# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0376/ # command:# Making conformation for sequence T0376 numbered 1 through 321 Created new target T0376 from T0376.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0376/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0376/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0376//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0376/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0376/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0376/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mzhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mzhA expands to /projects/compbio/data/pdb/1mzh.pdb.gz 1mzhA:# T0376 read from 1mzhA/merged-good-all-a2m # 1mzhA read from 1mzhA/merged-good-all-a2m # adding 1mzhA to template set # found chain 1mzhA in template set T0376 9 :VIPALM 1mzhA 108 :IDNAAL # choosing archetypes in rotamer library T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCG 1mzhA 114 :KPHLSEKEIEEFVLKSEELGIYAVCVNP T0376 64 :VERLVK 1mzhA 144 :VKLASS T0376 70 :AGIPVIVGTG 1mzhA 152 :KKVKVCCVIG T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRV 1mzhA 167 :NKTSVKVKEAVEAVRDGAQELDIVWNL T0376 109 :SRGSVIAAQKAHFKAILSAAPEIPAVIYNSPY 1mzhA 196 :FKSEKYDFVVEELKEIFRETPSAVHKVIVETP T0376 144 :ATRADLFFALR 1mzhA 228 :YLNEEEIKKAV T0376 155 :AEH 1mzhA 242 :IEA T0376 159 :NLVGFKEFGGP 1mzhA 245 :GADFIKTSTGF T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1mzhA 260 :TTLEEVRLIKSSAKGRIKVKASGG T0376 194 :TAVVHGFVNCGATGAIT 1mzhA 287 :LETAISMIEAGADRIGT T0376 220 :VIHLCKLSQAA 1mzhA 306 :GISIAEEFLKR Number of specific fragments extracted= 12 number of extra gaps= 0 total=12 Number of alignments=1 # 1mzhA read from 1mzhA/merged-good-all-a2m # found chain 1mzhA in template set T0376 9 :VIPALM 1mzhA 108 :IDNAAL T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCG 1mzhA 114 :KPHLSEKEIEEFVLKSEELGIYAVCVNP T0376 64 :VERLVK 1mzhA 144 :VKLASS T0376 70 :AGIPVIVGTGAV 1mzhA 152 :KKVKVCCVIGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRV 1mzhA 168 :KTSVKVKEAVEAVRDGAQELDIVWNL T0376 108 :LSRGSVIAAQKAHFKAILSAAPEIPAVIYNSPY 1mzhA 195 :AFKSEKYDFVVEELKEIFRETPSAVHKVIVETP T0376 144 :ATRADLFFALRA 1mzhA 228 :YLNEEEIKKAVE T0376 159 :NLVGFKEFGGPAD 1mzhA 245 :GADFIKTSTGFAP T0376 172 :MRYAAENITSRDDEVTLMIGVD 1mzhA 262 :LEEVRLIKSSAKGRIKVKASGG T0376 194 :TAVVHGFVNCGATGAITGI 1mzhA 287 :LETAISMIEAGADRIGTSS T0376 220 :VIHLCKLSQA 1mzhA 306 :GISIAEEFLK Number of specific fragments extracted= 11 number of extra gaps= 0 total=23 Number of alignments=2 # 1mzhA read from 1mzhA/merged-good-all-a2m # found chain 1mzhA in template set T0376 6 :FSGVIPALM 1mzhA 105 :RKYIDNAAL T0376 20 :DRTPDFDALVRKGKELIADGMSAVVY 1mzhA 114 :KPHLSEKEIEEFVLKSEELGIYAVCV T0376 64 :VERLVK 1mzhA 144 :VKLASS T0376 70 :AGIPVIVGTGA 1mzhA 152 :KKVKVCCVIGF T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPR 1mzhA 167 :NKTSVKVKEAVEAVRDGAQELDIVWN T0376 110 :RG 1mzhA 198 :SE T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYY 1mzhA 200 :KYDFVVEELKEIFRETPSAVHKVIVETPY T0376 146 :RADLFFALRAE 1mzhA 229 :LNEEEIKKAVE T0376 159 :NLVGFKEFGG 1mzhA 245 :GADFIKTSTG T0376 169 :PADMRYAAENITS 1mzhA 261 :TLEEVRLIKSSAK T0376 184 :DEVTLMIGVD 1mzhA 274 :GRIKVKASGG T0376 194 :TAVVHGFVNCGATGAITGIG 1mzhA 287 :LETAISMIEAGADRIGTSSG T0376 221 :IHLCKLSQAA 1mzhA 307 :ISIAEEFLKR Number of specific fragments extracted= 13 number of extra gaps= 0 total=36 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1w3iA/merged-good-all-a2m # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0376)V74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0376)I75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0376)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0376)I104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0376 9 :VIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVKAGIP 1w3iA 4 :IITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNK T0376 76 :VGTGAVNTASAVAHAVHAQKVGAKGLM 1w3iA 71 :FQVGGLNLDDAIRLAKLSKDFDIVGIA T0376 105 :PRVLSR 1w3iA 100 :APYYYP T0376 111 :GS 1w3iA 107 :MS T0376 114 :IAAQKAHFKAILSAAP 1w3iA 109 :EKHLVKYFKTLCEVSP T0376 131 :IPAVIYNSPYY 1w3iA 125 :HPVYLYNYPTA T0376 142 :GFATRADLFFAL 1w3iA 137 :GKDIDAKVAKEI T0376 158 :KNLVGFKEFGG 1w3iA 149 :GCFTGVKDTIE T0376 171 :DMRYAAENITSR 1w3iA 160 :NIIHTLDYKRLN T0376 184 :DEVTLMIG 1w3iA 172 :PNMLVYSG T0376 193 :DTAVVHGFVNCGATGA 1w3iA 180 :SDMLIATVASTGLDGN T0376 211 :GIGNVLPKEVIHLCKLSQA 1w3iA 198 :AGSNYLPEVTVTIKKLAME T0376 233 :GD 1w3iA 217 :RK T0376 235 :ADARARALELEQALAVLSSFD 1w3iA 220 :DEALKLQFLHDEVIEASRIFG T0376 260 :LVLYFKYMMVLK 1w3iA 241 :SLSSNYVLTKYF T0376 272 :GDKEYTLHFNETD 1w3iA 254 :GYDLGYPRPPIFP T0376 286 :LTDSQRGYVEAQFKLFNSWYADWSKL 1w3iA 267 :LDDEEERQLIKKVEGIRAKLVELKIL Number of specific fragments extracted= 17 number of extra gaps= 3 total=53 Number of alignments=4 # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0376)V74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0376)I75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0376)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0376)I104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0376 9 :VIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVKAGIP 1w3iA 4 :IITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNK T0376 76 :VGTGAVNTASAVAHAVHAQKVGAKGLM 1w3iA 71 :FQVGGLNLDDAIRLAKLSKDFDIVGIA T0376 105 :PRVLSRGSVIAAQKAHFKAILSAA 1w3iA 100 :APYYYPRMSEKHLVKYFKTLCEVS T0376 130 :EIPAVIYNSPYY 1w3iA 124 :PHPVYLYNYPTA T0376 142 :GFATRADLFFAL 1w3iA 137 :GKDIDAKVAKEI T0376 158 :KNLVGFKEFGG 1w3iA 149 :GCFTGVKDTIE T0376 171 :DMRYAAENITSRD 1w3iA 160 :NIIHTLDYKRLNP T0376 185 :EVTLMIG 1w3iA 173 :NMLVYSG T0376 193 :DTAVVHGFVNCGATGA 1w3iA 180 :SDMLIATVASTGLDGN T0376 211 :GIGNVLPKEVIHLCKLSQA 1w3iA 198 :AGSNYLPEVTVTIKKLAME T0376 233 :GDAD 1w3iA 217 :RKID T0376 238 :RARAL 1w3iA 221 :EALKL T0376 244 :LEQALAVLSSFDEGPD 1w3iA 226 :QFLHDEVIEASRIFGS T0376 261 :VLYFKYMMVLK 1w3iA 242 :LSSNYVLTKYF T0376 272 :GDKEYTLHFNET 1w3iA 254 :GYDLGYPRPPIF T0376 285 :ALTDSQRGYVEAQFKLFNSWYADWSKL 1w3iA 266 :PLDDEEERQLIKKVEGIRAKLVELKIL Number of specific fragments extracted= 16 number of extra gaps= 3 total=69 Number of alignments=5 # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0376)V74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0376)I75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0376)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0376)I104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0376 9 :VIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVKAGIP 1w3iA 4 :IITPIITPFTKDNRIDKEKLKIHAENLIRKGIDKLFVNGTTGLGPSLSPEEKLENLKAVYDVTNK T0376 76 :VGTGAVNTASAVAHAVHAQKVGAKGLM 1w3iA 71 :FQVGGLNLDDAIRLAKLSKDFDIVGIA T0376 105 :PRVLSRGSVIAAQKAHFKAILSA 1w3iA 100 :APYYYPRMSEKHLVKYFKTLCEV T0376 129 :PEIPAVIYNSPYYGFATRADLFFALR 1w3iA 123 :SPHPVYLYNYPTATGKDIDAKVAKEI T0376 158 :KNLVGFKEFGGPADMRYAAENIT 1w3iA 149 :GCFTGVKDTIENIIHTLDYKRLN T0376 185 :EVTLMIGVDTAVVHGFVNCGATGA 1w3iA 172 :PNMLVYSGSDMLIATVASTGLDGN T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1w3iA 198 :AGSNYLPEVTVTIKKLAMERKIDEALKLQFLHDEVIEASRIFGSLSSNYVLTKYFQGY T0376 269 :VLKGDKEYTLHFNE 1w3iA 257 :LGYPRPPIFPLDDE T0376 286 :LTDSQRGYVEAQFKLFNSW 1w3iA 271 :EERQLIKKVEGIRAKLVEL Number of specific fragments extracted= 9 number of extra gaps= 3 total=78 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w8sA expands to /projects/compbio/data/pdb/1w8s.pdb.gz 1w8sA:Skipped atom 267, because occupancy 0.35 <= existing 0.650 in 1w8sA Skipped atom 269, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 271, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 273, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 790, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 792, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1672, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1674, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1676, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1678, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1680, because occupancy 0.350 <= existing 0.650 in 1w8sA # T0376 read from 1w8sA/merged-good-all-a2m # 1w8sA read from 1w8sA/merged-good-all-a2m # adding 1w8sA to template set # found chain 1w8sA in template set Warning: unaligning (T0376)Q228 because last residue in template chain is (1w8sA)Y252 T0376 9 :VIPALMT 1w8sA 18 :SIILAYD T0376 17 :CRQD 1w8sA 34 :FMDN T0376 24 :DFDALVRKGK 1w8sA 42 :DPEYILRLAR T0376 37 :ADGMSAVVYC 1w8sA 52 :DAGFDGVVFQ T0376 66 :RLVK 1w8sA 64 :IAEK T0376 70 :AGIPVIVGTG 1w8sA 71 :GSVPLILKLN T0376 80 :AVNTASA 1w8sA 95 :NCSVEEA T0376 94 :QKVGAKGLMVIPRVLSR 1w8sA 102 :VSLGASAVGYTIYPGSG T0376 111 :GSVIAAQKAHFKAILSA 1w8sA 121 :WKMFEELARIKRDAVKF T0376 130 :EIPAVIYNSPYY 1w8sA 138 :DLPLVVESFPRG T0376 142 :GFAT 1w8sA 151 :KVVN T0376 147 :ADLFF 1w8sA 158 :PEIVA T0376 152 :ALRAEHK 1w8sA 166 :RIALELG T0376 160 :LVGFK 1w8sA 173 :ADAMK T0376 165 :EFGG 1w8sA 179 :KYTG T0376 171 :DMRYAAENITSR 1w8sA 183 :DPKTFSWAVKVA T0376 184 :DEVTLMIGVD 1w8sA 195 :GKVPVLMSGG T0376 196 :VVHGFVNCGATGAITGIGNV 1w8sA 216 :QVEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 19 number of extra gaps= 0 total=97 Number of alignments=7 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set Warning: unaligning (T0376)Q228 because last residue in template chain is (1w8sA)Y252 T0376 24 :DFDALVRKGK 1w8sA 42 :DPEYILRLAR T0376 37 :ADGMSAVVYC 1w8sA 52 :DAGFDGVVFQ T0376 57 :DE 1w8sA 62 :RG T0376 66 :RLVK 1w8sA 64 :IAEK T0376 70 :AGIPVIVGT 1w8sA 71 :GSVPLILKL T0376 79 :GAVNTAS 1w8sA 94 :ANCSVEE T0376 93 :AQKVGAKGLMVIPRVLSRGS 1w8sA 101 :AVSLGASAVGYTIYPGSGFE T0376 115 :AAQKAHFKAILSAA 1w8sA 121 :WKMFEELARIKRDA T0376 130 :EIPAVIYNSPYY 1w8sA 138 :DLPLVVESFPRG T0376 142 :GFA 1w8sA 151 :KVV T0376 145 :TRADLFF 1w8sA 156 :TAPEIVA T0376 152 :ALRAEHK 1w8sA 166 :RIALELG T0376 159 :NLVGFKEFG 1w8sA 174 :DAMKIKYTG T0376 171 :DMRYAAENITSRDDEVTLMIG 1w8sA 183 :DPKTFSWAVKVAGKVPVLMSG T0376 193 :D 1w8sA 204 :G T0376 194 :TAV 1w8sA 212 :DFL T0376 197 :VHGFVNCGATGAITGIGNV 1w8sA 217 :VEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 18 number of extra gaps= 0 total=115 Number of alignments=8 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set Warning: unaligning (T0376)Q228 because last residue in template chain is (1w8sA)Y252 T0376 24 :DFDALVRKGKEL 1w8sA 42 :DPEYILRLARDA T0376 39 :GMSAVVYC 1w8sA 54 :GFDGVVFQ T0376 61 :MEGVER 1w8sA 62 :RGIAEK T0376 70 :AGIPVIVGT 1w8sA 71 :GSVPLILKL T0376 80 :AVNTA 1w8sA 95 :NCSVE T0376 92 :HAQKVGAKGLMVIPRVLSRG 1w8sA 100 :EAVSLGASAVGYTIYPGSGF T0376 114 :IAAQKAHFKAILSAA 1w8sA 120 :EWKMFEELARIKRDA T0376 129 :PEIPAVIYNSPYYGFAT 1w8sA 137 :FDLPLVVESFPRGGKVV T0376 146 :RADLFFALRAE 1w8sA 156 :TAPEIVAYAAR T0376 159 :NL 1w8sA 172 :GA T0376 161 :VGFKEFGGPADMRYAAENIT 1w8sA 175 :AMKIKYTGDPKTFSWAVKVA T0376 184 :DEVTLMIGVD 1w8sA 195 :GKVPVLMSGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1w8sA 214 :LKQVEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 14 number of extra gaps= 0 total=129 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1gteA/merged-good-all-a2m # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0376)R110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gteA)M680 Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gteA)M680 Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0376 9 :VIPALMTPCR 1gteA 546 :FGLASAAPTT T0376 24 :DFDA 1gteA 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1gteA 560 :IRRAFEAGWGFALTK T0376 48 :SM 1gteA 575 :TF T0376 50 :GDWP 1gteA 601 :GPGQ T0376 56 :TDEQRMEGVERLVK 1gteA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gteA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLS 1gteA 645 :YNKNDWMELSRKAEASGADALELNLSCPH T0376 112 :S 1gteA 681 :G T0376 113 :VIAAQKAHFKAILSAA 1gteA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gteA 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1gteA 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1gteA 728 :GADGVT T0376 167 :GG 1gteA 736 :NT T0376 171 :DMRYAAENITSR 1gteA 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1gteA 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gteA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gteA 819 :VQN T0376 233 :GD 1gteA 822 :QD T0376 246 :QALAV 1gteA 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gteA 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gteA 848 :G T0376 279 :HFNETDA 1gteA 864 :PVPRIAE T0376 289 :SQRGYVEAQFKLFNSWY 1gteA 881 :PYLEQRKKIIAEEKMRL Number of specific fragments extracted= 24 number of extra gaps= 2 total=153 Number of alignments=10 # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0376)R110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gteA)M680 Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gteA)M680 Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0376 6 :FSG 1gteA 542 :FIN T0376 9 :VIPALMTPCR 1gteA 546 :FGLASAAPTT T0376 24 :DFDALVR 1gteA 556 :SSSMIRR T0376 35 :LIADGMSAVVYCGSM 1gteA 563 :AFEAGWGFALTKTFS T0376 50 :GDWPLL 1gteA 601 :GPGQSS T0376 56 :TDEQRMEGVERLVK 1gteA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gteA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLS 1gteA 645 :YNKNDWMELSRKAEASGADALELNLSCPH T0376 112 :S 1gteA 681 :G T0376 113 :VIAAQKAHFKAILSAA 1gteA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gteA 703 :QIPFFAKLTPNV T0376 142 :G 1gteA 716 :D T0376 147 :ADLFFALRAE 1gteA 718 :VSIARAAKEG T0376 157 :HKNLV 1gteA 729 :ADGVT T0376 172 :MRYAAENITSRD 1gteA 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gteA 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gteA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gteA 819 :VQN T0376 233 :GDADA 1gteA 822 :QDFTV T0376 239 :ARAL 1gteA 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gteA 831 :CTGLKALLYLKSIE T0376 275 :EY 1gteA 847 :QG T0376 278 :LHFNET 1gteA 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSW 1gteA 880 :GPYLEQRKKIIAEEKMR Number of specific fragments extracted= 24 number of extra gaps= 2 total=177 Number of alignments=11 # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0376)R110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gteA)M680 Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gteA)M680 Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0376 30 :RKGKELIADGMS 1gteA 558 :SMIRRAFEAGWG T0376 43 :VVYCGSMG 1gteA 570 :FALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gteA 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gteA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLS 1gteA 645 :YNKNDWMELSRKAEASGADALELNLSCPH T0376 112 :SVIAAQKAHFKAILSA 1gteA 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gteA 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1gteA 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1gteA 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gteA 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gteA 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1gteA 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKE 1gteA 849 :WDGQSPG T0376 276 :YTLHFNETDALTDSQR 1gteA 875 :KLPNFGPYLEQRKKII T0376 298 :FKLFNSWYA 1gteA 891 :AEEKMRLKE Number of specific fragments extracted= 15 number of extra gaps= 2 total=192 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dhpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dhpA expands to /projects/compbio/data/pdb/1dhp.pdb.gz 1dhpA:# T0376 read from 1dhpA/merged-good-all-a2m # 1dhpA read from 1dhpA/merged-good-all-a2m # adding 1dhpA to template set # found chain 1dhpA in template set T0376 1 :M 1dhpA 1 :M T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1dhpA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1dhpA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPS T0376 114 :IAAQKAHFKAILSAA 1dhpA 112 :QEGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 1dhpA 127 :DLPQILYNVPSR T0376 142 :GFATRADLFFAL 1dhpA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 1dhpA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 1dhpA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1dhpA 187 :DDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAE T0376 233 :GD 1dhpA 224 :GH T0376 235 :ADARARALELEQALAVLS 1dhpA 227 :AEARVINQRLMPLHNKLF T0376 254 :FDEGPDLV 1dhpA 245 :VEPNPIPV T0376 265 :KYMMVLKGDKE 1dhpA 253 :KWACKELGLVA T0376 276 :YTLHFNETD 1dhpA 265 :DTLRLPMTP T0376 286 :LTDSQRGYVEAQFKLFN 1dhpA 274 :ITDSGRETVRAALKHAG Number of specific fragments extracted= 15 number of extra gaps= 0 total=207 Number of alignments=13 # 1dhpA read from 1dhpA/merged-good-all-a2m # found chain 1dhpA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1dhpA)M1 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1dhpA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1dhpA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQ T0376 115 :AAQKAHFKAILSAA 1dhpA 113 :EGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 1dhpA 127 :DLPQILYNVPSR T0376 142 :GFATRADLFFAL 1dhpA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 1dhpA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 1dhpA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1dhpA 187 :DDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAE T0376 233 :GDA 1dhpA 224 :GHF T0376 237 :ARARAL 1dhpA 227 :AEARVI T0376 244 :LEQALAVLSSFDEGPD 1dhpA 233 :NQRLMPLHNKLFVEPN T0376 261 :VLYFKYMMVLKGDK 1dhpA 249 :PIPVKWACKELGLV T0376 275 :EYTLHFNET 1dhpA 264 :TDTLRLPMT T0376 285 :ALTDSQRGYVEAQFKLFNS 1dhpA 273 :PITDSGRETVRAALKHAGL Number of specific fragments extracted= 14 number of extra gaps= 0 total=221 Number of alignments=14 # 1dhpA read from 1dhpA/merged-good-all-a2m # found chain 1dhpA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1dhpA)M1 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1dhpA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1dhpA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRP T0376 113 :VIAAQKAHFKAILSA 1dhpA 111 :SQEGLYQHFKAIAEH T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1dhpA 126 :TDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELV T0376 184 :DEVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1dhpA 178 :SDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGYV 1dhpA 264 :TDTLRLPMTPITDSGRETVRAALKHA Number of specific fragments extracted= 6 number of extra gaps= 0 total=227 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xxxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376/1xxxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0376/1xxxA/merged-good-all-a2m.gz for input Trying 1xxxA/merged-good-all-a2m Error: Couldn't open file 1xxxA/merged-good-all-a2m or 1xxxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1o5kA/merged-good-all-a2m # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0376)F163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0376)E165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0376 5 :IFSGVIPALMTPCR 1o5kA 1 :MFRGVGTAIVTPFK T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1o5kA 15 :NGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSRTLE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1o5kA 68 :GKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPT T0376 114 :IAAQKAHFKAILSAA 1o5kA 111 :QEGLYQHYKYISERT T0376 130 :EIPAVIYNSPYY 1o5kA 126 :DLGIVVYNVPGR T0376 142 :GFATRADLFFALRAEHKNLVG 1o5kA 139 :GVNVLPETAARIAADLKNVVG T0376 166 :FGG 1o5kA 163 :ANP T0376 171 :DMRYAAENITSR 1o5kA 166 :DIDQIDRTVSLT T0376 183 :DDEVTLMIGVDTA 1o5kA 181 :RSDFMVWSGNDDR T0376 197 :VHGFVNCGATGA 1o5kA 194 :TFYLLCAGGDGV T0376 211 :GIGNVLPKEVIHLCKLSQA 1o5kA 208 :VVSNVAPKQMVELCAEYFS T0376 233 :GD 1o5kA 227 :GN T0376 235 :ADARARALELEQALAVLS 1o5kA 230 :EKSREVHRKLRPLMKALF T0376 254 :FDEGPDLV 1o5kA 248 :VETNPIPV T0376 265 :KYMMVLKGDKEYTLHFNETD 1o5kA 256 :KAALNLMGFIENELRLPLVP T0376 286 :LTDSQRGYVEAQFKLFN 1o5kA 276 :ASEKTVELLRNVLKESG Number of specific fragments extracted= 16 number of extra gaps= 1 total=243 Number of alignments=16 # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0376)S4 because first residue in template chain is (1o5kA)H0 Warning: unaligning (T0376)F163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0376)E165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0376 5 :IFSGVIPALMTPCR 1o5kA 1 :MFRGVGTAIVTPFK T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1o5kA 15 :NGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSRTLE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1o5kA 68 :GKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQ T0376 115 :AAQKAHFKAILSAA 1o5kA 112 :EGLYQHYKYISERT T0376 130 :EIPAVIYNSPYY 1o5kA 126 :DLGIVVYNVPGR T0376 142 :GFATRADLFFALRAEHKNLVG 1o5kA 139 :GVNVLPETAARIAADLKNVVG T0376 166 :FGG 1o5kA 163 :ANP T0376 171 :DMRYAAENITSR 1o5kA 166 :DIDQIDRTVSLT T0376 183 :DDEVTLMIGVDTAV 1o5kA 181 :RSDFMVWSGNDDRT T0376 198 :HGFVNCGATGA 1o5kA 195 :FYLLCAGGDGV T0376 211 :GIGNVLPKEVIHLCKLSQA 1o5kA 208 :VVSNVAPKQMVELCAEYFS T0376 233 :GDAD 1o5kA 227 :GNLE T0376 238 :RARAL 1o5kA 231 :KSREV T0376 244 :LEQALAVLSSFDEGPD 1o5kA 236 :HRKLRPLMKALFVETN T0376 261 :VLYFKYMMVLKGDKEYTLHFNET 1o5kA 252 :PIPVKAALNLMGFIENELRLPLV T0376 285 :ALTDSQRGYVEAQFKLFN 1o5kA 275 :PASEKTVELLRNVLKESG Number of specific fragments extracted= 16 number of extra gaps= 1 total=259 Number of alignments=17 # 1o5kA read from 1o5kA/merged-good-all-a2m # found chain 1o5kA in training set Warning: unaligning (T0376)S4 because first residue in template chain is (1o5kA)H0 Warning: unaligning (T0376)F163 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o5kA)E162 Warning: unaligning (T0376)E165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o5kA)E162 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o5kA)S207 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o5kA)S207 T0376 5 :IFSGVIPALMTPCR 1o5kA 1 :MFRGVGTAIVTPFK T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1o5kA 15 :NGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSRTLE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1o5kA 68 :GKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKP T0376 113 :VIAAQKAHFKAILSA 1o5kA 110 :TQEGLYQHYKYISER T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAE 1o5kA 125 :TDLGIVVYNVPGRTGVNVLPETAARIAA T0376 157 :HKNLVG 1o5kA 154 :LKNVVG T0376 166 :FGGPADMRYAAENITSRDDEVTLMIGVDTAVVHGFVNCGATGA 1o5kA 163 :ANPDIDQIDRTVSLTKQARSDFMVWSGNDDRTFYLLCAGGDGV T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMMVLKGDKEYTLHFNETDALTDSQRGY 1o5kA 208 :VVSNVAPKQMVELCAEYFSGNLEKSREVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVLKE Number of specific fragments extracted= 8 number of extra gaps= 1 total=267 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b4gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b4gA expands to /projects/compbio/data/pdb/2b4g.pdb.gz 2b4gA:Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1854, because occupancy 0.200 <= existing 0.400 in 2b4gA Skipped atom 1855, because occupancy 0.400 <= existing 0.400 in 2b4gA Skipped atom 1859, because occupancy 0.200 <= existing 0.400 in 2b4gA Skipped atom 1860, because occupancy 0.400 <= existing 0.400 in 2b4gA Skipped atom 1862, because occupancy 0.200 <= existing 0.400 in 2b4gA Skipped atom 1863, because occupancy 0.400 <= existing 0.400 in 2b4gA Skipped atom 1865, because occupancy 0.200 <= existing 0.400 in 2b4gA Skipped atom 1866, because occupancy 0.400 <= existing 0.400 in 2b4gA Skipped atom 1868, because occupancy 0.200 <= existing 0.400 in 2b4gA Skipped atom 1869, because occupancy 0.400 <= existing 0.400 in 2b4gA Skipped atom 1954, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1958, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1962, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in 2b4gA Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 2b4gA # T0376 read from 2b4gA/merged-good-all-a2m # 2b4gA read from 2b4gA/merged-good-all-a2m # adding 2b4gA to template set # found chain 2b4gA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2b4gA)V194 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (2b4gA)V194 Warning: unaligning (T0376)Q228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4gA)E278 Warning: unaligning (T0376)A229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4gA)E278 T0376 7 :SG 2b4gA 13 :SN T0376 9 :VIPALMTPCR 2b4gA 16 :FMNAAGVLCT T0376 24 :DFD 2b4gA 26 :TEE T0376 31 :KGKELIADGMSAVVYCGSM 2b4gA 29 :DLRRMTESESGSLIGKSCT T0376 52 :WPLLTDE 2b4gA 72 :LPNLGVD T0376 62 :EGVERLVK 2b4gA 79 :FYLSYAAQ T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQ 2b4gA 91 :SRKPLFLSMSGLSVEESVEMVKKLV T0376 95 :KVGAKGLMVIPRVLSRG 2b4gA 120 :EKGTILELNLSCPNVPG T0376 112 :S 2b4gA 138 :P T0376 113 :VIAAQKAHFKAILSAA 2b4gA 143 :DFDTTRTYLQKVSEAY T0376 130 :EIPAVIYNSPYYGFA 2b4gA 159 :GLPFGVKMPPYFDIA T0376 146 :RADLFFALRAEHKNLVGFK 2b4gA 174 :HFDMAAAVLNDFPLVKFIT T0376 167 :GG 2b4gA 195 :NS T0376 170 :AD 2b4gA 206 :AN T0376 172 :MRYAAENITSR 2b4gA 231 :LANVNAFFRRC T0376 184 :DEVTLMIGVD 2b4gA 242 :PDKLVFGCGG T0376 194 :TAVVHGFVNCGATGAITGIG 2b4gA 255 :GEEAFLHILAGASMVQVGTA T0376 226 :LS 2b4gA 275 :LH T0376 233 :GDADARARALELEQALAV 2b4gA 279 :GPIIFARLNKELQEIMTN T0376 255 :DE 2b4gA 297 :KG Number of specific fragments extracted= 20 number of extra gaps= 2 total=287 Number of alignments=19 # 2b4gA read from 2b4gA/merged-good-all-a2m # found chain 2b4gA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2b4gA)V194 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (2b4gA)V194 Warning: unaligning (T0376)Q228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4gA)E278 Warning: unaligning (T0376)A229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4gA)E278 T0376 6 :FSG 2b4gA 12 :FSN T0376 9 :VIPALMTPCR 2b4gA 16 :FMNAAGVLCT T0376 24 :DFDALVRKG 2b4gA 26 :TEEDLRRMT T0376 37 :ADGMSAVVYCGSM 2b4gA 35 :ESESGSLIGKSCT T0376 52 :WPLLTDE 2b4gA 72 :LPNLGVD T0376 62 :EGVERLVK 2b4gA 79 :FYLSYAAQ T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQ 2b4gA 91 :SRKPLFLSMSGLSVEESVEMVKKLV T0376 95 :KVGAKGLMVIPRVLSRGS 2b4gA 120 :EKGTILELNLSCPNVPGK T0376 113 :VIAAQKAHFKAILSAA 2b4gA 143 :DFDTTRTYLQKVSEAY T0376 130 :EIPAVIYNSPYY 2b4gA 159 :GLPFGVKMPPYF T0376 146 :R 2b4gA 171 :D T0376 147 :ADLFFALRAEHKNLVGFK 2b4gA 175 :FDMAAAVLNDFPLVKFIT T0376 167 :GG 2b4gA 195 :NS T0376 169 :PAD 2b4gA 205 :PAN T0376 172 :MRYAAENITSRD 2b4gA 231 :LANVNAFFRRCP T0376 185 :EVTLMIGVD 2b4gA 243 :DKLVFGCGG T0376 194 :TAVVHGFVNCGATGAITGIG 2b4gA 255 :GEEAFLHILAGASMVQVGTA T0376 226 :LS 2b4gA 275 :LH T0376 233 :GDA 2b4gA 279 :GPI T0376 237 :A 2b4gA 282 :I T0376 239 :ARAL 2b4gA 283 :FARL T0376 244 :LEQALAVLSSFD 2b4gA 287 :NKELQEIMTNKG Number of specific fragments extracted= 22 number of extra gaps= 2 total=309 Number of alignments=20 # 2b4gA read from 2b4gA/merged-good-all-a2m # found chain 2b4gA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (2b4gA)V194 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (2b4gA)V194 Warning: unaligning (T0376)L216 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4gA)E278 T0376 8 :GVIPALMTPCR 2b4gA 65 :GSINSMGLPNL T0376 24 :DFDA 2b4gA 76 :GVDF T0376 63 :GVERLVK 2b4gA 80 :YLSYAAQ T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQ 2b4gA 91 :SRKPLFLSMSGLSVEESVEMVKKLV T0376 95 :KVGAKGLMVIPRVLSRG 2b4gA 120 :EKGTILELNLSCPNVPG T0376 112 :SVIAAQKAHFKAILSA 2b4gA 142 :YDFDTTRTYLQKVSEA T0376 129 :PEIPAVIYNSPYYG 2b4gA 158 :YGLPFGVKMPPYFD T0376 148 :DLFFALRAE 2b4gA 175 :FDMAAAVLN T0376 157 :HKNLVGFK 2b4gA 185 :FPLVKFIT T0376 167 :GG 2b4gA 195 :NS T0376 170 :ADMRYAAENIT 2b4gA 231 :LANVNAFFRRC T0376 184 :DEVTLMIGVD 2b4gA 242 :PDKLVFGCGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 2b4gA 255 :GEEAFLHILAGASMVQVGTALH T0376 217 :PKEVIHLCK 2b4gA 280 :PIIFARLNK T0376 234 :DADARARAL 2b4gA 289 :ELQEIMTNK Number of specific fragments extracted= 15 number of extra gaps= 2 total=324 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xkyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xkyA expands to /projects/compbio/data/pdb/1xky.pdb.gz 1xkyA:# T0376 read from 1xkyA/merged-good-all-a2m # 1xkyA read from 1xkyA/merged-good-all-a2m # adding 1xkyA to template set # found chain 1xkyA in template set Warning: unaligning (T0376)A144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)I145 Warning: unaligning (T0376)T145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)I145 Warning: unaligning (T0376)A208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 Warning: unaligning (T0376)G257 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)P251 Warning: unaligning (T0376)P258 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)P251 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1xkyA 2 :IDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVS T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1xkyA 71 :KRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPS T0376 114 :IAAQKAHFKAILSAA 1xkyA 114 :QEGMYQHFKAIAEST T0376 130 :EIPAVIYNSPYY 1xkyA 129 :PLPVMLYNVPGR T0376 142 :GF 1xkyA 142 :IV T0376 146 :RADLFFAL 1xkyA 146 :SVDTVVRL T0376 155 :AEHKNLVGFKEFGG 1xkyA 154 :SEIENIVAIKDAGG T0376 171 :DMRYAAENITSRDDEVTLMIG 1xkyA 168 :DVLTMTEIIEKTADDFAVYSG T0376 193 :DTAVVHGFVNCGATG 1xkyA 189 :DDGLTLPAMAVGAKG T0376 211 :GIGNVLPKEVIHLCKLSQA 1xkyA 207 :VASHVIGNEMQEMIAAFQA T0376 233 :GD 1xkyA 226 :GE T0376 235 :ADARARALELEQALAVLS 1xkyA 229 :KKAQKLHQLLVRVTDSLF T0376 254 :FDE 1xkyA 247 :MAP T0376 259 :DLV 1xkyA 252 :TPV T0376 265 :KYMMVLKGDKEYTLHFNETD 1xkyA 255 :KTALQMVGLDVGSVRLPLLP T0376 286 :LTDSQRGYVEAQFKLF 1xkyA 275 :LTEEERVTLQSVMQSI Number of specific fragments extracted= 16 number of extra gaps= 3 total=340 Number of alignments=22 # 1xkyA read from 1xkyA/merged-good-all-a2m # found chain 1xkyA in template set Warning: unaligning (T0376)A3 because first residue in template chain is (1xkyA)M1 Warning: unaligning (T0376)A144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)I145 Warning: unaligning (T0376)T145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)I145 Warning: unaligning (T0376)A208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 Warning: unaligning (T0376)D259 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)P251 Warning: unaligning (T0376)V261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)P251 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1xkyA 2 :IDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVS T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1xkyA 71 :KRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQ T0376 115 :AAQKAHFKAILSAA 1xkyA 115 :EGMYQHFKAIAEST T0376 130 :EIPAVIYNSPYY 1xkyA 129 :PLPVMLYNVPGR T0376 142 :GF 1xkyA 142 :IV T0376 146 :RADLFFAL 1xkyA 146 :SVDTVVRL T0376 155 :AEHKNLVGFKEFGG 1xkyA 154 :SEIENIVAIKDAGG T0376 171 :DMRYAAENITSRDDEVTLMIG 1xkyA 168 :DVLTMTEIIEKTADDFAVYSG T0376 193 :DTAVVHGFVNCGATG 1xkyA 189 :DDGLTLPAMAVGAKG T0376 211 :GIGNVLPKEVIHLCKLSQA 1xkyA 207 :VASHVIGNEMQEMIAAFQA T0376 233 :GDAD 1xkyA 226 :GEFK T0376 238 :RARAL 1xkyA 230 :KAQKL T0376 244 :LEQALAVLSSFDEGP 1xkyA 235 :HQLLVRVTDSLFMAP T0376 262 :LYFKYMMVLKGDKEYTLHFNET 1xkyA 252 :TPVKTALQMVGLDVGSVRLPLL T0376 285 :ALTDSQRGYVEAQFKLF 1xkyA 274 :PLTEEERVTLQSVMQSI Number of specific fragments extracted= 15 number of extra gaps= 3 total=355 Number of alignments=23 # 1xkyA read from 1xkyA/merged-good-all-a2m # found chain 1xkyA in template set Warning: unaligning (T0376)A3 because first residue in template chain is (1xkyA)M1 Warning: unaligning (T0376)T145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)I145 Warning: unaligning (T0376)R146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)I145 Warning: unaligning (T0376)A208 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)V205 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)V205 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)S206 Warning: unaligning (T0376)F254 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xkyA)P251 Warning: unaligning (T0376)D255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xkyA)P251 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1xkyA 2 :IDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVS T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1xkyA 71 :KRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKP T0376 113 :VIAAQKAHFKAILSA 1xkyA 113 :SQEGMYQHFKAIAES T0376 129 :PEIPAVIYNSPYYGFA 1xkyA 128 :TPLPVMLYNVPGRSIV T0376 147 :ADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1xkyA 146 :SVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKT T0376 184 :DEVTLMIGVDTAVVHGFVNCGATG 1xkyA 180 :ADDFAVYSGDDGLTLPAMAVGAKG T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSS 1xkyA 207 :VASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAP T0376 256 :EGPDLVLYFKYMMVLKGDKEYTLHFNETDALTDSQRG 1xkyA 252 :TPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQ Number of specific fragments extracted= 8 number of extra gaps= 3 total=363 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h7xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h7xA expands to /projects/compbio/data/pdb/1h7x.pdb.gz 1h7xA:# T0376 read from 1h7xA/merged-good-all-a2m # 1h7xA read from 1h7xA/merged-good-all-a2m # adding 1h7xA to template set # found chain 1h7xA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7xA)T735 T0376 6 :FSGVIPALMTPCRQ 1h7xA 542 :FINPFGLASAAPTT T0376 24 :DFDA 1h7xA 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1h7xA 560 :IRRAFEAGWGFALTK T0376 47 :GSM 1h7xA 593 :GTT T0376 50 :GDWPL 1h7xA 601 :GPGQS T0376 56 :TDEQRMEGVERLVK 1h7xA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7xA 645 :YNKNDWMELSRKAEASGADALELNLSAPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7xA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7xA 703 :QIPFFAKLTPNV T0376 145 :T 1h7xA 716 :D T0376 147 :ADLFFALRAE 1h7xA 718 :VSIARAAKEG T0376 159 :NLVGFK 1h7xA 728 :GADGVT T0376 167 :GG 1h7xA 736 :NT T0376 172 :MRYAAENITSR 1h7xA 775 :LRAVTTIARAL T0376 184 :DEVTLMIGVD 1h7xA 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7xA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7xA 819 :VQN T0376 233 :GD 1h7xA 822 :QD T0376 246 :QALAV 1h7xA 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1h7xA 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1h7xA 848 :G T0376 279 :HFNETDA 1h7xA 864 :PVPRIAE T0376 289 :SQRGYVEAQFKLFNSWYA 1h7xA 881 :PYLEQRKKIIAEEKMRLK Number of specific fragments extracted= 24 number of extra gaps= 1 total=387 Number of alignments=25 # 1h7xA read from 1h7xA/merged-good-all-a2m # found chain 1h7xA in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xA)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1h7xA)T735 T0376 6 :FSGVIPALMTPCRQ 1h7xA 542 :FINPFGLASAAPTT T0376 24 :DFDALVR 1h7xA 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1h7xA 563 :AFEAGWGFALT T0376 47 :GSM 1h7xA 593 :GTT T0376 50 :GDWPLL 1h7xA 601 :GPGQSS T0376 56 :TDEQRMEGVERLVK 1h7xA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7xA 645 :YNKNDWMELSRKAEASGADALELNLSAPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7xA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7xA 703 :QIPFFAKLTPNV T0376 142 :G 1h7xA 716 :D T0376 147 :ADLFFALRA 1h7xA 718 :VSIARAAKE T0376 156 :EHKNLV 1h7xA 728 :GADGVT T0376 172 :MRYAAENITSRD 1h7xA 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1h7xA 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7xA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7xA 819 :VQN T0376 233 :GDADA 1h7xA 822 :QDFTV T0376 239 :ARAL 1h7xA 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1h7xA 831 :CTGLKALLYLKSIE T0376 275 :EY 1h7xA 847 :QG T0376 278 :LHFNET 1h7xA 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSW 1h7xA 880 :GPYLEQRKKIIAEEKMR Number of specific fragments extracted= 23 number of extra gaps= 1 total=410 Number of alignments=26 # 1h7xA read from 1h7xA/merged-good-all-a2m # found chain 1h7xA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7xA)T735 T0376 30 :RKGKELIADGMSA 1h7xA 558 :SMIRRAFEAGWGF T0376 44 :VYCGSMG 1h7xA 571 :ALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1h7xA 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1h7xA 645 :YNKNDWMELSRKAEASGADALELNLSAPHGM T0376 113 :VIAAQKAHFKAILSA 1h7xA 687 :DPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1h7xA 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1h7xA 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1h7xA 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1h7xA 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1h7xA 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1h7xA 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1h7xA 849 :WDGQSPGTE T0376 278 :LHFNETDALTDSQRG 1h7xA 877 :PNFGPYLEQRKKIIA T0376 299 :KLFNSWYA 1h7xA 892 :EEKMRLKE Number of specific fragments extracted= 15 number of extra gaps= 1 total=425 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h7xC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h7xC expands to /projects/compbio/data/pdb/1h7x.pdb.gz 1h7xC:# T0376 read from 1h7xC/merged-good-all-a2m # 1h7xC read from 1h7xC/merged-good-all-a2m # adding 1h7xC to template set # found chain 1h7xC in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xC)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7xC)T735 T0376 6 :FSGVIPALMTPCRQ 1h7xC 542 :FINPFGLASAAPTT T0376 24 :DFDA 1h7xC 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1h7xC 560 :IRRAFEAGWGFALTK T0376 47 :GSM 1h7xC 593 :GTT T0376 50 :GDWPL 1h7xC 601 :GPGQS T0376 56 :TDEQRMEGVERLVK 1h7xC 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xC 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7xC 645 :YNKNDWMELSRKAEASGADALELNLSAPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7xC 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7xC 703 :QIPFFAKLTPNV T0376 142 :G 1h7xC 716 :D T0376 147 :ADLFFALRAE 1h7xC 718 :VSIARAAKEG T0376 159 :NLVGFK 1h7xC 728 :GADGVT T0376 167 :GG 1h7xC 736 :NT T0376 171 :DMRYAAENITSR 1h7xC 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1h7xC 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7xC 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7xC 819 :VQN T0376 233 :GD 1h7xC 822 :QD T0376 246 :QALAV 1h7xC 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1h7xC 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1h7xC 848 :G T0376 280 :FNETD 1h7xC 865 :VPRIA T0376 289 :SQRGYVEAQFKLFNSWYADWS 1h7xC 881 :PYLEQRKKIIAEEKMRLKEQN Number of specific fragments extracted= 24 number of extra gaps= 1 total=449 Number of alignments=28 # 1h7xC read from 1h7xC/merged-good-all-a2m # found chain 1h7xC in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xC)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1h7xC)T735 T0376 6 :FSGVIPALMTPCRQ 1h7xC 542 :FINPFGLASAAPTT T0376 24 :DFDALVR 1h7xC 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1h7xC 563 :AFEAGWGFALT T0376 47 :GSM 1h7xC 593 :GTT T0376 50 :GDWPLL 1h7xC 601 :GPGQSS T0376 56 :TDEQRMEGVERLVK 1h7xC 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xC 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7xC 645 :YNKNDWMELSRKAEASGADALELNLSAPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7xC 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7xC 703 :QIPFFAKLTPNV T0376 142 :G 1h7xC 716 :D T0376 147 :ADLFFALRAE 1h7xC 718 :VSIARAAKEG T0376 157 :HKNLV 1h7xC 729 :ADGVT T0376 172 :MRYAAENITSRD 1h7xC 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1h7xC 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7xC 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7xC 819 :VQN T0376 233 :GDADA 1h7xC 822 :QDFTV T0376 239 :ARAL 1h7xC 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1h7xC 831 :CTGLKALLYLKSIE T0376 275 :EY 1h7xC 847 :QG T0376 278 :LHFNET 1h7xC 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSWYAD 1h7xC 880 :GPYLEQRKKIIAEEKMRLKE Number of specific fragments extracted= 23 number of extra gaps= 1 total=472 Number of alignments=29 # 1h7xC read from 1h7xC/merged-good-all-a2m # found chain 1h7xC in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7xC)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7xC)T735 T0376 8 :GVIPALMTP 1h7xC 547 :GLASAAPTT T0376 24 :DF 1h7xC 556 :SS T0376 30 :RKGKELIADGMSA 1h7xC 558 :SMIRRAFEAGWGF T0376 44 :VYCGSMG 1h7xC 571 :ALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1h7xC 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7xC 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1h7xC 645 :YNKNDWMELSRKAEASGADALELNLSAPHGM T0376 113 :VIAAQKAHFKAILSA 1h7xC 687 :DPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1h7xC 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1h7xC 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1h7xC 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1h7xC 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1h7xC 799 :AESGLQFLHSGASVLQVCSAVQ T0376 229 :AAA 1h7xC 821 :NQD T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1h7xC 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1h7xC 849 :WDGQSPGTE T0376 278 :LHFNETDA 1h7xC 877 :PNFGPYLE T0376 296 :AQFKLFNSWYADWSKLPG 1h7xC 885 :QRKKIIAEEKMRLKEQNA Number of specific fragments extracted= 18 number of extra gaps= 1 total=490 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yxcA expands to /projects/compbio/data/pdb/1yxc.pdb.gz 1yxcA:# T0376 read from 1yxcA/merged-good-all-a2m # 1yxcA read from 1yxcA/merged-good-all-a2m # adding 1yxcA to template set # found chain 1yxcA in template set Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0376 1 :M 1yxcA 1 :M T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 1yxcA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 1yxcA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1yxcA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPS T0376 114 :IAAQKAHFKAILSAA 1yxcA 112 :QEGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 1yxcA 127 :DLPQILYNVPSR T0376 142 :GFATRADLFFAL 1yxcA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 1yxcA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 1yxcA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 1yxcA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 1yxcA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GD 1yxcA 224 :GH T0376 235 :ADARARALELEQALAVLS 1yxcA 227 :AEARVINQRLMPLHNKLF T0376 254 :FDEGPDLV 1yxcA 245 :VEPNPIPV T0376 265 :KYMMVLKGDKE 1yxcA 253 :KWACKELGLVA T0376 276 :YTLHFNETD 1yxcA 265 :DTLRLPMTP T0376 286 :LTDSQRGYVEAQFKLFN 1yxcA 274 :ITDSGRETVRAALKHAG Number of specific fragments extracted= 17 number of extra gaps= 2 total=507 Number of alignments=31 # 1yxcA read from 1yxcA/merged-good-all-a2m # found chain 1yxcA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1yxcA)M1 Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 1yxcA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 1yxcA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1yxcA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQ T0376 115 :AAQKAHFKAILSAA 1yxcA 113 :EGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 1yxcA 127 :DLPQILYNVPSR T0376 142 :GFATRADLFFAL 1yxcA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 1yxcA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 1yxcA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 1yxcA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 1yxcA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GDA 1yxcA 224 :GHF T0376 237 :ARARAL 1yxcA 227 :AEARVI T0376 244 :LEQALAVLSSFDEGPD 1yxcA 233 :NQRLMPLHNKLFVEPN T0376 261 :VLYFKYMMVLKGDK 1yxcA 249 :PIPVKWACKELGLV T0376 275 :EYTLHFNET 1yxcA 264 :TDTLRLPMT T0376 285 :ALTDSQRGYVEAQFKLFN 1yxcA 273 :PITDSGRETVRAALKHAG Number of specific fragments extracted= 16 number of extra gaps= 2 total=523 Number of alignments=32 # 1yxcA read from 1yxcA/merged-good-all-a2m # found chain 1yxcA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1yxcA)M1 Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 1yxcA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 1yxcA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1yxcA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRP T0376 113 :VIAAQKAHFKAILSA 1yxcA 111 :SQEGLYQHFKAIAEH T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1yxcA 126 :TDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELV T0376 184 :DEVTLMIGVDTAVVHGFVNCGATGA 1yxcA 178 :SDDFVLLSGDDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1yxcA 205 :VTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGY 1yxcA 264 :TDTLRLPMTPITDSGRETVRAALKH Number of specific fragments extracted= 8 number of extra gaps= 2 total=531 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1thfD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1thfD/merged-good-all-a2m # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0376 7 :SGVIPAL 1thfD 4 :KRIIACL T0376 19 :QD 1thfD 14 :DG T0376 21 :RT 1thfD 27 :RD T0376 28 :LVRKGKELIADGMSAVVYCGSMG 1thfD 32 :PVELGKFYSEIGIDELVFLDITA T0376 57 :DEQRMEGVERLVK 1thfD 59 :RKTMLELVEKVAE T0376 71 :GIPVIVGTGAVNTASA 1thfD 74 :DIPFTVGGGIHDFETA T0376 91 :VHAQKVGAKGLMVIPRVLSRGSVIAA 1thfD 90 :SELILRGADKVSINTAAVENPSLITQ T0376 117 :QKAHFKAILSA 1thfD 153 :LRDWVVEVEKR T0376 130 :EIPAVIYNSPYY 1thfD 164 :GAGEILLTSIDR T0376 142 :GFATRADLFFAL 1thfD 179 :KSGYDTEMIRFV T0376 179 :ITSRDDEVTLMIGVD 1thfD 191 :RPLTTLPIIASGGAG T0376 195 :A 1thfD 207 :M T0376 196 :VVHGFVNCGATGAITG 1thfD 209 :HFLEAFLAGADAALAA T0376 225 :KLSQA 1thfD 225 :SVFHF T0376 233 :GD 1thfD 230 :RE T0376 236 :DARARALELEQ 1thfD 233 :DVRELKEYLKK Number of specific fragments extracted= 16 number of extra gaps= 0 total=547 Number of alignments=34 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0376 6 :FS 1thfD 4 :KR T0376 9 :VIPAL 1thfD 6 :IIACL T0376 14 :M 1thfD 12 :V T0376 21 :RT 1thfD 27 :RD T0376 28 :LVRKGKELIADGMSAVVYCGSMGDW 1thfD 32 :PVELGKFYSEIGIDELVFLDITASV T0376 55 :LTDEQRMEGVERLVK 1thfD 57 :EKRKTMLELVEKVAE T0376 71 :GIPVIVGTGAVNTA 1thfD 74 :DIPFTVGGGIHDFE T0376 89 :HAVHAQKVGAKGLMVIPRVLSRGSVIAA 1thfD 88 :TASELILRGADKVSINTAAVENPSLITQ T0376 117 :QKAHFKAILSAAP 1thfD 153 :LRDWVVEVEKRGA T0376 131 :IPAVIYNSPYY 1thfD 166 :GEILLTSIDRD T0376 142 :GFATRADLFFALR 1thfD 179 :KSGYDTEMIRFVR T0376 180 :TSRDDE 1thfD 192 :PLTTLP T0376 187 :TLMIGV 1thfD 198 :IIASGG T0376 194 :TA 1thfD 208 :EH T0376 197 :VHGFVNCGATGAITG 1thfD 210 :FLEAFLAGADAALAA T0376 225 :KLSQA 1thfD 225 :SVFHF T0376 233 :GDAD 1thfD 230 :REID T0376 239 :ARAL 1thfD 234 :VREL T0376 244 :LEQALA 1thfD 238 :KEYLKK Number of specific fragments extracted= 19 number of extra gaps= 0 total=566 Number of alignments=35 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0376 8 :GVIPAL 1thfD 5 :RIIACL T0376 17 :CRQD 1thfD 12 :VKDG T0376 21 :RT 1thfD 27 :RD T0376 28 :LVRKGKELIADGMSAVVYCGSMGDW 1thfD 32 :PVELGKFYSEIGIDELVFLDITASV T0376 55 :LTDEQRMEGVERLVK 1thfD 57 :EKRKTMLELVEKVAE T0376 70 :AGIPVIVGTGAVNTAS 1thfD 73 :IDIPFTVGGGIHDFET T0376 90 :AVHAQKVGAKGLM 1thfD 89 :ASELILRGADKVS T0376 103 :VIP 1thfD 126 :VVA T0376 117 :QKAHFKAILSA 1thfD 153 :LRDWVVEVEKR T0376 130 :EIPAVIYNSPYYG 1thfD 164 :GAGEILLTSIDRD T0376 143 :FATRADLFFALR 1thfD 179 :KSGYDTEMIRFV T0376 177 :E 1thfD 191 :R T0376 182 :RDDEVTLMIGVD 1thfD 192 :PLTTLPIIASGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1thfD 207 :MEHFLEAFLAGADAALAASVFH T0376 220 :VIHLCKLSQAA 1thfD 234 :VRELKEYLKKH Number of specific fragments extracted= 15 number of extra gaps= 0 total=581 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a6lA expands to /projects/compbio/data/pdb/2a6l.pdb.gz 2a6lA:# T0376 read from 2a6lA/merged-good-all-a2m # 2a6lA read from 2a6lA/merged-good-all-a2m # adding 2a6lA to template set # found chain 2a6lA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (2a6lA)M1 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 2a6lA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 2a6lA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPS T0376 114 :IAAQKAHFKAILSAA 2a6lA 112 :QEGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 2a6lA 127 :DLPQILYNVPSH T0376 142 :GFATRADLFFAL 2a6lA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 2a6lA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 2a6lA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 2a6lA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 2a6lA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GD 2a6lA 224 :GH T0376 235 :ADARARALELEQALAVLS 2a6lA 227 :AEARVINQRLMPLHNKLF T0376 254 :FDEGPDLV 2a6lA 245 :VEPNPIPV T0376 265 :KYMMVLKGDKE 2a6lA 253 :KWACKELGLVA T0376 276 :YTLHFNETD 2a6lA 265 :DTLRLPMTP T0376 286 :LTDSQRGYVEAQFKLFN 2a6lA 274 :ITDSGRETVRAALKHAG Number of specific fragments extracted= 15 number of extra gaps= 1 total=596 Number of alignments=37 # 2a6lA read from 2a6lA/merged-good-all-a2m # found chain 2a6lA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (2a6lA)M1 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 2a6lA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 2a6lA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQ T0376 115 :AAQKAHFKAILSAA 2a6lA 113 :EGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 2a6lA 127 :DLPQILYNVPSH T0376 142 :GFATRADLFFAL 2a6lA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 2a6lA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 2a6lA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 2a6lA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 2a6lA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GDA 2a6lA 224 :GHF T0376 237 :ARARAL 2a6lA 227 :AEARVI T0376 244 :LEQALAVLSSFDEGPD 2a6lA 233 :NQRLMPLHNKLFVEPN T0376 261 :VLYFKYMMVLKGDK 2a6lA 249 :PIPVKWACKELGLV T0376 275 :EYTLHFNET 2a6lA 264 :TDTLRLPMT T0376 285 :ALTDSQRGYVEAQFKLFN 2a6lA 273 :PITDSGRETVRAALKHAG Number of specific fragments extracted= 15 number of extra gaps= 1 total=611 Number of alignments=38 # 2a6lA read from 2a6lA/merged-good-all-a2m # found chain 2a6lA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (2a6lA)M1 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 2a6lA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 2a6lA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRP T0376 113 :VIAAQKAHFKAILSA 2a6lA 111 :SQEGLYQHFKAIAEH T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 2a6lA 126 :TDLPQILYNVPSHTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELV T0376 184 :DEVTLMIGVDTAVVHGFVNCGATGA 2a6lA 178 :SDDFVLLSGDDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 2a6lA 205 :VTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGY 2a6lA 264 :TDTLRLPMTPITDSGRETVRAALKH Number of specific fragments extracted= 7 number of extra gaps= 1 total=618 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s2wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1s2wA/merged-good-all-a2m # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set T0376 9 :VIPALMTPCR 1s2wA 82 :ILLDADTGYG T0376 24 :DFDALVRKGKELIADGMSAVVYCG 1s2wA 92 :NFNNARRLVRKLEDRGVAGACLED T0376 51 :DWPLLTDEQRMEGVERLVK 1s2wA 129 :AQPLADIEEFALKIKACKD T0376 70 :AGIPVIVGTGAV 1s2wA 152 :PDFCIVARVEAF T0376 82 :NTASAVAHAVHAQKVGAKGLMVIP 1s2wA 168 :GLDEALKRAEAYRNAGADAILMHS T0376 109 :SRGS 1s2wA 192 :KKAD T0376 114 :IAAQKAHFKA 1s2wA 196 :PSDIEAFMKA T0376 128 :APE 1s2wA 206 :WNN T0376 131 :IPAVI 1s2wA 210 :GPVVI T0376 138 :SPYYGFATRADLFFAL 1s2wA 215 :VPTKYYKTPTDHFRDM T0376 159 :NLVGFKEFGG 1s2wA 231 :GVSMVIWANH T0376 171 :DMRYAAENITSR 1s2wA 241 :NLRASVSAIQQT Number of specific fragments extracted= 12 number of extra gaps= 0 total=630 Number of alignments=40 # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set T0376 9 :VIPALMTPCR 1s2wA 82 :ILLDADTGYG T0376 24 :DFDALVRKGKELIADGMSAVVYCGSM 1s2wA 92 :NFNNARRLVRKLEDRGVAGACLEDKL T0376 51 :DWPLLTDEQRMEGVERLVK 1s2wA 129 :AQPLADIEEFALKIKACKD T0376 70 :AGIPVIVGTGAV 1s2wA 152 :PDFCIVARVEAF T0376 83 :TASAVAHAVHAQKVGAKGLMVIP 1s2wA 169 :LDEALKRAEAYRNAGADAILMHS T0376 109 :SRGSV 1s2wA 192 :KKADP T0376 115 :AAQKAHFKAI 1s2wA 197 :SDIEAFMKAW T0376 130 :E 1s2wA 207 :N T0376 131 :IPAVI 1s2wA 210 :GPVVI T0376 138 :SPYYGFATRADLFFAL 1s2wA 215 :VPTKYYKTPTDHFRDM T0376 185 :EVTLMIGVDTAV 1s2wA 231 :GVSMVIWANHNL T0376 238 :RARALELEQALAVLSSFDEGPDL 1s2wA 243 :RASVSAIQQTTKQIYDDQSLVNV T0376 282 :ETDALTDSQRGY 1s2wA 266 :EDKIVSVKEIFR Number of specific fragments extracted= 13 number of extra gaps= 0 total=643 Number of alignments=41 # 1s2wA read from 1s2wA/merged-good-all-a2m # found chain 1s2wA in training set Warning: unaligning (T0376)D57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s2wA)W64 Warning: unaligning (T0376)L108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s2wA)G127 T0376 29 :VRKGKELIADGMSAVVYCG 1s2wA 29 :GLSARIVQEAGFKGIWGSG T0376 58 :EQRMEGVERLVK 1s2wA 65 :TQVVEVLEFMSD T0376 70 :AGIPVIVGT 1s2wA 78 :SDVPILLDA T0376 79 :GAVNTASAVAHAVHAQKVGAKGLMVIPRV 1s2wA 89 :GYGNFNNARRLVRKLEDRGVAGACLEDKL T0376 112 :SVIAAQKAHFKAILSAA 1s2wA 133 :ADIEEFALKIKACKDSQ T0376 129 :PEIPAVIYN 1s2wA 152 :PDFCIVARV T0376 139 :P 1s2wA 161 :E T0376 141 :YGFATRADLFFALRAE 1s2wA 162 :AFIAGWGLDEALKRAE T0376 157 :HKNLVGFKEFG 1s2wA 181 :NAGADAILMHS T0376 168 :GPADMRYAAENIT 1s2wA 194 :ADPSDIEAFMKAW T0376 184 :DEVTLMIGVDTAV 1s2wA 207 :NNQGPVVIVPTKY T0376 197 :VHGFVNCGATGAITGIG 1s2wA 224 :TDHFRDMGVSMVIWANH T0376 234 :DADARARALELEQALAVLSS 1s2wA 241 :NLRASVSAIQQTTKQIYDDQ T0376 270 :LKGDKEYTLHFNETDAL 1s2wA 261 :SLVNVEDKIVSVKEIFR Number of specific fragments extracted= 14 number of extra gaps= 0 total=657 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rvkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1rvkA/merged-good-all-a2m # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set Warning: unaligning (T0376)G211 because of BadResidue code BAD_PEPTIDE in next template residue (1rvkA)L332 Warning: unaligning (T0376)I212 because of BadResidue code BAD_PEPTIDE at template residue (1rvkA)L332 T0376 8 :GVIPALMTPCRQDR 1rvkA 133 :AYGSIMCGDELEGG T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSMG 1rvkA 148 :ATPEDYGRFAETLVKRGYKGIKLHTWMP T0376 51 :DWPLLTDEQRMEGVERLVK 1rvkA 177 :VSWAPDVKMDLKACAAVRE T0376 70 :AGIPVIVGTGA 1rvkA 199 :PDIRLMIDAFH T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIP 1rvkA 211 :YSRTDALALGRGLEKLGFDWIEEPM T0376 110 :RGSVIAA 1rvkA 236 :DEQSLSS T0376 121 :FKAILSAA 1rvkA 243 :YKWLSDNL T0376 130 :EIPAVI 1rvkA 251 :DIPVVG T0376 141 :Y 1rvkA 257 :P T0376 142 :GFATRADLFFALRAE 1rvkA 259 :SAAGKHWHRAEWIKA T0376 158 :KNLVGFK 1rvkA 274 :GACDILR T0376 165 :EFGGPADMRYAAENITSR 1rvkA 285 :DVGGITPALKTMHLAEAF T0376 185 :EVTLMIGVDTAVVHGFVNCG 1rvkA 303 :GMECEVHGNTAMNLHVVAAT T0376 205 :ATGAIT 1rvkA 325 :CRWYER T0376 213 :GN 1rvkA 333 :LH Number of specific fragments extracted= 15 number of extra gaps= 1 total=672 Number of alignments=43 # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set Warning: unaligning (T0376)G211 because of BadResidue code BAD_PEPTIDE in next template residue (1rvkA)L332 Warning: unaligning (T0376)I212 because of BadResidue code BAD_PEPTIDE at template residue (1rvkA)L332 T0376 3 :ASIFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLL 1rvkA 128 :RDKVLAYGSIMCGDELEGGLATPEDYGRFAETLVKRGYKGIKLHTWMPPVSWA T0376 56 :TDEQRMEGVERLVK 1rvkA 182 :DVKMDLKACAAVRE T0376 70 :AGIPVIVGTGA 1rvkA 199 :PDIRLMIDAFH T0376 81 :VNTASAVAHAVHAQKVGAKGLMVI 1rvkA 211 :YSRTDALALGRGLEKLGFDWIEEP T0376 109 :SRGSVIAA 1rvkA 235 :MDEQSLSS T0376 121 :FKAILSAA 1rvkA 243 :YKWLSDNL T0376 130 :EIPAVI 1rvkA 251 :DIPVVG T0376 139 :PY 1rvkA 257 :PE T0376 142 :GFATRADLFFALRAE 1rvkA 259 :SAAGKHWHRAEWIKA T0376 158 :KNLVGFKEFGG 1rvkA 274 :GACDILRTGVN T0376 171 :DM 1rvkA 285 :DV T0376 173 :RYAAENITSRDDEVTL 1rvkA 293 :LKTMHLAEAFGMECEV T0376 190 :IG 1rvkA 309 :HG T0376 193 :DTAVVHGFVNC 1rvkA 311 :NTAMNLHVVAA T0376 204 :GATGAIT 1rvkA 324 :NCRWYER T0376 213 :GN 1rvkA 333 :LH Number of specific fragments extracted= 16 number of extra gaps= 1 total=688 Number of alignments=44 # 1rvkA read from 1rvkA/merged-good-all-a2m # found chain 1rvkA in training set Warning: unaligning (T0376)G211 because of BadResidue code BAD_PEPTIDE in next template residue (1rvkA)L332 Warning: unaligning (T0376)I212 because of BadResidue code BAD_PEPTIDE at template residue (1rvkA)L332 T0376 4 :SIFSGVIPALMTPCRQD 1rvkA 129 :DKVLAYGSIMCGDELEG T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSMGDW 1rvkA 148 :ATPEDYGRFAETLVKRGYKGIKLHTWMPPV T0376 53 :PLLTDEQRMEGVERLVK 1rvkA 179 :WAPDVKMDLKACAAVRE T0376 70 :AGIPVIVGTGA 1rvkA 199 :PDIRLMIDAFH T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPR 1rvkA 211 :YSRTDALALGRGLEKLGFDWIEEPMD T0376 110 :RG 1rvkA 237 :EQ T0376 113 :VIAAQKA 1rvkA 239 :SLSSYKW T0376 124 :ILSA 1rvkA 246 :LSDN T0376 129 :PEIPAV 1rvkA 250 :LDIPVV T0376 140 :YYGFATRADLFFALRAEHKNLVGFKEFG 1rvkA 256 :GPESAAGKHWHRAEWIKAGACDILRTGV T0376 168 :GPADMRYAAENITSRDDEVTLMIGVDTAVVHGFVN 1rvkA 287 :GGITPALKTMHLAEAFGMECEVHGNTAMNLHVVAA T0376 205 :ATGAIT 1rvkA 325 :CRWYER T0376 213 :GN 1rvkA 333 :LH Number of specific fragments extracted= 13 number of extra gaps= 1 total=701 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a6nA expands to /projects/compbio/data/pdb/2a6n.pdb.gz 2a6nA:# T0376 read from 2a6nA/merged-good-all-a2m # 2a6nA read from 2a6nA/merged-good-all-a2m # adding 2a6nA to template set # found chain 2a6nA in template set Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)S204 T0376 1 :M 2a6nA 1 :M T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 2a6nA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 2a6nA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 2a6nA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPS T0376 114 :IAAQKAHFKAILSAA 2a6nA 112 :QEGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 2a6nA 127 :DLPQILYNVPSA T0376 142 :GFATRADLFFAL 2a6nA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 2a6nA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 2a6nA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 2a6nA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 2a6nA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GD 2a6nA 224 :GH T0376 235 :ADARARALELEQALAVLS 2a6nA 227 :AEARVINQRLMPLHNKLF T0376 254 :FDEGPDLV 2a6nA 245 :VEPNPIPV T0376 265 :KYMMVLKGDKE 2a6nA 253 :KWACKELGLVA T0376 276 :YTLHFNETD 2a6nA 265 :DTLRLPMTP T0376 286 :LTDSQRGYVEAQFKLFN 2a6nA 274 :ITDSGRETVRAALKHAG Number of specific fragments extracted= 17 number of extra gaps= 2 total=718 Number of alignments=46 # 2a6nA read from 2a6nA/merged-good-all-a2m # found chain 2a6nA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (2a6nA)M1 Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 2a6nA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 2a6nA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 2a6nA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQ T0376 115 :AAQKAHFKAILSAA 2a6nA 113 :EGLYQHFKAIAEHT T0376 130 :EIPAVIYNSPYY 2a6nA 127 :DLPQILYNVPSA T0376 142 :GFATRADLFFAL 2a6nA 140 :GCDLLPETVGRL T0376 155 :AEHKNLVGFKEFGG 2a6nA 152 :AKVKNIIGIKEATG T0376 171 :DMRYAAENITSRDDEVTLMIG 2a6nA 166 :NLTRVNQIKELVSDDFVLLSG T0376 193 :DTAVVHGFVNCGATGA 2a6nA 187 :DDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQA 2a6nA 205 :VTANVAARDMAQMCKLAAE T0376 233 :GDA 2a6nA 224 :GHF T0376 237 :ARARAL 2a6nA 227 :AEARVI T0376 244 :LEQALAVLSSFDEGPD 2a6nA 233 :NQRLMPLHNKLFVEPN T0376 261 :VLYFKYMMVLKGDK 2a6nA 249 :PIPVKWACKELGLV T0376 275 :EYTLHFNET 2a6nA 264 :TDTLRLPMT T0376 285 :ALTDSQRGYVEAQFKLFN 2a6nA 273 :PITDSGRETVRAALKHAG Number of specific fragments extracted= 16 number of extra gaps= 2 total=734 Number of alignments=47 # 2a6nA read from 2a6nA/merged-good-all-a2m # found chain 2a6nA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (2a6nA)M1 Warning: unaligning (T0376)C46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)G43 Warning: unaligning (T0376)G47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)G43 Warning: unaligning (T0376)I209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6nA)S204 Warning: unaligning (T0376)T210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6nA)S204 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVY 2a6nA 2 :FTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVS T0376 48 :SMGDWPLLTDEQRMEGVERLVK 2a6nA 44 :TTGESATLNHDEHADVVMMTLD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 2a6nA 69 :GRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRP T0376 113 :VIAAQKAHFKAILSA 2a6nA 111 :SQEGLYQHFKAIAEH T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 2a6nA 126 :TDLPQILYNVPSATGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELV T0376 184 :DEVTLMIGVDTAVVHGFVNCGATGA 2a6nA 178 :SDDFVLLSGDDASALDFMQLGGHGV T0376 211 :GIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 2a6nA 205 :VTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGY 2a6nA 264 :TDTLRLPMTPITDSGRETVRAALKH Number of specific fragments extracted= 8 number of extra gaps= 2 total=742 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376/1s5wA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0376/1s5wA/merged-good-all-a2m.gz for input Trying 1s5wA/merged-good-all-a2m Error: Couldn't open file 1s5wA/merged-good-all-a2m or 1s5wA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1qwgA/merged-good-all-a2m # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0376)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0376)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0376 3 :ASIFSGVIPALM 1qwgA 9 :EDFQRGLTVVLD T0376 21 :RTPDFDALVRKGKELIAD 1qwgA 21 :KGLPPKFVEDYLKVCGDY T0376 40 :MSAVVY 1qwgA 39 :IDFVKF T0376 48 :SMGDWPLLTDEQRMEGVERLVKAGIPVIV 1qwgA 45 :GWGTSAVIDRDVVKEKINYYKDWGIKVYP T0376 79 :GAVNTASAV 1qwgA 74 :GGTLFEYAY T0376 88 :AHAVHAQKVG 1qwgA 118 :NAIKRAKDNG T0376 100 :GLMVIPRVLSR 1qwgA 130 :VLTEVGKKMPD T0376 111 :GS 1qwgA 145 :LT T0376 114 :IAAQKAHFKAILSA 1qwgA 147 :IDDRIKLINFDLDA T0376 130 :EIPAVIYNS 1qwgA 161 :GADYVIIEG T0376 139 :PYY 1qwgA 177 :GLF T0376 142 :GFATRADLFFALRAEHK 1qwgA 182 :EGKVKENELDVLAKNVD T0376 159 :NLVG 1qwgA 201 :KVIF T0376 164 :K 1qwgA 205 :E T0376 167 :GG 1qwgA 206 :AP T0376 171 :DMRYAAENITSRDDEVTLM 1qwgA 208 :QKSQQVAFILKFGSSVNLA T0376 190 :IGVDTAVVHGFVNCGAT 1qwgA 228 :IAFDEVISLETLRRGLR Number of specific fragments extracted= 17 number of extra gaps= 1 total=759 Number of alignments=49 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0376)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0376)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0376 3 :ASIFSGVIPALM 1qwgA 9 :EDFQRGLTVVLD T0376 21 :RTPDFDALVRKGKELIAD 1qwgA 21 :KGLPPKFVEDYLKVCGDY T0376 40 :MSAVVY 1qwgA 39 :IDFVKF T0376 48 :SMGDWPLLTDEQRMEGVERLVKAGIPVI 1qwgA 45 :GWGTSAVIDRDVVKEKINYYKDWGIKVY T0376 76 :VGTGAV 1qwgA 102 :VEISDG T0376 82 :NTASAVAHAVHAQKVG 1qwgA 112 :SLEERNNAIKRAKDNG T0376 100 :GLMVIPRVL 1qwgA 130 :VLTEVGKKM T0376 109 :SRGSVIAAQKAHFKAILSA 1qwgA 142 :DKQLTIDDRIKLINFDLDA T0376 130 :EIPAVIYNS 1qwgA 161 :GADYVIIEG T0376 139 :PYY 1qwgA 177 :GLF T0376 142 :GFATRADLFFALRAEHK 1qwgA 182 :EGKVKENELDVLAKNVD T0376 159 :NLVGF 1qwgA 201 :KVIFE T0376 167 :GG 1qwgA 206 :AP T0376 171 :DMRYAAENITSRDDEVTLM 1qwgA 208 :QKSQQVAFILKFGSSVNLA T0376 190 :IGVDTAVVHGFVNCGAT 1qwgA 228 :IAFDEVISLETLRRGLR Number of specific fragments extracted= 15 number of extra gaps= 1 total=774 Number of alignments=50 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0376)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0376)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0376 2 :TASIFSGVIPALM 1qwgA 8 :YEDFQRGLTVVLD T0376 21 :RTPDFDALVRKGKELIA 1qwgA 21 :KGLPPKFVEDYLKVCGD T0376 40 :MSAVVY 1qwgA 39 :IDFVKF T0376 48 :SMGDWPLLTDEQRMEGVERLVKAGIPVI 1qwgA 45 :GWGTSAVIDRDVVKEKINYYKDWGIKVY T0376 76 :VGTGAVN 1qwgA 102 :VEISDGS T0376 83 :TASAVAHAVHAQKVG 1qwgA 113 :LEERNNAIKRAKDNG T0376 100 :GLMVIPRVL 1qwgA 130 :VLTEVGKKM T0376 112 :SVIAAQKAHFKAILSA 1qwgA 145 :LTIDDRIKLINFDLDA T0376 130 :EIPAVIYNSPYYG 1qwgA 161 :GADYVIIEGRESG T0376 143 :FATRADLFFALRAE 1qwgA 182 :EGKVKENELDVLAK T0376 157 :HKNLVGF 1qwgA 199 :INKVIFE T0376 167 :GGPADMRYAAENIT 1qwgA 206 :APQKSQQVAFILKF T0376 184 :DEVTLMIGVDTAVVHGF 1qwgA 220 :GSSVNLANIAFDEVISL T0376 201 :VNCG 1qwgA 239 :LRRG Number of specific fragments extracted= 14 number of extra gaps= 1 total=788 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tx2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tx2A expands to /projects/compbio/data/pdb/1tx2.pdb.gz 1tx2A:# T0376 read from 1tx2A/merged-good-all-a2m # 1tx2A read from 1tx2A/merged-good-all-a2m # adding 1tx2A to template set # found chain 1tx2A in template set Warning: unaligning (T0376)M14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0376)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0376)R21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)G36 Warning: unaligning (T0376)T22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)G36 Warning: unaligning (T0376)W52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0376 6 :FS 1tx2A 20 :TL T0376 9 :VIPAL 1tx2A 22 :IMGIL T0376 16 :PCRQD 1tx2A 29 :TPDSF T0376 25 :FDALVRKGKELIADGMSAVVYCG 1tx2A 42 :VDAAVRHAKEMRDEGAHIIDIGG T0376 53 :PLLTDEQRME 1tx2A 72 :AKVSVEEEIK T0376 63 :GVERLVK 1tx2A 86 :MIQAVSK T0376 70 :AGIPVIVGTGA 1tx2A 94 :VKLPISIDTYK T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1tx2A 105 :AEVAKQAIEAGAHIINDIWGAKAEPK T0376 120 :HFKAILSA 1tx2A 131 :IAEVAAHY T0376 130 :EIPAVIYNSPYY 1tx2A 139 :DVPIILMHNRDN T0376 142 :GFAT 1tx2A 152 :NYRN T0376 147 :ADLFFALR 1tx2A 158 :ADMIADLY T0376 155 :AEHK 1tx2A 172 :KDAG T0376 159 :NLVGFKEFGGPADMRYAAENITSRDD 1tx2A 180 :NIILDPGIGFAKTPEQNLEAMRNLEQ T0376 185 :EVTLMIGVD 1tx2A 210 :GYPVLLGTS T0376 194 :TAVVHGFV 1tx2A 220 :KSFIGHVL T0376 202 :NCGATGAIT 1tx2A 247 :EKGCEFVRV T0376 220 :VIHLCKLSQAAA 1tx2A 258 :VKEMSRMAKMMD T0376 246 :Q 1tx2A 270 :A Number of specific fragments extracted= 19 number of extra gaps= 2 total=807 Number of alignments=52 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0376)M14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0376)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0376)T22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)G36 Warning: unaligning (T0376)W52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0376 7 :S 1tx2A 21 :L T0376 9 :VIPAL 1tx2A 22 :IMGIL T0376 16 :PCRQDR 1tx2A 29 :TPDSFS T0376 25 :FDALVRKGKELIADGMSAVVYCG 1tx2A 42 :VDAAVRHAKEMRDEGAHIIDIGG T0376 53 :PLLTDEQRME 1tx2A 72 :AKVSVEEEIK T0376 63 :GVERLVK 1tx2A 86 :MIQAVSK T0376 70 :AGIPVIVGTGA 1tx2A 94 :VKLPISIDTYK T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1tx2A 105 :AEVAKQAIEAGAHIINDIWGAKAEPK T0376 120 :HFKAILSA 1tx2A 131 :IAEVAAHY T0376 130 :EIPAVIYNSPYY 1tx2A 139 :DVPIILMHNRDN T0376 142 :GFATRADLFFA 1tx2A 152 :NYRNLMADMIA T0376 153 :LRA 1tx2A 164 :LYD T0376 156 :EHK 1tx2A 173 :DAG T0376 159 :NLVGFKEFGGPADMRYAAENITSRDD 1tx2A 180 :NIILDPGIGFAKTPEQNLEAMRNLEQ T0376 185 :EVTLMIGVD 1tx2A 210 :GYPVLLGTS T0376 194 :TAVVHGFVNCGATGAIT 1tx2A 239 :GATVCLGIEKGCEFVRV T0376 220 :VIHLCKLSQAAA 1tx2A 258 :VKEMSRMAKMMD T0376 239 :A 1tx2A 270 :A Number of specific fragments extracted= 18 number of extra gaps= 2 total=825 Number of alignments=53 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0376)M14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0376)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0376)W52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0376 9 :VIPAL 1tx2A 22 :IMGIL T0376 16 :PCRQD 1tx2A 29 :TPDSF T0376 25 :FDALVRKGKELIADGMSAVVYCG 1tx2A 42 :VDAAVRHAKEMRDEGAHIIDIGG T0376 53 :PLLTDEQRME 1tx2A 72 :AKVSVEEEIK T0376 63 :GVERLVK 1tx2A 86 :MIQAVSK T0376 70 :AGIPVIVGTGA 1tx2A 94 :VKLPISIDTYK T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRG 1tx2A 105 :AEVAKQAIEAGAHIINDIWGAKAEP T0376 119 :AHFKAILSA 1tx2A 130 :KIAEVAAHY T0376 130 :EIPAVIYNSPYYGFATRADLFFALRA 1tx2A 139 :DVPIILMHNRDNMNYRNLMADMIADL T0376 156 :E 1tx2A 172 :K T0376 157 :HKNLVGFKEFGG 1tx2A 178 :DENIILDPGIGF T0376 169 :PADMRYAAENITS 1tx2A 192 :TPEQNLEAMRNLE T0376 182 :RDDEVTLMIGVD 1tx2A 207 :NVLGYPVLLGTS T0376 194 :TAVVHGFVNCGATGAITGIG 1tx2A 239 :GATVCLGIEKGCEFVRVHDV T0376 218 :KEVIHLCK 1tx2A 259 :KEMSRMAK T0376 237 :ARARA 1tx2A 267 :MMDAM Number of specific fragments extracted= 16 number of extra gaps= 1 total=841 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xg4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1xg4A/merged-good-all-a2m # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set T0376 29 :VRKGKELIADGMSAVVYC 1xg4A 28 :ANHALLAQRAGYQAIYLS T0376 47 :GSMG 1xg4A 52 :GSLG T0376 51 :DWPLLTDEQRMEGVERLVK 1xg4A 58 :DLGISTLDDVLTDIRRITD T0376 70 :AGIPVIVGTG 1xg4A 78 :CSLPLLVDAD T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIP 1xg4A 91 :GSSAFNVARTVKSMIKAGAAGLHIED T0376 106 :RVLSRGS 1xg4A 122 :RSGHRPN T0376 113 :VIAAQKAHFKAILSAA 1xg4A 133 :SKEEMVDRIRAAVDAK T0376 129 :PEIPAVIYNSPYY 1xg4A 151 :PDFVIMARTDALA T0376 142 :GFATRADLFFALRAE 1xg4A 166 :GLDAAIERAQAYVEA T0376 159 :NL 1xg4A 181 :GA T0376 161 :VGFKEFGG 1xg4A 184 :MLFPEAIT T0376 171 :DMRYAAENITSRDDE 1xg4A 192 :ELAMYRQFADAVQVP T0376 188 :LMIGVDT 1xg4A 207 :ILANITE T0376 195 :AVVHGFVNCGATGAITGIG 1xg4A 220 :FTTDELRSAHVAMALYPLS T0376 226 :LSQAAAK 1xg4A 239 :AFRAMNR T0376 237 :ARARALE 1xg4A 246 :AAEHVYN T0376 250 :VLSSFDEGPDL 1xg4A 253 :VLRQEGTQKSV T0376 282 :ETDALTDSQR 1xg4A 264 :IDTMQTRNEL Number of specific fragments extracted= 18 number of extra gaps= 0 total=859 Number of alignments=55 # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set T0376 9 :VIPALMTPCRQ 1xg4A 82 :LLVDADIGFGS T0376 24 :DFDALVRKGKELIADGMSAVVYCGSMG 1xg4A 93 :SAFNVARTVKSMIKAGAAGLHIEDQVG T0376 51 :DWPLLTDEQRMEGVERLVK 1xg4A 128 :NKAIVSKEEMVDRIRAAVD T0376 70 :AGIPVIVGTGAVNTA 1xg4A 151 :PDFVIMARTDALAVE T0376 85 :SAVAHAVHAQKVGAKGLMVI 1xg4A 169 :AAIERAQAYVEAGAEMLFPE T0376 110 :RGSVIA 1xg4A 189 :AITELA T0376 120 :HFKAILSAA 1xg4A 195 :MYRQFADAV T0376 130 :EIPAVIYNSPYY 1xg4A 204 :QVPILANITEFG T0376 142 :GFATRADLFFAL 1xg4A 217 :TPLFTTDELRSA T0376 185 :EVTLMIGVDTAV 1xg4A 229 :HVAMALYPLSAF T0376 228 :QA 1xg4A 241 :RA T0376 239 :ARAL 1xg4A 243 :MNRA T0376 244 :LEQALAVLSSFDEGPDL 1xg4A 247 :AEHVYNVLRQEGTQKSV T0376 282 :ETDALTDSQR 1xg4A 264 :IDTMQTRNEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=873 Number of alignments=56 # 1xg4A read from 1xg4A/merged-good-all-a2m # found chain 1xg4A in training set T0376 29 :VRKGKELIADGMSAVVYC 1xg4A 28 :ANHALLAQRAGYQAIYLS T0376 47 :GSMG 1xg4A 52 :GSLG T0376 51 :DWPLLTDEQRMEGVERLVK 1xg4A 58 :DLGISTLDDVLTDIRRITD T0376 70 :AGIPVIVGT 1xg4A 78 :CSLPLLVDA T0376 79 :GAVNTASAVAHAVHAQKVGAKGLMVI 1xg4A 90 :FGSSAFNVARTVKSMIKAGAAGLHIE T0376 105 :PRVLSRG 1xg4A 121 :KRSGHRP T0376 112 :SVIAAQKAHFKAILSAA 1xg4A 132 :VSKEEMVDRIRAAVDAK T0376 129 :PEIPAVIYNSPY 1xg4A 151 :PDFVIMARTDAL T0376 147 :ADLFFALRAE 1xg4A 166 :GLDAAIERAQ T0376 161 :VGFKEFGGPADMRYAAENIT 1xg4A 184 :MLFPEAITELAMYRQFADAV T0376 184 :DEVTLMIGVD 1xg4A 204 :QVPILANITE T0376 197 :VHGFVNCGATGAITGIG 1xg4A 222 :TDELRSAHVAMALYPLS T0376 234 :DADARARALELEQALAVLSS 1xg4A 239 :AFRAMNRAAEHVYNVLRQEG T0376 269 :VLKGDKEYTLHFNETDAL 1xg4A 259 :TQKSVIDTMQTRNELYES Number of specific fragments extracted= 14 number of extra gaps= 0 total=887 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ojxA expands to /projects/compbio/data/pdb/1ojx.pdb.gz 1ojxA:# T0376 read from 1ojxA/merged-good-all-a2m # 1ojxA read from 1ojxA/merged-good-all-a2m # adding 1ojxA to template set # found chain 1ojxA in template set Warning: unaligning (T0376)Q228 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0376)A229 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0376 9 :VIPALMT 1ojxA 18 :SIILAYD T0376 24 :DFDALVRKGK 1ojxA 42 :DPEYILRLAR T0376 37 :ADGMSAVVYC 1ojxA 52 :DAGFDGVVFQ T0376 65 :ERLVK 1ojxA 63 :GIAEK T0376 70 :AGIPVIVGTG 1ojxA 71 :GSVPLILKLN T0376 80 :AVNTASA 1ojxA 95 :NCSVEEA T0376 94 :QKVGAKGLMVIPRVLSR 1ojxA 102 :VSLGASAVGYTIYPGSG T0376 111 :GSVIAAQKAHFKAILSA 1ojxA 121 :WKMFEELARIKRDAVKF T0376 130 :EIPAVIYNSPYY 1ojxA 138 :DLPLVVWSYPRG T0376 142 :GFAT 1ojxA 151 :KVVN T0376 147 :ADLFFALRAEH 1ojxA 161 :VAYAARIALEL T0376 159 :NLVGFK 1ojxA 172 :GADAMK T0376 165 :EFGG 1ojxA 179 :KYTG T0376 171 :DMRYAAENITSRDDEVTLMIGVD 1ojxA 183 :DPKTFSWAVKVAGKVPVLMSGGP T0376 196 :VVHGFVNCGATGAITGIGNV 1ojxA 216 :QVEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 16 number of extra gaps= 1 total=903 Number of alignments=58 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set Warning: unaligning (T0376)Q228 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0376)A229 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0376 24 :DFDALVRKGK 1ojxA 42 :DPEYILRLAR T0376 37 :ADGMSAVVYC 1ojxA 52 :DAGFDGVVFQ T0376 65 :ERLVK 1ojxA 63 :GIAEK T0376 70 :AGIPVIVGT 1ojxA 71 :GSVPLILKL T0376 79 :GAVNTAS 1ojxA 94 :ANCSVEE T0376 93 :AQKVGAKGLMVIPRVLSRGS 1ojxA 101 :AVSLGASAVGYTIYPGSGFE T0376 115 :AAQKAHFKAILSAA 1ojxA 121 :WKMFEELARIKRDA T0376 130 :EIPAVIYNSPYY 1ojxA 138 :DLPLVVWSYPRG T0376 142 :GFA 1ojxA 151 :KVV T0376 145 :TRADLFF 1ojxA 156 :TAPEIVA T0376 152 :ALRAEHK 1ojxA 166 :RIALELG T0376 159 :NLVGFKEF 1ojxA 174 :DAMKIKYT T0376 168 :G 1ojxA 182 :G T0376 171 :DMRYAAENITSRDDEVTLMIG 1ojxA 183 :DPKTFSWAVKVAGKVPVLMSG T0376 193 :D 1ojxA 204 :G T0376 194 :TAV 1ojxA 212 :DFL T0376 197 :VHGFVNCGATGAITGIGNV 1ojxA 217 :VEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 18 number of extra gaps= 1 total=921 Number of alignments=59 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set Warning: unaligning (T0376)Q228 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0376)A229 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0376 24 :DFDALVRKGKEL 1ojxA 42 :DPEYILRLARDA T0376 39 :GMSAVVYC 1ojxA 54 :GFDGVVFQ T0376 61 :MEGVER 1ojxA 62 :RGIAEK T0376 70 :AGIPVIVGT 1ojxA 71 :GSVPLILKL T0376 80 :AVNTA 1ojxA 95 :NCSVE T0376 92 :HAQKVGAKGLMVIPRVLSRG 1ojxA 100 :EAVSLGASAVGYTIYPGSGF T0376 114 :IAAQKAHFKAILSAA 1ojxA 120 :EWKMFEELARIKRDA T0376 129 :PEIPAVIYNSPYYGFAT 1ojxA 137 :FDLPLVVWSYPRGGKVV T0376 146 :RADLFFALRAE 1ojxA 156 :TAPEIVAYAAR T0376 159 :NLVGFKE 1ojxA 172 :GADAMKI T0376 166 :FGGPADMRYAAENIT 1ojxA 180 :YTGDPKTFSWAVKVA T0376 184 :DEVTLMIGVD 1ojxA 195 :GKVPVLMSGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1ojxA 214 :LKQVEGVLEAGALGIAVGRNVW T0376 216 :LPKEVIHLCKLS 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 14 number of extra gaps= 1 total=935 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y0eA expands to /projects/compbio/data/pdb/1y0e.pdb.gz 1y0eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0376 read from 1y0eA/merged-good-all-a2m # 1y0eA read from 1y0eA/merged-good-all-a2m # adding 1y0eA to template set # found chain 1y0eA in template set Warning: unaligning (T0376)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0376)R106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 Warning: unaligning (T0376)A128 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y0eA)P117 Warning: unaligning (T0376)P129 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y0eA)P117 T0376 7 :SGVIPALMT 1y0eA 4 :HGLIVSCQA T0376 18 :RQDRT 1y0eA 13 :LPDEP T0376 23 :PDFDALVRKGKELIADGMSAVVYC 1y0eA 19 :HSSFIMSKMALAAYEGGAVGIRAN T0376 56 :TDEQRMEGVER 1y0eA 43 :TKEDILAIKET T0376 70 :AGIPVIVGTG 1y0eA 54 :VDLPVIGIVK T0376 80 :AVNTASA 1y0eA 74 :TATSKEV T0376 91 :VHAQKVGAKGLMVI 1y0eA 81 :DELIESQCEVIALD T0376 107 :VL 1y0eA 97 :LQ T0376 109 :SRGS 1y0eA 101 :PKET T0376 114 :IAAQKAHFK 1y0eA 105 :LDELVSYIR T0376 126 :SA 1y0eA 114 :TH T0376 130 :EIPAVIYN 1y0eA 118 :NVEIMADI T0376 145 :TRADLFFAL 1y0eA 126 :ATVEEAKNA T0376 155 :AEHK 1y0eA 135 :ARLG T0376 160 :LVGFK 1y0eA 139 :FDYIG T0376 170 :ADMRYAAENITSRDD 1y0eA 161 :NDFQFLKDVLQSVDA T0376 187 :TLMIGVD 1y0eA 176 :KVIAEGN T0376 194 :TAVVHGFVNCGATGAITG 1y0eA 186 :PDMYKRVMDLGVHCSVVG T0376 225 :KLSQ 1y0eA 204 :GAIT T0376 234 :DADARARALE 1y0eA 208 :RPKEITKRFV Number of specific fragments extracted= 20 number of extra gaps= 2 total=955 Number of alignments=61 # 1y0eA read from 1y0eA/merged-good-all-a2m # found chain 1y0eA in template set Warning: unaligning (T0376)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0376)R106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 Warning: unaligning (T0376)A128 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y0eA)P117 Warning: unaligning (T0376)P129 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y0eA)P117 T0376 7 :SGVIPALM 1y0eA 4 :HGLIVSCQ T0376 17 :CRQDRTP 1y0eA 12 :ALPDEPL T0376 24 :DFDALVRKGKELIADGMSAVVYCG 1y0eA 20 :SSFIMSKMALAAYEGGAVGIRANT T0376 57 :DEQ 1y0eA 44 :KED T0376 64 :VERLVK 1y0eA 47 :ILAIKE T0376 70 :AGIPVIVGT 1y0eA 54 :VDLPVIGIV T0376 79 :GAVNTA 1y0eA 73 :ITATSK T0376 89 :HAVHAQKVGAKGLMVI 1y0eA 79 :EVDELIESQCEVIALD T0376 107 :VLSRG 1y0eA 97 :LQQRP T0376 112 :SVIAAQKAHFK 1y0eA 103 :ETLDELVSYIR T0376 126 :SA 1y0eA 114 :TH T0376 130 :EIPAVIYN 1y0eA 118 :NVEIMADI T0376 145 :TRADLFFAL 1y0eA 126 :ATVEEAKNA T0376 155 :AEHK 1y0eA 135 :ARLG T0376 159 :NLVGF 1y0eA 140 :DYIGT T0376 166 :FGGPADMRYAAENITSRDDEV 1y0eA 157 :LLYQNDFQFLKDVLQSVDAKV T0376 188 :LMIG 1y0eA 178 :IAEG T0376 193 :D 1y0eA 182 :N T0376 194 :TAV 1y0eA 187 :DMY T0376 198 :HGFVNCGATGAITGIGNVLPKE 1y0eA 190 :KRVMDLGVHCSVVGGAITRPKE Number of specific fragments extracted= 20 number of extra gaps= 2 total=975 Number of alignments=62 # 1y0eA read from 1y0eA/merged-good-all-a2m # found chain 1y0eA in template set Warning: unaligning (T0376)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0376)R106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 Warning: unaligning (T0376)A128 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y0eA)P117 Warning: unaligning (T0376)P129 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y0eA)P117 T0376 7 :SGVIPAL 1y0eA 4 :HGLIVSC T0376 16 :PCRQDRTP 1y0eA 11 :QALPDEPL T0376 24 :DFDALVRKGKELIADGMSAVVYC 1y0eA 20 :SSFIMSKMALAAYEGGAVGIRAN T0376 56 :TDEQRMEGVERL 1y0eA 43 :TKEDILAIKETV T0376 71 :GIPVIVGT 1y0eA 55 :DLPVIGIV T0376 79 :GAVNTA 1y0eA 73 :ITATSK T0376 89 :HAVHAQKVGAKGLMVI 1y0eA 79 :EVDELIESQCEVIALD T0376 107 :VLSRG 1y0eA 97 :LQQRP T0376 112 :SVIAAQ 1y0eA 103 :ETLDEL T0376 121 :FKAILSA 1y0eA 109 :VSYIRTH T0376 130 :EIPAVIYN 1y0eA 118 :NVEIMADI T0376 146 :RADLFFALRAEH 1y0eA 126 :ATVEEAKNAARL T0376 159 :NLVGFKEFGG 1y0eA 138 :GFDYIGTTLH T0376 169 :PADMRYAAENIT 1y0eA 162 :DFQFLKDVLQSV T0376 185 :EVTLMIGVD 1y0eA 174 :DAKVIAEGN T0376 194 :TAVVHGFVNCGATGAITGIGNVLPK 1y0eA 186 :PDMYKRVMDLGVHCSVVGGAITRPK T0376 234 :DADARAR 1y0eA 211 :EITKRFV Number of specific fragments extracted= 17 number of extra gaps= 2 total=992 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt8B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gt8B expands to /projects/compbio/data/pdb/1gt8.pdb.gz 1gt8B:# T0376 read from 1gt8B/merged-good-all-a2m # 1gt8B read from 1gt8B/merged-good-all-a2m # adding 1gt8B to template set # found chain 1gt8B in template set Warning: unaligning (T0376)S112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gt8B)M680 Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8B)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gt8B)T735 T0376 6 :FSGVIPALMTPCRQD 1gt8B 542 :FINPFGLASAAPTTS T0376 25 :F 1gt8B 557 :S T0376 30 :RKGKELIADGMSAVVYC 1gt8B 558 :SMIRRAFEAGWGFALTK T0376 47 :GSM 1gt8B 593 :GTT T0376 50 :GDWP 1gt8B 601 :GPGQ T0376 56 :TDEQRMEGVERLVK 1gt8B 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8B 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8B 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSAA 1gt8B 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gt8B 703 :QIPFFAKLTPNV T0376 144 :ATRADLFFALRAE 1gt8B 715 :TDIVSIARAAKEG T0376 159 :NLVGFK 1gt8B 728 :GADGVT T0376 167 :GG 1gt8B 736 :NT T0376 172 :MRYAAENITSR 1gt8B 775 :LRAVTTIARAL T0376 184 :DEVTLMIGVD 1gt8B 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8B 799 :AESGLQFLHSGASVLQVCSAVQN T0376 233 :GD 1gt8B 822 :QD T0376 246 :QALAV 1gt8B 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gt8B 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gt8B 848 :G T0376 278 :LHFNETDA 1gt8B 863 :KPVPRIAE T0376 289 :SQRGYVEAQFKLFNSWYA 1gt8B 881 :PYLEQRKKIIAEEKMRLK Number of specific fragments extracted= 22 number of extra gaps= 1 total=1014 Number of alignments=64 # 1gt8B read from 1gt8B/merged-good-all-a2m # found chain 1gt8B in template set Warning: unaligning (T0376)S112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gt8B)M680 Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8B)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gt8B)T735 T0376 6 :FSGVIPALMTPCRQ 1gt8B 542 :FINPFGLASAAPTT T0376 24 :DFDA 1gt8B 556 :SSSM T0376 32 :GKELIADGMSAVVY 1gt8B 560 :IRRAFEAGWGFALT T0376 47 :GSM 1gt8B 593 :GTT T0376 51 :DWPLLTDEQRMEGVERLVK 1gt8B 612 :LISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8B 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8B 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSAA 1gt8B 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gt8B 703 :QIPFFAKLTPNV T0376 142 :G 1gt8B 716 :D T0376 147 :ADLFFALRAE 1gt8B 718 :VSIARAAKEG T0376 159 :NLVGFK 1gt8B 728 :GADGVT T0376 167 :GG 1gt8B 736 :NT T0376 169 :PAD 1gt8B 745 :KAD T0376 172 :MRYAAENITSRD 1gt8B 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gt8B 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8B 799 :AESGLQFLHSGASVLQVCSAVQN T0376 233 :GDADA 1gt8B 822 :QDFTV T0376 239 :ARAL 1gt8B 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gt8B 831 :CTGLKALLYLKSIE T0376 275 :EY 1gt8B 847 :QG T0376 278 :LHFNET 1gt8B 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSW 1gt8B 880 :GPYLEQRKKIIAEEKMR Number of specific fragments extracted= 23 number of extra gaps= 1 total=1037 Number of alignments=65 # 1gt8B read from 1gt8B/merged-good-all-a2m # found chain 1gt8B in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8B)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gt8B)T735 T0376 30 :RKGKELIADGMSAV 1gt8B 558 :SMIRRAFEAGWGFA T0376 45 :YC 1gt8B 572 :LT T0376 47 :GSMG 1gt8B 593 :GTTS T0376 52 :WPLLTDEQRMEGVERLVK 1gt8B 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8B 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8B 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 112 :SVIAAQKAHFKAILSA 1gt8B 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gt8B 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1gt8B 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1gt8B 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gt8B 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8B 799 :AESGLQFLHSGASVLQVCSAVQN T0376 249 :AVLSSFDEGPDLVLYFKYMM 1gt8B 825 :TVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1gt8B 849 :WDGQSPGTE T0376 278 :LHFNETDALTDSQR 1gt8B 877 :PNFGPYLEQRKKII T0376 298 :FKLFNSWYA 1gt8B 891 :AEEKMRLKE Number of specific fragments extracted= 16 number of extra gaps= 1 total=1053 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aj2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aj2 expands to /projects/compbio/data/pdb/1aj2.pdb.gz 1aj2:Warning: there is no chain 1aj2 will retry with 1aj2A # T0376 read from 1aj2/merged-good-all-a2m # 1aj2 read from 1aj2/merged-good-all-a2m # adding 1aj2 to template set # found chain 1aj2 in template set Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0376 9 :VIPALMTPCRQD 1aj2 15 :PHVMGILNVTPD T0376 25 :FDALVRKGKELIADGMSAVVYCG 1aj2 37 :LIDAVKHANLMINAGATIIDVGG T0376 48 :SMGDWPLLTDEQRME 1aj2 62 :TRPGAAEVSVEEELQ T0376 63 :GVERLVK 1aj2 81 :VVEAIAQ T0376 71 :GIPVIVGTGAV 1aj2 90 :EVWISVDTSKP T0376 88 :AHAVHAQKVGAKGL 1aj2 101 :EVIRESAKVGAHII T0376 103 :VIPRVLSRGSVIAAQKAH 1aj2 115 :NDIRSLSEPGALEAAAET T0376 130 :EIPAVIYNS 1aj2 133 :GLPVCLMHM T0376 139 :PYYGFATR 1aj2 145 :PKTMQEAP T0376 147 :ADLFFALRAEH 1aj2 162 :NRYFIEQIARC T0376 158 :KNLVGFKEFGGPADMRYAAENITSRDD 1aj2 180 :EKLLLDPGFGFGKNLSHNYSLLARLAE T0376 185 :EVTLMIGVDTAVVHGFV 1aj2 211 :NLPLLVGMSRKSMIGQL T0376 202 :NCGATGAIT 1aj2 248 :MQGAHIIRV T0376 233 :GD 1aj2 257 :HD T0376 235 :ADARARALELEQALA 1aj2 260 :KETVEAMRVVEATLS T0376 253 :SFDEG 1aj2 275 :AKENK Number of specific fragments extracted= 16 number of extra gaps= 1 total=1069 Number of alignments=67 # 1aj2 read from 1aj2/merged-good-all-a2m # found chain 1aj2 in template set Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0376 9 :VIPALMTPCRQD 1aj2 15 :PHVMGILNVTPD T0376 25 :FDALVRKGKELIADGMSAVVYCG 1aj2 37 :LIDAVKHANLMINAGATIIDVGG T0376 48 :SMGDWPLLTDEQRME 1aj2 62 :TRPGAAEVSVEEELQ T0376 63 :GVERLVK 1aj2 81 :VVEAIAQ T0376 71 :GIPVIVGTGAV 1aj2 90 :EVWISVDTSKP T0376 88 :AHAVHAQKVGAKGL 1aj2 101 :EVIRESAKVGAHII T0376 103 :VIPRVLSRGSVIAAQKAH 1aj2 115 :NDIRSLSEPGALEAAAET T0376 130 :EIPAVIYNS 1aj2 133 :GLPVCLMHM T0376 139 :PYYGFATR 1aj2 145 :PKTMQEAP T0376 147 :ADLFFALRAEH 1aj2 162 :NRYFIEQIARC T0376 158 :KNLVGFKEFGGPADMRYAAENITSRDD 1aj2 180 :EKLLLDPGFGFGKNLSHNYSLLARLAE T0376 185 :EVTLMIGVDTAVVHGFVN 1aj2 211 :NLPLLVGMSRKSMIGQLL T0376 203 :CGATGAIT 1aj2 249 :QGAHIIRV T0376 233 :GDAD 1aj2 257 :HDVK T0376 238 :RARAL 1aj2 261 :ETVEA T0376 244 :LEQALA 1aj2 266 :MRVVEA T0376 253 :SFDEGPD 1aj2 272 :TLSAKEN Number of specific fragments extracted= 17 number of extra gaps= 1 total=1086 Number of alignments=68 # 1aj2 read from 1aj2/merged-good-all-a2m # found chain 1aj2 in template set Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1aj2)F89 T0376 9 :VIPALMTPCRQD 1aj2 15 :PHVMGILNVTPD T0376 25 :FDALVRKGKELIADGMSAVVYCG 1aj2 37 :LIDAVKHANLMINAGATIIDVGG T0376 48 :SMGDWPLLTDEQRME 1aj2 62 :TRPGAAEVSVEEELQ T0376 63 :GVERLVK 1aj2 81 :VVEAIAQ T0376 71 :GIPVIVGTGAV 1aj2 90 :EVWISVDTSKP T0376 88 :AHAVHAQKVGAKGL 1aj2 101 :EVIRESAKVGAHII T0376 102 :MVIPRVLSRG 1aj2 136 :VCLMHMQGNP T0376 114 :IAAQKAHFKAILSAA 1aj2 158 :FAEVNRYFIEQIARC T0376 129 :PEI 1aj2 179 :KEK T0376 134 :VIYN 1aj2 182 :LLLD T0376 139 :P 1aj2 186 :P T0376 141 :YGFATRADLFFALRAE 1aj2 187 :GFGFGKNLSHNYSLLA T0376 158 :K 1aj2 209 :H T0376 159 :NLVGFKEFGGP 1aj2 211 :NLPLLVGMSRK T0376 174 :YAAENITSRDDEVT 1aj2 222 :SMIGQLLNVGPSER T0376 192 :VDTAVVHGFVNCGATGAIT 1aj2 238 :GSLACAVIAAMQGAHIIRV T0376 230 :AAKGDADARARALELEQA 1aj2 257 :HDVKETVEAMRVVEATLS Number of specific fragments extracted= 17 number of extra gaps= 1 total=1103 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gt8D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gt8D expands to /projects/compbio/data/pdb/1gt8.pdb.gz 1gt8D:# T0376 read from 1gt8D/merged-good-all-a2m # 1gt8D read from 1gt8D/merged-good-all-a2m # adding 1gt8D to template set # found chain 1gt8D in template set Warning: unaligning (T0376)S112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gt8D)M680 Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8D)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gt8D)T735 T0376 6 :FSGVIPALMTPCRQ 1gt8D 542 :FINPFGLASAAPTT T0376 24 :DFDA 1gt8D 556 :SSSM T0376 32 :GKELIADGMSAVVYCGSM 1gt8D 560 :IRRAFEAGWGFALTKTFS T0376 50 :GDWPL 1gt8D 601 :GPGQS T0376 56 :TDEQRMEGVERLVK 1gt8D 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8D 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8D 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSAA 1gt8D 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gt8D 703 :QIPFFAKLTPNV T0376 144 :ATRADLFFALRAE 1gt8D 715 :TDIVSIARAAKEG T0376 159 :NLVGFK 1gt8D 728 :GADGVT T0376 167 :GG 1gt8D 736 :NT T0376 172 :MRYAAENITSR 1gt8D 775 :LRAVTTIARAL T0376 184 :DEVTLMIGVD 1gt8D 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8D 799 :AESGLQFLHSGASVLQVCSAVQN T0376 233 :GD 1gt8D 822 :QD T0376 246 :QALAV 1gt8D 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gt8D 830 :YCTGLKALLYLKSIEE T0376 276 :YT 1gt8D 847 :QG T0376 280 :FNETDA 1gt8D 865 :VPRIAE T0376 289 :SQRGYVEAQFKLFNSWY 1gt8D 881 :PYLEQRKKIIAEEKMRL Number of specific fragments extracted= 21 number of extra gaps= 1 total=1124 Number of alignments=70 # 1gt8D read from 1gt8D/merged-good-all-a2m # found chain 1gt8D in template set Warning: unaligning (T0376)S112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gt8D)M680 Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8D)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1gt8D)T735 T0376 6 :FSG 1gt8D 542 :FIN T0376 9 :VIPALMTPCR 1gt8D 546 :FGLASAAPTT T0376 24 :DFDALVR 1gt8D 556 :SSSMIRR T0376 35 :LIADGMSAVVYCGSM 1gt8D 563 :AFEAGWGFALTKTFS T0376 50 :GD 1gt8D 601 :GP T0376 52 :WPLLTDEQRMEGVERLVK 1gt8D 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8D 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8D 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSAA 1gt8D 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gt8D 703 :QIPFFAKLTPNV T0376 142 :G 1gt8D 716 :D T0376 147 :ADLFFALRAE 1gt8D 718 :VSIARAAKEG T0376 157 :HKNLV 1gt8D 729 :ADGVT T0376 172 :MRYAAENITSRD 1gt8D 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gt8D 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8D 799 :AESGLQFLHSGASVLQVCSAVQN T0376 233 :GDADA 1gt8D 822 :QDFTV T0376 239 :ARAL 1gt8D 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gt8D 831 :CTGLKALLYLKSIE T0376 275 :EYT 1gt8D 846 :LQG T0376 278 :LHFNETD 1gt8D 866 :PRIAELM T0376 289 :SQRGYVEAQFKLFNSW 1gt8D 881 :PYLEQRKKIIAEEKMR Number of specific fragments extracted= 22 number of extra gaps= 1 total=1146 Number of alignments=71 # 1gt8D read from 1gt8D/merged-good-all-a2m # found chain 1gt8D in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gt8D)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gt8D)T735 T0376 31 :KGKELIADGMSA 1gt8D 559 :MIRRAFEAGWGF T0376 44 :VYCGSMG 1gt8D 571 :ALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gt8D 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gt8D 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gt8D 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 112 :SVIAAQKAHFKAILSA 1gt8D 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gt8D 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1gt8D 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1gt8D 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gt8D 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gt8D 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYM 1gt8D 824 :FTVIQDYCTGLKALLYLKSI T0376 268 :M 1gt8D 866 :P T0376 269 :VLKGDKEYTLHFNETDALTDSQR 1gt8D 868 :IAELMGKKLPNFGPYLEQRKKII T0376 298 :FKLFNSWYAD 1gt8D 891 :AEEKMRLKEQ Number of specific fragments extracted= 15 number of extra gaps= 1 total=1161 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1eyeA/merged-good-all-a2m # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0376)G47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0376)S48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 T0376 6 :FS 1eyeA 6 :VQ T0376 9 :VIPALMTPCRQDRT 1eyeA 8 :VMGVLNVTDDSFSD T0376 23 :PDFDALVRKGKELIADGMSAVVYC 1eyeA 26 :LDLDDAVKHGLAMAAAGAGIVDVG T0376 57 :DEQRMEGVERLVKAGIPVIVGTGA 1eyeA 66 :TSRVIPVVKELAAQGITVSIDTMR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGSVIAAQKAH 1eyeA 90 :ADVARAALQNGAQMVNDVSGGRADPAMGPLLAEA T0376 130 :EIPAVIYNS 1eyeA 124 :DVPWVLMHW T0376 139 :PYYGFATR 1eyeA 140 :PHVPVRYG T0376 147 :ADLFFALRAE 1eyeA 158 :LASVADAVAA T0376 157 :H 1eyeA 169 :V T0376 158 :KNLVGFKEFGGPADMRYAAENITSR 1eyeA 172 :ARLVLDPGLGFAKTAQHNWAILHAL T0376 183 :DDEVTLMIGVDTAVVHGFV 1eyeA 201 :ATGIPVLVGASRKRFLGAL T0376 202 :NCGATGAITG 1eyeA 246 :LHGAWGVRVH T0376 216 :LPKEVIHLCKLSQAAA 1eyeA 256 :DVRASVDAIKVVEAWM Number of specific fragments extracted= 13 number of extra gaps= 1 total=1174 Number of alignments=73 # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0376)G47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0376)S48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 T0376 6 :FS 1eyeA 6 :VQ T0376 9 :VIPALMTPCRQDRT 1eyeA 8 :VMGVLNVTDDSFSD T0376 23 :PDFDALVRKGKELIADGMSAVVYC 1eyeA 26 :LDLDDAVKHGLAMAAAGAGIVDVG T0376 57 :DEQRMEGVERLVKAGIPVIVGTGA 1eyeA 66 :TSRVIPVVKELAAQGITVSIDTMR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGSVIAAQKAH 1eyeA 90 :ADVARAALQNGAQMVNDVSGGRADPAMGPLLAEA T0376 130 :EIPAVIYNS 1eyeA 124 :DVPWVLMHW T0376 139 :PYYGFATR 1eyeA 140 :PHVPVRYG T0376 147 :ADLFFALRAE 1eyeA 154 :RADLLASVAD T0376 158 :KNLVGFKEFGGPADMRYAAENITSR 1eyeA 172 :ARLVLDPGLGFAKTAQHNWAILHAL T0376 183 :DDEVTLMIGVD 1eyeA 201 :ATGIPVLVGAS T0376 194 :TAVVHGFVNCGATGAITGIG 1eyeA 238 :AVISALAALHGAWGVRVHDV T0376 218 :KEVIHLCKLSQAA 1eyeA 258 :RASVDAIKVVEAW Number of specific fragments extracted= 12 number of extra gaps= 1 total=1186 Number of alignments=74 # 1eyeA read from 1eyeA/merged-good-all-a2m # found chain 1eyeA in training set Warning: unaligning (T0376)G47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eyeA)E65 Warning: unaligning (T0376)S48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eyeA)E65 T0376 9 :VIPALMTPCRQD 1eyeA 8 :VMGVLNVTDDSF T0376 23 :PDFDALVRKGKELIADGMSAVVYC 1eyeA 26 :LDLDDAVKHGLAMAAAGAGIVDVG T0376 57 :DEQRMEGVERLVKAGIPVIVGTGA 1eyeA 66 :TSRVIPVVKELAAQGITVSIDTMR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRG 1eyeA 90 :ADVARAALQNGAQMVNDVSGGRADP T0376 119 :AHFKAILSA 1eyeA 115 :AMGPLLAEA T0376 130 :EIPAVIYNSPYYG 1eyeA 124 :DVPWVLMHWRAVS T0376 143 :FATRA 1eyeA 141 :HVPVR T0376 148 :DLFFALRA 1eyeA 150 :VAEVRADL T0376 157 :HKNLVGFKEFGG 1eyeA 171 :PARLVLDPGLGF T0376 169 :PADMRYAAENITS 1eyeA 185 :TAQHNWAILHALP T0376 182 :RDDEVTLMIGVDTA 1eyeA 201 :ATGIPVLVGASRKR T0376 261 :VLYFKYMMVLKGDKEYTLHFNETDALTDSQRGY 1eyeA 215 :FLGALLAGPDGVMRPTDGRDTATAVISALAALH T0376 294 :VEAQFKLFNSWYADW 1eyeA 257 :VRASVDAIKVVEAWM Number of specific fragments extracted= 13 number of extra gaps= 1 total=1199 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ad4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ad4A expands to /projects/compbio/data/pdb/1ad4.pdb.gz 1ad4A:# T0376 read from 1ad4A/merged-good-all-a2m # 1ad4A read from 1ad4A/merged-good-all-a2m # adding 1ad4A to template set # found chain 1ad4A in template set Warning: unaligning (T0376)T2 because first residue in template chain is (1ad4A)T2 Warning: unaligning (T0376)A12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ad4A)N25 Warning: unaligning (T0376)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ad4A)N25 Warning: unaligning (T0376)C46 because of BadResidue code BAD_PEPTIDE in next template residue (1ad4A)G48 Warning: unaligning (T0376)G47 because of BadResidue code BAD_PEPTIDE at template residue (1ad4A)G48 T0376 3 :ASIFSGVIP 1ad4A 3 :KTKIMGILN T0376 25 :FDALVRKGKELIADGMSAVVY 1ad4A 26 :VESAVTRVKAMMDEGADIIDV T0376 48 :SMGD 1ad4A 49 :VSTR T0376 52 :WPLLTDEQRMEGVERLVK 1ad4A 55 :HEMITVEEELNRVLPVVE T0376 70 :AGIPVIVGTGA 1ad4A 77 :FDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1ad4A 88 :SEVAEACLKLGVDIINDQWAGLYDHR T0376 120 :HFKAILSA 1ad4A 114 :MFQVVAKY T0376 130 :EIPAVIYNSPYYGFATR 1ad4A 122 :DAEIVLMHNGNGNRDEP T0376 147 :ADLFFALR 1ad4A 148 :LAQAHQAK T0376 155 :AEHK 1ad4A 157 :AGIP T0376 159 :NLVGFKEFGGPADMRYAAENITSR 1ad4A 163 :KIWLDPGIGFAKTRNEEAEVMARL T0376 185 :EVTLMIGVD 1ad4A 193 :EYPVLLATS T0376 194 :TAVVHGFV 1ad4A 203 :KRFTKEMM T0376 202 :NCGATGAIT 1ad4A 232 :MKGVRAVRV T0376 220 :VIHLCKLSQA 1ad4A 243 :VELNAKLAKG T0376 240 :RALELEQ 1ad4A 253 :IDFLKEN Number of specific fragments extracted= 16 number of extra gaps= 1 total=1215 Number of alignments=76 # 1ad4A read from 1ad4A/merged-good-all-a2m # found chain 1ad4A in template set Warning: unaligning (T0376)T2 because first residue in template chain is (1ad4A)T2 Warning: unaligning (T0376)A12 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ad4A)N25 Warning: unaligning (T0376)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ad4A)N25 Warning: unaligning (T0376)C46 because of BadResidue code BAD_PEPTIDE in next template residue (1ad4A)G48 Warning: unaligning (T0376)G47 because of BadResidue code BAD_PEPTIDE at template residue (1ad4A)G48 T0376 3 :ASIFSGVIP 1ad4A 3 :KTKIMGILN T0376 25 :FDALVRKGKELIADGMSAVVY 1ad4A 26 :VESAVTRVKAMMDEGADIIDV T0376 48 :SMGD 1ad4A 49 :VSTR T0376 52 :WPLLTDEQR 1ad4A 55 :HEMITVEEE T0376 61 :MEGVERLVKAGIPVIVGTGA 1ad4A 68 :LPVVEAIVGFDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1ad4A 88 :SEVAEACLKLGVDIINDQWAGLYDHR T0376 120 :HFKAILSA 1ad4A 114 :MFQVVAKY T0376 130 :EIPAVIYNSPYYGFATRA 1ad4A 122 :DAEIVLMHNGNGNRDEPV T0376 148 :DLFFALRAE 1ad4A 142 :EMLTSLLAQ T0376 157 :HK 1ad4A 159 :IP T0376 159 :NLVGFKEFGGPADMRYAAENITSR 1ad4A 163 :KIWLDPGIGFAKTRNEEAEVMARL T0376 184 :DEVTLMIGVD 1ad4A 192 :TEYPVLLATS T0376 194 :TAVVHGFVNCGATGAITGI 1ad4A 224 :AATTAYGIMKGVRAVRVHN T0376 220 :VIHLCKLSQA 1ad4A 243 :VELNAKLAKG T0376 237 :ARARAL 1ad4A 253 :IDFLKE T0376 244 :LE 1ad4A 259 :NE Number of specific fragments extracted= 16 number of extra gaps= 1 total=1231 Number of alignments=77 # 1ad4A read from 1ad4A/merged-good-all-a2m # found chain 1ad4A in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1ad4A)T2 Warning: unaligning (T0376)M14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ad4A)N25 Warning: unaligning (T0376)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ad4A)N25 Warning: unaligning (T0376)C46 because of BadResidue code BAD_PEPTIDE in next template residue (1ad4A)G48 Warning: unaligning (T0376)G47 because of BadResidue code BAD_PEPTIDE at template residue (1ad4A)G48 T0376 5 :IFSGVIPAL 1ad4A 3 :KTKIMGILN T0376 25 :FDALVRKGKELIADGMSAVVY 1ad4A 26 :VESAVTRVKAMMDEGADIIDV T0376 48 :S 1ad4A 49 :V T0376 53 :PLLTDEQRME 1ad4A 56 :EMITVEEELN T0376 63 :GVERLVKAGIPVIVGTGA 1ad4A 70 :VVEAIVGFDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRG 1ad4A 88 :SEVAEACLKLGVDIINDQWAGLYDH T0376 119 :AHFKAILSA 1ad4A 113 :RMFQVVAKY T0376 130 :EIPAVIYNSPYYGFATRADLFFALRA 1ad4A 122 :DAEIVLMHNGNGNRDEPVVEEMLTSL T0376 156 :E 1ad4A 152 :H T0376 157 :HKNLVGFKEFGG 1ad4A 161 :SNKIWLDPGIGF T0376 169 :PADMRYAAENITS 1ad4A 175 :TRNEEAEVMARLD T0376 183 :DDEVTLMIGVD 1ad4A 191 :ATEYPVLLATS T0376 194 :TAVVHGFVNCGATGAITGIG 1ad4A 224 :AATTAYGIMKGVRAVRVHNV T0376 218 :KEVIHL 1ad4A 244 :ELNAKL T0376 235 :ADARARALELEQA 1ad4A 250 :AKGIDFLKENENA Number of specific fragments extracted= 15 number of extra gaps= 1 total=1246 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1ub3A/merged-good-all-a2m # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0376 12 :ALMTPCRQD 1ub3A 7 :IDHTLLKPT T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSM 1ub3A 16 :ATLEEVAKAAEEALEYGFYGLCIPPSY T0376 64 :VERLVK 1ub3A 43 :VAWVRA T0376 70 :AG 1ub3A 51 :PH T0376 72 :IPVIVGTGAV 1ub3A 55 :FRLVTVVGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRV 1ub3A 69 :EKEVKALEAALACARGADEVDMVLHL T0376 108 :LSRGSVIAAQKAHFKAILSAAPEIPAVIYNSPYY 1ub3A 96 :RAKAGDLDYLEAEVRAVREAVPQAVLKVILETGY T0376 145 :TRADLFFAL 1ub3A 130 :FSPEEIARL T0376 155 :AEH 1ub3A 139 :AEA T0376 159 :NLVGFKEFGGP 1ub3A 146 :GADFLKTSTGF T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1ub3A 161 :ASLEDVALLVRVAQGRAQVKAAGG T0376 194 :TAVVHGFVNCGATGAIT 1ub3A 188 :RETALRMLKAGASRLGT Number of specific fragments extracted= 12 number of extra gaps= 0 total=1258 Number of alignments=79 # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0376 12 :ALMTPCRQD 1ub3A 7 :IDHTLLKPT T0376 23 :PDFDALVRKGKELIADGMSAVVY 1ub3A 16 :ATLEEVAKAAEEALEYGFYGLCI T0376 64 :VERLVK 1ub3A 43 :VAWVRA T0376 70 :AGI 1ub3A 51 :PHA T0376 73 :PVIVGTGAV 1ub3A 56 :RLVTVVGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRV 1ub3A 69 :EKEVKALEAALACARGADEVDMVLHL T0376 108 :LSRGSVIAAQKAHFKAILSAAPEIPAVIYNSPYY 1ub3A 96 :RAKAGDLDYLEAEVRAVREAVPQAVLKVILETGY T0376 145 :TRADLFFALRAE 1ub3A 130 :FSPEEIARLAEA T0376 159 :NLVGFKEFGGP 1ub3A 146 :GADFLKTSTGF T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1ub3A 161 :ASLEDVALLVRVAQGRAQVKAAGG T0376 194 :TAVVHGFVNCGATGAIT 1ub3A 188 :RETALRMLKAGASRLGT Number of specific fragments extracted= 11 number of extra gaps= 0 total=1269 Number of alignments=80 # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0376 14 :MTPCRQD 1ub3A 9 :HTLLKPT T0376 23 :PDFDALVRKGKELIADGMSAVVY 1ub3A 16 :ATLEEVAKAAEEALEYGFYGLCI T0376 64 :VERLVK 1ub3A 43 :VAWVRA T0376 70 :AGIPVIVGTGAV 1ub3A 53 :APFRLVTVVGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPR 1ub3A 69 :EKEVKALEAALACARGADEVDMVLH T0376 110 :RG 1ub3A 99 :AG T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYG 1ub3A 101 :DLDYLEAEVRAVREAVPQAVLKVILETGYF T0376 147 :ADLFFALRAE 1ub3A 131 :SPEEIARLAE T0376 159 :NLVGFKEFGG 1ub3A 146 :GADFLKTSTG T0376 169 :PADMRYAAENIT 1ub3A 162 :SLEDVALLVRVA T0376 184 :DEVTLMIGVD 1ub3A 174 :QGRAQVKAAG T0376 194 :TAVVHGFVNCGATGAIT 1ub3A 188 :RETALRMLKAGASRLGT Number of specific fragments extracted= 12 number of extra gaps= 0 total=1281 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jubA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1jubA/merged-good-all-a2m # 1jubA read from 1jubA/merged-good-all-a2m # found chain 1jubA in training set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1jubA)V192 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1jubA)V192 T0376 10 :IPALMTPCR 1jubA 66 :INSMGLPNL T0376 24 :DFDALVRKGKELIADGM 1jubA 75 :GFDYYLDYVLKNQKENA T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAK 1jubA 92 :QEGPIFFSIAGMSAAENIAMLKKIQESDFS T0376 100 :GLMVIPRVLSRGS 1jubA 123 :ITELNLSCPNVPG T0376 113 :VIAAQKAHFKAILSAA 1jubA 142 :DFEATEKLLKEVFTFF T0376 130 :EIPAVIYNSPYY 1jubA 158 :TKPLGVKLPPYF T0376 143 :F 1jubA 171 :L T0376 145 :TRADLFFALRAEHK 1jubA 172 :VHFDIMAEILNQFP T0376 160 :LVGFK 1jubA 186 :LTYVN T0376 167 :GG 1jubA 193 :NS T0376 169 :PADMRYAAENITSRDDEVTLMIGVD 1jubA 226 :PTALANVRAFYTRLKPEIQIIGTGG T0376 194 :TAVVHGFVNCGATGAITGI 1jubA 254 :GQDAFEHLLCGATMLQIGT T0376 225 :KLSQA 1jubA 273 :ALHKE T0376 233 :GDADARARALELEQALAV 1jubA 278 :GPAIFDRIIKELEEIMNQ T0376 255 :DEG 1jubA 296 :KGY Number of specific fragments extracted= 15 number of extra gaps= 1 total=1296 Number of alignments=82 # 1jubA read from 1jubA/merged-good-all-a2m # found chain 1jubA in training set Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE in next template residue (1jubA)V192 T0376 8 :GVIPALMTPCR 1jubA 64 :GSINSMGLPNL T0376 24 :DFDALVRKGKELIADGM 1jubA 75 :GFDYYLDYVLKNQKENA T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGA 1jubA 92 :QEGPIFFSIAGMSAAENIAMLKKIQESDF T0376 99 :KGLMVIPRVLSRGS 1jubA 122 :GITELNLSCPNVPG T0376 113 :VIAAQKAHFKAILSAA 1jubA 142 :DFEATEKLLKEVFTFF T0376 130 :EIPAVIYNSPYY 1jubA 158 :TKPLGVKLPPYF T0376 146 :RADLFFALRAEHK 1jubA 173 :HFDIMAEILNQFP T0376 159 :NLVG 1jubA 187 :TYVN T0376 168 :GPAD 1jubA 211 :KPKD T0376 172 :MRYAAENITSRDDEVTLMIGVD 1jubA 229 :LANVRAFYTRLKPEIQIIGTGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1jubA 254 :GQDAFEHLLCGATMLQIGTALHK T0376 217 :PKEVIHLCKLSQA 1jubA 279 :PAIFDRIIKELEE T0376 250 :VLSS 1jubA 292 :IMNQ Number of specific fragments extracted= 13 number of extra gaps= 1 total=1309 Number of alignments=83 # 1jubA read from 1jubA/merged-good-all-a2m # found chain 1jubA in training set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1jubA)V192 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1jubA)V192 T0376 8 :GVIPALMTPCR 1jubA 64 :GSINSMGLPNL T0376 24 :DFDALVRKGKELIADGM 1jubA 75 :GFDYYLDYVLKNQKENA T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAK 1jubA 92 :QEGPIFFSIAGMSAAENIAMLKKIQESDFS T0376 100 :GLMVIPRVLSRG 1jubA 123 :ITELNLSCPNVP T0376 112 :SVIAAQKAHFKAILSA 1jubA 141 :YDFEATEKLLKEVFTF T0376 129 :PEIPAVIYNSPYYG 1jubA 157 :FTKPLGVKLPPYFD T0376 147 :ADLFFALRAE 1jubA 173 :HFDIMAEILN T0376 157 :HK 1jubA 184 :FP T0376 160 :LVGFK 1jubA 186 :LTYVN T0376 167 :G 1jubA 193 :N T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1jubA 226 :PTALANVRAFYTRLKPEIQIIGTG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1jubA 254 :GQDAFEHLLCGATMLQIGTALHK T0376 217 :PKEVIHLCK 1jubA 279 :PAIFDRIIK T0376 234 :DADARARA 1jubA 288 :ELEEIMNQ Number of specific fragments extracted= 14 number of extra gaps= 1 total=1323 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f6kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f6kA expands to /projects/compbio/data/pdb/1f6k.pdb.gz 1f6kA:Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 2143, because occupancy 0.500 <= existing 0.500 in 1f6kA Skipped atom 2145, because occupancy 0.500 <= existing 0.500 in 1f6kA # T0376 read from 1f6kA/merged-good-all-a2m # 1f6kA read from 1f6kA/merged-good-all-a2m # adding 1f6kA to template set # found chain 1f6kA in template set Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f6kA)P271 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f6kA)P271 T0376 1 :MTA 1f6kA 1 :MRD T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f6kA 4 :LKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f6kA 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1f6kA 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFS T0376 114 :IAAQKAHFKAILSAA 1f6kA 115 :FPEIKHYYDTIIAET T0376 130 :EIPAVIYNSPYY 1f6kA 130 :GSNMIVYSIPFL T0376 142 :GFATRADLFFAL 1f6kA 143 :GVNMGIEQFGEL T0376 155 :AEHKNLVGFKEFGG 1f6kA 155 :YKNPKVLGVKFTAG T0376 171 :DMRYAAENITSR 1f6kA 169 :DFYLLERLKKAY T0376 184 :DEVTLMIGVDTA 1f6kA 181 :PNHLIWAGFDEM T0376 197 :VHGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1f6kA 193 :MLPAASLGVDGAIGSTFNVNGVRARQIFELTKA T0376 233 :GD 1f6kA 226 :GK T0376 235 :ADARARALELEQALAVLSSFD 1f6kA 229 :KEALEIQHVTNDLIEGILANG T0376 260 :LVLYFKYMMVLKGDKEYTLH 1f6kA 250 :LYLTIKELLKLEGVDAGYCR T0376 282 :ETDALTDSQRGYVEAQFKLF 1f6kA 272 :MTSKATAEQVAKAKDLKAKF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1338 Number of alignments=85 # 1f6kA read from 1f6kA/merged-good-all-a2m # found chain 1f6kA in template set Warning: unaligning (T0376)A3 because first residue in template chain is (1f6kA)M1 Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f6kA)P271 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f6kA)P271 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f6kA 2 :RDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f6kA 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1f6kA 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSF T0376 115 :AAQKAHFKAILSAA 1f6kA 116 :PEIKHYYDTIIAET T0376 130 :EIPAVIYNSPYY 1f6kA 130 :GSNMIVYSIPFL T0376 142 :GFATRADLFFALR 1f6kA 143 :GVNMGIEQFGELY T0376 156 :EHKNLVGFKEFGG 1f6kA 156 :KNPKVLGVKFTAG T0376 171 :DMRYAAENITSRD 1f6kA 169 :DFYLLERLKKAYP T0376 185 :EVTLMIGVDTAV 1f6kA 182 :NHLIWAGFDEMM T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1f6kA 194 :LPAASLGVDGAIGSTFNVNGVRARQIFELTKA T0376 233 :GDAD 1f6kA 226 :GKLK T0376 238 :RARAL 1f6kA 230 :EALEI T0376 244 :LEQALAVLSSFDEGPD 1f6kA 235 :QHVTNDLIEGILANGL T0376 261 :VLYFKYMMVLKGDKEYTLH 1f6kA 251 :YLTIKELLKLEGVDAGYCR T0376 282 :ETDALTDSQRGYVEAQFKLF 1f6kA 272 :MTSKATAEQVAKAKDLKAKF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1353 Number of alignments=86 # 1f6kA read from 1f6kA/merged-good-all-a2m # found chain 1f6kA in template set Warning: unaligning (T0376)K274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f6kA)P271 Warning: unaligning (T0376)E275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f6kA)P271 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f6kA 2 :RDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f6kA 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1f6kA 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKF T0376 113 :VIAAQKAHFKAILSA 1f6kA 114 :SFPEIKHYYDTIIAE T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1f6kA 129 :TGSNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAY T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMMVLKGD 1f6kA 181 :PNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCR T0376 276 :YT 1f6kA 272 :MT T0376 278 :LHFNETDALTDSQRGY 1f6kA 275 :KATAEQVAKAKDLKAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=1361 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nal1 expands to /projects/compbio/data/pdb/1nal.pdb.gz 1nal1:# T0376 read from 1nal1/merged-good-all-a2m # 1nal1 read from 1nal1/merged-good-all-a2m # adding 1nal1 to template set # found chain 1nal1 in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1nal1)N4 Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)G72 Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nal1)P273 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nal1)P273 Warning: unaligning (T0376)N302 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)Q294 Warning: unaligning (T0376)S303 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)Q294 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal1 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 71 :GIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1nal1 73 :KIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFS T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNSPYY 1nal1 115 :FEEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1nal1 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1nal1 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSR 1nal1 170 :DLYQMEQIRREH T0376 184 :DEVTLMIGVDTAVVHGF 1nal1 182 :PDLVLYNGYDEIFASGL T0376 202 :NCGATGAITGIGNVLPKEVIHLCKLSQA 1nal1 199 :LAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GD 1nal1 227 :GD T0376 235 :ADARARALELEQALAVLSSFD 1nal1 230 :QTAQKLQTECNKVIDLLIKTG T0376 260 :LVLYFKYMMVLKGDKE 1nal1 251 :VFRGLKTVLHYMDVVS T0376 276 :YTLH 1nal1 268 :PLCR T0376 282 :ETD 1nal1 274 :FGP T0376 286 :LTDSQRGYVEAQFKLF 1nal1 277 :VDEKYQPELKALAQQL Number of specific fragments extracted= 14 number of extra gaps= 3 total=1375 Number of alignments=88 # 1nal1 read from 1nal1/merged-good-all-a2m # found chain 1nal1 in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1nal1)N4 Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)G72 Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nal1)P273 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nal1)P273 Warning: unaligning (T0376)N302 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)Q294 Warning: unaligning (T0376)S303 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)Q294 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal1 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 71 :GIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1nal1 73 :KIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSF T0376 115 :AAQKAHFKAILSAAPEIPAVIYNSPYY 1nal1 116 :EEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1nal1 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1nal1 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSRD 1nal1 170 :DLYQMEQIRREHP T0376 185 :EVTLMIGVDTAV 1nal1 183 :DLVLYNGYDEIF T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1nal1 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GDAD 1nal1 227 :GDIQ T0376 238 :RARAL 1nal1 231 :TAQKL T0376 244 :LEQALAVLSSFDEGPD 1nal1 236 :QTECNKVIDLLIKTGV T0376 261 :VLYFKYMMVLKGDK 1nal1 252 :FRGLKTVLHYMDVV T0376 275 :EYTLH 1nal1 267 :VPLCR T0376 282 :ET 1nal1 274 :FG T0376 285 :ALTDSQRGYVEAQFKLF 1nal1 276 :PVDEKYQPELKALAQQL Number of specific fragments extracted= 15 number of extra gaps= 3 total=1390 Number of alignments=89 # 1nal1 read from 1nal1/merged-good-all-a2m # found chain 1nal1 in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1nal1)N4 Warning: unaligning (T0376)A70 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)G72 Warning: unaligning (T0376)K274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nal1)P273 Warning: unaligning (T0376)E275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nal1)P273 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal1 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 71 :GIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1nal1 73 :KIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPF T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1nal1 114 :SFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREH T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1nal1 182 :PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVV T0376 269 :VLKGD 1nal1 267 :VPLCR T0376 276 :YTLHFNETDALTDSQRGYV 1nal1 274 :FGPVDEKYQPELKALAQQL Number of specific fragments extracted= 6 number of extra gaps= 2 total=1396 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal3/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nal3 expands to /projects/compbio/data/pdb/1nal.pdb.gz 1nal3:# T0376 read from 1nal3/merged-good-all-a2m # 1nal3 read from 1nal3/merged-good-all-a2m # adding 1nal3 to template set # found chain 1nal3 in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1nal3)N4 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal3 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1nal3 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFS T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNSPYY 1nal3 115 :FEEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1nal3 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1nal3 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSR 1nal3 170 :DLYQMEQIRREH T0376 184 :DEVTLMIGVDTAVVHGF 1nal3 182 :PDLVLYNGYDEIFASGL T0376 202 :NCGATGAITGIGNVLPKEVIHLCKLSQA 1nal3 199 :LAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GD 1nal3 227 :GD T0376 235 :ADARARALELEQALAVLSSFD 1nal3 230 :QTAQKLQTECNKVIDLLIKTG T0376 260 :LVLYFKYMMVLKGDKE 1nal3 251 :VFRGLKTVLHYMDVVS T0376 276 :YTLHFNETD 1nal3 268 :PLCRKPFGP T0376 286 :LTDSQRGYVEAQFKLFN 1nal3 277 :VDEKYQPELKALAQQLM Number of specific fragments extracted= 13 number of extra gaps= 0 total=1409 Number of alignments=91 # 1nal3 read from 1nal3/merged-good-all-a2m # found chain 1nal3 in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1nal3)N4 Warning: unaligning (T0376)S303 because last residue in template chain is (1nal3)Q294 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal3 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1nal3 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSF T0376 115 :AAQKAHFKAILSAAPEIPAVIYNSPYY 1nal3 116 :EEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1nal3 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1nal3 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSRD 1nal3 170 :DLYQMEQIRREHP T0376 185 :EVTLMIGVDTAV 1nal3 183 :DLVLYNGYDEIF T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1nal3 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GDAD 1nal3 227 :GDIQ T0376 238 :RARAL 1nal3 231 :TAQKL T0376 244 :LEQALAVLSSFDEGPD 1nal3 236 :QTECNKVIDLLIKTGV T0376 261 :VLYFKYMMVLKGDK 1nal3 252 :FRGLKTVLHYMDVV T0376 275 :EYTLHFNET 1nal3 267 :VPLCRKPFG T0376 285 :ALTDSQRGYVEAQFKLFN 1nal3 276 :PVDEKYQPELKALAQQLM Number of specific fragments extracted= 14 number of extra gaps= 0 total=1423 Number of alignments=92 # 1nal3 read from 1nal3/merged-good-all-a2m # found chain 1nal3 in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1nal3)N4 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1nal3 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1nal3 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPF T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1nal3 114 :SFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREH T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1nal3 182 :PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGY 1nal3 267 :VPLCRKPFGPVDEKYQPELKALAQQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=1428 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n7kA expands to /projects/compbio/data/pdb/1n7k.pdb.gz 1n7kA:# T0376 read from 1n7kA/merged-good-all-a2m # 1n7kA read from 1n7kA/merged-good-all-a2m # adding 1n7kA to template set # found chain 1n7kA in template set T0376 12 :ALMTPCRQD 1n7kA 25 :IDSTLLSPR T0376 23 :PDFDALVRKGKELIADGMSAVVY 1n7kA 34 :ATEEDVRNLVREASDYGFRCAVL T0376 56 :TDEQRMEGVERLVKAGIPVIVGTGAV 1n7kA 57 :TPVYTVKISGLAEKLGVKLCSVIGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLS 1n7kA 87 :PLEVKLVEAQTVLEAGATELDVVPHLSL T0376 112 :S 1n7kA 115 :G T0376 114 :IAAQKAHFKAILSAA 1n7kA 116 :PEAVYREVSGIVKLA T0376 129 :PEIPAVIYNSPYY 1n7kA 133 :YGAVVKVILEAPL T0376 145 :TRADLFFALRAEH 1n7kA 146 :WDDKTLSLLVDSS T0376 159 :NLVGFKEFGGPA 1n7kA 162 :GADIVKTSTGVY T0376 171 :DMRYAAENITSRDD 1n7kA 178 :DPVTVFRLASLAKP T0376 185 :EVTLMIGVD 1n7kA 193 :GMGVKASGG T0376 194 :TAVVHGFVNCGATGAIT 1n7kA 205 :GIDAVLAVGAGADIIGT T0376 220 :VIHLCKLSQ 1n7kA 224 :AVKVLESFK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1441 Number of alignments=94 # 1n7kA read from 1n7kA/merged-good-all-a2m # found chain 1n7kA in template set T0376 12 :ALMTPCRQD 1n7kA 25 :IDSTLLSPR T0376 23 :PDFDALVRKGKELIADGMSAVVY 1n7kA 34 :ATEEDVRNLVREASDYGFRCAVL T0376 56 :TDEQRMEGVERLVKAGIPVIVGTGAV 1n7kA 57 :TPVYTVKISGLAEKLGVKLCSVIGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLSR 1n7kA 87 :PLEVKLVEAQTVLEAGATELDVVPHLSLG T0376 114 :IAAQKAHFKAILSAA 1n7kA 116 :PEAVYREVSGIVKLA T0376 129 :PEIPAVIYNSPYY 1n7kA 133 :YGAVVKVILEAPL T0376 145 :TRADLFFALRAE 1n7kA 146 :WDDKTLSLLVDS T0376 159 :NLVGFKEFGGPA 1n7kA 162 :GADIVKTSTGVY T0376 171 :DMRYAAENITSRDD 1n7kA 178 :DPVTVFRLASLAKP T0376 185 :EVTLMIGVD 1n7kA 193 :GMGVKASGG T0376 194 :TAVVHGFVNCGATGAIT 1n7kA 205 :GIDAVLAVGAGADIIGT T0376 220 :VIHLCKLSQ 1n7kA 224 :AVKVLESFK Number of specific fragments extracted= 12 number of extra gaps= 0 total=1453 Number of alignments=95 # 1n7kA read from 1n7kA/merged-good-all-a2m # found chain 1n7kA in template set T0376 9 :VIP 1n7kA 25 :IDS T0376 15 :TPCRQD 1n7kA 28 :TLLSPR T0376 23 :PDFDALVRKGKELIADGMSAVVY 1n7kA 34 :ATEEDVRNLVREASDYGFRCAVL T0376 56 :TDEQRMEGVERLVKAGIPVIVGTGAV 1n7kA 57 :TPVYTVKISGLAEKLGVKLCSVIGFP T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLS 1n7kA 87 :PLEVKLVEAQTVLEAGATELDVVPHLSL T0376 113 :VIAAQKAHFKAILSAA 1n7kA 115 :GPEAVYREVSGIVKLA T0376 129 :PEIPAVIYNSPYYG 1n7kA 133 :YGAVVKVILEAPLW T0376 147 :ADLFFALRAE 1n7kA 147 :DDKTLSLLVD T0376 157 :HKNLVGFKEFGG 1n7kA 160 :RAGADIVKTSTG T0376 169 :PADMRYAAENITSRDDEVTLMIGVD 1n7kA 178 :DPVTVFRLASLAKPLGMGVKASGGI T0376 194 :TAVVHGFVNCGATGAITG 1n7kA 205 :GIDAVLAVGAGADIIGTS T0376 219 :EVIHLCKLSQ 1n7kA 223 :SAVKVLESFK Number of specific fragments extracted= 12 number of extra gaps= 0 total=1465 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p0kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p0kA expands to /projects/compbio/data/pdb/1p0k.pdb.gz 1p0kA:# T0376 read from 1p0kA/merged-good-all-a2m # 1p0kA read from 1p0kA/merged-good-all-a2m # adding 1p0kA to template set # found chain 1p0kA in template set Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0376)G167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)R226 T0376 9 :VIPALMTPCR 1p0kA 57 :PIFINAMTGG T0376 21 :R 1p0kA 67 :G T0376 25 :FDALVRKGKELIADGMSAV 1p0kA 72 :YEINKSLARAASQAGIPLA T0376 46 :CGS 1p0kA 91 :VGS T0376 50 :GDWPLLTDEQRM 1p0kA 94 :QMSALKDPSERL T0376 63 :GVERLVK 1p0kA 106 :SYEIVRK T0376 70 :AGIPVIVGTGAVNTA 1p0kA 115 :PNGLIFANLGSEATA T0376 88 :AHAVHAQKV 1p0kA 130 :AQAKEAVEM T0376 97 :GAKGLMVIPRVLSR 1p0kA 140 :GANALQIHLNVIQE T0376 117 :QKAHFKAILSAA 1p0kA 166 :ALKRIEQICSRV T0376 130 :EIPAVIYN 1p0kA 178 :SVPVIVKE T0376 141 :YGFATRADLFFALRAE 1p0kA 186 :VGFGMSKASAGKLYEA T0376 159 :NLVGFKEF 1p0kA 202 :GAAAVDIG T0376 170 :AD 1p0kA 228 :IS T0376 172 :MRYAAENITSR 1p0kA 239 :AASLAEIRSEF T0376 184 :DEVTLMIGVD 1p0kA 250 :PASTMIASGG T0376 194 :TAVVHGFVNCGATGAIT 1p0kA 263 :ALDVAKAIALGASCTGM T0376 217 :PKE 1p0kA 280 :AGH T0376 223 :LCKLSQA 1p0kA 283 :FLKALTD T0376 233 :GD 1p0kA 290 :SG T0376 235 :ADARARALELEQAL 1p0kA 293 :EGLLEEIQLILEEL T0376 265 :KYMMVLKGDKE 1p0kA 307 :KLIMTVLGART T0376 278 :LHFNET 1p0kA 322 :QKAPLV T0376 286 :LTDSQRGYVEA 1p0kA 328 :IKGETHHWLTE Number of specific fragments extracted= 24 number of extra gaps= 0 total=1489 Number of alignments=97 # 1p0kA read from 1p0kA/merged-good-all-a2m # found chain 1p0kA in template set Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0376)E165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)R226 T0376 11 :PALMTPCRQDR 1p0kA 57 :PIFINAMTGGG T0376 25 :FDALVRKGKELIADGMSAV 1p0kA 72 :YEINKSLARAASQAGIPLA T0376 46 :C 1p0kA 91 :V T0376 50 :GDWPLL 1p0kA 92 :GSQMSA T0376 56 :TDEQRME 1p0kA 100 :DPSERLS T0376 64 :VERLVK 1p0kA 107 :YEIVRK T0376 70 :AGIPVIVGTGAVN 1p0kA 115 :PNGLIFANLGSEA T0376 89 :HAVHAQKV 1p0kA 131 :QAKEAVEM T0376 97 :GAKGLMVIPRVLSR 1p0kA 140 :GANALQIHLNVIQE T0376 117 :QKAHFKAILSAA 1p0kA 166 :ALKRIEQICSRV T0376 130 :EIPAVIYN 1p0kA 178 :SVPVIVKE T0376 141 :YGFATRADLFFALRAEHKNLVGFK 1p0kA 186 :VGFGMSKASAGKLYEAGAAAVDIG T0376 169 :PAD 1p0kA 227 :QIS T0376 172 :MRYAAENITSRDDEVTLMIG 1p0kA 239 :AASLAEIRSEFPASTMIASG T0376 194 :TAVVHGFVNCGATGAITG 1p0kA 263 :ALDVAKAIALGASCTGMA T0376 221 :IHLCKLSQA 1p0kA 281 :GHFLKALTD T0376 242 :LELEQALAVLSSF 1p0kA 290 :SGEEGLLEEIQLI T0376 261 :VLYFKYMMVLKGDK 1p0kA 303 :LEELKLIMTVLGAR T0376 275 :EYTLHFNET 1p0kA 319 :ADLQKAPLV T0376 286 :LTDSQRGYVEA 1p0kA 328 :IKGETHHWLTE Number of specific fragments extracted= 20 number of extra gaps= 0 total=1509 Number of alignments=98 # 1p0kA read from 1p0kA/merged-good-all-a2m # found chain 1p0kA in template set Warning: unaligning (T0376)G111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)F163 Warning: unaligning (T0376)I114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0kA)F163 Warning: unaligning (T0376)G167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0kA)R226 T0376 9 :VIPALMTP 1p0kA 58 :IFINAMTG T0376 20 :D 1p0kA 66 :G T0376 25 :FDALVRKGKELIADGMSA 1p0kA 72 :YEINKSLARAASQAGIPL T0376 45 :YCGSMG 1p0kA 90 :AVGSQM T0376 52 :WPLLTDEQRME 1p0kA 96 :SALKDPSERLS T0376 64 :VERLVK 1p0kA 107 :YEIVRK T0376 70 :AGIPVIVGTGAVNTAS 1p0kA 115 :PNGLIFANLGSEATAA T0376 89 :HAVHAQKV 1p0kA 131 :QAKEAVEM T0376 97 :GAKGLMVIPRVLSR 1p0kA 140 :GANALQIHLNVIQE T0376 115 :AAQKAHFKAILSA 1p0kA 164 :SGALKRIEQICSR T0376 129 :PEIPAVIYNS 1p0kA 177 :VSVPVIVKEV T0376 143 :FATRADLFFALRAE 1p0kA 187 :GFGMSKASAGKLYE T0376 159 :NLVGFKEF 1p0kA 202 :GAAAVDIG T0376 170 :ADMRYAAENIT 1p0kA 239 :AASLAEIRSEF T0376 184 :DEVTLMIGVD 1p0kA 250 :PASTMIASGG T0376 194 :TAVVHGFVNCGATGAITG 1p0kA 263 :ALDVAKAIALGASCTGMA T0376 221 :IHLCKLSQAAAKGDADARARALELEQALAVLSS 1p0kA 281 :GHFLKALTDSGEEGLLEEIQLILEELKLIMTVL T0376 261 :VLYFKYMM 1p0kA 318 :IADLQKAP T0376 280 :FNETDALTDS 1p0kA 329 :KGETHHWLTE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1528 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hl2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1hl2A/merged-good-all-a2m # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set Warning: unaligning (T0376)S4 because first residue in template chain is (1hl2A)T3 T0376 5 :IFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1hl2A 4 :NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1hl2A 72 :GKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFS T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNSPYY 1hl2A 115 :FEEHCDHYRAIIDSADGLPMVVYNIPAR T0376 142 :GFATRADLFFAL 1hl2A 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1hl2A 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSR 1hl2A 170 :DLYQMEQIRREH T0376 184 :DEVTLMIGVDTAVVHGF 1hl2A 182 :PDLVLYNGYDEIFASGL T0376 202 :NCGATGAITGIGNVLPKEVIHLCKLSQA 1hl2A 199 :LAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GD 1hl2A 227 :GD T0376 235 :ADARARALELEQALAVLSSFD 1hl2A 230 :QTAQKLQTECNKVIDLLIKTG T0376 260 :LVLYFKYMMVLKGDKE 1hl2A 251 :VFRGLKTVLHYMDVVS T0376 276 :YTLHFNETD 1hl2A 268 :PLCRKPFGP T0376 286 :LTDSQRGYVEAQFKLFNSW 1hl2A 277 :VDEKYLPELKALAQQLMQE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1541 Number of alignments=100 # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set Warning: unaligning (T0376)S4 because first residue in template chain is (1hl2A)T3 T0376 5 :IFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1hl2A 4 :NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1hl2A 72 :GKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSF T0376 115 :AAQKAHFKAILSAAPEIPAVIYNSPYY 1hl2A 116 :EEHCDHYRAIIDSADGLPMVVYNIPAR T0376 142 :GFATRADLFFAL 1hl2A 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1hl2A 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSRD 1hl2A 170 :DLYQMEQIRREHP T0376 185 :EVTLMIGVDTAV 1hl2A 183 :DLVLYNGYDEIF T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1hl2A 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GDAD 1hl2A 227 :GDIQ T0376 238 :RARAL 1hl2A 231 :TAQKL T0376 244 :LEQALAVLSSFDEGPD 1hl2A 236 :QTECNKVIDLLIKTGV T0376 261 :VLYFKYMMVLKGDK 1hl2A 252 :FRGLKTVLHYMDVV T0376 275 :EYTLHFNET 1hl2A 267 :VPLCRKPFG T0376 285 :ALTDSQRGYVEAQFKLFNSW 1hl2A 276 :PVDEKYLPELKALAQQLMQE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1555 Number of alignments=101 # 1hl2A read from 1hl2A/merged-good-all-a2m # found chain 1hl2A in training set Warning: unaligning (T0376)S4 because first residue in template chain is (1hl2A)T3 T0376 5 :IFSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1hl2A 4 :NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1hl2A 72 :GKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPF T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1hl2A 114 :SFEEHCDHYRAIIDSADGLPMVVYNIPARSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREH T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1hl2A 182 :PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGYVEA 1hl2A 267 :VPLCRKPFGPVDEKYLPELKALAQQLMQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=1560 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h7wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h7wA expands to /projects/compbio/data/pdb/1h7w.pdb.gz 1h7wA:# T0376 read from 1h7wA/merged-good-all-a2m # 1h7wA read from 1h7wA/merged-good-all-a2m # adding 1h7wA to template set # found chain 1h7wA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7wA)T735 T0376 6 :FSG 1h7wA 542 :FIN T0376 9 :VIPALMTPCR 1h7wA 546 :FGLASAAPTT T0376 24 :DFDA 1h7wA 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1h7wA 560 :IRRAFEAGWGFALTK T0376 47 :GSM 1h7wA 593 :GTT T0376 50 :GDW 1h7wA 601 :GPG T0376 56 :TDEQRMEGVERLVK 1h7wA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7wA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7wA 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7wA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7wA 703 :QIPFFAKLTPNV T0376 145 :T 1h7wA 716 :D T0376 147 :ADLFFALRAE 1h7wA 718 :VSIARAAKEG T0376 159 :NLVGFK 1h7wA 728 :GADGVT T0376 167 :GG 1h7wA 736 :NT T0376 171 :DMRYAAENITSR 1h7wA 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1h7wA 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7wA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7wA 819 :VQN T0376 233 :GD 1h7wA 822 :QD T0376 246 :QALAV 1h7wA 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1h7wA 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1h7wA 848 :G T0376 280 :FNETD 1h7wA 865 :VPRIA T0376 289 :SQRGYVEAQFKLFNSW 1h7wA 881 :PYLEQRKKIIAEEKMR Number of specific fragments extracted= 25 number of extra gaps= 1 total=1585 Number of alignments=103 # 1h7wA read from 1h7wA/merged-good-all-a2m # found chain 1h7wA in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wA)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1h7wA)T735 T0376 6 :FSGVIPALMTPC 1h7wA 542 :FINPFGLASAAP T0376 18 :R 1h7wA 555 :T T0376 24 :DFDALVR 1h7wA 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1h7wA 563 :AFEAGWGFALT T0376 47 :GSM 1h7wA 593 :GTT T0376 52 :WPLLTDEQRMEGVERLVK 1h7wA 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7wA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7wA 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7wA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7wA 703 :QIPFFAKLTPNV T0376 142 :G 1h7wA 716 :D T0376 147 :ADLFFALRA 1h7wA 718 :VSIARAAKE T0376 156 :EHKNLV 1h7wA 728 :GADGVT T0376 172 :MRYAAENITSRD 1h7wA 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1h7wA 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7wA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7wA 819 :VQN T0376 233 :GDADA 1h7wA 822 :QDFTV T0376 239 :ARAL 1h7wA 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1h7wA 831 :CTGLKALLYLKSIE T0376 275 :EY 1h7wA 847 :QG T0376 278 :LHFNET 1h7wA 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNS 1h7wA 880 :GPYLEQRKKIIAEEKM Number of specific fragments extracted= 23 number of extra gaps= 1 total=1608 Number of alignments=104 # 1h7wA read from 1h7wA/merged-good-all-a2m # found chain 1h7wA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7wA)T735 T0376 30 :RKGKELIADGMSA 1h7wA 558 :SMIRRAFEAGWGF T0376 44 :VYCGSMG 1h7wA 571 :ALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1h7wA 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7wA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1h7wA 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSA 1h7wA 687 :DPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1h7wA 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1h7wA 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1h7wA 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1h7wA 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1h7wA 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1h7wA 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1h7wA 849 :WDGQSPGTE T0376 278 :LHFNETDALTDSQR 1h7wA 877 :PNFGPYLEQRKKII T0376 298 :FKLFNSWYA 1h7wA 891 :AEEKMRLKE Number of specific fragments extracted= 15 number of extra gaps= 1 total=1623 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h7wB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h7wB expands to /projects/compbio/data/pdb/1h7w.pdb.gz 1h7wB:# T0376 read from 1h7wB/merged-good-all-a2m # 1h7wB read from 1h7wB/merged-good-all-a2m # adding 1h7wB to template set # found chain 1h7wB in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wB)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7wB)T735 T0376 6 :FSGVIPALMTPCRQ 1h7wB 542 :FINPFGLASAAPTT T0376 24 :DFDA 1h7wB 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1h7wB 560 :IRRAFEAGWGFALTK T0376 47 :GSM 1h7wB 593 :GTT T0376 50 :GDWPL 1h7wB 601 :GPGQS T0376 56 :TDEQRMEGVERLVK 1h7wB 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7wB 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7wB 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7wB 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7wB 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1h7wB 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1h7wB 728 :GADGVT T0376 167 :GG 1h7wB 736 :NT T0376 172 :MRYAAENITSR 1h7wB 775 :LRAVTTIARAL T0376 184 :DEVTLMIGVD 1h7wB 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7wB 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7wB 819 :VQN T0376 233 :GD 1h7wB 822 :QD T0376 246 :QALAV 1h7wB 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1h7wB 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1h7wB 848 :G T0376 281 :NETD 1h7wB 866 :PRIA T0376 289 :SQRGYVEAQFKLFNSWYA 1h7wB 881 :PYLEQRKKIIAEEKMRLK Number of specific fragments extracted= 23 number of extra gaps= 1 total=1646 Number of alignments=106 # 1h7wB read from 1h7wB/merged-good-all-a2m # found chain 1h7wB in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wB)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7wB)T735 T0376 6 :FSGVIPALMTPCRQ 1h7wB 542 :FINPFGLASAAPTT T0376 24 :DFDALVR 1h7wB 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1h7wB 563 :AFEAGWGFALT T0376 47 :GSM 1h7wB 593 :GTT T0376 50 :GDWPLL 1h7wB 601 :GPGQSS T0376 56 :TDEQRMEGVERLVK 1h7wB 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGAV 1h7wB 633 :PDNIVIASIMCS T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1h7wB 646 :NKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1h7wB 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1h7wB 703 :QIPFFAKLTPNV T0376 142 :G 1h7wB 716 :D T0376 147 :ADLFFALRAE 1h7wB 718 :VSIARAAKEG T0376 159 :NLVGFK 1h7wB 728 :GADGVT T0376 167 :GG 1h7wB 736 :NT T0376 169 :PAD 1h7wB 745 :KAD T0376 172 :MRYAAENITSRD 1h7wB 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1h7wB 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1h7wB 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1h7wB 819 :VQN T0376 233 :GDADA 1h7wB 822 :QDFTV T0376 239 :ARAL 1h7wB 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1h7wB 831 :CTGLKALLYLKSIE T0376 275 :EY 1h7wB 847 :QG T0376 278 :LHFNET 1h7wB 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSWY 1h7wB 880 :GPYLEQRKKIIAEEKMRL Number of specific fragments extracted= 25 number of extra gaps= 1 total=1671 Number of alignments=107 # 1h7wB read from 1h7wB/merged-good-all-a2m # found chain 1h7wB in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1h7wB)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1h7wB)T735 T0376 8 :GVIPALMTP 1h7wB 547 :GLASAAPTT T0376 24 :DF 1h7wB 556 :SS T0376 30 :RKGKELIADGMSAV 1h7wB 558 :SMIRRAFEAGWGFA T0376 45 :YCGSMG 1h7wB 572 :LTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1h7wB 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1h7wB 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1h7wB 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSA 1h7wB 687 :DPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1h7wB 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1h7wB 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1h7wB 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1h7wB 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1h7wB 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1h7wB 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1h7wB 849 :WDGQSPGTE T0376 278 :LHFNETDALTDSQR 1h7wB 877 :PNFGPYLEQRKKII T0376 295 :E 1h7wB 891 :A T0376 299 :KLFNSWYA 1h7wB 892 :EEKMRLKE Number of specific fragments extracted= 18 number of extra gaps= 1 total=1689 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gthA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gthA expands to /projects/compbio/data/pdb/1gth.pdb.gz 1gthA:# T0376 read from 1gthA/merged-good-all-a2m # 1gthA read from 1gthA/merged-good-all-a2m # adding 1gthA to template set # found chain 1gthA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthA)T735 T0376 6 :FSGVIPALMTPCRQ 1gthA 542 :FINPFGLASAAPTT T0376 24 :DFDA 1gthA 556 :SSSM T0376 32 :GKELIADGMSAVVYCGSM 1gthA 560 :IRRAFEAGWGFALTKTFS T0376 56 :TDEQRMEGVERLVK 1gthA 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthA 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthA 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1gthA 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1gthA 728 :GADGVT T0376 167 :GG 1gthA 736 :NT T0376 171 :DMRYAAENITSR 1gthA 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1gthA 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthA 819 :VQN T0376 233 :GD 1gthA 822 :QD T0376 246 :QALAV 1gthA 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gthA 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gthA 848 :G T0376 279 :HFNETD 1gthA 864 :PVPRIA T0376 289 :SQRGYVEAQF 1gthA 881 :PYLEQRKKII T0376 299 :KLFNSWYADWSKLPG 1gthA 892 :EEKMRLKEQNAAFPP Number of specific fragments extracted= 22 number of extra gaps= 1 total=1711 Number of alignments=109 # 1gthA read from 1gthA/merged-good-all-a2m # found chain 1gthA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthA)T735 T0376 6 :FSGVIPALMTPCRQ 1gthA 542 :FINPFGLASAAPTT T0376 24 :DFDALVR 1gthA 556 :SSSMIRR T0376 35 :LIADGMSAVVYCGSM 1gthA 563 :AFEAGWGFALTKTFS T0376 51 :DWPLLTDEQRMEGVERLVK 1gthA 612 :LISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTG 1gthA 633 :PDNIVIASIM T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthA 644 :SYNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthA 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthA 703 :QIPFFAKLTPNV T0376 142 :G 1gthA 716 :D T0376 147 :ADLFFALRAE 1gthA 718 :VSIARAAKEG T0376 159 :NLVGFK 1gthA 728 :GADGVT T0376 167 :GG 1gthA 736 :NT T0376 172 :MRYAAENITSRD 1gthA 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gthA 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthA 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthA 819 :VQN T0376 233 :GDADA 1gthA 822 :QDFTV T0376 239 :ARAL 1gthA 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gthA 831 :CTGLKALLYLKSIE T0376 275 :EY 1gthA 847 :QG T0376 278 :LHFNET 1gthA 874 :KKLPNF T0376 288 :DSQRGYVEAQF 1gthA 880 :GPYLEQRKKII T0376 299 :KLFNSWYADWSKLPG 1gthA 892 :EEKMRLKEQNAAFPP Number of specific fragments extracted= 23 number of extra gaps= 1 total=1734 Number of alignments=110 # 1gthA read from 1gthA/merged-good-all-a2m # found chain 1gthA in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthA)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthA)T735 T0376 31 :KGKELIADGMS 1gthA 559 :MIRRAFEAGWG T0376 43 :VVYCGSMG 1gthA 570 :FALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gthA 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthA 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gthA 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 112 :SVIAAQKAHFKAILSA 1gthA 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gthA 702 :VQIPFFAKLTPNVT T0376 147 :ADLFFALRAEHKNLVGFK 1gthA 716 :DIVSIARAAKEGGADGVT T0376 167 :GG 1gthA 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gthA 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gthA 799 :AESGLQFLHSGASVLQVCSAVQN T0376 231 :A 1gthA 823 :D T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1gthA 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKE 1gthA 849 :WDGQSPG T0376 276 :YTLHFNETDALTDSQR 1gthA 875 :KLPNFGPYLEQRKKII T0376 298 :FKLFNSWYAD 1gthA 891 :AEEKMRLKEQ Number of specific fragments extracted= 16 number of extra gaps= 1 total=1750 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gthB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gthB expands to /projects/compbio/data/pdb/1gth.pdb.gz 1gthB:# T0376 read from 1gthB/merged-good-all-a2m # 1gthB read from 1gthB/merged-good-all-a2m # adding 1gthB to template set # found chain 1gthB in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthB)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthB)T735 T0376 6 :FSGVIPALMTPCRQ 1gthB 542 :FINPFGLASAAPTT T0376 24 :DFDA 1gthB 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1gthB 560 :IRRAFEAGWGFALTK T0376 48 :SM 1gthB 575 :TF T0376 50 :GDWP 1gthB 601 :GPGQ T0376 56 :TDEQRMEGVERLVK 1gthB 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthB 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthB 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthB 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthB 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1gthB 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1gthB 728 :GADGVT T0376 167 :GG 1gthB 736 :NT T0376 171 :DMRYAAENITSR 1gthB 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1gthB 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthB 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthB 819 :VQN T0376 233 :GD 1gthB 822 :QD T0376 246 :QALAV 1gthB 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gthB 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gthB 848 :G T0376 279 :HFNETD 1gthB 864 :PVPRIA T0376 289 :SQRGYVEAQFKLFNSWYA 1gthB 881 :PYLEQRKKIIAEEKMRLK Number of specific fragments extracted= 23 number of extra gaps= 1 total=1773 Number of alignments=112 # 1gthB read from 1gthB/merged-good-all-a2m # found chain 1gthB in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1gthB)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1gthB)T735 T0376 6 :FSG 1gthB 542 :FIN T0376 9 :VIPALMTPCR 1gthB 546 :FGLASAAPTT T0376 24 :DFDALVR 1gthB 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1gthB 563 :AFEAGWGFALT T0376 47 :GSM 1gthB 574 :KTF T0376 51 :DWPLLTDEQRMEGVERLVK 1gthB 612 :LISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTG 1gthB 633 :PDNIVIASIM T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthB 644 :SYNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthB 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthB 703 :QIPFFAKLTPNV T0376 142 :G 1gthB 716 :D T0376 147 :ADLFFALRA 1gthB 718 :VSIARAAKE T0376 156 :EHKNLV 1gthB 728 :GADGVT T0376 172 :MRYAAENITSRD 1gthB 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gthB 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthB 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthB 819 :VQN T0376 233 :GDADA 1gthB 822 :QDFTV T0376 239 :ARAL 1gthB 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gthB 831 :CTGLKALLYLKSIE T0376 275 :EY 1gthB 847 :QG T0376 278 :LHFNET 1gthB 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSW 1gthB 880 :GPYLEQRKKIIAEEKMR Number of specific fragments extracted= 23 number of extra gaps= 1 total=1796 Number of alignments=113 # 1gthB read from 1gthB/merged-good-all-a2m # found chain 1gthB in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthB)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthB)T735 T0376 31 :KGKELIADGMS 1gthB 559 :MIRRAFEAGWG T0376 43 :VVYCGSMG 1gthB 570 :FALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gthB 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthB 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gthB 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 112 :SVIAAQKAHFKAILSA 1gthB 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gthB 702 :VQIPFFAKLTPNVT T0376 146 :RADLFFALRAE 1gthB 716 :DIVSIARAAKE T0376 159 :NLVGFK 1gthB 728 :GADGVT T0376 167 :GG 1gthB 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gthB 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gthB 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1gthB 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKEYT 1gthB 849 :WDGQSPGTE T0376 278 :LHFNETDALTDSQR 1gthB 877 :PNFGPYLEQRKKII T0376 298 :FKLFNSWYA 1gthB 891 :AEEKMRLKE Number of specific fragments extracted= 16 number of extra gaps= 1 total=1812 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gthC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gthC expands to /projects/compbio/data/pdb/1gth.pdb.gz 1gthC:# T0376 read from 1gthC/merged-good-all-a2m # 1gthC read from 1gthC/merged-good-all-a2m # adding 1gthC to template set # found chain 1gthC in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthC)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthC)T735 T0376 6 :FSGVIPALMTPCRQ 1gthC 542 :FINPFGLASAAPTT T0376 24 :DFDA 1gthC 556 :SSSM T0376 32 :GKELIADGMSAVVYC 1gthC 560 :IRRAFEAGWGFALTK T0376 48 :SM 1gthC 575 :TF T0376 56 :TDEQRMEGVERLVK 1gthC 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthC 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthC 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthC 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthC 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1gthC 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1gthC 728 :GADGVT T0376 167 :GG 1gthC 736 :NT T0376 172 :MRYAAENITSR 1gthC 775 :LRAVTTIARAL T0376 184 :DEVTLMIGVD 1gthC 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthC 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthC 819 :VQN T0376 233 :GD 1gthC 822 :QD T0376 246 :QALAV 1gthC 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gthC 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gthC 848 :G T0376 279 :HFNETDA 1gthC 864 :PVPRIAE T0376 289 :SQRGYVEAQF 1gthC 881 :PYLEQRKKII T0376 299 :KLFNSWYA 1gthC 892 :EEKMRLKE Number of specific fragments extracted= 23 number of extra gaps= 1 total=1835 Number of alignments=115 # 1gthC read from 1gthC/merged-good-all-a2m # found chain 1gthC in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1gthC)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1gthC)T735 T0376 6 :FSGVIPALMTPCR 1gthC 542 :FINPFGLASAAPT T0376 21 :R 1gthC 555 :T T0376 24 :DFDALVR 1gthC 556 :SSSMIRR T0376 35 :LIADGMSAVVY 1gthC 563 :AFEAGWGFALT T0376 47 :GSM 1gthC 574 :KTF T0376 51 :DWPLLTDEQRMEGVERLVK 1gthC 612 :LISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGAV 1gthC 633 :PDNIVIASIMCS T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthC 646 :NKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthC 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthC 703 :QIPFFAKLTPNV T0376 142 :G 1gthC 716 :D T0376 147 :ADLFFALRAE 1gthC 718 :VSIARAAKEG T0376 157 :HKNLV 1gthC 729 :ADGVT T0376 172 :MRYAAENITSRD 1gthC 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gthC 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthC 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthC 819 :VQN T0376 233 :GDADA 1gthC 822 :QDFTV T0376 239 :ARAL 1gthC 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gthC 831 :CTGLKALLYLKSIE T0376 275 :EY 1gthC 847 :QG T0376 278 :LHFNET 1gthC 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNS 1gthC 880 :GPYLEQRKKIIAEEKM Number of specific fragments extracted= 23 number of extra gaps= 1 total=1858 Number of alignments=116 # 1gthC read from 1gthC/merged-good-all-a2m # found chain 1gthC in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthC)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthC)T735 T0376 31 :KGKELIADGMS 1gthC 559 :MIRRAFEAGWG T0376 43 :VVYCGSMG 1gthC 570 :FALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gthC 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthC 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gthC 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 112 :SVIAAQKAHFKAILSA 1gthC 686 :QDPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gthC 702 :VQIPFFAKLTPNVT T0376 146 :RADLFFALRAE 1gthC 716 :DIVSIARAAKE T0376 159 :NLVGFK 1gthC 728 :GADGVT T0376 167 :GG 1gthC 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gthC 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gthC 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1gthC 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKE 1gthC 849 :WDGQSPG T0376 276 :YTLHFNETDALTDSQR 1gthC 875 :KLPNFGPYLEQRKKII T0376 298 :FKLFNSWYAD 1gthC 891 :AEEKMRLKEQ Number of specific fragments extracted= 16 number of extra gaps= 1 total=1874 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gthD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gthD expands to /projects/compbio/data/pdb/1gth.pdb.gz 1gthD:# T0376 read from 1gthD/merged-good-all-a2m # 1gthD read from 1gthD/merged-good-all-a2m # adding 1gthD to template set # found chain 1gthD in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthD)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthD)T735 T0376 6 :FSGVIPALMTPCRQD 1gthD 542 :FINPFGLASAAPTTS T0376 25 :FDA 1gthD 557 :SSM T0376 32 :GKELIADGMSAVVYCGSM 1gthD 560 :IRRAFEAGWGFALTKTFS T0376 50 :GDW 1gthD 601 :GPG T0376 56 :TDEQRMEGVERLVK 1gthD 617 :TAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthD 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthD 645 :YNKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthD 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthD 703 :QIPFFAKLTPNV T0376 145 :TRADLFFALRAE 1gthD 716 :DIVSIARAAKEG T0376 159 :NLVGFK 1gthD 728 :GADGVT T0376 167 :GG 1gthD 736 :NT T0376 171 :DMRYAAENITSR 1gthD 774 :ALRAVTTIARAL T0376 184 :DEVTLMIGVD 1gthD 786 :PGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthD 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthD 819 :VQN T0376 233 :GD 1gthD 822 :QD T0376 246 :QALAV 1gthD 825 :TVIQD T0376 260 :LVLYFKYMMVLKGDKE 1gthD 830 :YCTGLKALLYLKSIEE T0376 276 :Y 1gthD 848 :G T0376 279 :HFNETDA 1gthD 864 :PVPRIAE T0376 289 :SQRGYVEAQFKLFNSWYADWSK 1gthD 881 :PYLEQRKKIIAEEKMRLKEQNA Number of specific fragments extracted= 22 number of extra gaps= 1 total=1896 Number of alignments=118 # 1gthD read from 1gthD/merged-good-all-a2m # found chain 1gthD in template set Warning: unaligning (T0376)G162 because of BadResidue code BAD_PEPTIDE in next template residue (1gthD)T735 Warning: unaligning (T0376)F163 because of BadResidue code BAD_PEPTIDE at template residue (1gthD)T735 T0376 6 :FSGVIPALMTPCRQ 1gthD 542 :FINPFGLASAAPTT T0376 24 :DFDALVR 1gthD 556 :SSSMIRR T0376 35 :LIADGMSAVVYCGSM 1gthD 563 :AFEAGWGFALTKTFS T0376 51 :DWPLLTDEQRMEGVERLVK 1gthD 612 :LISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGAV 1gthD 633 :PDNIVIASIMCS T0376 82 :NTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1gthD 646 :NKNDWMELSRKAEASGADALELNLSCPHGMG T0376 113 :VIAAQKAHFKAILSAA 1gthD 687 :DPELVRNICRWVRQAV T0376 130 :EIPAVIYNSPYY 1gthD 703 :QIPFFAKLTPNV T0376 142 :G 1gthD 716 :D T0376 147 :ADLFFALRAE 1gthD 718 :VSIARAAKEG T0376 157 :HKNLV 1gthD 729 :ADGVT T0376 172 :MRYAAENITSRD 1gthD 775 :LRAVTTIARALP T0376 185 :EVTLMIGVD 1gthD 787 :GFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIG 1gthD 799 :AESGLQFLHSGASVLQVCSA T0376 227 :SQA 1gthD 819 :VQN T0376 233 :GDADA 1gthD 822 :QDFTV T0376 239 :ARAL 1gthD 827 :IQDY T0376 261 :VLYFKYMMVLKGDK 1gthD 831 :CTGLKALLYLKSIE T0376 275 :EY 1gthD 847 :QG T0376 278 :LHFNET 1gthD 874 :KKLPNF T0376 288 :DSQRGYVEAQFKLFNSWY 1gthD 880 :GPYLEQRKKIIAEEKMRL Number of specific fragments extracted= 21 number of extra gaps= 1 total=1917 Number of alignments=119 # 1gthD read from 1gthD/merged-good-all-a2m # found chain 1gthD in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1gthD)T735 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1gthD)T735 T0376 31 :KGKELIADGMSA 1gthD 559 :MIRRAFEAGWGF T0376 44 :VYCGSMG 1gthD 571 :ALTKTFS T0376 52 :WPLLTDEQRMEGVERLVK 1gthD 613 :ISEKTAAYWCQSVTELKA T0376 70 :AGIPVIVGTGA 1gthD 633 :PDNIVIASIMC T0376 81 :VNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1gthD 645 :YNKNDWMELSRKAEASGADALELNLSCPHGM T0376 113 :VIAAQKAHFKAILSA 1gthD 687 :DPELVRNICRWVRQA T0376 129 :PEIPAVIYNSPYYG 1gthD 702 :VQIPFFAKLTPNVT T0376 146 :RADLFFALRAE 1gthD 716 :DIVSIARAAKE T0376 159 :NLVGFK 1gthD 728 :GADGVT T0376 167 :GG 1gthD 736 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1gthD 772 :PIALRAVTTIARALPGFPILATGG T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1gthD 799 :AESGLQFLHSGASVLQVCSAVQN T0376 248 :LAVLSSFDEGPDLVLYFKYMM 1gthD 824 :FTVIQDYCTGLKALLYLKSIE T0376 269 :VLKGDKE 1gthD 849 :WDGQSPG T0376 276 :YTLHFNETDALTDSQR 1gthD 875 :KLPNFGPYLEQRKKII T0376 298 :FKLFNSWYAD 1gthD 891 :AEEKMRLKEQ Number of specific fragments extracted= 16 number of extra gaps= 1 total=1933 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w37A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376/1w37A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0376/1w37A/merged-good-all-a2m.gz for input Trying 1w37A/merged-good-all-a2m Error: Couldn't open file 1w37A/merged-good-all-a2m or 1w37A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cw6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cw6A expands to /projects/compbio/data/pdb/2cw6.pdb.gz 2cw6A:# T0376 read from 2cw6A/merged-good-all-a2m # 2cw6A read from 2cw6A/merged-good-all-a2m # adding 2cw6A to template set # found chain 2cw6A in template set T0376 4 :SIFS 2cw6A 31 :KRVK T0376 11 :PALMTPC 2cw6A 35 :IVEVGPR T0376 18 :RQDRTPDFDALVRKGKELIADGMSAVVYCGSM 2cw6A 46 :NEKNIVSTPVKIKLIDMLSEAGLSVIETTSFV T0376 64 :VERLVK 2cw6A 88 :HTEVLK T0376 70 :AGIPVIVGT 2cw6A 99 :PGINYPVLT T0376 81 :VNTA 2cw6A 108 :PNLK T0376 89 :HAVHAQKVGAKGLMVIPRVL 2cw6A 112 :GFEAAVAAGAKEVVIFGAAS T0376 109 :SRGS 2cw6A 139 :INCS T0376 114 :IAAQKAHFKAILSAA 2cw6A 143 :IEESFQRFDAILKAA T0376 129 :PEIPAVIYNS 2cw6A 160 :ANISVRGYVS T0376 139 :PY 2cw6A 175 :PY T0376 142 :GFATRADLFFALRAEH 2cw6A 177 :EGKISPAKVAEVTKKF T0376 159 :NLVGFKEFGGPADMRYAAENITSR 2cw6A 198 :YEISLGDTIGVGTPGIMKDMLSAV T0376 183 :D 2cw6A 226 :P T0376 184 :DEVTLMIGVD 2cw6A 228 :AALAVHCHDT T0376 194 :TAVVHGFVNCGATGAITGIGNVL 2cw6A 242 :LANTLMALQMGVSVVDSSVAGLG T0376 220 :VIHLCKLSQAA 2cw6A 278 :TEDLVYMLEGL T0376 233 :G 2cw6A 289 :G T0376 234 :D 2cw6A 295 :N T0376 242 :LELEQALAVLSSFDE 2cw6A 297 :QKLLEAGNFICQALN Number of specific fragments extracted= 20 number of extra gaps= 0 total=1953 Number of alignments=121 # 2cw6A read from 2cw6A/merged-good-all-a2m # found chain 2cw6A in template set T0376 19 :QDRTPDFDALVRKGKELIADGMSAVVYCGSM 2cw6A 47 :EKNIVSTPVKIKLIDMLSEAGLSVIETTSFV T0376 64 :VERLVK 2cw6A 88 :HTEVLK T0376 70 :AGI 2cw6A 99 :PGI T0376 73 :PVI 2cw6A 104 :PVL T0376 78 :TGA 2cw6A 107 :TPN T0376 89 :HAVHAQKVGAKGLMVIPRVL 2cw6A 112 :GFEAAVAAGAKEVVIFGAAS T0376 109 :SRGSVIAAQKAHFKAILSAA 2cw6A 138 :NINCSIEESFQRFDAILKAA T0376 129 :PEIPAVIYNS 2cw6A 160 :ANISVRGYVS T0376 141 :Y 2cw6A 175 :P T0376 142 :GFATRADLFFALRAE 2cw6A 177 :EGKISPAKVAEVTKK T0376 157 :HK 2cw6A 197 :CY T0376 160 :LVGFKEFGGPADMRYAAENITSR 2cw6A 199 :EISLGDTIGVGTPGIMKDMLSAV T0376 183 :D 2cw6A 226 :P T0376 184 :DEVTLMIGVD 2cw6A 228 :AALAVHCHDT T0376 194 :TAVVHGFVNCGATGAITGIGNVL 2cw6A 242 :LANTLMALQMGVSVVDSSVAGLG T0376 219 :EVIHLCKLSQAA 2cw6A 277 :ATEDLVYMLEGL T0376 233 :G 2cw6A 289 :G T0376 234 :DADARARAL 2cw6A 291 :HTGVNLQKL T0376 244 :LEQALAVLSSFDEGPD 2cw6A 300 :LEAGNFICQALNRKTS Number of specific fragments extracted= 19 number of extra gaps= 0 total=1972 Number of alignments=122 # 2cw6A read from 2cw6A/merged-good-all-a2m # found chain 2cw6A in template set T0376 2 :TASIFSGVIPALM 2cw6A 29 :LPKRVKIVEVGPR T0376 20 :DRTPDFDALVRKGKELIADGMSAVVYCGSMG 2cw6A 48 :KNIVSTPVKIKLIDMLSEAGLSVIETTSFVS T0376 60 :RMEGVERLV 2cw6A 88 :HTEVLKGIQ T0376 70 :AGI 2cw6A 99 :PGI T0376 73 :PVI 2cw6A 104 :PVL T0376 78 :TGA 2cw6A 107 :TPN T0376 83 :T 2cw6A 110 :L T0376 89 :HAVHAQKVGAKGLMVIPRVL 2cw6A 112 :GFEAAVAAGAKEVVIFGAAS T0376 110 :RG 2cw6A 140 :NC T0376 113 :VIAAQKAHFKAILSAA 2cw6A 142 :SIEESFQRFDAILKAA T0376 129 :PEIPAVIYNSPYYG 2cw6A 160 :ANISVRGYVSCALG T0376 143 :FATRADLFFALRAE 2cw6A 177 :EGKISPAKVAEVTK T0376 157 :H 2cw6A 197 :C T0376 159 :NLVGFKEFGG 2cw6A 198 :YEISLGDTIG T0376 169 :PADMRYAAENITS 2cw6A 210 :TPGIMKDMLSAVM T0376 182 :RDDEVTLMIGVD 2cw6A 225 :VPLAALAVHCHD T0376 194 :TAVVHGFVNCGATGAITGIGNVL 2cw6A 242 :LANTLMALQMGVSVVDSSVAGLG T0376 220 :VIHLCKLSQA 2cw6A 278 :TEDLVYMLEG T0376 231 :AKGDADARARALELE 2cw6A 295 :NLQKLLEAGNFICQA Number of specific fragments extracted= 19 number of extra gaps= 0 total=1991 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376/1s5tA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0376/1s5tA/merged-good-all-a2m.gz for input Trying 1s5tA/merged-good-all-a2m Error: Couldn't open file 1s5tA/merged-good-all-a2m or 1s5tA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0376/1s5vA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0376/1s5vA/merged-good-all-a2m.gz for input Trying 1s5vA/merged-good-all-a2m Error: Couldn't open file 1s5vA/merged-good-all-a2m or 1s5vA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o0yA expands to /projects/compbio/data/pdb/1o0y.pdb.gz 1o0yA:# T0376 read from 1o0yA/merged-good-all-a2m # 1o0yA read from 1o0yA/merged-good-all-a2m # adding 1o0yA to template set # found chain 1o0yA in template set Warning: unaligning (T0376)G162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0376)F163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0376)E165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)S181 Warning: unaligning (T0376)F166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0376)G168 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 Warning: unaligning (T0376)P169 because of BadResidue code BAD_PEPTIDE at template residue (1o0yA)F184 T0376 12 :ALMTPCRQD 1o0yA 35 :IEHTNLKPF T0376 23 :PDFDALVRKGKELIADGMSAVVYCGS 1o0yA 44 :ATPDDIKKLCLEARENRFHGVCVNPC T0376 63 :GVERLVK 1o0yA 70 :YVKLARE T0376 70 :AGIPVIVGTG 1o0yA 81 :TDVKVVTVVG T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPRV 1o0yA 95 :ANETRTKAHEAIFAVESGADEIDMVINV T0376 108 :LSRGS 1o0yA 125 :LKAKE T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNSPY 1o0yA 130 :WEYVYEDIRSVVESVKGKVVKVIIETC T0376 144 :ATRADLFFALR 1o0yA 157 :YLDTEEKIAAC T0376 155 :AEHKNLV 1o0yA 170 :SKLAGAH T0376 164 :K 1o0yA 179 :K T0376 167 :G 1o0yA 182 :T T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1o0yA 189 :ATAEDVHLMKWIVGDEMGVKASGG T0376 196 :VVHGFVNCGATGAITGI 1o0yA 218 :DAVKMIMYGADRIGTSS T0376 220 :VIHLCKLSQA 1o0yA 235 :GVKIVQGGEE Number of specific fragments extracted= 14 number of extra gaps= 3 total=2005 Number of alignments=124 # 1o0yA read from 1o0yA/merged-good-all-a2m # found chain 1o0yA in template set Warning: unaligning (T0376)G162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0376)F163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0376)E165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)S181 Warning: unaligning (T0376)F166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0376)G168 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 Warning: unaligning (T0376)P169 because of BadResidue code BAD_PEPTIDE at template residue (1o0yA)F184 T0376 12 :ALMTPCRQDR 1o0yA 35 :IEHTNLKPFA T0376 24 :DFDALVRKGKELIADGMSAVVYCG 1o0yA 45 :TPDDIKKLCLEARENRFHGVCVNP T0376 64 :VERLVK 1o0yA 71 :VKLARE T0376 70 :AGIPVIVGTG 1o0yA 81 :TDVKVVTVVG T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPRV 1o0yA 95 :ANETRTKAHEAIFAVESGADEIDMVINV T0376 108 :LSRGSVIAAQKAHFKAILSAAPEIPAVIYNSPY 1o0yA 124 :MLKAKEWEYVYEDIRSVVESVKGKVVKVIIETC T0376 144 :ATRADLFFALR 1o0yA 157 :YLDTEEKIAAC T0376 155 :AEHKNLV 1o0yA 170 :SKLAGAH T0376 164 :K 1o0yA 179 :K T0376 167 :G 1o0yA 182 :T T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1o0yA 189 :ATAEDVHLMKWIVGDEMGVKASGG T0376 195 :AVVHGFVNCGATGAITGI 1o0yA 217 :EDAVKMIMYGADRIGTSS T0376 220 :VIHLCKLSQA 1o0yA 235 :GVKIVQGGEE Number of specific fragments extracted= 13 number of extra gaps= 3 total=2018 Number of alignments=125 # 1o0yA read from 1o0yA/merged-good-all-a2m # found chain 1o0yA in template set Warning: unaligning (T0376)G162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0376)F163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0376)E165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)S181 Warning: unaligning (T0376)F166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0376)G168 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 T0376 13 :LMTPCRQD 1o0yA 36 :EHTNLKPF T0376 24 :DFDALVRKGKELIADGMSAVVY 1o0yA 45 :TPDDIKKLCLEARENRFHGVCV T0376 63 :GVERLVK 1o0yA 70 :YVKLARE T0376 70 :AGIPVIVGTG 1o0yA 81 :TDVKVVTVVG T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPR 1o0yA 95 :ANETRTKAHEAIFAVESGADEIDMVIN T0376 110 :RG 1o0yA 127 :AK T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYG 1o0yA 129 :EWEYVYEDIRSVVESVKGKVVKVIIETCYL T0376 147 :ADLFFALRA 1o0yA 159 :DTEEKIAAC T0376 156 :EHKNLV 1o0yA 171 :KLAGAH T0376 164 :K 1o0yA 179 :K T0376 167 :G 1o0yA 182 :T T0376 169 :PADMRYAAENITS 1o0yA 190 :TAEDVHLMKWIVG T0376 184 :DEVTLMIGVD 1o0yA 203 :DEMGVKASGG T0376 194 :TAVVHGFVNCGATGAITGIG 1o0yA 216 :FEDAVKMIMYGADRIGTSSG T0376 221 :IHLCKLSQA 1o0yA 236 :VKIVQGGEE Number of specific fragments extracted= 15 number of extra gaps= 3 total=2033 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rqbA expands to /projects/compbio/data/pdb/1rqb.pdb.gz 1rqbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0376 read from 1rqbA/merged-good-all-a2m # 1rqbA read from 1rqbA/merged-good-all-a2m # adding 1rqbA to template set # found chain 1rqbA in template set Warning: unaligning (T0376)V103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rqbA)D185 Warning: unaligning (T0376)P105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rqbA)D185 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDW 1rqbA 86 :SRLQMLLRGQNLLGYRHYNDEVVDRFVDKSAENGMDVFRVFDAMNDP T0376 58 :EQRMEGVERLVKAGIPVIVGTGAV 1rqbA 133 :RNMAHAMAAVKKAGKHAQGTICYT T0376 82 :NTASAVAHAVHAQKVGAKGLM 1rqbA 162 :TVEGYVKLAGQLLDMGADSIA T0376 106 :RVL 1rqbA 186 :MAA T0376 110 :RGS 1rqbA 189 :LLK T0376 114 :IAAQKAHFKAILSAAP 1rqbA 192 :PQPAYDIIKAIKDTYG T0376 130 :EIPAVIYNSPYYGF 1rqbA 209 :KTQINLHCHSTTGV T0376 146 :RADLFFALRAE 1rqbA 223 :TEVSLMKAIEA T0376 159 :NLVGFKEFGG 1rqbA 234 :GVDVVDTAIS T0376 171 :DM 1rqbA 244 :SM T0376 175 :AAENITSRDD 1rqbA 254 :TESVAEMLEG T0376 185 :EVT 1rqbA 265 :GYT T0376 190 :IGVDTAVVHGFV 1rqbA 268 :TNLDYDRLHKIR T0376 213 :GNVLPKEVIHLCKLSQA 1rqbA 305 :SQIPGGMLSNMESQLRA T0376 232 :KGD 1rqbA 322 :QGA T0376 235 :ADARARALELEQALAVLSSF 1rqbA 326 :DKMDEVMAEVPRVRKAAGFP T0376 255 :DEGPDLVLYFKYMMVLKGDKEY 1rqbA 349 :TPSSQIVGTQAVFNVMMGEYKR T0376 277 :TLHFNETD 1rqbA 382 :YYGASPAD T0376 286 :LTDSQRGYVEAQF 1rqbA 390 :RDPKVVKLAEEQS Number of specific fragments extracted= 19 number of extra gaps= 0 total=2052 Number of alignments=127 # 1rqbA read from 1rqbA/merged-good-all-a2m # found chain 1rqbA in template set Warning: unaligning (T0376)I135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rqbA)D185 Warning: unaligning (T0376)N137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rqbA)D185 T0376 30 :RKGKELIAD 1rqbA 74 :ERLRTFRKL T0376 39 :GMSAVVYCG 1rqbA 85 :NSRLQMLLR T0376 50 :GDWP 1rqbA 94 :GQNL T0376 54 :LLTDEQRMEGVERLVKAGIPVIVGTGAVNTASAVAHA 1rqbA 102 :HYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHA T0376 91 :VHAQKVGAKGLMVIPRVLSRGSVIAAQKAHFKAILSAAP 1rqbA 140 :AAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDMGA T0376 131 :IPAV 1rqbA 179 :DSIA T0376 141 :YGFATRADLFFAL 1rqbA 186 :MAALLKPQPAYDI T0376 175 :AAENITSRDDEVTLMIGVD 1rqbA 199 :IKAIKDTYGQKTQINLHCH T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1rqbA 224 :EVSLMKAIEAGVDVVDTAISSMS T0376 217 :PKEVIHLCKLSQAAAK 1rqbA 272 :YDRLHKIRDHFKAIRP T0376 236 :DARARAL 1rqbA 299 :DTSIFKS T0376 243 :ELEQALAVLSSFDEGPDL 1rqbA 311 :MLSNMESQLRAQGAEDKM T0376 261 :VLYFKYMMVLKGDKEYT 1rqbA 354 :IVGTQAVFNVMMGEYKR T0376 278 :LHFNE 1rqbA 384 :GASPA T0376 285 :ALTDSQRGYVEAQF 1rqbA 389 :DRDPKVVKLAEEQS Number of specific fragments extracted= 15 number of extra gaps= 0 total=2067 Number of alignments=128 # 1rqbA read from 1rqbA/merged-good-all-a2m # found chain 1rqbA in template set Warning: unaligning (T0376)I135 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rqbA)D185 Warning: unaligning (T0376)N137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rqbA)D185 T0376 30 :RKGKELIA 1rqbA 74 :ERLRTFRK T0376 38 :DGMSAVVYCGSMGDWP 1rqbA 84 :PNSRLQMLLRGQNLLG T0376 54 :LLTDEQRMEGVERLVKAGIPVIVGTGAVNTASAVAHA 1rqbA 102 :HYNDEVVDRFVDKSAENGMDVFRVFDAMNDPRNMAHA T0376 91 :VHAQKVGAKGLMVIPRVLSRGSVIAAQKAHFKAILSA 1rqbA 140 :AAVKKAGKHAQGTICYTISPVHTVEGYVKLAGQLLDM T0376 129 :PEIPAV 1rqbA 177 :GADSIA T0376 142 :GFATRADLFFALR 1rqbA 186 :MAALLKPQPAYDI T0376 173 :RYAAENITS 1rqbA 199 :IKAIKDTYG T0376 184 :DEVTLMIGVD 1rqbA 208 :QKTQINLHCH T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1rqbA 224 :EVSLMKAIEAGVDVVDTAISSMS T0376 219 :EVIHLCKLSQAA 1rqbA 253 :PTESVAEMLEGT T0376 231 :AKGDADARARALELEQALAVLSS 1rqbA 271 :DYDRLHKIRDHFKAIRPKYKKFE T0376 254 :FDEGPDLV 1rqbA 308 :PGGMLSNM T0376 302 :NSWYADWSKLPGA 1rqbA 316 :ESQLRAQGAEDKM Number of specific fragments extracted= 13 number of extra gaps= 0 total=2080 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ad1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ad1A expands to /projects/compbio/data/pdb/1ad1.pdb.gz 1ad1A:# T0376 read from 1ad1A/merged-good-all-a2m # 1ad1A read from 1ad1A/merged-good-all-a2m # adding 1ad1A to template set # found chain 1ad1A in template set T0376 5 :IFSGVIPALMT 1ad1A 3 :KTKIMGILNVT T0376 16 :PCRQDRT 1ad1A 16 :SFSDGGK T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSMGDWPL 1ad1A 24 :NNVESAVTRVKAMMDEGADIIDVGGVSTRPGH T0376 55 :LTDEQRMEGVERLVK 1ad1A 58 :ITVEEELNRVLPVVE T0376 70 :AGIPVIVGTGA 1ad1A 77 :FDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1ad1A 88 :SEVAEACLKLGVDIINDQWAGLYDHR T0376 120 :HFKAILSA 1ad1A 114 :MFQVVAKY T0376 130 :EIPAVIYNSPYYGFATR 1ad1A 122 :DAEIVLMHNGNGNRDEP T0376 147 :ADLFFALR 1ad1A 148 :LAQAHQAK T0376 155 :AEHK 1ad1A 157 :AGIP T0376 159 :NLVGFKEFGGPADMRYAAENITSR 1ad1A 163 :KIWLDPGIGFAKTRNEEAEVMARL T0376 184 :DEVTLMIGVD 1ad1A 192 :TEYPVLLATS T0376 194 :TAVVHGFVNCGATGAIT 1ad1A 224 :AATTAYGIMKGVRAVRV T0376 217 :PKEVI 1ad1A 243 :VELNA T0376 225 :KLSQA 1ad1A 248 :KLAKG T0376 240 :RALELEQ 1ad1A 253 :IDFLKEN Number of specific fragments extracted= 16 number of extra gaps= 0 total=2096 Number of alignments=130 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1ad1A)T2 T0376 5 :IFSGVIPALMTP 1ad1A 3 :KTKIMGILNVTP T0376 17 :CRQDRT 1ad1A 17 :FSDGGK T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSMGD 1ad1A 24 :NNVESAVTRVKAMMDEGADIIDVGGVSTR T0376 52 :WPLLTDEQRME 1ad1A 55 :HEMITVEEELN T0376 63 :GVERLVKAGIPVIVGTGA 1ad1A 70 :VVEAIVGFDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRGS 1ad1A 88 :SEVAEACLKLGVDIINDQWAGLYDHR T0376 120 :HFKAILSA 1ad1A 114 :MFQVVAKY T0376 130 :EIPAVIYNSPYYGFATRA 1ad1A 122 :DAEIVLMHNGNGNRDEPV T0376 148 :DLFFALRAE 1ad1A 142 :EMLTSLLAQ T0376 157 :HK 1ad1A 159 :IP T0376 159 :NLVGFKEFGGPADMRYAAENITSR 1ad1A 163 :KIWLDPGIGFAKTRNEEAEVMARL T0376 184 :DEVTLMIGVD 1ad1A 192 :TEYPVLLATS T0376 194 :TAVVHGFVNCGATGAIT 1ad1A 224 :AATTAYGIMKGVRAVRV T0376 220 :VIHLCKLSQA 1ad1A 243 :VELNAKLAKG T0376 237 :ARARAL 1ad1A 253 :IDFLKE T0376 244 :LE 1ad1A 259 :NE Number of specific fragments extracted= 16 number of extra gaps= 0 total=2112 Number of alignments=131 # 1ad1A read from 1ad1A/merged-good-all-a2m # found chain 1ad1A in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1ad1A)T2 T0376 5 :IFSGVIPALMT 1ad1A 3 :KTKIMGILNVT T0376 17 :CRQDRT 1ad1A 17 :FSDGGK T0376 23 :PDFDALVRKGKELIADGMSAVVYCGSMGD 1ad1A 24 :NNVESAVTRVKAMMDEGADIIDVGGVSTR T0376 52 :WPLLTDEQRME 1ad1A 55 :HEMITVEEELN T0376 63 :GVERLVKAGIPVIVGTGA 1ad1A 70 :VVEAIVGFDVKISVDTFR T0376 87 :VAHAVHAQKVGAKGLMVIPRVLSRG 1ad1A 88 :SEVAEACLKLGVDIINDQWAGLYDH T0376 119 :AHFKAILSA 1ad1A 113 :RMFQVVAKY T0376 130 :EIPAVIYNSPYYGFATRADLFFALRA 1ad1A 122 :DAEIVLMHNGNGNRDEPVVEEMLTSL T0376 157 :HKNLVGFKEFGGP 1ad1A 161 :SNKIWLDPGIGFA T0376 170 :ADMRYAAENITS 1ad1A 180 :AEVMARLDELVA T0376 184 :DEVTLMIGVD 1ad1A 192 :TEYPVLLATS T0376 194 :TAVVHGFVNCGATGAITGIG 1ad1A 224 :AATTAYGIMKGVRAVRVHNV T0376 218 :KEVIHLCK 1ad1A 244 :ELNAKLAK T0376 237 :ARARALELE 1ad1A 252 :GIDFLKENE T0376 250 :VLS 1ad1A 261 :NAR Number of specific fragments extracted= 15 number of extra gaps= 0 total=2127 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vh7A expands to /projects/compbio/data/pdb/1vh7.pdb.gz 1vh7A:Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 688, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 690, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 692, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 694, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 890, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 892, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 894, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 896, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 925, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1031, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1033, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1035, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1037, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1039, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1370, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1372, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1374, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1376, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1835, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1837, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1839, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1841, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1843, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1923, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1925, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1927, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1929, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1931, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1933, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1935, because occupancy 0.350 <= existing 0.650 in 1vh7A # T0376 read from 1vh7A/merged-good-all-a2m # 1vh7A read from 1vh7A/merged-good-all-a2m # adding 1vh7A to template set # found chain 1vh7A in template set T0376 5 :IF 1vh7A 3 :AK T0376 8 :GVIPAL 1vh7A 5 :RIIACL T0376 15 :TPCRQDRT 1vh7A 21 :TNFENLRD T0376 28 :LVRKGKELIADGMSAVVYCGSM 1vh7A 32 :PVELGKFYSEIGIDELVFLDIT T0376 57 :DEQRMEGVERLVK 1vh7A 59 :RKTMLELVEKVAE T0376 70 :AGIPVIVGTGAVNTASA 1vh7A 73 :IDIPFTVGGGIHDFETA T0376 91 :VHAQKVGAKGLMVIPRVLSRGSVIAA 1vh7A 90 :SELILRGADKVSINTAAVENPSLITQ T0376 117 :QKAHFKAILSA 1vh7A 153 :LRDWVVEVEKR T0376 130 :EIPAVIYNSPYY 1vh7A 164 :GAGEILLTSIDR T0376 142 :GFATRADLFFALR 1vh7A 179 :KSGYDTEMIRFVR T0376 158 :K 1vh7A 192 :P T0376 165 :EFGG 1vh7A 193 :LTTL T0376 185 :EVTLMIGVD 1vh7A 197 :PIIASGGAG T0376 194 :TAVVHGFVNCGATGAITG 1vh7A 207 :MEHFLEAFLAGADAALAA T0376 225 :KLSQA 1vh7A 225 :SVFHF T0376 233 :GD 1vh7A 230 :RE T0376 236 :DAR 1vh7A 233 :DVR T0376 246 :QALAVLSS 1vh7A 236 :ELKEYLKK Number of specific fragments extracted= 18 number of extra gaps= 0 total=2145 Number of alignments=133 # 1vh7A read from 1vh7A/merged-good-all-a2m # found chain 1vh7A in template set Warning: unaligning (T0376)S4 because first residue in template chain is (1vh7A)L2 T0376 5 :IFS 1vh7A 3 :AKR T0376 9 :VIPAL 1vh7A 6 :IIACL T0376 14 :M 1vh7A 12 :V T0376 15 :TPCR 1vh7A 21 :TNFE T0376 20 :D 1vh7A 25 :N T0376 21 :RT 1vh7A 27 :RD T0376 28 :LVRKGKELIADGMSAVVYCGSM 1vh7A 32 :PVELGKFYSEIGIDELVFLDIT T0376 57 :DEQRMEGVERLVK 1vh7A 59 :RKTMLELVEKVAE T0376 70 :AGIPVIVGTGAVNTA 1vh7A 73 :IDIPFTVGGGIHDFE T0376 89 :HAVHAQKVGAKGLMVIPRVLSRGSVIAA 1vh7A 88 :TASELILRGADKVSINTAAVENPSLITQ T0376 117 :QKAHFKAILSAAP 1vh7A 153 :LRDWVVEVEKRGA T0376 131 :IPAVIYNSPYY 1vh7A 166 :GEILLTSIDRD T0376 142 :GFATRADLFFALRAEHKNLVGFKEFGG 1vh7A 179 :KSGYDTEMIRFVRPLTTLPIIASGGAG T0376 171 :DMRYA 1vh7A 206 :KMEHF T0376 198 :HGFVNCGATGAITG 1vh7A 211 :LEAFLAGADAALAA T0376 225 :KLSQA 1vh7A 225 :SVFHF T0376 233 :GDAD 1vh7A 230 :REID T0376 239 :ARAL 1vh7A 234 :VREL T0376 244 :LEQALA 1vh7A 238 :KEYLKK Number of specific fragments extracted= 19 number of extra gaps= 0 total=2164 Number of alignments=134 # 1vh7A read from 1vh7A/merged-good-all-a2m # found chain 1vh7A in template set T0376 6 :FSGVIPA 1vh7A 4 :KRIIACL T0376 16 :PCRQD 1vh7A 11 :DVKDG T0376 21 :RT 1vh7A 27 :RD T0376 28 :LVRKGKELIADGMSAVVYCGSM 1vh7A 32 :PVELGKFYSEIGIDELVFLDIT T0376 57 :DEQRMEGVERLVK 1vh7A 59 :RKTMLELVEKVAE T0376 70 :AGIPVIVGTGAVNTAS 1vh7A 73 :IDIPFTVGGGIHDFET T0376 90 :AVHAQKVGAKGLMVI 1vh7A 89 :ASELILRGADKVSIN T0376 113 :VIAA 1vh7A 109 :NPSL T0376 117 :QKAHFKAILSA 1vh7A 153 :LRDWVVEVEKR T0376 129 :P 1vh7A 164 :G T0376 131 :IPAVIYNSPYYG 1vh7A 165 :AGEILLTSIDRD T0376 143 :FATRADLFFALRAE 1vh7A 179 :KSGYDTEMIRFVRP T0376 183 :DDEVTLMIGVD 1vh7A 193 :LTTLPIIASGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1vh7A 207 :MEHFLEAFLAGADAALAASVFH T0376 220 :VIHLCKLSQAA 1vh7A 234 :VRELKEYLKKH Number of specific fragments extracted= 15 number of extra gaps= 0 total=2179 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fdyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fdyA expands to /projects/compbio/data/pdb/1fdy.pdb.gz 1fdyA:# T0376 read from 1fdyA/merged-good-all-a2m # 1fdyA read from 1fdyA/merged-good-all-a2m # adding 1fdyA to template set # found chain 1fdyA in template set Warning: unaligning (T0376)A3 because first residue in template chain is (1fdyA)N4 Warning: unaligning (T0376)W304 because last residue in template chain is (1fdyA)E295 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1fdyA 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1fdyA 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFS T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNSPYY 1fdyA 115 :FEEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1fdyA 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1fdyA 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSR 1fdyA 170 :DLYQMEQIRREH T0376 184 :DEVTLMIGVDTAVVHGF 1fdyA 182 :PDLVLYNGYDEIFASGL T0376 202 :NCGATGAITGIGNVLPKEVIHLCKLSQA 1fdyA 199 :LAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GD 1fdyA 227 :GD T0376 235 :ADARARALELEQALAVLSSFD 1fdyA 230 :QTAQKLQTECNKVIDLLIKTG T0376 260 :LVLYFKYMMVLKGDKE 1fdyA 251 :VFRGLKTVLHYMDVVS T0376 276 :YTLHFNETD 1fdyA 268 :PLCRKPFGP T0376 286 :LTDSQRGYVEAQFKLFNS 1fdyA 277 :VDEKYLPELKALAQQLMQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=2192 Number of alignments=136 # 1fdyA read from 1fdyA/merged-good-all-a2m # found chain 1fdyA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1fdyA)N4 Warning: unaligning (T0376)W304 because last residue in template chain is (1fdyA)E295 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1fdyA 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1fdyA 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSF T0376 115 :AAQKAHFKAILSAAPEIPAVIYNSPYY 1fdyA 116 :EEHCDHYRAIIDSADGLPMVVYNIPAL T0376 142 :GFATRADLFFAL 1fdyA 144 :GVKLTLDQINTL T0376 155 :AEHKNLVGFKEFGG 1fdyA 156 :VTLPGVGALKQTSG T0376 171 :DMRYAAENITSRD 1fdyA 170 :DLYQMEQIRREHP T0376 185 :EVTLMIGVDTAV 1fdyA 183 :DLVLYNGYDEIF T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1fdyA 195 :ASGLLAGADGGIGSTYNIMGWRYQGIVKALKE T0376 233 :GDAD 1fdyA 227 :GDIQ T0376 238 :RARAL 1fdyA 231 :TAQKL T0376 244 :LEQALAVLSSFDEGPD 1fdyA 236 :QTECNKVIDLLIKTGV T0376 261 :VLYFKYMMVLKGDK 1fdyA 252 :FRGLKTVLHYMDVV T0376 275 :EYTLHFNET 1fdyA 267 :VPLCRKPFG T0376 285 :ALTDSQRGYVEAQFKLFNS 1fdyA 276 :PVDEKYLPELKALAQQLMQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=2206 Number of alignments=137 # 1fdyA read from 1fdyA/merged-good-all-a2m # found chain 1fdyA in template set Warning: unaligning (T0376)I5 because first residue in template chain is (1fdyA)N4 T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIADGMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1fdyA 5 :LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1fdyA 72 :GKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPF T0376 113 :VIAAQKAHFKAILSAAPEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1fdyA 114 :SFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREH T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMM 1fdyA 182 :PDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVV T0376 269 :VLKGDKEYTLHFNETDALTDSQRGYVEA 1fdyA 267 :VPLCRKPFGPVDEKYLPELKALAQQLMQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=2211 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f74A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0376 read from 1f74A/merged-good-all-a2m # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f74A)P271 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f74A)P271 T0376 1 :MTA 1f74A 1 :MRD T0376 6 :FSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f74A 4 :LKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f74A 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGS 1f74A 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFS T0376 114 :IAAQKAHFKAILSAA 1f74A 115 :FPEIKHYYDTIIAET T0376 130 :EIPAVIYNSPYY 1f74A 130 :GSNMIVYSIPFL T0376 142 :GFATRADLFFAL 1f74A 143 :GVNMGIEQFGEL T0376 155 :AEHKNLVGFKEFGG 1f74A 155 :YKNPKVLGVKFTAG T0376 171 :DMRYAAENITSR 1f74A 169 :DFYLLERLKKAY T0376 184 :DEVTLMIGVDTAVVHGF 1f74A 181 :PNHLIWAGFDEMMLPAA T0376 202 :NCGATGAITGIGNVLPKEVIHLCKLSQA 1f74A 198 :SLGVDGAIGSTFNVNGVRARQIFELTKA T0376 233 :GD 1f74A 226 :GK T0376 235 :ADARARALELEQALAVLSSFD 1f74A 229 :KEALEIQHVTNDLIEGILANG T0376 260 :LVLYFKYMMVLKGDKEYTLH 1f74A 250 :LYLTIKELLKLEGVDAGYCR T0376 282 :ETDALTDSQRGYVEAQFKLF 1f74A 272 :MTSKATAEQVAKAKDLKAKF Number of specific fragments extracted= 15 number of extra gaps= 1 total=2226 Number of alignments=139 # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set Warning: unaligning (T0376)A3 because first residue in template chain is (1f74A)M1 Warning: unaligning (T0376)F280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f74A)P271 Warning: unaligning (T0376)N281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f74A)P271 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f74A 2 :RDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f74A 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRGSV 1f74A 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSF T0376 115 :AAQKAHFKAILSAA 1f74A 116 :PEIKHYYDTIIAET T0376 130 :EIPAVIYNSPYY 1f74A 130 :GSNMIVYSIPFL T0376 142 :GFATRADLFFAL 1f74A 143 :GVNMGIEQFGEL T0376 155 :AEHKNLVGFKEFGG 1f74A 155 :YKNPKVLGVKFTAG T0376 171 :DMRYAAENITSRD 1f74A 169 :DFYLLERLKKAYP T0376 185 :EVTLMIGVDTAV 1f74A 182 :NHLIWAGFDEMM T0376 198 :HGFVNCGATGAITGIGNVLPKEVIHLCKLSQA 1f74A 194 :LPAASLGVDGAIGSTFNVNGVRARQIFELTKA T0376 233 :GDAD 1f74A 226 :GKLK T0376 238 :RARAL 1f74A 230 :EALEI T0376 244 :LEQALAVLSSFDEGPD 1f74A 235 :QHVTNDLIEGILANGL T0376 261 :VLYFKYMMVLKGDKEYTLH 1f74A 251 :YLTIKELLKLEGVDAGYCR T0376 282 :ETDALTDSQRGYVEAQFKLF 1f74A 272 :MTSKATAEQVAKAKDLKAKF Number of specific fragments extracted= 15 number of extra gaps= 1 total=2241 Number of alignments=140 # 1f74A read from 1f74A/merged-good-all-a2m # found chain 1f74A in training set Warning: unaligning (T0376)K274 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1f74A)P271 Warning: unaligning (T0376)E275 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1f74A)P271 T0376 4 :SIFSGVIPALMTPCRQDRTPDFDALVRKGKELIAD 1f74A 2 :RDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDK T0376 39 :GMSAVVYCGSMGDWPLLTDEQRMEGVERLVK 1f74A 38 :KVDGLYVGGSTGENFMLSTEEKKEIFRIAKD T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1f74A 72 :DQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKF T0376 113 :VIAAQKAHFKAILSA 1f74A 114 :SFPEIKHYYDTIIAE T0376 129 :PEIPAVIYNSPYYGFATRADLFFALRAEHKNLVGFKEFGGPADMRYAAENIT 1f74A 129 :TGSNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAY T0376 185 :EVTLMIGVDTAVVHGFVNCGATGAITGIGNVLPKEVIHLCKLSQAAAKGDADARARALELEQALAVLSSFDEGPDLVLYFKYMMVLKGD 1f74A 181 :PNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCR T0376 276 :YT 1f74A 272 :MT T0376 278 :LHFNETDALTDSQRGY 1f74A 275 :KATAEQVAKAKDLKAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=2249 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ep3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ep3A expands to /projects/compbio/data/pdb/1ep3.pdb.gz 1ep3A:# T0376 read from 1ep3A/merged-good-all-a2m # 1ep3A read from 1ep3A/merged-good-all-a2m # adding 1ep3A to template set # found chain 1ep3A in template set Warning: unaligning (T0376)V103 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0376)I104 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0376 9 :VIPALMT 1ep3A 101 :IIANVAG T0376 17 :C 1ep3A 108 :S T0376 24 :DFDALVRKGKELIA 1ep3A 109 :EEADYVAVCAKIGD T0376 38 :DGMSAVVYCGSM 1ep3A 124 :ANVKAIELNISC T0376 50 :GDWPLLTDEQRMEGVERLVK 1ep3A 142 :GQAFGTDPEVAAALVKACKA T0376 70 :AGIPVIVGTGAV 1ep3A 163 :SKVPLYVKLSPN T0376 87 :VAHAVHAQKVGAKGLM 1ep3A 179 :VPIAKAVEAAGADGLT T0376 105 :P 1ep3A 197 :N T0376 106 :RVLSRG 1ep3A 211 :PILANI T0376 113 :VIAAQKAHFKAILSAA 1ep3A 225 :IKPVALKLIHQVAQDV T0376 130 :EIPAVIYN 1ep3A 241 :DIPIIGMG T0376 166 :FGG 1ep3A 249 :GVA T0376 171 :DMRY 1ep3A 252 :NAQD T0376 197 :VHGFVNCGATGAITGIGNVL 1ep3A 256 :VLEMYMAGASAVAVGTANFA T0376 217 :PKEVIHLCKLSQA 1ep3A 277 :PFVCPKIIDKLPE T0376 240 :RALE 1ep3A 290 :LMDQ T0376 244 :LEQALAVLSS 1ep3A 299 :LESLIQEVKE Number of specific fragments extracted= 17 number of extra gaps= 1 total=2266 Number of alignments=142 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0376)V103 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0376)I104 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0376 9 :VIPALMTP 1ep3A 101 :IIANVAGS T0376 24 :DFDALVRKGKELIA 1ep3A 109 :EEADYVAVCAKIGD T0376 38 :DGMSAVVYCGSM 1ep3A 124 :ANVKAIELNISC T0376 50 :GDWPLLTDEQRMEGVERLVK 1ep3A 142 :GQAFGTDPEVAAALVKACKA T0376 70 :AGIPVIVGTGAV 1ep3A 163 :SKVPLYVKLSPN T0376 88 :AHAVHAQKVGAKGLM 1ep3A 180 :PIAKAVEAAGADGLT T0376 105 :PRVL 1ep3A 197 :NTLM T0376 109 :SRGS 1ep3A 222 :GPAI T0376 114 :IAAQKAHFKAILSAA 1ep3A 226 :KPVALKLIHQVAQDV T0376 130 :EIPAVIYN 1ep3A 241 :DIPIIGMG T0376 166 :FGG 1ep3A 249 :GVA T0376 171 :DM 1ep3A 252 :NA T0376 195 :AVVHGFVNCGATGAITGIGNVL 1ep3A 254 :QDVLEMYMAGASAVAVGTANFA T0376 217 :PKEVIHLCK 1ep3A 277 :PFVCPKIID T0376 238 :RARAL 1ep3A 286 :KLPEL T0376 244 :LEQ 1ep3A 291 :MDQ T0376 247 :ALAVLSSFDEG 1ep3A 299 :LESLIQEVKEG Number of specific fragments extracted= 17 number of extra gaps= 1 total=2283 Number of alignments=143 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0376)E165 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0376)F166 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0376 64 :VERLVK 1ep3A 89 :LPWLNE T0376 70 :AGIPVIVGTGAVNTASAVAHAVHAQKV 1ep3A 97 :PELPIIANVAGSEEADYVAVCAKIGDA T0376 97 :GAKGLMVIPRVLSRG 1ep3A 125 :NVKAIELNISCPNVK T0376 112 :SVIAAQKAHFKAILSA 1ep3A 147 :TDPEVAAALVKACKAV T0376 129 :PEIPAVIYNSPY 1ep3A 163 :SKVPLYVKLSPN T0376 144 :ATRADLFFALRAE 1ep3A 175 :VTDIVPIAKAVEA T0376 159 :NLVGFK 1ep3A 189 :GADGLT T0376 167 :GG 1ep3A 197 :NT T0376 170 :ADMRYAAENITSRDDEVTLMIGVD 1ep3A 227 :PVALKLIHQVAQDVDIPIIGMGGV T0376 194 :TAVVHGFVNCGATGAITGIGNVL 1ep3A 253 :AQDVLEMYMAGASAVAVGTANFA T0376 217 :PKEVIHLCK 1ep3A 277 :PFVCPKIID T0376 234 :DADARARA 1ep3A 286 :KLPELMDQ T0376 242 :LELEQALAV 1ep3A 299 :LESLIQEVK Number of specific fragments extracted= 13 number of extra gaps= 1 total=2296 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zfjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zfjA expands to /projects/compbio/data/pdb/1zfj.pdb.gz 1zfjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0376 read from 1zfjA/merged-good-all-a2m # 1zfjA read from 1zfjA/merged-good-all-a2m # adding 1zfjA to template set # found chain 1zfjA in template set T0376 24 :DFDALVRKGK 1zfjA 172 :DLETAERILH T0376 37 :ADGMSAVVYCGSMGD 1zfjA 182 :EHRIEKLPLVDNSGR T0376 61 :MEGVERLVK 1zfjA 203 :IKDIEKVIE T0376 70 :AGIPVIVGTGAV 1zfjA 221 :GRLLVAAAVGVT T0376 85 :SAVAHAVHAQKVGAKGLMVIPRVLS 1zfjA 234 :DTFERAEALFEAGADAIVIDTAHGH T0376 114 :IAAQKAHFKAILSAAPEIPAVIYNS 1zfjA 259 :SAGVLRKIAEIRAHFPNRTLIAGNI T0376 145 :TRADLFFALRAE 1zfjA 284 :ATAEGARALYDA T0376 159 :NLVGFKEFGG 1zfjA 296 :GVDVVKVGIG T0376 170 :ADMRYAAENITSR 1zfjA 324 :TAIYDAAAVAREY T0376 184 :DEVTLMIG 1zfjA 337 :GKTIIADG T0376 193 :D 1zfjA 345 :G T0376 194 :TAVVHGFVNCGATGAITGIGNV 1zfjA 349 :SGDIVKALAAGGNAVMLGSMFA T0376 218 :KEVI 1zfjA 396 :IAAM T0376 236 :DARARALELEQAL 1zfjA 432 :AASDIVFQMLGGI T0376 265 :KYMMVLKGDKE 1zfjA 445 :RSGMGYVGAGD T0376 277 :TLH 1zfjA 464 :QFV T0376 285 :ALTDSQRGY 1zfjA 467 :EMSGAGLIE Number of specific fragments extracted= 17 number of extra gaps= 0 total=2313 Number of alignments=145 # 1zfjA read from 1zfjA/merged-good-all-a2m # found chain 1zfjA in template set Warning: unaligning (T0376)G233 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zfjA)N416 T0376 23 :PDFDALVRKGK 1zfjA 171 :TDLETAERILH T0376 37 :ADGMSAVVYCGSMGDWPLL 1zfjA 182 :EHRIEKLPLVDNSGRLSGL T0376 61 :MEGVERLVK 1zfjA 203 :IKDIEKVIE T0376 70 :AGIPVIVGTGAV 1zfjA 221 :GRLLVAAAVGVT T0376 86 :AVAHAVHAQKVGAKGLMVIPRV 1zfjA 235 :TFERAEALFEAGADAIVIDTAH T0376 111 :GSV 1zfjA 257 :GHS T0376 115 :AAQKAHFKAILSAAPEIPAVIYNS 1zfjA 260 :AGVLRKIAEIRAHFPNRTLIAGNI T0376 145 :TRADLFFALRAE 1zfjA 284 :ATAEGARALYDA T0376 159 :NLVGFKEFGGP 1zfjA 296 :GVDVVKVGIGP T0376 172 :MRYAAENITSRD 1zfjA 326 :IYDAAAVAREYG T0376 185 :EVTLMIG 1zfjA 338 :KTIIADG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1zfjA 349 :SGDIVKALAAGGNAVMLGSMFA T0376 217 :PKEVI 1zfjA 395 :SIAAM T0376 234 :DA 1zfjA 417 :KL T0376 236 :D 1zfjA 431 :G T0376 238 :RARAL 1zfjA 432 :AASDI T0376 244 :LEQALAVLSSF 1zfjA 437 :VFQMLGGIRSG T0376 255 :DEGPD 1zfjA 451 :VGAGD T0376 261 :VLYFKYM 1zfjA 456 :IQELHEN T0376 276 :YTLH 1zfjA 463 :AQFV T0376 285 :ALTDSQRGY 1zfjA 467 :EMSGAGLIE Number of specific fragments extracted= 21 number of extra gaps= 0 total=2334 Number of alignments=146 # 1zfjA read from 1zfjA/merged-good-all-a2m # found chain 1zfjA in template set T0376 24 :DFDALVRKGK 1zfjA 172 :DLETAERILH T0376 37 :ADGMS 1zfjA 182 :EHRIE T0376 61 :MEGVERLVK 1zfjA 203 :IKDIEKVIE T0376 70 :AGIPVIVGTGAV 1zfjA 221 :GRLLVAAAVGVT T0376 84 :ASAVAHAVHAQKVGAKGLMVIPRVLSR 1zfjA 233 :SDTFERAEALFEAGADAIVIDTAHGHS T0376 115 :AAQKAHFKAILSAAPEIPAVIYNSP 1zfjA 260 :AGVLRKIAEIRAHFPNRTLIAGNIA T0376 147 :ADLFFALRAE 1zfjA 285 :TAEGARALYD T0376 159 :NLVGFKEFGGP 1zfjA 296 :GVDVVKVGIGP T0376 170 :ADMRYAAENITSRD 1zfjA 323 :VTAIYDAAAVAREY T0376 185 :EVTLMIGVD 1zfjA 337 :GKTIIADGG T0376 194 :TAVVHGFVNCGATGAITGIGNV 1zfjA 349 :SGDIVKALAAGGNAVMLGSMFA Number of specific fragments extracted= 11 number of extra gaps= 0 total=2345 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mumA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mumA expands to /projects/compbio/data/pdb/1mum.pdb.gz 1mumA:# T0376 read from 1mumA/merged-good-all-a2m # 1mumA read from 1mumA/merged-good-all-a2m # adding 1mumA to template set # found chain 1mumA in template set T0376 29 :VRKGKELIADGMSAVVYC 1mumA 28 :ANHALLAQRAGYQAIYLS T0376 47 :GSMG 1mumA 52 :GSLG T0376 51 :DWPLLTDEQRMEGVERLVK 1mumA 58 :DLGISTLDDVLTDIRRITD T0376 70 :AGIPVIVGTG 1mumA 78 :CSLPLLVDAD T0376 80 :AVNTASAVAHAVHAQKVGAKGLMVIPRVLSR 1mumA 91 :GSSAFNVARTVKSMIKAGAAGLHIEDQVGAK T0376 113 :VIAAQKAHFKAILSAA 1mumA 133 :SKEEMVDRIRAAVDAK T0376 129 :PEIPAVIYNSPYY 1mumA 151 :PDFVIMARTDALA T0376 142 :GFATRADLFFALRAE 1mumA 166 :GLDAAIERAQAYVEA T0376 159 :NL 1mumA 181 :GA T0376 161 :VGFKEFGG 1mumA 184 :MLFPEAIT T0376 171 :DMRYAAENITSRD 1mumA 192 :ELAMYRQFADAVQ T0376 186 :VTLMIGVDT 1mumA 205 :VPILANITE T0376 195 :AVVHGFVNCGATGAITGIG 1mumA 220 :FTTDELRSAHVAMALYPLS T0376 226 :LSQA 1mumA 239 :AFRA T0376 240 :RALELEQALAVLSSFDEGPDLV 1mumA 243 :MNRAAEHVYNVLRQEGTQKSVI T0376 282 :ETD 1mumA 265 :DTM T0376 286 :LTDSQR 1mumA 268 :QTRNEL Number of specific fragments extracted= 17 number of extra gaps= 0 total=2362 Number of alignments=148 # 1mumA read from 1mumA/merged-good-all-a2m # found chain 1mumA in template set T0376 9 :VIPALMTPCRQ 1mumA 82 :LLVDADIGFGS T0376 24 :DFDALVRKGKELIADGMSAVVYCGSMG 1mumA 93 :SAFNVARTVKSMIKAGAAGLHIEDQVG T0376 51 :DWPLLTDEQRMEGVERLVK 1mumA 128 :NKAIVSKEEMVDRIRAAVD T0376 70 :AGIPVIVGTGAV 1mumA 151 :PDFVIMARTDAL T0376 82 :NTASAVAHAVHAQKVGAKGLMV 1mumA 166 :GLDAAIERAQAYVEAGAEMLFP T0376 110 :RGSVIA 1mumA 189 :AITELA T0376 120 :HFKAILSAA 1mumA 195 :MYRQFADAV T0376 130 :EIPAVIYNSPYY 1mumA 204 :QVPILANITEFG T0376 142 :GFATRAD 1mumA 217 :TPLFTTD T0376 199 :GFVNCGATGAITGIG 1mumA 224 :ELRSAHVAMALYPLS T0376 226 :LSQA 1mumA 239 :AFRA T0376 237 :A 1mumA 243 :M T0376 240 :RAL 1mumA 244 :NRA T0376 244 :LEQALAVLSSFDEGPDL 1mumA 247 :AEHVYNVLRQEGTQKSV T0376 282 :ETDALTDSQRG 1mumA 264 :IDTMQTRNELY Number of specific fragments extracted= 15 number of extra gaps= 0 total=2377 Number of alignments=149 # 1mumA read from 1mumA/merged-good-all-a2m # found chain 1mumA in template set T0376 29 :VRKGKELIADGMSAVVYC 1mumA 28 :ANHALLAQRAGYQAIYLS T0376 47 :GSMG 1mumA 52 :GSLG T0376 51 :DWPLLTDEQRMEGVERLVK 1mumA 58 :DLGISTLDDVLTDIRRITD T0376 70 :AGIPVIVGT 1mumA 78 :CSLPLLVDA T0376 79 :GAVNTASAVAHAVHAQKVGAKGLMVIPRVLSRG 1mumA 90 :FGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKR T0376 112 :SVIAAQKAHFKAILSAA 1mumA 132 :VSKEEMVDRIRAAVDAK T0376 129 :PEIPAVIYNSP 1mumA 151 :PDFVIMARTDA T0376 147 :ADLFFALRAE 1mumA 166 :GLDAAIERAQ T0376 161 :VGFKEFGGPADMRYAAENIT 1mumA 184 :MLFPEAITELAMYRQFADAV T0376 184 :DEVTLMIGVD 1mumA 204 :QVPILANITE T0376 197 :VHGFVNCGATGAITGIG 1mumA 222 :TDELRSAHVAMALYPLS T0376 234 :DADARARALELEQALAVLSS 1mumA 239 :AFRAMNRAAEHVYNVLRQEG T0376 270 :LKGDKEYTLHFNETDAL 1mumA 260 :QKSVIDTMQTRNELYES Number of specific fragments extracted= 13 number of extra gaps= 0 total=2390 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pymA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pymA expands to /projects/compbio/data/pdb/1pym.pdb.gz 1pymA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 419, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 550, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1776, because occupancy 0.500 <= existing 0.500 in 1pymA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0376 read from 1pymA/merged-good-all-a2m # 1pymA read from 1pymA/merged-good-all-a2m # adding 1pymA to template set # found chain 1pymA in template set T0376 5 :IFSGVIPAL 1pymA 19 :DLEFIMEAH T0376 29 :VRKGKELIADGMSAVVYCG 1pymA 29 :GLSARIVQEAGFKGIWGSG T0376 49 :MGDWPLLTDEQRMEGVERLVK 1pymA 56 :VRDSNEASWTQVVEVLEFMSD T0376 70 :AGIPVIVGTGAVN 1pymA 78 :SDVPILLDADTGY T0376 83 :TASAVAHAVHAQKVGAKGLMVIPRVL 1pymA 93 :FNNARRLVRKLEDRGVAGACLEDKLF T0376 111 :GS 1pymA 133 :AD T0376 114 :IAAQKAHFKAILSAA 1pymA 135 :IEEFALKIKACKDSQ T0376 129 :PEIPAVIYNSPYY 1pymA 152 :PDFCIVARVEAFI T0376 142 :GFATR 1pymA 166 :GWGLD T0376 147 :ADLFFALRAE 1pymA 173 :LKRAEAYRNA T0376 159 :NLVGFKEFGGPADMRYAAENITSRDDEVTLMIGVDTAV 1pymA 183 :GADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYY T0376 197 :VHGFVNCGATGAITGI 1pymA 224 :TDHFRDMGVSMVIWAN T0376 225 :KL 1pymA 240 :HN T0376 237 :ARARALELEQALAVLSSFDEGPDLV 1pymA 242 :LRASVSAIQQTTKQIYDDQSLVNVE T0376 282 :ET 1pymA 267 :DK T0376 285 :ALTDSQRGYV 1pymA 269 :IVSVKEIFRL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2406 Number of alignments=151 # 1pymA read from 1pymA/merged-good-all-a2m # found chain 1pymA in template set T0376 29 :VRKGKELIADGMSAVVYCG 1pymA 29 :GLSARIVQEAGFKGIWGSG T0376 51 :DWPLLTDEQRMEGVERLVK 1pymA 58 :DSNEASWTQVVEVLEFMSD T0376 70 :AGIPVIVGTGAVN 1pymA 78 :SDVPILLDADTGY T0376 83 :TASAVAHAVHAQKVGAKGLMVIPRVL 1pymA 93 :FNNARRLVRKLEDRGVAGACLEDKLF T0376 109 :SRGSVIAAQKAHFKAILSAA 1pymA 130 :QPLADIEEFALKIKACKDSQ T0376 129 :PEIPAVIYNSPYY 1pymA 152 :PDFCIVARVEAFI T0376 142 :GFATR 1pymA 166 :GWGLD T0376 147 :ADLFFALRAE 1pymA 173 :LKRAEAYRNA T0376 159 :NLVGFKEFGGPADMRYAAENITSRDDEVTLMIGVDTAV 1pymA 183 :GADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYY T0376 197 :VHGFVNCGATGAITGI 1pymA 224 :TDHFRDMGVSMVIWAN T0376 222 :HLCKLSQA 1pymA 240 :HNLRASVS T0376 238 :RARAL 1pymA 248 :AIQQT T0376 244 :LEQ 1pymA 253 :TKQ T0376 251 :LSSFDEGPDL 1pymA 256 :IYDDQSLVNV T0376 284 :DALTDSQRGYV 1pymA 268 :KIVSVKEIFRL Number of specific fragments extracted= 15 number of extra gaps= 0 total=2421 Number of alignments=152 # 1pymA read from 1pymA/merged-good-all-a2m # found chain 1pymA in template set T0376 29 :VRKGKELIADGMSAVVYCG 1pymA 29 :GLSARIVQEAGFKGIWGSG T0376 51 :DWPLLTDEQRMEGVERLVK 1pymA 58 :DSNEASWTQVVEVLEFMSD T0376 70 :AGIPVIVGTGAVN 1pymA 78 :SDVPILLDADTGY T0376 83 :TASAVAHAVHAQKVGAKGLMVIPRVLSRG 1pymA 93 :FNNARRLVRKLEDRGVAGACLEDKLFPKT T0376 112 :SVIAAQKAHFKAILSAA 1pymA 133 :ADIEEFALKIKACKDSQ T0376 129 :PEIPAVIYNSPYYG 1pymA 152 :PDFCIVARVEAFIA T0376 145 :TRADLFFALRAE 1pymA 166 :GWGLDEALKRAE T0376 157 :HKNLVGFKEFG 1pymA 181 :NAGADAILMHS T0376 168 :GPADMRYAAENITS 1pymA 194 :ADPSDIEAFMKAWN T0376 184 :DEVTLMIGVDTAV 1pymA 208 :NQGPVVIVPTKYY T0376 197 :VHGFVNCGATGAITGIGN 1pymA 224 :TDHFRDMGVSMVIWANHN T0376 235 :ADARARALELEQALAVLSSFDEGPD 1pymA 242 :LRASVSAIQQTTKQIYDDQSLVNVE T0376 276 :YTLHFNETDALT 1pymA 267 :DKIVSVKEIFRL T0376 288 :DSQR 1pymA 285 :VQAE Number of specific fragments extracted= 14 number of extra gaps= 0 total=2435 Number of alignments=153 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 153 Adding 4989 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -539.8654, CN propb: -539.8654 weights: 0.2527 constraints: 1203 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1203 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1203 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 3786 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 3786 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 4989 # command: