLASELQIPFVYGSD 1vflA 276 :AVIRFKNDQVNYSLNTD Number of specific fragments extracted= 17 number of extra gaps= 0 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 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 2 :KRDGHTHTEFC 1vflA 8 :KVELHVHLDGA T0440 19 :DVEEMVLKAIELDFD 1vflA 20 :KPETILYYGKRRGIA T0440 41 :APL 1vflA 35 :LPA T0440 44 :SSEFMKNTAGDKEAVT 1vflA 39 :TPEELQNIIGMDKPLT T0440 62 :S 1vflA 55 :L T0440 76 :NHIKKKY 1vflA 56 :PDFLAKF T0440 94 :VDYLIGYEDFTRDFLNEYGP 1vflA 70 :AGCRDAIKRIAYEFVEMKAK T0440 115 :TDDGVLSLHFLEGQGGF 1vflA 90 :DGVVYVEVRYSPHLLAN T0440 132 :RSIDFSAEDY 1vflA 112 :IPWNQAEGDL T0440 151 :GFEQAQLAYLEGVKQSIEA 1vflA 122 :TPDEVVSLVNQGLQEGERD T0440 171 :LG 1vflA 141 :FG T0440 173 :LFKPRRMGHISLCQKF 1vflA 154 :HQPSWSSEVVELCKKY T0440 189 :QQFFGED 1vflA 184 :TIEGSSL T0440 204 :MEKFRVILALVKKRDYELDFNTAGLFK 1vflA 191 :FPGHVQAYAEAVKSGVHRTVHAGEVGS T0440 234 :GETYPPKKIVTLASELQIPFVY 1vflA 237 :YHTLEDTTLYNRLRQENMHFEI Number of specific fragments extracted= 15 number of extra gaps= 0 total=254 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 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 125 :L 1vflA 180 :A T0440 126 :EGQGGFRS 1vflA 184 :TIEGSSLF 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= 16 number of extra gaps= 0 total=270 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 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)G118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ob3A)V170 Warning: unaligning (T0440)L120 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 :GHTHTEFCPHGT 2ob3A 54 :THEHICGSSAGF T0440 18 :DDVEE 2ob3A 74 :GSRKA T0440 23 :MVLKAIELDFDEYSIVE 2ob3A 86 :GLRRARAAGVRTIVDVS T0440 41 :APLSSEFMKNTAG 2ob3A 107 :GRDVSLLAEVSRA T0440 54 :DKEAVT 2ob3A 121 :DVHIVA T0440 62 :SM 2ob3A 129 :GL T0440 66 :SDLPY 2ob3A 133 :DPPLS T0440 78 :IKKKYA 2ob3A 138 :MRLRSV T0440 98 :IGYEDFTRDFL 2ob3A 144 :EELTQFFLREI T0440 109 :NEYGPQTDD 2ob3A 159 :EDTGIRAGI T0440 121 :SLHF 2ob3A 171 :ATTG T0440 151 :GFEQAQLAYLEGVKQSIE 2ob3A 175 :KATPFQELVLKAAARASL T0440 173 :LF 2ob3A 193 :AT T0440 177 :RRM 2ob3A 197 :PVT T0440 184 :LCQKF 2ob3A 204 :ASQRD T0440 207 :FRVILALVKKRDY 2ob3A 209 :GEQQAAIFESEGL T0440 220 :ELDFNTAGLF 2ob3A 225 :RVCIGHSDDT T0440 234 :GE 2ob3A 235 :DD T0440 239 :PKKIVTLA 2ob3A 237 :LSYLTALA T0440 248 :ELQIPFVYGS 2ob3A 245 :ARGYLIGLDH Number of specific fragments extracted= 20 number of extra gaps= 4 total=290 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 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)G172 because of BadResidue code BAD_PEPTIDE in next template residue (2ob3A)V196 Warning: unaligning (T0440)L173 because of BadResidue code BAD_PEPTIDE at template residue (2ob3A)V196 Warning: unaligning (T0440)K175 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 :YEDFTRDFLN 2ob3A 142 :SVEELTQFFL T0440 110 :EYG 2ob3A 160 :DTG T0440 115 :TDDGV 2ob3A 163 :IRAGI T0440 123 :HFLEGQ 2ob3A 171 :ATTGKA T0440 152 :FEQ 2ob3A 177 :TPF T0440 156 :QLAYLEGVKQSIEAD 2ob3A 180 :QELVLKAAARASLAT T0440 174 :F 2ob3A 197 :P T0440 176 :PRRMGHISLCQKF 2ob3A 204 :ASQRDGEQQAAIF T0440 189 :QQFFGED 2ob3A 219 :EGLSPSR T0440 196 :TSDFSEE 2ob3A 230 :HSDDTDD T0440 204 :MEKFRVILA 2ob3A 237 :LSYLTALAA T0440 217 :RDYELDFNTAGLFKPLCGE 2ob3A 246 :RGYLIGLDHIPYSAIGLED T0440 236 :TYPPKKIVTLAS 2ob3A 274 :IRSWQTRALLIK T0440 248 :ELQIP 2ob3A 289 :DQGYM T0440 253 :FVYGSDSH 2ob3A 296 :ILVSNDWT Number of specific fragments extracted= 22 number of extra gaps= 4 total=312 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 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 19 :DVEEMVLKAIELDFD 2ob3A 82 :KAVRGLRRARAAGVR 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=330 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 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)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0440)S121 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 :DDVEEMVLKAIELDFDEYSIVEH 1j6oA 14 :DDRNAVISSFEENNIEFVVNVGV T0440 42 :P 1j6oA 37 :N T0440 69 :PYYFKKMNHIKKKY 1j6oA 38 :LEDSKKSLDLSKTS T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDD 1j6oA 52 :DRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKV T0440 118 :GV 1j6oA 87 :AI T0440 122 :LHF 1j6oA 91 :TGL T0440 126 :EGQGGFR 1j6oA 94 :DFFRNIS T0440 151 :G 1j6oA 101 :P T0440 156 :QLAYLEGVKQSIEADLGLFKPRRM 1j6oA 102 :AEVQKRVFVEQIELAGKLNLPLVV T0440 181 :H 1j6oA 126 :H T0440 182 :ISLCQKFQQFFG 1j6oA 131 :YSEAYEILRTES T0440 209 :VILALVKKRDYELDF 1j6oA 158 :EWAKKFIDLGFLLGI T0440 225 :TAGLFKP 1j6oA 173 :GGPVTYP T0440 238 :PPKKIVTLASELQI 1j6oA 180 :KNEALREVVKRVGL T0440 252 :PFVYGSDSHGVQDIGRG 1j6oA 195 :YIVLETDCPFLPPQPFR Number of specific fragments extracted= 18 number of extra gaps= 1 total=348 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 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)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0440)S121 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 :SDLLIHIGFE 1j6oA 52 :DRIFCSVGVH T0440 94 :VDYL 1j6oA 65 :AKEV T0440 98 :IGYEDFTRDFLNE 1j6oA 70 :EDFIEHLEKFAKD T0440 114 :QTDDGV 1j6oA 83 :EKVVAI T0440 122 :LHFLEGQGGF 1j6oA 91 :TGLDFFRNIS T0440 151 :GFEQA 1j6oA 101 :PAEVQ T0440 157 :LAYLEGVKQSIEAD 1j6oA 106 :KRVFVEQIELAGKL T0440 172 :GLF 1j6oA 120 :NLP T0440 177 :RRMGHISLCQK 1j6oA 130 :AYSEAYEILRT T0440 189 :QQFFGED 1j6oA 141 :ESLPEKR 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= 19 number of extra gaps= 1 total=367 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 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=380 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 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)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 :RDGHTHTEFC 2gzxA 3 :IDTHVHLNDE T0440 14 :HGT 2gzxA 13 :QYD T0440 18 :DDVEEMVLKAIELDFDEYSIVEH 2gzxA 16 :DDLSEVITRAREAGVDRMFVVGF T0440 42 :P 2gzxA 39 :N T0440 69 :PYYFKKMNHIKKKY 2gzxA 40 :KSTIERAMKLIDEY T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDD 2gzxA 54 :DFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKV T0440 118 :GV 2gzxA 89 :GI T0440 122 :LHFLEGQGGFR 2gzxA 93 :MGLDYHWDKSP T0440 156 :QLAYLEGVKQSIEADLGLFKPRRM 2gzxA 104 :ADVQKEVFRKQIALAKRLKLPIII T0440 181 :HI 2gzxA 128 :HN T0440 198 :DF 2gzxA 131 :EA T0440 207 :FRVILALVKKRDY 2gzxA 133 :TQDCIDILLEEHA T0440 220 :ELDF 2gzxA 149 :GGIM T0440 226 :AGLF 2gzxA 153 :HSFS T0440 234 :G 2gzxA 157 :G T0440 238 :PPKKIVTLASELQIPFVYG 2gzxA 158 :SPEIADIVTNKLNFYISLG Number of specific fragments extracted= 16 number of extra gaps= 1 total=396 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 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 12 :CPHGT 2gzxA 11 :DEQYD T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 2gzxA 16 :DDLSEVITRAREAGVDRMFVVGFNKSTIERA T0440 62 :SMAMSDL 2gzxA 47 :MKLIDEY T0440 84 :SDLLIHIGFEVDYLIGYE 2gzxA 54 :DFLYGIIGWHPVDAIDFT T0440 102 :DFTRDFLNEYGPQTDDGV 2gzxA 73 :EHLEWIESLAQHPKVIGI T0440 122 :LHFLEGQ 2gzxA 93 :MGLDYHW T0440 151 :G 2gzxA 100 :D T0440 173 :LFK 2gzxA 101 :KSP T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGL 2gzxA 104 :ADVQKEVFRKQIALAKRLKLPIIIHNREA T0440 239 :PKKIVTLASELQ 2gzxA 133 :TQDCIDILLEEH T0440 251 :IPFVY 2gzxA 148 :VGGIM Number of specific fragments extracted= 12 number of extra gaps= 1 total=408 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 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=419 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)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 T0440 2 :KRDGHTHTEF 1zzmA 5 :FIDTHCHFDF T0440 14 :HGTHDDVEEMVLKAIELDFDEYSIVEH 1zzmA 15 :PPFSGDEEASLQRAAQAGVGKIIVPAT T0440 42 :P 1zzmA 42 :E T0440 69 :PYYFKKMNHIKKKY 1zzmA 43 :AENFARVLALAENY T0440 84 :SDLLIHIGFEV 1zzmA 57 :QPLYAALGLHP T0440 95 :DYLIGYEDFTRDFLNE 1zzmA 72 :KHSDVSLEQLQQALER T0440 112 :GPQTDDGV 1zzmA 88 :RPAKVVAV T0440 122 :LHF 1zzmA 98 :IGL T0440 126 :EGQGGFR 1zzmA 101 :DLFGDDP T0440 151 :G 1zzmA 108 :Q T0440 156 :QLAYLEGVKQSIEADLGLFKPRRM 1zzmA 109 :FERQQWLLDEQLKLAKRYDLPVIL T0440 181 :HI 1zzmA 133 :HS T0440 198 :DFSEEVMEKFR 1zzmA 136 :RTHDKLAMHLK T0440 209 :VILALVKKRDYELDF 1zzmA 164 :QQAERFVQLGYKIGV T0440 225 :TAGLFKPLCGE 1zzmA 179 :GGTITYPRASK T0440 242 :IVTLASELQI 1zzmA 190 :TRDVIAKLPL T0440 252 :PFVYGSDSHGVQDIGRG 1zzmA 201 :SLLLETDAPDMPLNGFQ Number of specific fragments extracted= 17 number of extra gaps= 1 total=436 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 :KRDGHTHTE 1zzmA 5 :FIDTHCHFD T0440 12 :CPHGT 1zzmA 14 :FPPFS T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPLSSEFM 1zzmA 19 :GDEEASLQRAAQAGVGKIIVPATEAENFARV T0440 62 :SMAMSDL 1zzmA 50 :LALAENY T0440 84 :SDLLIHIGFEV 1zzmA 57 :QPLYAALGLHP T0440 95 :DYL 1zzmA 71 :EKH T0440 98 :IGYEDFTRDFLNE 1zzmA 75 :DVSLEQLQQALER T0440 114 :QTDDGVLS 1zzmA 88 :RPAKVVAV T0440 124 :FLEGQ 1zzmA 98 :IGLDL T0440 151 :G 1zzmA 103 :F T0440 171 :LGLFK 1zzmA 104 :GDDPQ T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGL 1zzmA 109 :FERQQWLLDEQLKLAKRYDLPVILHSRRT T0440 239 :PKKIVTLASELQIP 1zzmA 138 :HDKLAMHLKRHDLP T0440 253 :FVY 1zzmA 154 :GVV Number of specific fragments extracted= 15 number of extra gaps= 1 total=451 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 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=462 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 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)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vc7A)I138 Warning: unaligning (T0440)F124 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 19 :DVEEMVLKAIELDFDEYSI 2vc7A 48 :NAVNEVKRAMQFGVKTIVD T0440 63 :MAMSDLPYYFKKMNHIKKKYASDLLIHIGFEV 2vc7A 67 :PTVMGLGRDIRFMEKVVKATGINLVAGTGIYI T0440 95 :DYLIGYEDFTRDFLNEY 2vc7A 105 :YFLNRSIDEIADLFIHD T0440 115 :TDD 2vc7A 126 :IQG T0440 120 :LS 2vc7A 134 :GF T0440 125 :LE 2vc7A 139 :AA T0440 148 :FYGGFEQAQLAYLEGVKQSIE 2vc7A 141 :DEPGITKDVEKVIRAAAIANK T0440 173 :LFKPRRMGH 2vc7A 162 :ETKVPIITH T0440 182 :I 2vc7A 178 :G T0440 183 :SLCQKFQQ 2vc7A 180 :EQQRILTE T0440 192 :FGEDTS 2vc7A 188 :EGVDPG T0440 198 :DFSEE 2vc7A 204 :DNIDY T0440 207 :FRVILA 2vc7A 209 :IKKIAD T0440 217 :RDYELD 2vc7A 215 :KGSFIG T0440 225 :TAGLF 2vc7A 223 :RYGLD T0440 235 :ETYPPKKIVTLAS 2vc7A 228 :LFLPVDKRNETTL T0440 248 :ELQI 2vc7A 244 :KDGY T0440 252 :PFVYGSDSHGVQ 2vc7A 250 :KIMISHDYCCTI T0440 264 :DIGRG 2vc7A 265 :TAKPE Number of specific fragments extracted= 19 number of extra gaps= 1 total=481 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 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)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vc7A)I138 Warning: unaligning (T0440)F124 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 :SSEFM 2vc7A 75 :DIRFM T0440 62 :SMAMSDLP 2vc7A 80 :EKVVKATG T0440 86 :LLIHIGFEVDYLIG 2vc7A 88 :INLVAGTGIYIYID T0440 100 :YEDFTRDFLNEYGPQTDDGVLS 2vc7A 114 :IADLFIHDIKEGIQGTLNKAGF T0440 125 :LEGQG 2vc7A 139 :AADEP T0440 151 :GFEQAQLAYLEGVKQSIEAD 2vc7A 144 :GITKDVEKVIRAAAIANKET T0440 173 :LFK 2vc7A 164 :KVP T0440 176 :PRRMGHISLCQKF 2vc7A 173 :AHNNTGLEQQRIL T0440 189 :QQFFGED 2vc7A 188 :EGVDPGK T0440 196 :TSDF 2vc7A 199 :HLGD T0440 204 :MEKFRVILA 2vc7A 206 :IDYIKKIAD T0440 217 :RDYELD 2vc7A 215 :KGSFIG T0440 225 :TAGL 2vc7A 223 :RYGL T0440 234 :GETYPPKKIVTLASE 2vc7A 227 :DLFLPVDKRNETTLR T0440 249 :LQIP 2vc7A 245 :DGYS T0440 253 :FVYGSDSHGV 2vc7A 251 :IMISHDYCCT Number of specific fragments extracted= 17 number of extra gaps= 1 total=498 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 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 19 :DVEEMVLKAIELDFDEYSIVEHAPLSSE 2vc7A 48 :NAVNEVKRAMQFGVKTIVDPTVMGLGRD 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 111 :YGPQTDDGV 2vc7A 127 :QGTLNKAGF 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=513 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 3c86A/T0440-3c86A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3c86A expands to /projects/compbio/data/pdb/3c86.pdb.gz 3c86A:Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms # T0440 read from 3c86A/T0440-3c86A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c86A read from 3c86A/T0440-3c86A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3c86A to template set # found chain 3c86A in template set Warning: unaligning (T0440)T60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)T128 Warning: unaligning (T0440)A61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)T128 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3c86A)V170 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c86A)V170 Warning: unaligning (T0440)H123 because of BadResidue code BAD_PEPTIDE in next template residue (3c86A)T172 Warning: unaligning (T0440)F124 because of BadResidue code BAD_PEPTIDE at template residue (3c86A)T172 Warning: unaligning (T0440)I182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)S203 Warning: unaligning (T0440)S183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)S203 Warning: unaligning (T0440)Y255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)D253 Warning: unaligning (T0440)G256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)D253 T0440 1 :M 3c86A 49 :A T0440 2 :KRDGHTHTEFCPHGT 3c86A 51 :FTLTHEHICGSSAGF T0440 17 :HDDVEEMVLKAIELDFDEYSIVEH 3c86A 80 :AEKAVRGLRHARAAGVQTIVDVST T0440 42 :PLS 3c86A 104 :FDI T0440 45 :SEFMKNTAG 3c86A 111 :RLLAEVSRA T0440 54 :DKEAVT 3c86A 121 :DVHIVA T0440 62 :SMAMSDLPY 3c86A 129 :GLWFDPPLS T0440 78 :IKKKY 3c86A 138 :MRMRS T0440 101 :EDFTRDFLNEY 3c86A 143 :VEELTQFFLRE T0440 112 :GPQTDDGV 3c86A 160 :DTGIRAGI T0440 125 :LE 3c86A 173 :TG T0440 151 :GFEQAQLAYLEGVKQSIE 3c86A 175 :KATPFQELVLKAAARASL T0440 173 :LFKPRRMGH 3c86A 193 :ATGVPVTTH T0440 184 :LCQKF 3c86A 204 :ASQRD T0440 207 :FRVILALVKKRDY 3c86A 209 :GEQQAAIFESEGL T0440 220 :ELDFNTAGLF 3c86A 225 :RVCIGHSDDT T0440 234 :GE 3c86A 235 :DD T0440 239 :PKKIVTLA 3c86A 237 :LSYLTGLA T0440 248 :ELQIPFV 3c86A 245 :ARGYLVG T0440 257 :SDSHGVQDIGR 3c86A 254 :RMPYSAIGLEG Number of specific fragments extracted= 20 number of extra gaps= 3 total=533 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 3c86A/T0440-3c86A-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 3c86A/T0440-3c86A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c86A read from 3c86A/T0440-3c86A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c86A in template set Warning: unaligning (T0440)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)T128 Warning: unaligning (T0440)F92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)T128 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3c86A)V170 Warning: unaligning (T0440)L122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c86A)V170 Warning: unaligning (T0440)H123 because of BadResidue code BAD_PEPTIDE in next template residue (3c86A)T172 Warning: unaligning (T0440)F124 because of BadResidue code BAD_PEPTIDE at template residue (3c86A)T172 Warning: unaligning (T0440)F174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)S203 Warning: unaligning (T0440)K175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)S203 Warning: unaligning (T0440)F223 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)D253 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)D253 T0440 20 :VEEMVLKAIELDFDEYSIVEHAPL 3c86A 83 :AVRGLRHARAAGVQTIVDVSTFDI T0440 44 :SSEFM 3c86A 109 :DVRLL T0440 62 :SMAMSDLP 3c86A 114 :AEVSRAAD T0440 86 :LLIHI 3c86A 122 :VHIVA T0440 93 :EVDYL 3c86A 129 :GLWFD T0440 98 :IG 3c86A 136 :LS T0440 100 :YEDFTRDFLN 3c86A 142 :SVEELTQFFL T0440 112 :GPQTDDGV 3c86A 160 :DTGIRAGI T0440 125 :LEGQ 3c86A 173 :TGKA T0440 152 :FEQ 3c86A 177 :TPF T0440 156 :QLAYLEGVKQSIEAD 3c86A 180 :QELVLKAAARASLAT T0440 172 :G 3c86A 195 :G T0440 173 :L 3c86A 201 :H T0440 176 :PRRMGHISLCQKF 3c86A 204 :ASQRDGEQQAAIF T0440 189 :QQFFGED 3c86A 219 :EGLSPSR T0440 196 :TSDFS 3c86A 230 :HSDDT T0440 204 :MEKFRVILAL 3c86A 237 :LSYLTGLAAR T0440 218 :DYELD 3c86A 247 :GYLVG T0440 225 :TAGLFKPLCG 3c86A 254 :RMPYSAIGLE T0440 235 :ETYPPKKIVTLASE 3c86A 273 :GTRSWQTRALLIKA T0440 249 :LQIP 3c86A 290 :RGYK T0440 253 :FVYGSDSHG 3c86A 296 :ILVSHDWLF Number of specific fragments extracted= 22 number of extra gaps= 3 total=555 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 3c86A/T0440-3c86A-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 3c86A/T0440-3c86A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c86A read from 3c86A/T0440-3c86A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c86A in template set Warning: unaligning (T0440)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)T128 Warning: unaligning (T0440)F92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)T128 Warning: unaligning (T0440)G118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3c86A)V170 Warning: unaligning (T0440)L120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3c86A)V170 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE in next template residue (3c86A)T172 Warning: unaligning (T0440)L122 because of BadResidue code BAD_PEPTIDE at template residue (3c86A)T172 Warning: unaligning (T0440)I182 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)S203 Warning: unaligning (T0440)S183 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)S203 Warning: unaligning (T0440)F223 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3c86A)D253 Warning: unaligning (T0440)N224 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3c86A)D253 T0440 20 :VEEMVLKAIELDFDEYSIV 3c86A 83 :AVRGLRHARAAGVQTIVDV T0440 43 :LSSEFMKNT 3c86A 102 :STFDIGRDV T0440 73 :KKMNHIKKKY 3c86A 111 :RLLAEVSRAA T0440 85 :DLLIHI 3c86A 121 :DVHIVA T0440 95 :DYLIG 3c86A 129 :GLWFD T0440 100 :YEDFTRDFLNE 3c86A 146 :LTQFFLREIQH T0440 111 :YGPQTDD 3c86A 161 :TGIRAGI T0440 128 :QGG 3c86A 173 :TGK T0440 152 :FEQAQLAYLEGVKQSIEAD 3c86A 176 :ATPFQELVLKAAARASLAT T0440 175 :KPRRMGH 3c86A 195 :GVPVTTH T0440 184 :L 3c86A 204 :A T0440 191 :FFG 3c86A 232 :DDT T0440 198 :DFSEE 3c86A 235 :DDLSY T0440 207 :FRVIL 3c86A 240 :LTGLA T0440 216 :KRDYELD 3c86A 245 :ARGYLVG T0440 225 :TAGLFKPLCG 3c86A 254 :RMPYSAIGLE T0440 235 :ETYPPKKIVTLAS 3c86A 273 :GTRSWQTRALLIK T0440 248 :ELQI 3c86A 289 :DRGY T0440 253 :FVYGSD 3c86A 296 :ILVSHD Number of specific fragments extracted= 19 number of extra gaps= 3 total=574 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 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 42 :PLSSEFMKNT 2pgfA 111 :HAVFNKYKEG 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 116 :DDGVLSLHFLE 2pgfA 192 :ADFVGFDHGGH T0440 131 :FRSIDFSAEDYNEGIVQ 2pgfA 203 :EVDLKEYKEIFDYVRES T0440 151 :GFE 2pgfA 220 :GVP T0440 165 :QSIEADLGLFKPRRMGHISLCQK 2pgfA 237 :NTLYSAIQVLKVERIGHGIRVAE T0440 207 :FRVILALVKKRDYELDFN 2pgfA 260 :SQELIDMVKEKNILLEVC T0440 225 :TAGLFKPLCGE 2pgfA 283 :LLKNAKSMDTH T0440 238 :PPKKIV 2pgfA 294 :PIRQLY T0440 248 :ELQIPFVYGSD 2pgfA 300 :DAGVKVSVNSD Number of specific fragments extracted= 17 number of extra gaps= 0 total=591 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 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 57 :AVTTASMAMSDLPYYFKKMNHIKKKY 2pgfA 87 :EFVEKAIKVADIFHDYEVIEDLAKHA T0440 84 :SDLLIHIGFEV 2pgfA 119 :EGVVLMEFRYS T0440 96 :YL 2pgfA 130 :PT T0440 100 :YEDFTRDFLNEYGPQTDDGVLSLHFLEGQGG 2pgfA 148 :IVKGIKEVVELLDHKIHVALMCIGDTGHEAA T0440 151 :GFEQAQLAYLEG 2pgfA 179 :NIKASADFCLKH T0440 171 :LGLFKPRRM 2pgfA 201 :GHEVDLKEY T0440 180 :GHISLCQKF 2pgfA 211 :EIFDYVRES T0440 196 :TSDFSEE 2pgfA 256 :RVAESQE T0440 210 :ILALVKKRDYELDFN 2pgfA 263 :LIDMVKEKNILLEVC T0440 226 :AGLFKPLCGET 2pgfA 284 :LKNAKSMDTHP T0440 239 :PK 2pgfA 295 :IR T0440 245 :LASELQIPFVYGSD 2pgfA 297 :QLYDAGVKVSVNSD Number of specific fragments extracted= 16 number of extra gaps= 0 total=607 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 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 :SEF 2pgfA 131 :TFV T0440 58 :VTTASMAMSD 2pgfA 134 :AFKYNLDIEL 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 199 :FSEE 2pgfA 259 :ESQE 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= 13 number of extra gaps= 0 total=620 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 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 :DDVEEMVLKAIELDFDEYSIVE 1yixA 20 :KDVDDVLAKAAARDVKFCLAVA T0440 42 :PL 1yixA 42 :TT T0440 69 :PYYFKKMNHIKKKY 1yixA 44 :LPSYLHMRDLVGER T0440 84 :SDLLIHIGFEVDYLIGY 1yixA 58 :DNVVFSCGVHPLNQNDP T0440 101 :EDFTRDFLN 1yixA 77 :VEDLRRLAA T0440 113 :PQTDDGV 1yixA 86 :EEGVVAL T0440 122 :LHFLEGQGGF 1yixA 95 :TGLDYYYTPE T0440 155 :AQLAYLEGVKQSIEADLGLFKPRRM 1yixA 105 :TKVRQQESFIHHIQIGRELNKPVIV T0440 181 :HI 1yixA 130 :HT T0440 197 :SDFSEEVMEKFR 1yixA 132 :RDARADTLAILR T0440 209 :VILALVKKRDYELDF 1yixA 162 :ETAGKLLDLGFYISF T0440 225 :TAGLFKPL 1yixA 177 :SGIVTFRN T0440 239 :PKKIVTLASELQI 1yixA 185 :AEQLRDAARYVPL T0440 252 :PFVYGSDSHGVQDIGR 1yixA 199 :RLLVETDSPYLAPVPH Number of specific fragments extracted= 17 number of extra gaps= 1 total=637 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 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)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 3 :RDGHTHTEFC 1yixA 4 :VDSHCHLDGL T0440 13 :PHGTHDDVEEMVLKAIELDFDEYSIVE 1yixA 15 :YESLHKDVDDVLAKAAARDVKFCLAVA T0440 43 :LSSEFMKNT 1yixA 42 :TTLPSYLHM T0440 62 :SMAMSDL 1yixA 51 :RDLVGER T0440 84 :SDLLIHIGFEVDYLIG 1yixA 58 :DNVVFSCGVHPLNQND T0440 100 :YEDFTRDFLNE 1yixA 76 :DVEDLRRLAAE T0440 115 :TD 1yixA 87 :EG T0440 117 :DGV 1yixA 90 :VAL T0440 122 :LHFLEGQGG 1yixA 95 :TGLDYYYTP T0440 150 :GGFEQA 1yixA 104 :ETKVRQ T0440 157 :LAYLEGVKQSIEA 1yixA 110 :QESFIHHIQIGRE T0440 171 :LGLF 1yixA 123 :LNKP T0440 175 :K 1yixA 134 :A T0440 178 :RMGHISLCQKF 1yixA 135 :RADTLAILREE T0440 190 :QFFGED 1yixA 146 :KVTDCG T0440 204 :MEK 1yixA 161 :RET T0440 211 :LALVKKRDYELDFNTAGLFKP 1yixA 164 :AGKLLDLGFYISFSGIVTFRN T0440 239 :PKKIVTLASELQIP 1yixA 185 :AEQLRDAARYVPLD T0440 253 :FVYGSDSHGVQDI 1yixA 200 :LLVETDSPYLAPV Number of specific fragments extracted= 19 number of extra gaps= 1 total=656 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 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=668 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 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)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0440)S121 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 42 :P 1xwyA 38 :N T0440 69 :PYYFKKMNHIKKKY 1xwyA 39 :LRESQQAQKLARQY T0440 84 :SDLLIHIGFEVDYLIGYEDFTRDFLNEYGPQTDD 1xwyA 53 :SSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEV T0440 118 :GV 1xwyA 88 :AI T0440 122 :LHF 1xwyA 92 :CGL T0440 126 :EGQGGFR 1xwyA 95 :DFNRNFS T0440 151 :GFEQ 1xwyA 102 :TPEE T0440 159 :YLEGVKQSIEADLGLFKPRRM 1xwyA 106 :QERAFVAQLRIAADLNMPVFM T0440 181 :HI 1xwyA 127 :HC T0440 198 :DFSEEVMEKFR 1xwyA 130 :DAHERFMTLLE T0440 209 :VILALVKKRDYELDF 1xwyA 159 :EEMQACVAHGIYIGI T0440 225 :TAGLFKPL 1xwyA 174 :TGWVCDER T0440 238 :PPKKIVTLASELQI 1xwyA 182 :RGLELRELLPLIPA T0440 252 :PFVYGSDSHGVQDIGR 1xwyA 197 :KLLIETDAPYLLPRDL Number of specific fragments extracted= 17 number of extra gaps= 1 total=685 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 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)L120 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0440)S121 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0440 3 :RDGHTHTE 1xwyA 2 :FDIGVNLT T0440 12 :CPHGT 1xwyA 10 :SSQFA T0440 18 :DDVEEMVLKAIELDFDEYSIVE 1xwyA 15 :KDRDDVVACAFDAGVNGLLITG T0440 44 :SSEFMKNT 1xwyA 38 :NLRESQQA T0440 62 :SMAMSD 1xwyA 46 :QKLARQ T0440 82 :Y 1xwyA 52 :Y T0440 84 :SDLLIHIGFEV 1xwyA 53 :SSCWSTAGVHP T0440 95 :DYL 1xwyA 67 :SQW T0440 98 :IGYEDFTRDFLNEY 1xwyA 71 :AATEEAIIELAAQP T0440 115 :TDDGV 1xwyA 85 :EVVAI T0440 122 :LHFLEGQ 1xwyA 92 :CGLDFNR T0440 172 :GLFK 1xwyA 99 :NFST T0440 200 :SEEVMEKFRVILALVKKRDYELDFNTAGL 1xwyA 103 :PEEQERAFVAQLRIAADLNMPVFMHCRDA T0440 239 :PKKIVTL 1xwyA 132 :HERFMTL T0440 246 :ASELQIPFVYGSDSHGVQDIG 1xwyA 164 :CVAHGIYIGITGWVCDERRGL T0440 268 :GYSTYCQK 1xwyA 185 :ELRELLPL Number of specific fragments extracted= 16 number of extra gaps= 1 total=701 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 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=713 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 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 :DDVEEMVLKAIELDFDEYSIVEH 2ffiA 40 :APLGDYLGQLRAHGFSHGVLVQP T0440 42 :PLS 2ffiA 63 :SFL T0440 69 :PYYFKKMNHIKKKYASDLL 2ffiA 66 :GTDNRYLLSALQTVPGQLR T0440 93 :EVDYLI 2ffiA 85 :GVVMLE T0440 99 :GYEDFTRDFLNEYG 2ffiA 92 :DVEQATLAEMARLG T0440 115 :TD 2ffiA 106 :VR T0440 118 :GVLSL 2ffiA 108 :GVRLN T0440 128 :QGGFRSIDFSAEDYNEGIVQFYG 2ffiA 113 :LMGQDMPDLTGAQWRPLLERIGE T0440 151 :GF 2ffiA 137 :GW T0440 161 :EGVKQSIEADLGLFKPRRMGHISLCQKF 2ffiA 147 :ADIPVLVRALQPYGLDIVIDHFGRPDAR T0440 194 :EDTSDFSEEVMEKFRVILALVKKRDY 2ffiA 202 :YRLQGSPEENLAFARQALCALEAHYG T0440 220 :ELDFNTAGLF 2ffiA 231 :LMWGSDWPHT T0440 231 :PL 2ffiA 241 :QH T0440 234 :GETYPPKKIVTLASELQIP 2ffiA 243 :ESEVSFGSAVEQFEALGCS Number of specific fragments extracted= 17 number of extra gaps= 0 total=730 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 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 :TDDGVLSLHFLEGQG 2ffiA 105 :GVRGVRLNLMGQDMP T0440 135 :DFSAE 2ffiA 120 :DLTGA T0440 151 :GFEQAQLAYLE 2ffiA 125 :QWRPLLERIGE T0440 171 :LGL 2ffiA 136 :QGW T0440 174 :FK 2ffiA 144 :RQ T0440 178 :RMGHISLCQKF 2ffiA 146 :VADIPVLVRAL T0440 192 :FGEDTSDFSEEVMEKFRVILALVKKRDY 2ffiA 200 :GIYRLQGSPEENLAFARQALCALEAHYG T0440 220 :ELDFNTAG 2ffiA 231 :LMWGSDWP T0440 229 :FKPL 2ffiA 239 :HTQH T0440 234 :GETYPPKKIVTLASELQIP 2ffiA 243 :ESEVSFGSAVEQFEALGCS Number of specific fragments extracted= 18 number of extra gaps= 0 total=748 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 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 :DLLIH 2ffiA 137 :GWHVE T0440 94 :VDYLIGYEDFTRDFLN 2ffiA 142 :LHRQVADIPVLVRALQ T0440 112 :GPQTDDGVL 2ffiA 158 :PYGLDIVID 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=762 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 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 :HDDVEEMVLKAIELDFDEYSIVE 2qahA 53 :DAGPDMLFALRDHLGFARNVIVQ T0440 42 :PLSSEFMKNTA 2qahA 84 :AATLDAIARAQ T0440 56 :EAVTTASM 2qahA 95 :GKARGIAV 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 :EDFTRDFLNEYG 2qahA 137 :KDKFLEVAGRLP T0440 115 :TDDGVLSLHF 2qahA 149 :AGWHVVIYFE T0440 126 :EG 2qahA 159 :AD T0440 151 :GFEQ 2qahA 161 :ILEE T0440 159 :YLEGVKQ 2qahA 165 :LRPFMDA T0440 173 :LFKPRRMGHISLCQKFQQFFG 2qahA 172 :IPVPIVIDHMGRPDVRQGPDG T0440 201 :EE 2qahA 193 :AD T0440 207 :FRVILALVKKRD 2qahA 195 :MKAFRRLLDSRE T0440 220 :ELDFNTAGLF 2qahA 207 :DIWFKATCPD T0440 230 :KPL 2qahA 219 :DPA T0440 234 :GETY 2qahA 222 :GPPW T0440 238 :PPKKIVTLASELQIPFVYGSD 2qahA 228 :FARSVAPLVADYADRVIWGTD T0440 261 :GVQDIGR 2qahA 251 :HPNMQDA Number of specific fragments extracted= 25 number of extra gaps= 5 total=787 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 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)H14 because of BadResidue code BAD_PEPTIDE in next template residue (2qahA)A47 Warning: unaligning (T0440)G15 because of BadResidue code BAD_PEPTIDE at template residue (2qahA)A47 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)G130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qahA)A135 Warning: unaligning (T0440)F131 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 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 2 :KR 2qahA 27 :AI T0440 6 :HTHTEFC 2qahA 31 :HCHVFGP T0440 13 :P 2qahA 45 :P T0440 16 :T 2qahA 48 :K T0440 18 :DDVEEMVLKAIELDFDEYSIVEHAPL 2qahA 54 :AGPDMLFALRDHLGFARNVIVQASCH T0440 44 :SSEFM 2qahA 82 :DNAAT T0440 62 :SMAMSDL 2qahA 87 :LDAIARA T0440 83 :ASDLL 2qahA 94 :QGKAR T0440 91 :GFEV 2qahA 99 :GIAV T0440 97 :LIGYEDFTR 2qahA 105 :PAIDEAELA T0440 108 :LNE 2qahA 116 :HEG T0440 115 :TDDGVLSLHFLEGQG 2qahA 119 :GMRGIRFNFLKRLVD T0440 152 :FEQAQLAYLE 2qahA 137 :KDKFLEVAGR T0440 163 :V 2qahA 147 :L T0440 168 :E 2qahA 148 :P T0440 171 :LGLF 2qahA 149 :AGWH T0440 175 :KPRRMGHISLCQKF 2qahA 159 :ADILEELRPFMDAI T0440 189 :QQFFGEDTSDF 2qahA 182 :GRPDVRQGPDG T0440 205 :EKFRVILALVKKRDY 2qahA 193 :ADMKAFRRLLDSRED T0440 220 :ELD 2qahA 209 :WFK T0440 225 :TAGLFKPLCGETYP 2qahA 212 :ATCPDRLDPAGPPW T0440 239 :PKKIVTLASELQIPFVYGSD 2qahA 229 :ARSVAPLVADYADRVIWGTD T0440 261 :GVQDIGRGYS 2qahA 251 :HPNMQDAIPD Number of specific fragments extracted= 23 number of extra gaps= 6 total=810 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 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 :SSEFMKNTAGDKEAVT 2qahA 76 :ASCHGTDNAATLDAIA T0440 63 :MAMSD 2qahA 92 :RAQGK 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=829 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 1i0dA/T0440-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i0dA expands to /projects/compbio/data/pdb/1i0d.pdb.gz 1i0dA:Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1442, because occupancy 0.300 <= existing 0.700 in 1i0dA Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1997, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 1998, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2000, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2001, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2003, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2004, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2006, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2007, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1i0dA # T0440 read from 1i0dA/T0440-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0440-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i0dA to template set # found chain 1i0dA in template set T0440 2 :KRDGHTHT 1i0dA 51 :FTLTHEHI T0440 10 :EFCPH 1i0dA 60 :GSSAG T0440 18 :DDVEE 1i0dA 74 :GSRKA T0440 23 :MVLKAIELDFDEYSIVE 1i0dA 86 :GLRRARAAGVRTIVDVS T0440 41 :APLSSEFMKNTAG 1i0dA 107 :GRDVSLLAEVSRA T0440 54 :DKEAVTTASMAMSDLPY 1i0dA 121 :DVHIVAATGLWFDPPLS T0440 78 :IKKKY 1i0dA 138 :MRLRS T0440 101 :EDFTRDFLNEY 1i0dA 143 :VEELTQFFLRE T0440 112 :GPQTDDGVLSLHFLE 1i0dA 160 :DTGIRAGIIKVATTG T0440 151 :GFEQAQLAYLEGVKQSIE 1i0dA 175 :KATPFQELVLKAAARASL T0440 173 :LFKPRRMGHISLCQKF 1i0dA 193 :ATGVPVTTHTAASQRD T0440 207 :FRVILALVKKRDY 1i0dA 209 :GEQQAAIFESEGL T0440 220 :ELDFNTAGLF 1i0dA 225 :RVCIGHSDDT T0440 234 :GE 1i0dA 235 :DD T0440 239 :PK 1i0dA 237 :LS T0440 242 :IVTLASELQIPFVYGSD 1i0dA 239 :YLTALAARGYLIGLDHI Number of specific fragments extracted= 16 number of extra gaps= 0 total=845 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 1i0dA/T0440-1i0dA-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 1i0dA/T0440-1i0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0440-1i0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i0dA in template set T0440 20 :VEEMVLKAIELDFDEYSIVEHAPL 1i0dA 83 :AVRGLRRARAAGVRTIVDVSTFDI T0440 44 :SSEFM 1i0dA 109 :DVSLL T0440 62 :SMAMSDLP 1i0dA 114 :AEVSRAAD T0440 86 :LLIHIGFEVDYL 1i0dA 122 :VHIVAATGLWFD T0440 98 :IG 1i0dA 135 :PL T0440 100 :YEDFTRDFLNEYGPQTDDGVLSLHFLEGQ 1i0dA 146 :LTQFFLREIQYGIEDTGIRAGIIKVATTG T0440 151 :GFEQAQLAYLEGVKQSIEAD 1i0dA 175 :KATPFQELVLKAAARASLAT T0440 172 :GL 1i0dA 195 :GV T0440 174 :FKPRRMGHISLCQKF 1i0dA 202 :TAASQRDGEQQAAIF T0440 189 :QQFFGED 1i0dA 219 :EGLSPSR T0440 196 :TSDF 1i0dA 230 :HSDD T0440 204 :MEKFRVILA 1i0dA 237 :LSYLTALAA T0440 217 :RDYELDFNTAGLFKPLCGE 1i0dA 246 :RGYLIGLDHIPHSAIGLED T0440 236 :TYPPKKIVTLASE 1i0dA 274 :IRSWQTRALLIKA T0440 249 :LQIP 1i0dA 290 :QGYM T0440 253 :FVYGSDS 1i0dA 296 :ILVSNDW Number of specific fragments extracted= 16 number of extra gaps= 0 total=861 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 1i0dA/T0440-1i0dA-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 1i0dA/T0440-1i0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0440-1i0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i0dA in template set T0440 20 :VEEMVLKAIELDFDEYSI 1i0dA 83 :AVRGLRRARAAGVRTIVD T0440 40 :HA 1i0dA 101 :VS T0440 44 :SSEFMKN 1i0dA 103 :TFDIGRD T0440 72 :FKKMNHIKKKY 1i0dA 110 :VSLLAEVSRAA T0440 85 :DLLIHIGF 1i0dA 121 :DVHIVAAT T0440 95 :DYLIG 1i0dA 129 :GLWFD T0440 100 :YEDFTRDFLNE 1i0dA 146 :LTQFFLREIQY T0440 111 :YGPQTDDGVLSL 1i0dA 161 :TGIRAGIIKVAT T0440 126 :E 1i0dA 173 :T T0440 150 :GGFEQAQLAYLEGVKQSIEAD 1i0dA 174 :GKATPFQELVLKAAARASLAT T0440 175 :KPRRMGHISLCQKFQQ 1i0dA 195 :GVPVTTHTAASQRDGE T0440 191 :FF 1i0dA 233 :DT T0440 198 :DFSEEVME 1i0dA 235 :DDLSYLTA T0440 214 :VKKRDYELDFNTAGLFKPLCG 1i0dA 243 :LAARGYLIGLDHIPHSAIGLE T0440 235 :ETYPPKKIVTLAS 1i0dA 273 :GIRSWQTRALLIK T0440 248 :ELQI 1i0dA 289 :DQGY T0440 253 :FVYGSD 1i0dA 296 :ILVSND Number of specific fragments extracted= 17 number of extra gaps= 0 total=878 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 2amxA/T0440-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2amxA expands to /projects/compbio/data/pdb/2amx.pdb.gz 2amxA:# T0440 read from 2amxA/T0440-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0440-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2amxA to template set # found chain 2amxA in template set Warning: unaligning (T0440)K2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0440 3 :RDGHTHT 2amxA 52 :VELHCHL T0440 14 :HGT 2amxA 59 :DLT T0440 18 :DDVEEMVLKAIELDFD 2amxA 62 :FSAEFFLKWARKYNLQ T0440 41 :APLSSEFMKNT 2amxA 80 :MSDDEILDHYL T0440 65 :MSDLPYYFKKMNHIKKKYASDLLI 2amxA 91 :FTKEGKSLAEFIRKAISVSDLYRD T0440 97 :LIGYEDFTRDFLNEYG 2amxA 115 :YDFIEDLAKWAVIEKY T0440 113 :PQTDDGVLSLH 2amxA 132 :EGVVLMEFRYS T0440 142 :NEGIVQFYG 2amxA 143 :PTFVSSSYG T0440 151 :GFEQAQLAYLEGVKQSIEADLGLFKPRRM 2amxA 153 :DVELIHKAFIKGIKNATELLNNKIHVALI T0440 183 :SLCQKFQQFFG 2amxA 195 :HSGDFAIKHKH T0440 194 :EDTSDFSEE 2amxA 217 :IDLKDHKDV T0440 207 :FR 2amxA 226 :YH T0440 209 :VILALVKKRDYELDFN 2amxA 275 :ELIELVKKKDILLEVC Number of specific fragments extracted= 13 number of extra gaps= 1 total=891 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 2amxA/T0440-2amxA-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 2amxA/T0440-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0440-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set Warning: unaligning (T0440)K2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0440 3 :RDGHTHTEFC 2amxA 52 :VELHCHLDLT T0440 19 :DVEEMVLKAIELDFD 2amxA 63 :SAEFFLKWARKYNLQ T0440 42 :PL 2amxA 78 :PN T0440 44 :SSEFMKNTA 2amxA 81 :SDDEILDHY T0440 53 :GDKEAVTTASMAMSDLPYYFKKMNHIKKKY 2amxA 93 :KEGKSLAEFIRKAISVSDLYRDYDFIEDLA T0440 83 :ASDLLIH 2amxA 131 :KEGVVLM T0440 91 :GFEVDYL 2amxA 138 :EFRYSPT T0440 100 :YEDFTRDFLNEYG 2amxA 161 :FIKGIKNATELLN T0440 115 :TDDGVLSLHFLEGQGGF 2amxA 174 :NKIHVALICISDTGHAA T0440 132 :RSIDFSAEDY 2amxA 213 :GGREIDLKDH T0440 153 :EQAQLAYLE 2amxA 223 :KDVYHSVRD T0440 171 :LGL 2amxA 232 :HGL T0440 174 :FKPRRMG 2amxA 242 :EDATLPN T0440 182 :ISLCQKFQQFFGED 2amxA 249 :LNTLYTAINILNVE T0440 196 :TSDFSEE 2amxA 269 :RVSESDE T0440 210 :ILALVKKRDYELDFN 2amxA 276 :LIELVKKKDILLEVC T0440 226 :AGLFKPLCGET 2amxA 297 :LNNVKSMDTHP T0440 239 :PKKIV 2amxA 308 :IRKLY T0440 248 :ELQIPFVYGSD 2amxA 313 :DAGVKVSVNSD Number of specific fragments extracted= 19 number of extra gaps= 1 total=910 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 2amxA/T0440-2amxA-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 2amxA/T0440-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0440-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set T0440 20 :VEEMVLKAIELDFDEYSIVEH 2amxA 122 :AKWAVIEKYKEGVVLMEFRYS T0440 54 :DKEAVTTASMAMSD 2amxA 143 :PTFVSSSYGLDVEL T0440 68 :LPYYFKKMNHIKKKYASDLLIHIGF 2amxA 158 :HKAFIKGIKNATELLNNKIHVALIC T0440 94 :VDYLIGYEDFTR 2amxA 183 :ISDTGHAAASIK T0440 106 :DFLNEYGPQ 2amxA 198 :DFAIKHKHD T0440 119 :VLSLHFLEGQGGFRS 2amxA 207 :FVGFDHGGREIDLKD T0440 141 :YNEGIVQFYGG 2amxA 222 :HKDVYHSVRDH T0440 165 :QSIEADLGLFKPRRMGHISLCQKF 2amxA 250 :NTLYTAINILNVERIGHGIRVSES T0440 201 :EE 2amxA 274 :DE T0440 210 :ILALVKKRDYELDFNT 2amxA 276 :LIELVKKKDILLEVCP T0440 226 :AGLFKPLCGET 2amxA 293 :SNLLLNNVKSM T0440 237 :YP 2amxA 306 :HP T0440 243 :VTLASELQIPFVYGSD 2amxA 308 :IRKLYDAGVKVSVNSD Number of specific fragments extracted= 13 number of extra gaps= 0 total=923 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 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 Warning: unaligning (T0440)S197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pajA)G264 T0440 10 :EFCP 2pajA 140 :VYYP T0440 14 :HGT 2pajA 145 :MPF T0440 18 :DDVEEMVLKAIELDFDEYSIVEHA 2pajA 148 :DSSAILFEEAEKLGLRFVLLRGGA T0440 42 :PLSSEFMKN 2pajA 176 :QLEADLPTA T0440 92 :FEVDYLIGYEDFTRDFLNEYG 2pajA 185 :LRPETLDAYVADIERLAARYH T0440 113 :PQTDDGVLSLHFLE 2pajA 207 :ASPRAMRRVVMAPT T0440 127 :GQGGFR 2pajA 222 :VLYSIS T0440 152 :F 2pajA 228 :P T0440 161 :EGVKQSIEADLGLFK 2pajA 229 :REMRETAAVARRLGL T0440 177 :RRMGHI 2pajA 244 :RMHSHL T0440 198 :DFS 2pajA 265 :KSP T0440 207 :F 2pajA 268 :V T0440 212 :ALVKKRDY 2pajA 269 :AFCGEHDW T0440 220 :ELDFNTA 2pajA 280 :DVWYAHL T0440 236 :TYPPKKIVTLASELQIPFVYG 2pajA 287 :VKVDADEIALLAQTGTGVAHC Number of specific fragments extracted= 15 number of extra gaps= 0 total=938 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 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 :SMAMSDL 2pajA 120 :RIGLIEL T0440 82 :YASDLLIHIGFEVDYLIG 2pajA 127 :ARSGCATVADHNYVYYPG T0440 100 :YEDFTRDFLNE 2pajA 149 :SSAILFEEAEK T0440 115 :TDDGVLSLHFLEGQGGF 2pajA 160 :LGLRFVLLRGGATQTRQ T0440 132 :RSIDFSA 2pajA 182 :PTALRPE T0440 151 :GFEQAQLAYLEGVKQSIE 2pajA 189 :TLDAYVADIERLAARYHD T0440 171 :LGLFK 2pajA 207 :ASPRA T0440 178 :RMG 2pajA 212 :MRR T0440 181 :H 2pajA 218 :A T0440 185 :C 2pajA 219 :P T0440 189 :QQFFGEDT 2pajA 220 :TTVLYSIS T0440 204 :MEKFRVILALVKKRDYELDFNT 2pajA 228 :PREMRETAAVARRLGLRMHSHL T0440 234 :GETYPPKKIVTLASELQIPFVY 2pajA 285 :HLVKVDADEIALLAQTGTGVAH Number of specific fragments extracted= 17 number of extra gaps= 0 total=955 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 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=967 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 23.285 sec, elapsed time= 28.404 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 5374 constraints to all_contacts Done adding distance constraints # command:CPU_time= 23.400 sec, elapsed time= 28.526 sec. # command:Reading probabilities from T0440.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 32.149 Optimizing... Probability sum: -496.080, CN propb: -496.080 weights: 0.198 constraints: 996 # command:CPU_time= 307.989 sec, elapsed time= 313.189 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 996 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 996 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 4378 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 4378 # 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= 308.084 sec, elapsed time= 314.237 sec. # command: