# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0375 numbered 1 through 296 Created new target T0375 from T0375.a2m # command:CPU_time= 6.438 sec, elapsed time= 6.465 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkd/T0375-1rkd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkd expands to /projects/compbio/data/pdb/1rkd.pdb.gz 1rkd:Warning: there is no chain 1rkd will retry with 1rkdA # T0375 read from 1rkd/T0375-1rkd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkd read from 1rkd/T0375-1rkd-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkd to template set # found chain 1rkd in template set T0375 2 :SQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVII 1rkd 5 :GSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFV # choosing archetypes in rotamer library T0375 101 :EASGSRTILYYDRSLPDVSATDFEKVD 1rkd 103 :NGEGENVIGIHAGANAALSPALVEAQR T0375 128 :LTQFKWIHIEGRNA 1rkd 132 :IANASALLMQLESP T0375 142 :SEQVKMLQRIDAHNTRQPPEQKIR 1rkd 147 :ESVMAAAKIAHQNKTIVALNPAPA T0375 171 :EKPRE 1rkd 171 :RELPD T0375 179 :QLFGYGDVVFVSKDVAKHL 1rkd 176 :ELLALVDIITPNETEAEKL T0375 198 :GFQ 1rkd 196 :GIR T0375 201 :SAEEALRGLYGRVRKGA 1rkd 201 :NDEDAAKAAQVLHEKGI T0375 218 :VLVCAWAEEGADALGPD 1rkd 219 :TVLITLGSRGVWASVNG T0375 236 :KLLHSDAF 1rkd 236 :EGQRVPGF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 1rkd 244 :RVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSV Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkd/T0375-1rkd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rkd/T0375-1rkd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkd read from 1rkd/T0375-1rkd-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkd in template set T0375 2 :SQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINE 1rkd 5 :GSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNG T0375 103 :SGSRTILYYDRSLPDVSATDFEKVD 1rkd 105 :EGENVIGIHAGANAALSPALVEAQR T0375 128 :LTQFKWIHIEGRNASEQ 1rkd 132 :IANASALLMQLESPLES T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEVE 1rkd 150 :MAAAKIAHQNKTIVALNPAPARELPDE T0375 180 :LFGYGDVVFVSKDVAKHL 1rkd 177 :LLALVDIITPNETEAEKL T0375 198 :GF 1rkd 196 :GI T0375 200 :QSAEEALRGLYGRV 1rkd 203 :EDAAKAAQVLHEKG T0375 216 :GAVLVCAWAEEGADALG 1rkd 217 :IRTVLITLGSRGVWASV T0375 234 :DGKLLHSDAF 1rkd 234 :NGEGQRVPGF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGI 1rkd 244 :RVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPS Number of specific fragments extracted= 10 number of extra gaps= 0 total=21 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkd/T0375-1rkd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rkd/T0375-1rkd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkd read from 1rkd/T0375-1rkd-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkd in template set T0375 2 :SQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINEASGSRTILYYDRSLP 1rkd 5 :GSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAA T0375 118 :VSATDFE 1rkd 120 :LSPALVE T0375 125 :KVDLTQFKWIHI 1rkd 129 :RERIANASALLM T0375 138 :GRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEK 1rkd 141 :QLESPLESVMAAAKIAHQNKTIVALNPAPARELPD T0375 179 :QLFGYGDVVFVSKDVAKHLGFQ 1rkd 176 :ELLALVDIITPNETEAEKLTGI T0375 201 :SAEE 1rkd 200 :ENDE T0375 205 :ALRGLYGRVRKGAVLVCAWAEEGADALGPDG 1rkd 206 :AKAAQVLHEKGIRTVLITLGSRGVWASVNGE T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1rkd 237 :GQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=29 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fv7A/T0375-2fv7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fv7A expands to /projects/compbio/data/pdb/2fv7.pdb.gz 2fv7A:Skipped atom 67, because occupancy 0.35 <= existing 0.650 in 2fv7A Skipped atom 69, because occupancy 0.350 <= existing 0.650 in 2fv7A Skipped atom 71, because occupancy 0.350 <= existing 0.650 in 2fv7A Skipped atom 73, because occupancy 0.350 <= existing 0.650 in 2fv7A Skipped atom 1002, because occupancy 0.350 <= existing 0.650 in 2fv7A Skipped atom 1004, because occupancy 0.350 <= existing 0.650 in 2fv7A # T0375 read from 2fv7A/T0375-2fv7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fv7A read from 2fv7A/T0375-2fv7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fv7A to template set # found chain 2fv7A in template set T0375 2 :SQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVII 2fv7A 16 :AAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIV T0375 101 :EASGSRTILYYDRSLPDVSATDFEKVD 2fv7A 114 :NNEGQNIIVIVAGANLLLNTEDLRAAA T0375 128 :LTQFKWIHIEGRNA 2fv7A 143 :ISRAKVMVCQLEIT T0375 142 :SEQVKMLQRIDAHNTRQPPEQ 2fv7A 158 :ATSLEALTMARRSGVKTLFNP T0375 169 :E 2fv7A 182 :I T0375 171 :EKPRE 2fv7A 183 :ADLDP T0375 179 :QLFGYGDVVFVSKDVAKHL 2fv7A 188 :QFYTLSDVFCCNESEAEIL T0375 198 :GFQ 2fv7A 208 :GLT T0375 201 :SAEEALRGLYGRVRKGA 2fv7A 213 :SAADAGEAALVLLKRGC T0375 218 :VLVCAWAEEGADALGPDG 2fv7A 231 :VVIITLGAEGCVVLSQTE T0375 236 :KLLHSDAF 2fv7A 250 :EPKHIPTE T0375 245 :PPRVVDTLGAGDTFNASVIFSLS 2fv7A 258 :KVKAVDTTGAGDSFVGALAFYLA T0375 268 :QGRSVQEALRFGCQVAGKKCGLQGFDGIV 2fv7A 283 :PNLSLEDMLNRSNFIAAVSVQAAGTQSSY Number of specific fragments extracted= 13 number of extra gaps= 0 total=42 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fv7A/T0375-2fv7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2fv7A/T0375-2fv7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fv7A read from 2fv7A/T0375-2fv7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fv7A in template set T0375 3 :QILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINE 2fv7A 17 :AVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNN T0375 103 :SGSRTILYYDRSLPDVSATDFEKVD 2fv7A 116 :EGQNIIVIVAGANLLLNTEDLRAAA T0375 128 :LTQFKWIHIEGRNASEQ 2fv7A 143 :ISRAKVMVCQLEITPAT T0375 145 :VKMLQRIDAHNTRQPPEQ 2fv7A 161 :LEALTMARRSGVKTLFNP T0375 166 :VSVEVE 2fv7A 179 :APAIAD T0375 177 :LF 2fv7A 185 :LD T0375 179 :QLFGYGDVVFVSKDVAKHL 2fv7A 188 :QFYTLSDVFCCNESEAEIL T0375 198 :GF 2fv7A 208 :GL T0375 200 :QSAEEALRGLYGRV 2fv7A 215 :ADAGEAALVLLKRG T0375 216 :GAVLVCAWAEEGADALGPDG 2fv7A 229 :CQVVIITLGAEGCVVLSQTE T0375 236 :KLLHSDAF 2fv7A 250 :EPKHIPTE T0375 245 :PPRVVDTLGAGDTFNASVIFSLS 2fv7A 258 :KVKAVDTTGAGDSFVGALAFYLA T0375 268 :QGRSVQEALRFGCQVAGKKCGLQGFDG 2fv7A 283 :PNLSLEDMLNRSNFIAAVSVQAAGTQS Number of specific fragments extracted= 13 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fv7A/T0375-2fv7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2fv7A/T0375-2fv7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fv7A read from 2fv7A/T0375-2fv7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fv7A in template set T0375 2 :SQILCVGLVVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINEASGSRTILYYDRSL 2fv7A 16 :AAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANL T0375 117 :DVSATDFEKV 2fv7A 130 :LLNTEDLRAA T0375 127 :DLTQFK 2fv7A 142 :VISRAK T0375 134 :IHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEV 2fv7A 148 :VMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIAD T0375 179 :QLFGYGDVVFVSKDVAKHLGFQ 2fv7A 188 :QFYTLSDVFCCNESEAEILTGL T0375 202 :AEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 2fv7A 215 :ADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAY T0375 269 :GRSVQEALRFGCQVAGKKCGLQGF 2fv7A 284 :NLSLEDMLNRSNFIAAVSVQAAGT Number of specific fragments extracted= 7 number of extra gaps= 0 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v1aA/T0375-1v1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v1aA expands to /projects/compbio/data/pdb/1v1a.pdb.gz 1v1aA:# T0375 read from 1v1aA/T0375-1v1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v1aA read from 1v1aA/T0375-1v1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v1aA to template set # found chain 1v1aA in template set T0375 1 :GSQILCVGLVVLDVISLVDKYPKE 1v1aA 1 :MLEVVTAGEPLVALVPQEPGHLRG T0375 30 :CLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 1v1aA 25 :KRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPG T0375 91 :SVPIATVIINEASGSRTILYYDR 1v1aA 85 :FTGLYLREYLPLGQGRVFYYRKG T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGRNAS 1v1aA 109 :AGSALAPGAFDPDYLEGVRFLHLSGITPA T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEV 1v1aA 145 :FSLWAMEEAKRRGVRVSLDVNYRQTLWS T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1v1aA 174 :EEARGFLERALPGVDLLFLSEEEAELL T0375 198 :G 1v1aA 202 :G T0375 201 :SAEEALRGL 1v1aA 203 :RVEEALRAL T0375 216 :GA 1v1aA 212 :SA T0375 218 :VLVCAWAEEGADALGPD 1v1aA 215 :EVVLKRGAKGAWAFVDG T0375 236 :KLLHSDAF 1v1aA 232 :RRVEGSAF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1v1aA 240 :AVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDH Number of specific fragments extracted= 12 number of extra gaps= 0 total=74 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v1aA/T0375-1v1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1v1aA/T0375-1v1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v1aA read from 1v1aA/T0375-1v1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v1aA in template set T0375 2 :SQILCVGLVVLDVISL 1v1aA 2 :LEVVTAGEPLVALVPQ T0375 23 :KEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 1v1aA 18 :EPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPG T0375 91 :SVPIATVIINEASGSRTILYYDR 1v1aA 85 :FTGLYLREYLPLGQGRVFYYRKG T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGR 1v1aA 109 :AGSALAPGAFDPDYLEGVRFLHLSGI T0375 140 :NASEQ 1v1aA 138 :LSPEA T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEV 1v1aA 147 :LWAMEEAKRRGVRVSLDVNYRQTLWS T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1v1aA 174 :EEARGFLERALPGVDLLFLSEEEAELL T0375 200 :QSAEEALRGL 1v1aA 202 :GRVEEALRAL T0375 215 :KGAVLVCAWAEEGADALG 1v1aA 212 :SAPEVVLKRGAKGAWAFV T0375 234 :DGKLLHSDAF 1v1aA 230 :DGRRVEGSAF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 1v1aA 240 :AVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGD Number of specific fragments extracted= 11 number of extra gaps= 0 total=85 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v1aA/T0375-1v1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1v1aA/T0375-1v1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v1aA read from 1v1aA/T0375-1v1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v1aA in template set T0375 1 :GSQILCVGLVVLDVISLVDKYP 1v1aA 1 :MLEVVTAGEPLVALVPQEPGHL T0375 24 :ED 1v1aA 23 :RG T0375 30 :CLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 1v1aA 25 :KRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPG T0375 91 :SVPIATVIINEASGSRTILYYDR 1v1aA 85 :FTGLYLREYLPLGQGRVFYYRKG T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGRNASE 1v1aA 109 :AGSALAPGAFDPDYLEGVRFLHLSGITPAL T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1v1aA 144 :AFSLWAMEEAKRRGVRVSLDVNYRQTLW T0375 172 :KPREELFQLFGYGDVVFVSKDVAKHLGFQ 1v1aA 175 :EARGFLERALPGVDLLFLSEEEAELLFGR T0375 208 :GLYGRVRKGAVLVCAWAEEGADALGPDG 1v1aA 205 :EEALRALSAPEVVLKRGAKGAWAFVDGR T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 1v1aA 233 :RVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGD Number of specific fragments extracted= 9 number of extra gaps= 0 total=94 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2afbA/T0375-2afbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2afbA expands to /projects/compbio/data/pdb/2afb.pdb.gz 2afbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 2afbA/T0375-2afbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2afbA read from 2afbA/T0375-2afbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2afbA to template set # found chain 2afbA in template set Warning: unaligning (T0375)Q33 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)D28 Warning: unaligning (T0375)R34 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)D28 Warning: unaligning (T0375)I94 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2afbA)Y88 Warning: unaligning (T0375)A95 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2afbA)Y88 Warning: unaligning (T0375)V189 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)N194 Warning: unaligning (T0375)S190 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)N194 Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2afbA)N217 Warning: unaligning (T0375)P246 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)H271 Warning: unaligning (T0375)R247 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)H271 T0375 1 :GSQILCVGLVVLDVI 2afbA 0 :HMKVVTFGEIMLRLS T0375 22 :PKEDSEIR 2afbA 15 :PPDHKRIF T0375 30 :CLS 2afbA 24 :TDS T0375 35 :WQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 2afbA 29 :VTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGN T0375 91 :SVP 2afbA 84 :RIG T0375 96 :TVIINEASGSRTILYYDR 2afbA 89 :FLEIGASQRPSKVVYDRA T0375 114 :SLPDVSATDFEKVD 2afbA 109 :AISEAKREDFDWEK T0375 128 :LTQFKWIHIEGRNAS 2afbA 124 :LDGARWFHFSGITPP T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEV 2afbA 146 :ILEDALKVANEKGVTVSCDLNYRARLWT T0375 171 :EKPREELFQLFGYGDVVF 2afbA 175 :EEAQKVMIPFMEYVDVLI T0375 191 :KDVAKHL 2afbA 195 :EEDIEKV T0375 198 :GFQ 2afbA 203 :GIS T0375 202 :AEEALRGLYGRVRK 2afbA 218 :REAYAKIAEEVTRK T0375 216 :GA 2afbA 233 :NF T0375 218 :VLVCAWAE 2afbA 236 :TVGITLRE T0375 228 :ADALGPD 2afbA 254 :VMVFENG T0375 236 :KLLHSDAF 2afbA 261 :QPHFSNRY T0375 245 :P 2afbA 269 :E T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2afbA 272 :IVDRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHTIPGD Number of specific fragments extracted= 19 number of extra gaps= 4 total=113 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2afbA/T0375-2afbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2afbA/T0375-2afbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2afbA read from 2afbA/T0375-2afbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2afbA in template set Warning: unaligning (T0375)Q33 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)D28 Warning: unaligning (T0375)R34 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)D28 Warning: unaligning (T0375)I94 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2afbA)Y88 Warning: unaligning (T0375)A95 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2afbA)Y88 Warning: unaligning (T0375)V189 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)N194 Warning: unaligning (T0375)S190 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)N194 Warning: unaligning (T0375)P246 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)H271 Warning: unaligning (T0375)R247 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)H271 T0375 1 :GSQILCVGLVVLDVISL 2afbA 0 :HMKVVTFGEIMLRLSPP T0375 19 :DKY 2afbA 17 :DHK T0375 26 :SEIRCLS 2afbA 20 :RIFQTDS T0375 35 :WQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 2afbA 29 :VTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGN T0375 91 :SVP 2afbA 84 :RIG T0375 96 :TVIINEASGSRTILYYDR 2afbA 89 :FLEIGASQRPSKVVYDRA T0375 114 :SLPDVSATDFEKVD 2afbA 109 :AISEAKREDFDWEK T0375 128 :LTQFKWIHIEGRNASEQ 2afbA 124 :LDGARWFHFSGITPPLG T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEV 2afbA 148 :EDALKVANEKGVTVSCDLNYRARLWT T0375 171 :EKPREELFQLFGYGDVVF 2afbA 175 :EEAQKVMIPFMEYVDVLI T0375 191 :KDVAKHL 2afbA 195 :EEDIEKV T0375 198 :GF 2afbA 203 :GI T0375 200 :QSAEEALRGLYGRV 2afbA 219 :EAYAKIAEEVTRKY T0375 215 :KGAVLVCAWAE 2afbA 233 :NFKTVGITLRE T0375 228 :ADALG 2afbA 254 :VMVFE T0375 234 :DGKLLHSDAF 2afbA 259 :NGQPHFSNRY T0375 245 :P 2afbA 269 :E T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2afbA 272 :IVDRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHTIPGD Number of specific fragments extracted= 18 number of extra gaps= 4 total=131 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2afbA/T0375-2afbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2afbA/T0375-2afbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2afbA read from 2afbA/T0375-2afbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2afbA in template set Warning: unaligning (T0375)Q33 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)D28 Warning: unaligning (T0375)R34 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)D28 Warning: unaligning (T0375)I94 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2afbA)Y88 Warning: unaligning (T0375)A95 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2afbA)Y88 Warning: unaligning (T0375)V189 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)N194 Warning: unaligning (T0375)S190 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)N194 Warning: unaligning (T0375)P246 because of BadResidue code BAD_PEPTIDE in next template residue (2afbA)H271 Warning: unaligning (T0375)R247 because of BadResidue code BAD_PEPTIDE at template residue (2afbA)H271 T0375 1 :GSQILCVGLVVLDVISL 2afbA 0 :HMKVVTFGEIMLRLSPP T0375 19 :DKYPKED 2afbA 17 :DHKRIFQ T0375 30 :CLS 2afbA 24 :TDS T0375 35 :WQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 2afbA 29 :VTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGN T0375 91 :SVP 2afbA 84 :RIG T0375 96 :TVIINEASGSRTILYYDR 2afbA 89 :FLEIGASQRPSKVVYDRA T0375 114 :SLPDVSATDFEKV 2afbA 109 :AISEAKREDFDWE T0375 127 :DLTQFKWIHIEGRNASE 2afbA 123 :ILDGARWFHFSGITPPL T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 2afbA 145 :LILEDALKVANEKGVTVSCDLNYRARLW T0375 172 :KPREELFQLFGYGDVVF 2afbA 176 :EAQKVMIPFMEYVDVLI T0375 191 :KDVAKHLGFQ 2afbA 195 :EEDIEKVLGI T0375 201 :SAEEALRGLYGRVRKGAVLVCAWAEE 2afbA 219 :EAYAKIAEEVTRKYNFKTVGITLRES T0375 227 :GADALGPDG 2afbA 253 :SVMVFENGQ T0375 238 :LHSDAFPP 2afbA 262 :PHFSNRYE T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2afbA 272 :IVDRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHTIPGD Number of specific fragments extracted= 15 number of extra gaps= 4 total=146 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dcnA/T0375-2dcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dcnA expands to /projects/compbio/data/pdb/2dcn.pdb.gz 2dcnA:Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1128, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1130, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1132, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1134, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 2dcnA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2dcnA # T0375 read from 2dcnA/T0375-2dcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dcnA read from 2dcnA/T0375-2dcnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dcnA to template set # found chain 2dcnA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2dcnA)A2 Warning: unaligning (T0375)L289 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2dcnA)R290 Warning: unaligning (T0375)Q290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2dcnA)R290 T0375 3 :QILCVGLVVLDVISLVDK 2dcnA 3 :KLITLGEILIEFNALSPG T0375 22 :PKED 2dcnA 21 :PLRH T0375 30 :CLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINEASG 2dcnA 25 :VSYFEKHVAGSEANYCVAFIKQGNECGIIAKVGDDEFGYNAIEWLRGQGVDVSHMKIDPSAPTGIFFIQRHYPVP T0375 105 :SRTILYYDR 2dcnA 102 :SESIYYRKG T0375 114 :SLPDVSATDFEKVDLTQFKWIHIE 2dcnA 112 :AGSKLSPEDVDEEYVKSADLVHSS T0375 140 :NASEQVKMLQRIDAHNTRQPPEQKIRVSVEV 2dcnA 141 :ISSTAKEAVYKAFEIASNRSFDTNIRLKLWS T0375 171 :EKPREELFQLFGY 2dcnA 173 :EEAKREILKLLSK T0375 184 :GDVVFVSKDVAKHL 2dcnA 188 :LKFLITDTDDSKII T0375 198 :GFQSAEEALRGLYG 2dcnA 203 :GESDPDKAAKAFSD T0375 216 :GA 2dcnA 217 :YA T0375 218 :VLVCAWAEEGADALGPD 2dcnA 220 :IIVMKLGPKGAIVYYDG T0375 236 :KLLHSDAF 2dcnA 237 :KKYYSSGY T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 2dcnA 245 :QVPVEDVTGAGDALGGTFLSLYYKGFEMEKALDYAIVASTLNVM T0375 291 :GFDGIV 2dcnA 291 :GDQENL Number of specific fragments extracted= 14 number of extra gaps= 1 total=160 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dcnA/T0375-2dcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2dcnA/T0375-2dcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dcnA read from 2dcnA/T0375-2dcnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dcnA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2dcnA)A2 Warning: unaligning (T0375)L289 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2dcnA)R290 Warning: unaligning (T0375)Q290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2dcnA)R290 T0375 3 :QILCVGLVVLDVISL 2dcnA 3 :KLITLGEILIEFNAL T0375 23 :KEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINEASG 2dcnA 18 :SPGPLRHVSYFEKHVAGSEANYCVAFIKQGNECGIIAKVGDDEFGYNAIEWLRGQGVDVSHMKIDPSAPTGIFFIQRHYPVP T0375 105 :SRTILYYDR 2dcnA 102 :SESIYYRKG T0375 114 :SLPDVSATDFEKVDLTQFKWIHIE 2dcnA 112 :AGSKLSPEDVDEEYVKSADLVHSS T0375 140 :NASEQVKMLQRIDAHNTRQPPEQKIRVSVEV 2dcnA 141 :ISSTAKEAVYKAFEIASNRSFDTNIRLKLWS T0375 171 :EKPREELFQLFGY 2dcnA 173 :EEAKREILKLLSK T0375 184 :GDVVFVSKDVAKHL 2dcnA 188 :LKFLITDTDDSKII T0375 198 :GFQSAEEALRGLYGR 2dcnA 203 :GESDPDKAAKAFSDY T0375 216 :GAVLVCAWAEEGADALG 2dcnA 218 :AEIIVMKLGPKGAIVYY T0375 234 :DGKLLHSDAF 2dcnA 235 :DGKKYYSSGY T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 2dcnA 245 :QVPVEDVTGAGDALGGTFLSLYYKGFEMEKALDYAIVASTLNVM T0375 291 :GFD 2dcnA 291 :GDQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=172 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dcnA/T0375-2dcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2dcnA/T0375-2dcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dcnA read from 2dcnA/T0375-2dcnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dcnA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2dcnA)A2 Warning: unaligning (T0375)L289 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2dcnA)R290 Warning: unaligning (T0375)Q290 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2dcnA)R290 T0375 3 :QILCVGLVVLDVISLVDK 2dcnA 3 :KLITLGEILIEFNALSPG T0375 22 :PKED 2dcnA 21 :PLRH T0375 30 :CLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIIN 2dcnA 25 :VSYFEKHVAGSEANYCVAFIKQGNECGIIAKVGDDEFGYNAIEWLRGQGVDVSHMKIDPSAPTGIFFIQRH T0375 101 :EASGSRTILYYDRSLPDVSATDFEKVDLTQFKWIHIEGRNASE 2dcnA 99 :PLKSESIYYRKGSAGSKLSPEDVDEEYVKSADLVHSSGITLAI T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 2dcnA 143 :STAKEAVYKAFEIASNRSFDTNIRLKLW T0375 172 :KPREELFQLFG 2dcnA 174 :EAKREILKLLS T0375 183 :YGDVVFVSKDVAKHLGFQSAEEALR 2dcnA 187 :HLKFLITDTDDSKIILGESDPDKAA T0375 210 :YGRVRKGAVLVCAWAEEGADALGPDG 2dcnA 212 :KAFSDYAEIIVMKLGPKGAIVYYDGK T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 2dcnA 238 :KYYSSGYQVPVEDVTGAGDALGGTFLSLYYKGFEMEKALDYAIVASTLNVM T0375 291 :GFD 2dcnA 291 :GDQ Number of specific fragments extracted= 10 number of extra gaps= 1 total=182 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bx4A/T0375-1bx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bx4A expands to /projects/compbio/data/pdb/1bx4.pdb.gz 1bx4A:# T0375 read from 1bx4A/T0375-1bx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bx4A read from 1bx4A/T0375-1bx4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bx4A to template set # found chain 1bx4A in template set T0375 4 :ILCVGLVVLDVISLVD 1bx4A 9 :LFGMGNPLLDISAVVD T0375 20 :K 1bx4A 32 :S T0375 22 :PKEDSE 1bx4A 33 :LKPNDQ T0375 32 :SQRWQRGGNASNSCTILSLL 1bx4A 57 :KVEYHAGGSTQNSIKVAQWM T0375 52 :G 1bx4A 82 :K T0375 54 :PCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1bx4A 83 :AATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQ T0375 88 :TTGSVPIATVII 1bx4A 116 :NEQPTGTCAACI T0375 101 :EAS 1bx4A 128 :TGD T0375 105 :SRTILYYDRSLPDVSATD 1bx4A 131 :NRSLIANLAAANCYKKEK T0375 123 :FE 1bx4A 150 :LD T0375 125 :KV 1bx4A 154 :KN T0375 127 :DLTQFKWIHIEGRN 1bx4A 158 :LVEKARVCYIAGFF T0375 141 :ASEQVKMLQRIDAHNTRQPPEQKIRVSV 1bx4A 176 :PESVLKVAHHASENNRIFTLNLSAPFIS T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1bx4A 204 :QFYKESLMKVMPYVDILFGNETEAATF T0375 198 :GFQ 1bx4A 235 :GFE T0375 201 :SAEEA 1bx4A 240 :DIKEI T0375 209 :LYGRVR 1bx4A 245 :AKKTQA T0375 215 :KGAVLVCAWAEEGADALGPD 1bx4A 258 :RQRIVIFTQGRDDTIMATES T0375 236 :KLLHSDAFP 1bx4A 278 :EVTAFAVLD T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1bx4A 289 :QKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCT Number of specific fragments extracted= 20 number of extra gaps= 0 total=202 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bx4A/T0375-1bx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1bx4A/T0375-1bx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bx4A read from 1bx4A/T0375-1bx4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bx4A in template set T0375 4 :ILCVGLVVLDVISLVD 1bx4A 9 :LFGMGNPLLDISAVVD T0375 20 :KYPKEDS 1bx4A 32 :SLKPNDQ T0375 32 :SQRWQRGGNASNSCTILSLL 1bx4A 57 :KVEYHAGGSTQNSIKVAQWM T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1bx4A 81 :HKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQ T0375 88 :TTGSVPIATVIIN 1bx4A 116 :NEQPTGTCAACIT T0375 103 :SGSRTILYYDRSLPDVSATD 1bx4A 129 :GDNRSLIANLAAANCYKKEK T0375 123 :FE 1bx4A 150 :LD T0375 125 :KVDLTQFKWIHIEG 1bx4A 156 :WMLVEKARVCYIAG T0375 139 :RNASEQVKMLQRIDAHNTRQPPEQK 1bx4A 174 :VSPESVLKVAHHASENNRIFTLNLS T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKHL 1bx4A 199 :APFISQFYKESLMKVMPYVDILFGNETEAATF T0375 198 :GF 1bx4A 235 :GF T0375 200 :QSAEEALRGLYGRV 1bx4A 239 :KDIKEIAKKTQALP T0375 214 :RKGAVLVCAWAEEGADALG 1bx4A 257 :KRQRIVIFTQGRDDTIMAT T0375 234 :DGKLLHSDAFP 1bx4A 276 :ESEVTAFAVLD T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1bx4A 289 :QKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCT T0375 294 :GI 1bx4A 339 :PE Number of specific fragments extracted= 16 number of extra gaps= 0 total=218 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bx4A/T0375-1bx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1bx4A/T0375-1bx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bx4A read from 1bx4A/T0375-1bx4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bx4A in template set T0375 4 :ILCVGLVVLDVISLVDK 1bx4A 9 :LFGMGNPLLDISAVVDK T0375 21 :YPKED 1bx4A 40 :LAEDK T0375 31 :LSQRWQRGGNASNSCTILSLL 1bx4A 56 :FKVEYHAGGSTQNSIKVAQWM T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTT 1bx4A 81 :HKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQ T0375 91 :SVPIATVIINEASGSRTILYYDR 1bx4A 119 :PTGTCAACITGDNRSLIANLAAA T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGRNASE 1bx4A 145 :KKEKHLDLEKNWMLVEKARVCYIAGFFLTV T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1bx4A 177 :ESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFARE T0375 201 :SAEEALRGLYGRVRKGA 1bx4A 238 :TKDIKEIAKKTQALPKM T0375 218 :VLVCAWAEEGADALGPDG 1bx4A 261 :IVIFTQGRDDTIMATESE T0375 238 :LHSDAFPPPR 1bx4A 279 :VTAFAVLDQD T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1bx4A 292 :IIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCT Number of specific fragments extracted= 11 number of extra gaps= 0 total=229 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abqA/T0375-2abqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2abqA expands to /projects/compbio/data/pdb/2abq.pdb.gz 2abqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 2abqA/T0375-2abqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abqA read from 2abqA/T0375-2abqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2abqA to template set # found chain 2abqA in template set T0375 4 :ILCVG 2abqA 2 :IYTVT T0375 9 :LVVLDVISLVDK 2abqA 8 :NPSIDYIVQVEN T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAP 2abqA 20 :FQQGVVNRSERDRKQPGGKGINVSRVLKRLGHETKALGFLGG T0375 65 :HVADFVLDDLRRYSVDLRYTVF 2abqA 62 :FTGAYVRNALEKEEIGLSFIEV T0375 89 :TGSVPIATVII 2abqA 84 :EGDTRINVKIK T0375 102 :ASGSR 2abqA 95 :GKQET T0375 110 :YYDRSLPDVSATDFEKVD 2abqA 100 :ELNGTAPLIKKEHVQALL T0375 128 :LTQF 2abqA 120 :LTEL T0375 132 :KWIHIEGRNAS 2abqA 127 :DVLVLAGSVPQ T0375 143 :EQVKMLQRIDAHNTRQPPEQK 2abqA 143 :IYRSMTQIAKERGAFVAVDTS T0375 174 :REELFQLF 2abqA 164 :GEALHEVL T0375 182 :GYGDVVFVSKDVAKHL 2abqA 173 :AKPSFIKPNHHELSEL T0375 198 :GFQ 2abqA 190 :SKP T0375 201 :SAEEALRGLYGRVRKGA 2abqA 195 :SIEDAIPHVQRLIGEGI T0375 218 :VLVCAWAEEGADALGPD 2abqA 213 :SILVSFAGDGALFASAE T0375 236 :KLLHSDAF 2abqA 230 :GMFHVNVP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2abqA 238 :SGEVRNSVGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDGF Number of specific fragments extracted= 17 number of extra gaps= 0 total=246 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abqA/T0375-2abqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2abqA/T0375-2abqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abqA read from 2abqA/T0375-2abqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2abqA in template set T0375 4 :ILCVG 2abqA 2 :IYTVT T0375 9 :LVVLDVISLVDKY 2abqA 8 :NPSIDYIVQVENF T0375 23 :KEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2abqA 21 :QQGVVNRSERDRKQPGGKGINVSRVLKRLGHETKALGFLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVF 2abqA 61 :GFTGAYVRNALEKEEIGLSFIEV T0375 89 :TGSVPIATVIIN 2abqA 84 :EGDTRINVKIKG T0375 103 :SGSRTI 2abqA 96 :KQETEL T0375 112 :DRSLPDVSATDFEKVD 2abqA 102 :NGTAPLIKKEHVQALL T0375 128 :LTQF 2abqA 120 :LTEL T0375 132 :KWIHIEGRNASEQ 2abqA 127 :DVLVLAGSVPQAM T0375 145 :VKMLQRIDAHNTRQPPEQK 2abqA 145 :RSMTQIAKERGAFVAVDTS T0375 174 :REELFQLFGY 2abqA 164 :GEALHEVLAA T0375 184 :GDVVFVSKDVAKHL 2abqA 175 :PSFIKPNHHELSEL T0375 198 :GF 2abqA 190 :SK T0375 200 :QSAEEA 2abqA 194 :ASIEDA T0375 206 :LRGLYGRV 2abqA 203 :VQRLIGEG T0375 216 :GAVLVCAWAEEGADALG 2abqA 211 :IESILVSFAGDGALFAS T0375 234 :DGKLLHSDAF 2abqA 228 :AEGMFHVNVP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2abqA 238 :SGEVRNSVGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDGF Number of specific fragments extracted= 18 number of extra gaps= 0 total=264 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abqA/T0375-2abqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2abqA/T0375-2abqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2abqA read from 2abqA/T0375-2abqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2abqA in template set T0375 4 :ILCVGLVVLDVISLVDK 2abqA 3 :YTVTLNPSIDYIVQVEN T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2abqA 20 :FQQGVVNRSERDRKQPGGKGINVSRVLKRLGHETKALGFLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATV 2abqA 61 :GFTGAYVRNALEKEEIGLSFIEVEGDTRINVKIK T0375 101 :EASGSRTIL 2abqA 95 :GKQETELNG T0375 114 :SLPDVSATDFEKV 2abqA 104 :TAPLIKKEHVQAL T0375 127 :DLTQFK 2abqA 119 :QLTELE T0375 133 :WIHIEGRNASE 2abqA 127 :DVLVLAGSVPQ T0375 144 :QVKMLQRIDAHNTRQPPEQKIR 2abqA 142 :TIYRSMTQIAKERGAFVAVDTS T0375 174 :REELFQLF 2abqA 164 :GEALHEVL T0375 182 :GYGDVVFVSKDVAKHLGFQ 2abqA 173 :AKPSFIKPNHHELSELVSK T0375 201 :S 2abqA 194 :A T0375 202 :AEEALRGLYGRVRKGAVLVCAWAEEGADALGPDG 2abqA 197 :EDAIPHVQRLIGEGIESILVSFAGDGALFASAEG T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 2abqA 231 :MFHVNVPSGEVRNSVGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDGF Number of specific fragments extracted= 13 number of extra gaps= 0 total=277 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f02A/T0375-2f02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f02A expands to /projects/compbio/data/pdb/2f02.pdb.gz 2f02A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 2f02A/T0375-2f02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f02A read from 2f02A/T0375-2f02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f02A to template set # found chain 2f02A in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2f02A)S0 T0375 3 :QILCVG 2f02A 1 :LIVTVT T0375 9 :LVVLDVISLVDK 2f02A 8 :NPSIDISYLLDH T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAP 2f02A 20 :LKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGG T0375 65 :HVADFVLDDLRRYSVDLRYTVF 2f02A 62 :FHGAFIANELKKANIPQAFTSI T0375 89 :TGSVPIATVIIN 2f02A 84 :KEETRDSIAILH T0375 103 :SGSRTILYYDR 2f02A 96 :EGNQTEILEAG T0375 116 :PDVSATDFEKVD 2f02A 107 :PTVSPEEISNFL T0375 128 :LTQFKWIHIEGRNA 2f02A 125 :IKQAEIVTISGSLA T0375 142 :S 2f02A 140 :G T0375 143 :EQVKMLQRIDAHNTRQPPEQKI 2f02A 145 :FYQELVQKAHAQEVKVLLDTSG T0375 175 :EELFQLFGY 2f02A 167 :DSLRQVLQG T0375 184 :GDVVFVSKDVAKHL 2f02A 179 :PYLIKPNLEELEGL T0375 198 :GFQ 2f02A 194 :GQD T0375 201 :SAEEALRGLY 2f02A 201 :PLAAVQTALT T0375 215 :KGA 2f02A 215 :AGI T0375 218 :VLVCAWAEEGADALGPD 2f02A 219 :WIVISLGKDGAIAKHHD T0375 236 :KLLHSDAF 2f02A 236 :QFYRVKIP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQ 2f02A 244 :TIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQER Number of specific fragments extracted= 18 number of extra gaps= 0 total=295 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f02A/T0375-2f02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2f02A/T0375-2f02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f02A read from 2f02A/T0375-2f02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f02A in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2f02A)S0 T0375 3 :QILCVG 2f02A 1 :LIVTVT T0375 9 :LVVLDVISLVDKY 2f02A 8 :NPSIDISYLLDHL T0375 23 :KEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2f02A 21 :KLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVF 2f02A 61 :GFHGAFIANELKKANIPQAFTSI T0375 89 :TGSVPIATVIIN 2f02A 84 :KEETRDSIAILH T0375 103 :SGSRTILYYDR 2f02A 96 :EGNQTEILEAG T0375 116 :PDVSATDFEKVD 2f02A 107 :PTVSPEEISNFL T0375 128 :LTQFKWIHIEGRNASEQ 2f02A 125 :IKQAEIVTISGSLAKGL T0375 145 :VKMLQRIDAHNTRQPPEQK 2f02A 147 :QELVQKAHAQEVKVLLDTS T0375 171 :E 2f02A 166 :G T0375 175 :EELFQLFGY 2f02A 167 :DSLRQVLQG T0375 184 :GDVVFVSKDVAKHL 2f02A 179 :PYLIKPNLEELEGL T0375 198 :GF 2f02A 194 :GQ T0375 200 :QSAEEALRGLYG 2f02A 200 :NPLAAVQTALTK T0375 212 :RVRKGAVLVCAWAEEGADALG 2f02A 213 :MFAGIEWIVISLGKDGAIAKH T0375 234 :DGKLLHSDA 2f02A 234 :HDQFYRVKI T0375 244 :PPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 2f02A 243 :PTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQE Number of specific fragments extracted= 17 number of extra gaps= 0 total=312 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f02A/T0375-2f02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2f02A/T0375-2f02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f02A read from 2f02A/T0375-2f02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f02A in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2f02A)S0 T0375 3 :QILCVG 2f02A 1 :LIVTVT T0375 9 :LVVLDVISLVDK 2f02A 8 :NPSIDISYLLDH T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2f02A 20 :LKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTGS 2f02A 61 :GFHGAFIANELKKANIPQAFTSIKEETR T0375 94 :IATVIINEASGSRTILYYDRSLPDVSATDFEKV 2f02A 89 :DSIAILHEGNQTEILEAGPTVSPEEISNFLENF T0375 127 :DLTQFKWIHIEGRNASE 2f02A 124 :LIKQAEIVTISGSLAKG T0375 144 :QVKMLQRIDAHNTRQPPEQKIR 2f02A 144 :DFYQELVQKAHAQEVKVLLDTS T0375 174 :REELFQLFG 2f02A 166 :GDSLRQVLQ T0375 183 :YGDVVFVSKDVAKHLGFQ 2f02A 178 :KPYLIKPNLEELEGLLGQ T0375 201 :SAEE 2f02A 200 :NPLA T0375 207 :RGLYGRV 2f02A 204 :AVQTALT T0375 214 :RKGAVLVCAWAEEGADALGPDG 2f02A 215 :AGIEWIVISLGKDGAIAKHHDQ T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQ 2f02A 237 :FYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQER Number of specific fragments extracted= 13 number of extra gaps= 0 total=325 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2absA/T0375-2absA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2absA/T0375-2absA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2absA read from 2absA/T0375-2absA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2absA in training set Warning: unaligning (T0375)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (2absA)S198 Warning: unaligning (T0375)K163 because of BadResidue code BAD_PEPTIDE at template residue (2absA)S198 Warning: unaligning (T0375)F199 because of BadResidue code BAD_PEPTIDE in next template residue (2absA)V237 Warning: unaligning (T0375)Q200 because of BadResidue code BAD_PEPTIDE at template residue (2absA)V237 Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2absA)N248 T0375 1 :GSQILCVGLVVLDVISLVD 2absA 12 :PMRVFAIGNPILDLVAEVP T0375 22 :PKEDSEIRCLSQ 2absA 39 :LKRGDATLATPE T0375 34 :RWQRGGNASNSCTILSLL 2absA 64 :TSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 2absA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 2absA 120 :PGQSTGVCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 2absA 133 :EKERTLCTHLGACGSFR T0375 120 :ATDFEK 2absA 151 :PEDWTT T0375 127 :DLTQFKWIHIEGRN 2absA 157 :FASGALIFYATAYT T0375 141 :ASEQVKMLQRIDAH 2absA 175 :PKNALEVAGYAHGI T0375 155 :NTRQPPE 2absA 190 :NAIFTLN T0375 164 :IRVSV 2absA 199 :APFCV T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 2absA 204 :ELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :G 2absA 235 :N T0375 202 :AEEALRGLYGRVR 2absA 249 :KEHAVEVCTGALR T0375 215 :KG 2absA 265 :AG T0375 217 :A 2absA 272 :T T0375 218 :VLVCAWAEEGADAL 2absA 274 :LVVMTRGHNPVIAA T0375 232 :GPDGKLL 2absA 290 :TADGTVV T0375 239 :HSDAFP 2absA 299 :EVGVPV T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 2absA 307 :AEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFSLSF Number of specific fragments extracted= 20 number of extra gaps= 2 total=345 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2absA/T0375-2absA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2absA/T0375-2absA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2absA read from 2absA/T0375-2absA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2absA in training set Warning: unaligning (T0375)Q162 because of BadResidue code BAD_PEPTIDE in next template residue (2absA)S198 Warning: unaligning (T0375)K163 because of BadResidue code BAD_PEPTIDE at template residue (2absA)S198 Warning: unaligning (T0375)F199 because of BadResidue code BAD_PEPTIDE in next template residue (2absA)V237 Warning: unaligning (T0375)I295 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2absA)T359 T0375 1 :GSQILCVGLVVLDVISLVD 2absA 12 :PMRVFAIGNPILDLVAEVP T0375 23 :KED 2absA 40 :KRG T0375 27 :EI 2absA 43 :DA T0375 29 :RCLSQRWQRGGNASNSCTILSLL 2absA 59 :DQFNPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 2absA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 2absA 120 :PGQSTGVCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 2absA 133 :EKERTLCTHLGACGSFR T0375 120 :ATDF 2absA 151 :PEDW T0375 125 :KVDLTQFKWIHIEGR 2absA 155 :TTFASGALIFYATAY T0375 140 :NASEQVKMLQRIDAH 2absA 174 :TPKNALEVAGYAHGI T0375 155 :NTRQPPE 2absA 190 :NAIFTLN T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKHL 2absA 199 :APFCVELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :G 2absA 235 :N T0375 200 :QSAEEALRGLYGR 2absA 250 :EHAVEVCTGALRL T0375 216 :GAVLVCAWAEEGADAL 2absA 272 :TKLVVMTRGHNPVIAA T0375 232 :GPDGKLLHS 2absA 290 :TADGTVVVH T0375 241 :DAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 2absA 303 :PVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFS T0375 294 :G 2absA 357 :S Number of specific fragments extracted= 18 number of extra gaps= 3 total=363 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2absA/T0375-2absA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2absA/T0375-2absA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2absA read from 2absA/T0375-2absA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2absA in training set Warning: unaligning (T0375)I164 because of BadResidue code BAD_PEPTIDE in next template residue (2absA)S198 Warning: unaligning (T0375)R165 because of BadResidue code BAD_PEPTIDE at template residue (2absA)S198 Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2absA)N248 T0375 2 :SQILCVGLVVLDVISLVDK 2absA 13 :MRVFAIGNPILDLVAEVPS T0375 21 :YPKEDSEIRCLSQRWQ 2absA 38 :FLKRGDATLATPEQMR T0375 37 :RGGNASNSCTILSLL 2absA 67 :PGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTV 2absA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMV T0375 87 :QTTGSVPIATVIINEASGSRTILYYDRSLPDVSATDF 2absA 119 :APGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWT T0375 126 :VDLTQFKWIHIEGRNASE 2absA 156 :TFASGALIFYATAYTLTA T0375 144 :QVKMLQRIDAHN 2absA 176 :KNALEVAGYAHG T0375 156 :TRQPPEQK 2absA 189 :PNAIFTLN T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 2absA 199 :APFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKV T0375 202 :AEE 2absA 249 :KEH T0375 205 :ALRGLYGRVRK 2absA 256 :CTGALRLLTAG T0375 216 :GAVLVCAWAEEGADALG 2absA 272 :TKLVVMTRGHNPVIAAE T0375 233 :PDGK 2absA 291 :ADGT T0375 237 :LLHSDAFPPPR 2absA 296 :VVHEVGVPVVA T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 2absA 310 :IVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 15 number of extra gaps= 1 total=378 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vm7A/T0375-1vm7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vm7A expands to /projects/compbio/data/pdb/1vm7.pdb.gz 1vm7A:# T0375 read from 1vm7A/T0375-1vm7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm7A read from 1vm7A/T0375-1vm7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vm7A to template set # found chain 1vm7A in template set Warning: unaligning (T0375)G8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm7A)S10 Warning: unaligning (T0375)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vm7A)S10 T0375 1 :GS 1vm7A 1 :MF T0375 3 :QILCV 1vm7A 4 :VISVV T0375 10 :VVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLL 1vm7A 11 :SNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKI T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSV 1vm7A 54 :EKGCRFVTCIGNDDYSDLLIENYEKLGI T0375 82 :RYTVFQT 1vm7A 82 :TGYIRVS T0375 90 :GSVPIATVII 1vm7A 89 :LPTGRAFIEV T0375 101 :EASGSRTILYYDRSLPDVSATDFEKVDLTQFKWIHIEGRNA 1vm7A 99 :DKTGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIP T0375 142 :SEQVKMLQRI 1vm7A 141 :ETTLECAKRF T0375 155 :NTRQPPEQ 1vm7A 151 :NGIVIFDP T0375 164 :IR 1vm7A 160 :PA T0375 171 :EKPRE 1vm7A 162 :QGINE T0375 179 :QLFGYGDVVFVSKDVAKH 1vm7A 167 :EIFQYLDYLTPNEKEIEA T0375 197 :L 1vm7A 190 :F T0375 198 :GFQSAEEA 1vm7A 192 :EFLTVEKA T0375 209 :LYGRVRKGA 1vm7A 200 :AEKFLELGV T0375 218 :VLVCAWAEEGADALGPD 1vm7A 210 :NVIVKLGDKGVLLVNKN T0375 236 :KLLHSDAF 1vm7A 227 :EKKHFPTF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGIV 1vm7A 235 :KVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSSI Number of specific fragments extracted= 18 number of extra gaps= 1 total=396 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vm7A/T0375-1vm7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vm7A/T0375-1vm7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm7A read from 1vm7A/T0375-1vm7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm7A in template set Warning: unaligning (T0375)G8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm7A)S10 Warning: unaligning (T0375)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vm7A)S10 T0375 2 :SQILCV 1vm7A 3 :LVISVV T0375 10 :VVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLL 1vm7A 11 :SNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKI T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSV 1vm7A 54 :EKGCRFVTCIGNDDYSDLLIENYEKLGI T0375 82 :RYTVFQTT 1vm7A 82 :TGYIRVSL T0375 91 :SVPIATVIINE 1vm7A 90 :PTGRAFIEVDK T0375 103 :SGSRTILYYDRSLPDVSATDFEKVDLTQFKWIHIEGRNASEQ 1vm7A 101 :TGQNRIIIFPGANAELKKELIDWNTLSESDILLLQNEIPFET T0375 145 :VKMLQRI 1vm7A 144 :LECAKRF T0375 155 :NTRQPPEQKIRVSVEVE 1vm7A 151 :NGIVIFDPAPAQGINEE T0375 180 :LFGYGDVVFVSKDVAKH 1vm7A 168 :IFQYLDYLTPNEKEIEA T0375 197 :L 1vm7A 190 :F T0375 198 :GFQSAEEALRGLYGRV 1vm7A 192 :EFLTVEKAAEKFLELG T0375 216 :GAVLVCAWAEEGADALG 1vm7A 208 :VKNVIVKLGDKGVLLVN T0375 234 :DGKLLHSDAF 1vm7A 225 :KNEKKHFPTF T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGI 1vm7A 235 :KVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGAQSS Number of specific fragments extracted= 14 number of extra gaps= 1 total=410 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vm7A/T0375-1vm7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vm7A/T0375-1vm7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm7A read from 1vm7A/T0375-1vm7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm7A in template set Warning: unaligning (T0375)G8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm7A)S10 Warning: unaligning (T0375)L9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vm7A)S10 T0375 2 :SQILCV 1vm7A 3 :LVISVV T0375 10 :VVLDVISLVDKYPKEDSEIRCLSQRWQRGGNASNSCTILSLL 1vm7A 11 :SNIDIVLKVDHFTKPGETQKAIEMNVFPGGKGANQAVTVAKI T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSV 1vm7A 54 :EKGCRFVTCIGNDDYSDLLIENYEKLGI T0375 82 :RYTVFQTT 1vm7A 82 :TGYIRVSL T0375 91 :SVPIATVIINEASGSRTILYYDRSLP 1vm7A 90 :PTGRAFIEVDKTGQNRIIIFPGANAE T0375 118 :VSATDFEKVDLTQFKWIHI 1vm7A 116 :LKKELIDWNTLSESDILLL T0375 138 :GRNASEQVKM 1vm7A 135 :QNEIPFETTL T0375 151 :IDAHNTRQPPEQKIRVSVEVEK 1vm7A 145 :ECAKRFNGIVIFDPAPAQGINE T0375 179 :QLFGYGDVVFVSKDVAKHLGFQ 1vm7A 167 :EIFQYLDYLTPNEKEIEALSKD T0375 201 :SAEEA 1vm7A 194 :LTVEK T0375 207 :RGLYGRVRKGAVLVCAWAEEGADALGPDG 1vm7A 199 :AAEKFLELGVKNVIVKLGDKGVLLVNKNE T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 1vm7A 228 :KKHFPTFKVKAVDTTAAGDVFNGAFAVALSEGKNPEEAVIFGTAAAAISVTRLGA Number of specific fragments extracted= 12 number of extra gaps= 1 total=422 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ajrA/T0375-2ajrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ajrA expands to /projects/compbio/data/pdb/2ajr.pdb.gz 2ajrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 920, because occupancy 0.500 <= existing 0.500 in 2ajrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 924, because occupancy 0.500 <= existing 0.500 in 2ajrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2ajrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2ajrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2ajrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 2ajrA/T0375-2ajrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ajrA read from 2ajrA/T0375-2ajrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ajrA to template set # found chain 2ajrA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2ajrA)H0 Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ajrA)L11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ajrA)L11 T0375 3 :QILCVG 2ajrA 1 :MVLTVT T0375 9 :LV 2ajrA 8 :NP T0375 13 :DVISLVDK 2ajrA 12 :DREIFIED T0375 22 :PKEDSEIRCLS 2ajrA 20 :FQVNRLYRIND T0375 33 :QRWQRGGNASNSCTILSLLGAPCAFMGSMAP 2ajrA 34 :TQMSPGGKGINVSIALSKLGVPSVATGFVGG T0375 65 :HVADFVLDDLRRY 2ajrA 65 :YMGKILVEELRKI T0375 78 :SVDLRYTVF 2ajrA 80 :LITTNFVYV T0375 89 :TGSVPIATVIINEASGSRTILYYDR 2ajrA 89 :EGETRENIEIIDEKNKTITAINFPG T0375 116 :PDVSATDFEKVD 2ajrA 114 :PDVTDMDVNHFL T0375 128 :LTQFKWIHIEGRNAS 2ajrA 132 :LSKVDCVVISGSIPP T0375 143 :EQVKMLQRIDAHNTRQPPEQ 2ajrA 152 :ICNELVRLARERGVFVFVEQ T0375 173 :PREELFQLF 2ajrA 172 :TPRLLERIY T0375 182 :GYGDVVFVS 2ajrA 184 :EFPNVVKPD T0375 197 :LGFQ 2ajrA 201 :LGVD T0375 201 :SAEEALRGLYGRVRK 2ajrA 207 :TFDDYVKLAEKLAEK T0375 217 :A 2ajrA 222 :S T0375 218 :VLVCAWAEEGADALGPD 2ajrA 224 :VSVVSYEVKNDIVATRE T0375 236 :KLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 2ajrA 241 :GVWLIRSKEEIDTSHLLGAGDAYVAGMVYYFIK T0375 269 :GRSVQEALRFGCQVAGKKCGLQG 2ajrA 275 :GANFLEMAKFGFASALAATRRKE Number of specific fragments extracted= 19 number of extra gaps= 1 total=441 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ajrA/T0375-2ajrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2ajrA/T0375-2ajrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ajrA read from 2ajrA/T0375-2ajrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ajrA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2ajrA)H0 Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ajrA)L11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ajrA)L11 T0375 3 :QILCVG 2ajrA 1 :MVLTVT T0375 9 :LV 2ajrA 8 :NP T0375 13 :DVISLVDKY 2ajrA 12 :DREIFIEDF T0375 23 :KEDSEIRCLSQ 2ajrA 21 :QVNRLYRINDL T0375 34 :RWQRGGNASNSCTILSLLGAPCAFMGSMA 2ajrA 35 :QMSPGGKGINVSIALSKLGVPSVATGFVG T0375 64 :GHVADFVLDDLRRY 2ajrA 64 :GYMGKILVEELRKI T0375 79 :VDLRYTVF 2ajrA 81 :ITTNFVYV T0375 89 :TGSVPIATVIINEASGSRTILYYDRS 2ajrA 89 :EGETRENIEIIDEKNKTITAINFPGP T0375 117 :DVSATDFEKVD 2ajrA 115 :DVTDMDVNHFL T0375 128 :LTQFKWIHIEGRNASEQ 2ajrA 132 :LSKVDCVVISGSIPPGV T0375 145 :VKMLQRIDAHNTRQPPEQK 2ajrA 154 :NELVRLARERGVFVFVEQT T0375 174 :REELFQLF 2ajrA 173 :PRLLERIY T0375 182 :GYGDVVFVS 2ajrA 184 :EFPNVVKPD T0375 197 :L 2ajrA 193 :L T0375 198 :GF 2ajrA 195 :GN T0375 200 :QSAEEALRGLYGR 2ajrA 209 :DDYVKLAEKLAEK T0375 216 :GAVLVCAWAEEGADALG 2ajrA 222 :SQVSVVSYEVKNDIVAT T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 2ajrA 239 :REGVWLIRSKEEIDTSHLLGAGDAYVAGMVYYFIK T0375 269 :GRSVQEALRFGCQVAGKKCGLQG 2ajrA 275 :GANFLEMAKFGFASALAATRRKE Number of specific fragments extracted= 19 number of extra gaps= 1 total=460 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ajrA/T0375-2ajrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2ajrA/T0375-2ajrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ajrA read from 2ajrA/T0375-2ajrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ajrA in template set Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ajrA)L11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ajrA)L11 T0375 4 :ILCVG 2ajrA 2 :VLTVT T0375 9 :LV 2ajrA 8 :NP T0375 13 :DVISLVDK 2ajrA 12 :DREIFIED T0375 22 :PKEDSEIRCL 2ajrA 20 :FQVNRLYRIN T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2ajrA 33 :KTQMSPGGKGINVSIALSKLGVPSVATGFVG T0375 64 :GHVADFVLDDLRRY 2ajrA 64 :GYMGKILVEELRKI T0375 78 :SVDLRYTVFQTTGSVPI 2ajrA 80 :LITTNFVYVEGETRENI T0375 97 :VIINEASGSRTILYYDR 2ajrA 97 :EIIDEKNKTITAINFPG T0375 117 :DVSATDFEKV 2ajrA 115 :DVTDMDVNHF T0375 127 :DLTQFKWIHIEGRNASE 2ajrA 131 :TLSKVDCVVISGSIPPG T0375 144 :QVKMLQRIDAHNTRQPPEQKIRV 2ajrA 151 :GICNELVRLARERGVFVFVEQTP T0375 175 :EELFQLF 2ajrA 174 :RLLERIY T0375 182 :GYGDVVFVS 2ajrA 184 :EFPNVVKPD T0375 197 :LGFQ 2ajrA 193 :LRGN T0375 201 :SAEEALRGLYGRVRKGAVLVCAWAEEGADALGPDGKL 2ajrA 207 :TFDDYVKLAEKLAEKSQVSVVSYEVKNDIVATREGVW T0375 239 :HSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 2ajrA 244 :LIRSKEEIDTSHLLGAGDAYVAGMVYYFIK T0375 269 :GRSVQEALRFGCQVAGKKCGL 2ajrA 275 :GANFLEMAKFGFASALAATRR Number of specific fragments extracted= 17 number of extra gaps= 1 total=477 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tyyA/T0375-1tyyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tyyA expands to /projects/compbio/data/pdb/1tyy.pdb.gz 1tyyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 1tyyA/T0375-1tyyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyyA read from 1tyyA/T0375-1tyyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tyyA to template set # found chain 1tyyA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1tyyA)N5 Warning: unaligning (T0375)I98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tyyA)S98 Warning: unaligning (T0375)T107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tyyA)S98 T0375 3 :QILCVGLVVLDVISLVDK 1tyyA 6 :KVWVIGDASVDLVPEKQN T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATV 1tyyA 24 :SYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIV T0375 108 :ILYYDR 1tyyA 99 :FTYLVH T0375 114 :SLPDVSATDFEK 1tyyA 107 :ADTYVSPQDLPP T0375 128 :LTQFKWIHIE 1tyyA 119 :FRQYEWFYFS T0375 140 :NAS 1tyyA 133 :TDR T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEV 1tyyA 140 :ACLEGARRMREAGGYVLFDVNLRSKMWG T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1tyyA 170 :DEIPELIARSAALASICKVSADELCQL T0375 198 :GFQSAEE 1tyyA 198 :GASHWQD T0375 211 :GRVRKGA 1tyyA 208 :YLRDLGC T0375 218 :VLVCAWAEEGADALGPDG 1tyyA 216 :TTIISLGADGALLITAEG T0375 237 :LLHSDAF 1tyyA 234 :EFHFPAP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1tyyA 241 :RVDVVDTTGAGDAFVGGLLFTLSR T0375 269 :GRS 1tyyA 267 :CWD T0375 272 :VQEALRFGCQVAGKKCGLQGFDGI 1tyyA 273 :LAEAISNANACGAMAVTAKGAMTA Number of specific fragments extracted= 15 number of extra gaps= 0 total=492 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tyyA/T0375-1tyyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1tyyA/T0375-1tyyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyyA read from 1tyyA/T0375-1tyyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tyyA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1tyyA)N5 Warning: unaligning (T0375)I98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tyyA)S98 Warning: unaligning (T0375)T107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tyyA)S98 T0375 3 :QILCVGLVVLDVISL 1tyyA 6 :KVWVIGDASVDLVPE T0375 23 :KED 1tyyA 21 :KQN T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATV 1tyyA 24 :SYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIV T0375 108 :ILYYDR 1tyyA 99 :FTYLVH T0375 114 :SLPDVSATDFEK 1tyyA 107 :ADTYVSPQDLPP T0375 128 :LTQFKWIHIE 1tyyA 119 :FRQYEWFYFS T0375 140 :NASEQ 1tyyA 133 :TDRPA T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEV 1tyyA 142 :LEGARRMREAGGYVLFDVNLRSKMWG T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1tyyA 170 :DEIPELIARSAALASICKVSADELCQL T0375 198 :GFQSA 1tyyA 198 :GASHW T0375 208 :GLYGRV 1tyyA 208 :YLRDLG T0375 216 :GAVLVCAWAEEGADALG 1tyyA 214 :CDTTIISLGADGALLIT T0375 234 :DGKLLHSDAF 1tyyA 231 :AEGEFHFPAP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1tyyA 241 :RVDVVDTTGAGDAFVGGLLFTLSR T0375 269 :GRS 1tyyA 267 :CWD T0375 272 :VQEALRFGCQVAGKKCGLQGFD 1tyyA 273 :LAEAISNANACGAMAVTAKGAM Number of specific fragments extracted= 16 number of extra gaps= 0 total=508 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tyyA/T0375-1tyyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1tyyA/T0375-1tyyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tyyA read from 1tyyA/T0375-1tyyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tyyA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1tyyA)N5 Warning: unaligning (T0375)I98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tyyA)S98 Warning: unaligning (T0375)R106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tyyA)S98 T0375 3 :QILCVGLVVLDVISLVDK 1tyyA 6 :KVWVIGDASVDLVPEKQN T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSVPIATV 1tyyA 24 :SYLKCPGGASANVGVCVARLGGECGFIGCLGDDDAGRFLRQVFQDNGVDVTFLRLDADLTSAVLIV T0375 107 :TILYYDR 1tyyA 99 :FTYLVHP T0375 114 :SLPDVSATDFEK 1tyyA 107 :ADTYVSPQDLPP T0375 128 :LTQFKWIHIEGRNASE 1tyyA 119 :FRQYEWFYFSSIGLTD T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1tyyA 139 :EACLEGARRMREAGGYVLFDVNLRSKMW T0375 172 :KPREELFQLFGYGDVVFVSKDVAKHLGFQSAEE 1tyyA 171 :EIPELIARSAALASICKVSADELCQLSGASHWQ T0375 211 :GRVRKGAVLVCAWAEEGADALGPDG 1tyyA 209 :LRDLGCDTTIISLGADGALLITAEG T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 1tyyA 234 :EFHFPAPRVDVVDTTGAGDAFVGGLLFTLSR T0375 269 :GRS 1tyyA 267 :CWD T0375 272 :VQEALRFGCQVAGKKCGLQGF 1tyyA 273 :LAEAISNANACGAMAVTAKGA Number of specific fragments extracted= 11 number of extra gaps= 0 total=519 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1liiA/T0375-1liiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1liiA expands to /projects/compbio/data/pdb/1lii.pdb.gz 1liiA:# T0375 read from 1liiA/T0375-1liiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1liiA read from 1liiA/T0375-1liiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1liiA to template set # found chain 1liiA in template set Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1liiA)G270 T0375 1 :GSQILCVGLVVLDVISLVD 1liiA 12 :PMRVFAIGNPILDLVAEVP T0375 22 :PKEDSEIRCL 1liiA 39 :LKRGDATLAT T0375 32 :SQRWQRGGNASNSCTILSLL 1liiA 62 :NPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1liiA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 1liiA 120 :PGQSTGTCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 1liiA 133 :EKERTLCTHLGACGSFR T0375 120 :ATDFEK 1liiA 151 :PENWTT T0375 127 :DLTQFKWIHIEGRNAS 1liiA 157 :FASGALIFYATAYTLT T0375 143 :EQVKMLQRIDAH 1liiA 177 :NALEVAGYAHGI T0375 155 :NTRQPPEQKIRVSV 1liiA 190 :NAIFTLNLSAPFCV T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1liiA 204 :ELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :GFQ 1liiA 235 :NLV T0375 216 :GA 1liiA 271 :AT T0375 218 :VLVCAWAEEGADAL 1liiA 274 :LVVMTRGHNPVIAA T0375 232 :GPDGKLL 1liiA 290 :TADGTVV T0375 239 :HSDAFP 1liiA 299 :EVGVPV T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDG 1liiA 307 :AEKIVDTNGAGDAFVGGFLYGLSQGKTVKQCIMCGNACAQDVIQHVGFSL Number of specific fragments extracted= 17 number of extra gaps= 0 total=536 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1liiA/T0375-1liiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1liiA/T0375-1liiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1liiA read from 1liiA/T0375-1liiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1liiA in template set Warning: unaligning (T0375)V213 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1liiA)G270 T0375 1 :GSQILCVGLVVLDVISLVD 1liiA 12 :PMRVFAIGNPILDLVAEVP T0375 24 :EDSEI 1liiA 40 :KRGDA T0375 29 :RCLSQRWQRGGNASNSCTILSLL 1liiA 59 :DQFNPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1liiA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 1liiA 120 :PGQSTGTCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 1liiA 133 :EKERTLCTHLGACGSFR T0375 123 :FE 1liiA 150 :IP T0375 125 :KVDLTQFKWIHIEGR 1liiA 155 :TTFASGALIFYATAY T0375 140 :NASEQVKMLQRIDAH 1liiA 174 :TPKNALEVAGYAHGI T0375 155 :NTRQPPEQK 1liiA 190 :NAIFTLNLS T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKHL 1liiA 199 :APFCVELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :GF 1liiA 235 :NL T0375 215 :KGAVLVCAWAEEGADAL 1liiA 271 :ATKLVVMTRGHNPVIAA T0375 232 :GPDGKLLHS 1liiA 290 :TADGTVVVH T0375 241 :DAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1liiA 303 :PVVAAEKIVDTNGAGDAFVGGFLYGLSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 15 number of extra gaps= 0 total=551 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1liiA/T0375-1liiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1liiA/T0375-1liiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1liiA read from 1liiA/T0375-1liiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1liiA in template set Warning: unaligning (T0375)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1liiA)G270 T0375 1 :GSQILCVGLVVLDVISLVDK 1liiA 12 :PMRVFAIGNPILDLVAEVPS T0375 21 :YPKED 1liiA 46 :LATPE T0375 26 :SEIRCLSQRWQRGGNASNSCTILSLL 1liiA 56 :STLDQFNPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1liiA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIINEA 1liiA 120 :PGQSTGTCAVLINEK T0375 104 :GSRTILYYDRSLP 1liiA 135 :ERTLCTHLGACGS T0375 118 :VSATDFEKVDLTQFKWIHIEGRNASE 1liiA 148 :FRIPENWTTFASGALIFYATAYTLTA T0375 144 :QVKMLQRIDAHN 1liiA 176 :KNALEVAGYAHG T0375 156 :TRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1liiA 189 :PNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKV T0375 215 :KGAVLVCAWAEEGADALG 1liiA 271 :ATKLVVMTRGHNPVIAAE T0375 233 :PDGK 1liiA 291 :ADGT T0375 237 :LLHSDAFPPPR 1liiA 296 :VVHEVGVPVVA T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1liiA 310 :IVDTNGAGDAFVGGFLYGLSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 13 number of extra gaps= 0 total=564 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0375-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0375 read from 1j5vA/T0375-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0375-1j5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0375-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0375 read from 1j5vA/T0375-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0375-1j5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5vA/T0375-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5vA expands to Error: no filename for 1j5vA # T0375 read from 1j5vA/T0375-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5vA read from 1j5vA/T0375-1j5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5vA to template set Error: can't find template for 1j5vA or 1j5vA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk4A/T0375-1vk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vk4A expands to /projects/compbio/data/pdb/1vk4.pdb.gz 1vk4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 232, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 1vk4A Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 1vk4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1392, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1394, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1396, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1402, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1404, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1406, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1408, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1507, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1509, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1511, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1513, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1515, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1517, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1765, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1767, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1977, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1979, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1981, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 1983, because occupancy 0.350 <= existing 0.650 in 1vk4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2198, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 2200, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 2202, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 2204, because occupancy 0.350 <= existing 0.650 in 1vk4A Skipped atom 2206, because occupancy 0.350 <= existing 0.650 in 1vk4A # T0375 read from 1vk4A/T0375-1vk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk4A read from 1vk4A/T0375-1vk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vk4A to template set # found chain 1vk4A in template set Warning: unaligning (T0375)I99 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk4A)T86 Warning: unaligning (T0375)S105 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk4A)T86 T0375 2 :SQILCVGLVVLDVISL 1vk4A 0 :HMITFIGHVSKDVNVV T0375 19 :DK 1vk4A 16 :DG T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPG 1vk4A 18 :KREIAYGGGVVMGAITSSLLGVKTKVITKCTRE T0375 74 :LRRYSVDLRYTVF 1vk4A 58 :LRDNGVEVVFLKS T0375 90 :GSVPIATVI 1vk4A 71 :PRTTSIENR T0375 106 :RTILYY 1vk4A 87 :RESFLI T0375 113 :RSLPDVSATDFEKV 1vk4A 93 :SAADPFTESDLAFI T0375 130 :QFKWIHIEGRN 1vk4A 107 :EGEAVHINPLW T0375 141 :A 1vk4A 122 :P T0375 142 :SEQVKMLQR 1vk4A 124 :DLIPVLRRK T0375 156 :T 1vk4A 133 :V T0375 157 :RQPPEQ 1vk4A 135 :FLSADA T0375 163 :KIRVSVEVEKPRE 1vk4A 149 :NEKLVYRDWEMKE T0375 179 :QLFGYGDVVFVSKDVAKHL 1vk4A 162 :KYLKYLDLFKVDSREAETL T0375 198 :GFQSAEEALRGLYGR 1vk4A 182 :GTNDLRESCRIIRSF T0375 216 :GA 1vk4A 197 :GA T0375 218 :VLVCAW 1vk4A 200 :IILATH T0375 225 :EEGADALGPD 1vk4A 206 :ASGVIVFDGN T0375 237 :LLHSDAF 1vk4A 216 :FYEASFR T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1vk4A 223 :SWSLEGRTGRGDTCTAAFLVGFVF T0375 269 :GRSVQEALRFGCQVAGKKCGLQGF 1vk4A 248 :KMSIEKATKFAAAVTSVKMRHPGP Number of specific fragments extracted= 21 number of extra gaps= 0 total=585 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk4A/T0375-1vk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vk4A/T0375-1vk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk4A read from 1vk4A/T0375-1vk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk4A in template set Warning: unaligning (T0375)N100 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vk4A)T86 Warning: unaligning (T0375)R106 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk4A)T86 T0375 3 :QILCVGLVVLDVISL 1vk4A 1 :MITFIGHVSKDVNVV T0375 24 :ED 1vk4A 16 :DG T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGHV 1vk4A 18 :KREIAYGGGVVMGAITSSLLGVKTKVITKCTREDV T0375 74 :LRRYSVDLRYTVF 1vk4A 58 :LRDNGVEVVFLKS T0375 91 :SVPIATVII 1vk4A 71 :PRTTSIENR T0375 107 :TILYYDRSLPDVSATDFEKV 1vk4A 87 :RESFLISAADPFTESDLAFI T0375 130 :QFKWIHIEGRNASEQ 1vk4A 107 :EGEAVHINPLWYGEF T0375 145 :VKMLQRIDAHNTRQPPEQ 1vk4A 123 :EDLIPVLRRKVMFLSADA T0375 163 :K 1vk4A 149 :N T0375 166 :VSVEVEKP 1vk4A 150 :EKLVYRDW T0375 175 :EELFQLFGYGDVVFVSKDVAKHL 1vk4A 158 :EMKEKYLKYLDLFKVDSREAETL T0375 198 :GFQSAEEALRGLYGRV 1vk4A 182 :GTNDLRESCRIIRSFG T0375 216 :GAVLVCAW 1vk4A 198 :AKIILATH T0375 225 :EEGADAL 1vk4A 206 :ASGVIVF T0375 234 :DGKLLHSDAF 1vk4A 213 :DGNFYEASFR T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1vk4A 223 :SWSLEGRTGRGDTCTAAFLVGFVF T0375 269 :GRSVQEALRFGCQVAGKKCGLQGFD 1vk4A 248 :KMSIEKATKFAAAVTSVKMRHPGPL Number of specific fragments extracted= 17 number of extra gaps= 0 total=602 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk4A/T0375-1vk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vk4A/T0375-1vk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk4A read from 1vk4A/T0375-1vk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk4A in template set Warning: unaligning (T0375)S103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vk4A)T86 T0375 2 :SQILCVGLVVLDVISL 1vk4A 0 :HMITFIGHVSKDVNVV T0375 24 :ED 1vk4A 16 :DG T0375 32 :SQRWQRGGNASNSCTILSLLGAPCAFMGSMAPGH 1vk4A 18 :KREIAYGGGVVMGAITSSLLGVKTKVITKCTRED T0375 74 :LRRYSVDLRYTVF 1vk4A 58 :LRDNGVEVVFLKS T0375 90 :GSVPIATVI 1vk4A 71 :PRTTSIENR T0375 104 :GSRTILYYD 1vk4A 87 :RESFLISAA T0375 116 :PDVSATDFEKV 1vk4A 96 :DPFTESDLAFI T0375 130 :QFKWIHIEGRNASE 1vk4A 107 :EGEAVHINPLWYGE T0375 144 :QVKMLQRIDA 1vk4A 124 :DLIPVLRRKV T0375 158 :QPPEQKIRVS 1vk4A 134 :MFLSADAQGF T0375 172 :KPREELFQLFGYGDVVFVSKDVAKHLGFQSAEEA 1vk4A 155 :RDWEMKEKYLKYLDLFKVDSREAETLTGTNDLRE T0375 207 :RGLYGRVRKGAVLVCAW 1vk4A 189 :SCRIIRSFGAKIILATH T0375 225 :EEGADALGPD 1vk4A 206 :ASGVIVFDGN T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 1vk4A 216 :FYEASFRSWSLEGRTGRGDTCTAAFLVGFVF T0375 269 :GRSVQEALRFGCQVAGKKCGLQGF 1vk4A 248 :KMSIEKATKFAAAVTSVKMRHPGP Number of specific fragments extracted= 15 number of extra gaps= 0 total=617 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub0A/T0375-1ub0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ub0A expands to /projects/compbio/data/pdb/1ub0.pdb.gz 1ub0A:Skipped atom 1460, because occupancy 0.350 <= existing 0.650 in 1ub0A # T0375 read from 1ub0A/T0375-1ub0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub0A read from 1ub0A/T0375-1ub0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ub0A to template set # found chain 1ub0A in template set Warning: unaligning (T0375)V170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ub0A)A116 Warning: unaligning (T0375)E226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ub0A)E181 T0375 1 :GSQILCVGL 1ub0A 1 :MRVALTIAG T0375 34 :RWQRGGNAS 1ub0A 10 :SDSGGGAGV T0375 68 :DFVLDDLRRYSVDLRYTVF 1ub0A 19 :QADLKVFFRFGVYGTSALT T0375 96 :TVIINEASGSRTILYYDR 1ub0A 38 :LVTAQNTLGVQRVHLLPP T0375 120 :ATDFEKVDLT 1ub0A 59 :YAQIESVAQD T0375 130 :QFKWIHIEGRNA 1ub0A 70 :PLHAAKTGALGD T0375 142 :SEQVKMLQRIDAHNT 1ub0A 83 :AIVEAVAEAVRRFGV T0375 157 :RQPPEQ 1ub0A 99 :PLVVDP T0375 171 :EKPREELF 1ub0A 117 :KEAAAALK T0375 179 :QLFGYGDVVFVSKDVAKHL 1ub0A 126 :RLFPLADLVTPNRLEAEAL T0375 198 :GFQ 1ub0A 146 :GRP T0375 201 :SAEEALRGLYGRVRKGA 1ub0A 151 :TLKEAEEAAKALLALGP T0375 218 :VLVCAWAE 1ub0A 169 :AVLLKGGH T0375 228 :ADALGPD 1ub0A 184 :DLLATRG T0375 236 :KLLHSDAF 1ub0A 191 :GVLRFSAP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 1ub0A 199 :RVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTRALKT T0375 290 :Q 1ub0A 247 :L Number of specific fragments extracted= 17 number of extra gaps= 0 total=634 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub0A/T0375-1ub0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ub0A/T0375-1ub0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub0A read from 1ub0A/T0375-1ub0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ub0A in template set Warning: unaligning (T0375)V170 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ub0A)A116 T0375 3 :QILCVGL 1ub0A 3 :VALTIAG T0375 34 :RWQRGGNAS 1ub0A 10 :SDSGGGAGV T0375 68 :DFVLDDLRRYSVDLRYTVFQ 1ub0A 19 :QADLKVFFRFGVYGTSALTL T0375 96 :TVIIN 1ub0A 39 :VTAQN T0375 102 :ASGSRTILY 1ub0A 44 :TLGVQRVHL T0375 118 :VSAT 1ub0A 53 :LPPE T0375 122 :DFEKVDLT 1ub0A 61 :QIESVAQD T0375 130 :QFKWIHIEGRNASEQVKML 1ub0A 70 :PLHAAKTGALGDAAIVEAV T0375 149 :QRIDAHNTR 1ub0A 90 :EAVRRFGVR T0375 158 :QPPEQ 1ub0A 100 :LVVDP T0375 171 :EKPREELFQ 1ub0A 117 :KEAAAALKE T0375 180 :LFGYGDVVFVSKDVAKHL 1ub0A 127 :LFPLADLVTPNRLEAEAL T0375 198 :GF 1ub0A 146 :GR T0375 200 :QSAEEALRGLYGRV 1ub0A 153 :KEAEEAAKALLALG T0375 216 :GAVLVCAWAE 1ub0A 167 :PKAVLLKGGH T0375 228 :ADALG 1ub0A 184 :DLLAT T0375 234 :DGKLLHSDA 1ub0A 189 :RGGVLRFSA T0375 244 :PPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 1ub0A 198 :PRVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTRALKT Number of specific fragments extracted= 18 number of extra gaps= 0 total=652 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub0A/T0375-1ub0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ub0A/T0375-1ub0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub0A read from 1ub0A/T0375-1ub0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ub0A in template set Warning: unaligning (T0375)V166 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ub0A)A116 T0375 1 :GSQILCVGL 1ub0A 1 :MRVALTIAG T0375 34 :RWQRGGNASNSCT 1ub0A 10 :SDSGGGAGVQADL T0375 47 :ILSLLGAPCAFMGSM 1ub0A 24 :VFFRFGVYGTSALTL T0375 96 :TVIINEASGSRTIL 1ub0A 39 :VTAQNTLGVQRVHL T0375 111 :YD 1ub0A 53 :LP T0375 115 :LPDVSATDFEKVDLTQFKWIHIEG 1ub0A 55 :PEVVYAQIESVAQDFPLHAAKTGA T0375 140 :NASEQVKMLQRIDAHNTR 1ub0A 79 :LGDAAIVEAVAEAVRRFG T0375 158 :QPPEQKIR 1ub0A 98 :RPLVVDPV T0375 172 :KPREELFQLF 1ub0A 118 :EAAAALKERL T0375 182 :GYGDVVFVSKDVAKHLGFQ 1ub0A 129 :PLADLVTPNRLEAEALLGR T0375 202 :AEEALRGLYGRVRKGAVLVCAWA 1ub0A 153 :KEAEEAAKALLALGPKAVLLKGG T0375 226 :EGADALGPDG 1ub0A 182 :AVDLLATRGG T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGK 1ub0A 192 :VLRFSAPRVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTR Number of specific fragments extracted= 13 number of extra gaps= 0 total=665 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awdA/T0375-2awdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2awdA expands to /projects/compbio/data/pdb/2awd.pdb.gz 2awdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 2awdA/T0375-2awdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awdA read from 2awdA/T0375-2awdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2awdA to template set # found chain 2awdA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2awdA)S0 Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2awdA)I11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2awdA)I11 Warning: unaligning (T0375)E137 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2awdA)G135 Warning: unaligning (T0375)G138 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2awdA)G135 T0375 3 :QILCVG 2awdA 1 :LIVTVT T0375 9 :LV 2awdA 8 :NP T0375 13 :DVISLVDK 2awdA 12 :DISYLLDH T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMAP 2awdA 20 :LKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLGG T0375 65 :HVADFVLDDLRRYSVDLRYTVF 2awdA 62 :FHGAFIANELKKANIPQAFTSI T0375 89 :TGSVPIATVIIN 2awdA 84 :KEETRDSIAILH T0375 103 :SGSRTILYYDR 2awdA 96 :EGNQTEILEAG T0375 116 :PDVSATDFEKVD 2awdA 107 :PTVSPEEISNFL T0375 128 :LTQFKWIHI 2awdA 125 :IKQAEIVTI T0375 139 :RNA 2awdA 136 :SLA T0375 142 :S 2awdA 140 :G T0375 143 :EQVKMLQRIDAHNTRQPPEQKI 2awdA 145 :FYQELVQKAHAQEVKVLLDTSG T0375 175 :EELFQLFGY 2awdA 167 :DSLRQVLQG T0375 184 :GDVVFVSKDVAKHL 2awdA 179 :PYLIKPNLEELEGL T0375 198 :GFQ 2awdA 194 :GQD T0375 201 :SAEEALRGLY 2awdA 201 :PLAAVQTALT T0375 215 :KGA 2awdA 215 :AGI T0375 218 :VLVCAWAEEGADALGPD 2awdA 219 :WIVISLGKDGAIAKHHD T0375 236 :KLLHSDAF 2awdA 236 :QFYRVKIP T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQ 2awdA 244 :TIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQER Number of specific fragments extracted= 20 number of extra gaps= 2 total=685 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awdA/T0375-2awdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2awdA/T0375-2awdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awdA read from 2awdA/T0375-2awdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2awdA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2awdA)S0 Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2awdA)I11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2awdA)I11 Warning: unaligning (T0375)E137 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2awdA)G135 Warning: unaligning (T0375)G138 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2awdA)G135 Warning: unaligning (T0375)Q200 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2awdA)E199 T0375 3 :QILCVG 2awdA 1 :LIVTVT T0375 9 :LV 2awdA 8 :NP T0375 13 :DVISLVDKY 2awdA 12 :DISYLLDHL T0375 23 :KEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2awdA 21 :KLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVF 2awdA 61 :GFHGAFIANELKKANIPQAFTSI T0375 89 :TGSVPIATVIIN 2awdA 84 :KEETRDSIAILH T0375 103 :SGSRTILYYDR 2awdA 96 :EGNQTEILEAG T0375 116 :PDVSATDFEKVD 2awdA 107 :PTVSPEEISNFL T0375 128 :LTQFKWIHI 2awdA 125 :IKQAEIVTI T0375 139 :RNASEQ 2awdA 136 :SLAKGL T0375 145 :VKMLQRIDAHNTRQPPEQK 2awdA 147 :QELVQKAHAQEVKVLLDTS T0375 171 :E 2awdA 166 :G T0375 175 :EELFQLFGY 2awdA 167 :DSLRQVLQG T0375 184 :GDVVFVSKDVAKHL 2awdA 179 :PYLIKPNLEELEGL T0375 198 :GF 2awdA 194 :GQ T0375 201 :SAEEALRGLYG 2awdA 200 :NPLAAVQTALT T0375 212 :RVRKGAVLVCAWAEEGADALG 2awdA 213 :MFAGIEWIVISLGKDGAIAKH T0375 234 :DGKLLHSDA 2awdA 234 :HDQFYRVKI T0375 244 :PPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQ 2awdA 243 :PTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQER Number of specific fragments extracted= 19 number of extra gaps= 3 total=704 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awdA/T0375-2awdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2awdA/T0375-2awdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2awdA read from 2awdA/T0375-2awdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2awdA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (2awdA)S0 Warning: unaligning (T0375)V11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2awdA)I11 Warning: unaligning (T0375)L12 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2awdA)I11 Warning: unaligning (T0375)E137 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2awdA)G135 Warning: unaligning (T0375)G138 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2awdA)G135 T0375 3 :QILCVG 2awdA 1 :LIVTVT T0375 9 :LV 2awdA 8 :NP T0375 13 :DVISLVDK 2awdA 12 :DISYLLDH T0375 22 :PKEDSEIRCLSQRWQRGGNASNSCTILSLLGAPCAFMGSMA 2awdA 20 :LKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTGSV 2awdA 61 :GFHGAFIANELKKANIPQAFTSIKEETRD T0375 95 :ATVIINEASGSRTILYYDRSLPDVSATDFEK 2awdA 90 :SIAILHEGNQTEILEAGPTVSPEEISNFLEN T0375 127 :DLTQFKWIHI 2awdA 124 :LIKQAEIVTI T0375 139 :RNASE 2awdA 136 :SLAKG T0375 144 :QVKMLQRIDAHNTRQPPEQKIR 2awdA 144 :DFYQELVQKAHAQEVKVLLDTS T0375 174 :REELFQLFG 2awdA 166 :GDSLRQVLQ T0375 183 :YGDVVFVSKDVAKHLGFQ 2awdA 178 :KPYLIKPNLEELEGLLGQ T0375 201 :SAEEALRGLY 2awdA 200 :NPLAAVQTAL T0375 212 :RVRKGAVLVCAWAEEGADALGPDG 2awdA 213 :MFAGIEWIVISLGKDGAIAKHHDQ T0375 238 :LHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 2awdA 237 :FYRVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQE Number of specific fragments extracted= 14 number of extra gaps= 2 total=718 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dgmA/T0375-1dgmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dgmA expands to /projects/compbio/data/pdb/1dgm.pdb.gz 1dgmA:Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1dgmA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1dgmA Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 1dgmA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 1dgmA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 1dgmA # T0375 read from 1dgmA/T0375-1dgmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dgmA read from 1dgmA/T0375-1dgmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dgmA to template set # found chain 1dgmA in template set Warning: unaligning (T0375)Q200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dgmA)T246 T0375 1 :GSQILCVGLVVLDVISLVD 1dgmA 12 :PMRVFAIGNPILDLVAEVP T0375 21 :YPKEDSEIRCL 1dgmA 38 :FLKRGDATLAT T0375 32 :SQRWQRGGNASNSCTILSLL 1dgmA 62 :NPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1dgmA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 1dgmA 120 :PGQSTGVCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 1dgmA 133 :EKERTLCTHLGACGSFR T0375 120 :ATDFEK 1dgmA 151 :PEDWTT T0375 127 :DLTQFKWIHIEGRNAS 1dgmA 157 :FASGALIFYATAYTLT T0375 143 :EQVKMLQRIDAH 1dgmA 177 :NAFEVAGYAHGI T0375 155 :NTRQPPEQKIRVSV 1dgmA 190 :NAIFTLNLSAPFCV T0375 171 :EKPREELFQLFGYGDVVFVSKDVAKHL 1dgmA 204 :ELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :GF 1dgmA 235 :NL T0375 201 :SAEEALRGLYGRVR 1dgmA 248 :NKEHAVEVCTGALR T0375 215 :KG 1dgmA 265 :AG T0375 217 :A 1dgmA 272 :T T0375 218 :VLVCAWAEEGADAL 1dgmA 274 :LVVMTRGHNPVIAA T0375 232 :GPDGKLL 1dgmA 290 :TADGTVV T0375 239 :HSDAFP 1dgmA 299 :EVGVPV T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1dgmA 307 :AEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 19 number of extra gaps= 0 total=737 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dgmA/T0375-1dgmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1dgmA/T0375-1dgmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dgmA read from 1dgmA/T0375-1dgmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dgmA in template set T0375 1 :GSQILCVGLVVLDVISLVD 1dgmA 12 :PMRVFAIGNPILDLVAEVP T0375 22 :PKEDSEI 1dgmA 38 :FLKRGDA T0375 30 :CLSQRWQRGGNASNSCTILSLL 1dgmA 60 :QFNPTSLPGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1dgmA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIIN 1dgmA 120 :PGQSTGVCAVLIN T0375 103 :SGSRTILYYDRSLPDVS 1dgmA 133 :EKERTLCTHLGACGSFR T0375 123 :FE 1dgmA 150 :LP T0375 125 :KVDLTQFKWIHIEGR 1dgmA 155 :TTFASGALIFYATAY T0375 140 :NASEQVKMLQRIDAH 1dgmA 174 :TPKNAFEVAGYAHGI T0375 155 :NTRQPPEQK 1dgmA 190 :NAIFTLNLS T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKHL 1dgmA 199 :APFCVELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :GF 1dgmA 235 :NL T0375 200 :QSAEEALRGLYGR 1dgmA 250 :EHAVEVCTGALRL T0375 216 :GAVLVCAWAEEGADAL 1dgmA 272 :TKLVVMTRGHNPVIAA T0375 232 :GPDGKLLHS 1dgmA 290 :TADGTVVVH T0375 241 :DAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1dgmA 303 :PVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 16 number of extra gaps= 0 total=753 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dgmA/T0375-1dgmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1dgmA/T0375-1dgmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dgmA read from 1dgmA/T0375-1dgmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dgmA in template set T0375 2 :SQILCVGLVVLDVISLVDK 1dgmA 13 :MRVFAIGNPILDLVAEVPS T0375 21 :YPKEDSEIRCLSQRWQ 1dgmA 38 :FLKRGDATLATPEQMR T0375 37 :RGGNASNSCTILSLL 1dgmA 67 :PGGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTVF 1dgmA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVA T0375 88 :TTGSVPIATVIINEASGSRTILYYDRSLPDVSATDF 1dgmA 120 :PGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWT T0375 126 :VDLTQFKWIHIEGRNASE 1dgmA 156 :TFASGALIFYATAYTLTA T0375 144 :QVKMLQRIDAHN 1dgmA 176 :KNAFEVAGYAHG T0375 156 :TRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1dgmA 189 :PNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKV T0375 201 :SAEE 1dgmA 247 :ANKE T0375 205 :ALRGLYGRVRK 1dgmA 256 :CTGALRLLTAG T0375 216 :GAVLVCAWAEEGADALG 1dgmA 272 :TKLVVMTRGHNPVIAAE T0375 233 :PDGKLLHSDAFPPPR 1dgmA 292 :DGTVVVHEVGVPVVA T0375 248 :VVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 1dgmA 310 :IVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFS Number of specific fragments extracted= 13 number of extra gaps= 0 total=766 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi9A/T0375-1vi9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vi9A expands to /projects/compbio/data/pdb/1vi9.pdb.gz 1vi9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1928, because occupancy 0.500 <= existing 0.500 in 1vi9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vi9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 1vi9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vi9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 1vi9A/T0375-1vi9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi9A read from 1vi9A/T0375-1vi9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vi9A to template set # found chain 1vi9A in template set Warning: unaligning (T0375)T84 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)Q40 Warning: unaligning (T0375)V85 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)Q40 Warning: unaligning (T0375)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)N43 Warning: unaligning (T0375)T88 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)N43 Warning: unaligning (T0375)I108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vi9A)V54 Warning: unaligning (T0375)Y110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vi9A)V54 T0375 1 :GSQILCVGL 1vi9A 2 :MKNILAIQS T0375 34 :RWQRGGNASNSCT 1vi9A 11 :HVVYGHAGNSAAE T0375 47 :ILSLLGAPCAFMG 1vi9A 25 :PMRRLGANVWPLN T0375 83 :Y 1vi9A 38 :T T0375 86 :F 1vi9A 41 :F T0375 89 :T 1vi9A 44 :H T0375 101 :EASGSRT 1vi9A 45 :TQYGKWT T0375 111 :Y 1vi9A 55 :M T0375 119 :SATDFEKVD 1vi9A 56 :PPSHLTEIV T0375 128 :LTQFKWIHIEGRNA 1vi9A 73 :LHTCDAVLSGYLGS T0375 142 :S 1vi9A 88 :E T0375 143 :EQVKMLQRIDAH 1vi9A 92 :HILGIVRQVKAA T0375 155 :NTRQPPEQ 1vi9A 106 :QAKYFCDP T0375 163 :KIRVSVEVEKPREELF 1vi9A 118 :PEKGCIVAPGVAEFHV T0375 179 :QLFGYGDVVFVSKDVAKHL 1vi9A 135 :HGLPASDIIAPNLVELEIL T0375 198 :GFQ 1vi9A 155 :EHA T0375 201 :SAEEALRGLYGRVRKGA 1vi9A 160 :NVEEAVLAARELIAQGP T0375 218 :VLVCAWAEEG 1vi9A 178 :IVLVKHLARA T0375 228 :ADALGPD 1vi9A 196 :MLLVTAD T0375 236 :KLLHSDAF 1vi9A 203 :EAWHISRP T0375 245 :PPRV 1vi9A 211 :LVDF T0375 249 :VDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKC 1vi9A 217 :RQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIM Number of specific fragments extracted= 22 number of extra gaps= 2 total=788 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi9A/T0375-1vi9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vi9A/T0375-1vi9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi9A read from 1vi9A/T0375-1vi9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi9A in template set Warning: unaligning (T0375)T84 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)Q40 Warning: unaligning (T0375)V85 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)Q40 Warning: unaligning (T0375)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)N43 Warning: unaligning (T0375)T88 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)N43 Warning: unaligning (T0375)I108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vi9A)V54 Warning: unaligning (T0375)Y110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vi9A)V54 T0375 2 :SQILCVGL 1vi9A 3 :KNILAIQS T0375 34 :RWQRGGNASNSCT 1vi9A 11 :HVVYGHAGNSAAE T0375 47 :ILSLLGAPCAFMG 1vi9A 25 :PMRRLGANVWPLN T0375 83 :Y 1vi9A 38 :T T0375 86 :F 1vi9A 41 :F T0375 89 :T 1vi9A 44 :H T0375 101 :EASGSRT 1vi9A 45 :TQYGKWT T0375 118 :VSATDFEKVD 1vi9A 55 :MPPSHLTEIV T0375 128 :LTQFKWIHIEGRNASEQ 1vi9A 73 :LHTCDAVLSGYLGSAEQ T0375 145 :VKMLQRIDAH 1vi9A 94 :LGIVRQVKAA T0375 155 :NTRQPPEQ 1vi9A 106 :QAKYFCDP T0375 165 :RVSVEVEKPREELFQ 1vi9A 120 :KGCIVAPGVAEFHVR T0375 180 :LFGYGDVVFVSKDVAKHL 1vi9A 136 :GLPASDIIAPNLVELEIL T0375 198 :GF 1vi9A 155 :EH T0375 200 :QSAE 1vi9A 159 :NNVE T0375 204 :EALRGLYGRV 1vi9A 166 :LAARELIAQG T0375 216 :GAVLVCAWAE 1vi9A 176 :PQIVLVKHLA T0375 228 :ADALG 1vi9A 196 :MLLVT T0375 234 :DGKLLHSDA 1vi9A 201 :ADEAWHISR T0375 244 :PPPRV 1vi9A 210 :PLVDF T0375 249 :VDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQV 1vi9A 217 :RQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAA T0375 283 :AGKKCGLQGFD 1vi9A 254 :IMVTTKAMQEY Number of specific fragments extracted= 22 number of extra gaps= 2 total=810 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi9A/T0375-1vi9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1vi9A/T0375-1vi9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi9A read from 1vi9A/T0375-1vi9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi9A in template set Warning: unaligning (T0375)M61 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)Q40 Warning: unaligning (T0375)A62 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)Q40 Warning: unaligning (T0375)G64 because of BadResidue code BAD_PEPTIDE in next template residue (1vi9A)N43 Warning: unaligning (T0375)H65 because of BadResidue code BAD_PEPTIDE at template residue (1vi9A)N43 Warning: unaligning (T0375)T107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vi9A)V54 Warning: unaligning (T0375)L109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vi9A)V54 T0375 1 :GSQILCVGL 1vi9A 2 :MKNILAIQS T0375 34 :RWQRGGNASNSC 1vi9A 11 :HVVYGHAGNSAA T0375 46 :TILSLLGAPCAFMGS 1vi9A 24 :FPMRRLGANVWPLNT T0375 63 :P 1vi9A 41 :F T0375 84 :TVFQ 1vi9A 44 :HTQY T0375 103 :SGSR 1vi9A 48 :GKWT T0375 110 :YYDRSLPDVSATDFEKVDLTQFKWIHIEGRNASE 1vi9A 55 :MPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAE T0375 144 :QVKMLQRIDAHN 1vi9A 91 :EHILGIVRQVKA T0375 156 :TRQPPEQKIRVS 1vi9A 105 :PQAKYFCDPVMG T0375 169 :EVE 1vi9A 117 :HPE T0375 172 :KPREELFQLF 1vi9A 127 :GVAEFHVRHG T0375 182 :GYGDVVFVSKDVAKHLGFQ 1vi9A 138 :PASDIIAPNLVELEILCEH T0375 202 :AEEALRGLYGRVRKGAVLVCAWAEE 1vi9A 162 :EEAVLAARELIAQGPQIVLVKHLAR T0375 227 :GADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGK 1vi9A 195 :EMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYE Number of specific fragments extracted= 14 number of extra gaps= 2 total=824 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lhpA/T0375-1lhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lhpA expands to /projects/compbio/data/pdb/1lhp.pdb.gz 1lhpA:# T0375 read from 1lhpA/T0375-1lhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lhpA read from 1lhpA/T0375-1lhpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lhpA to template set # found chain 1lhpA in template set Warning: unaligning (T0375)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lhpA)G212 T0375 1 :GSQILCVGL 1lhpA 4 :ECRVLSIQS T0375 17 :LVDKYPK 1lhpA 13 :HVVRGYV T0375 40 :NASNSCTILSLLGAPCAF 1lhpA 20 :GNRAATFPLQVLGFEVDA T0375 81 :LRYTVFQTT 1lhpA 38 :VNSVQFSNH T0375 101 :EASGSR 1lhpA 47 :TGYSHW T0375 118 :VSATDFEKVD 1lhpA 57 :LNSDELQELY T0375 128 :LT 1lhpA 71 :LN T0375 130 :QFKWIHIEGRNA 1lhpA 76 :QYDYVLTGYTRD T0375 142 :S 1lhpA 89 :S T0375 143 :EQVKMLQRIDAH 1lhpA 93 :MVVDIVQELKQQ T0375 155 :NTRQPPEQ 1lhpA 107 :RLVYVCDP T0375 163 :KIRVSVEVEKPREELF 1lhpA 122 :GEGAMYVPDDLLPVYR T0375 179 :QLFGYGDVVFVSKDVAKHL 1lhpA 139 :KVVPVADIITPNQFEAELL T0375 198 :GFQ 1lhpA 159 :GRK T0375 201 :SAEEALRGLYGRVRKGA 1lhpA 164 :SQEEALEVMDMLHSMGP T0375 218 :VLVCAWAE 1lhpA 182 :TVVITSSN T0375 226 :EG 1lhpA 194 :RG T0375 228 :ADAL 1lhpA 201 :ALGS T0375 236 :KLLHSDAF 1lhpA 217 :QRIRMEMH T0375 245 :PPRVV 1lhpA 225 :KVDAV T0375 251 :TLGAGDTFNASVIFSLSQ 1lhpA 230 :FVGTGDLFAAMLLAWTHK T0375 269 :GRSVQEALRFGCQVAGKKCGL 1lhpA 249 :PNNLKVACEKTVSAMHHVLQR Number of specific fragments extracted= 22 number of extra gaps= 0 total=846 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lhpA/T0375-1lhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1lhpA/T0375-1lhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lhpA read from 1lhpA/T0375-1lhpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lhpA in template set Warning: unaligning (T0375)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lhpA)G212 T0375 1 :GSQILCVGL 1lhpA 4 :ECRVLSIQS T0375 17 :LVDKY 1lhpA 13 :HVVRG T0375 64 :GHVADFVLDDLRRYSVDLRYTVF 1lhpA 18 :YVGNRAATFPLQVLGFEVDAVNS T0375 107 :TILYYDRSLPD 1lhpA 41 :VQFSNHTGYSH T0375 118 :VSATDFEKVD 1lhpA 57 :LNSDELQELY T0375 128 :LT 1lhpA 71 :LN T0375 130 :QFKWIHIEGRNASEQ 1lhpA 76 :QYDYVLTGYTRDKSF T0375 145 :VKMLQRIDAH 1lhpA 95 :VDIVQELKQQ T0375 155 :NTRQPPEQ 1lhpA 107 :RLVYVCDP T0375 163 :KIRVSVEVEKPREELFQ 1lhpA 122 :GEGAMYVPDDLLPVYRE T0375 180 :LFGYGDVVFVSKDVAKHL 1lhpA 140 :VVPVADIITPNQFEAELL T0375 198 :GF 1lhpA 159 :GR T0375 200 :QSAEEALRGLYGRV 1lhpA 166 :EEALEVMDMLHSMG T0375 216 :GAVLVCAWAE 1lhpA 180 :PDTVVITSSN T0375 226 :EG 1lhpA 194 :RG T0375 228 :ADALG 1lhpA 201 :ALGSQ T0375 236 :K 1lhpA 213 :S T0375 237 :LLHSDAF 1lhpA 218 :RIRMEMH T0375 245 :PPRVV 1lhpA 225 :KVDAV T0375 251 :TLGAGDTFNASVIFSLSQG 1lhpA 230 :FVGTGDLFAAMLLAWTHKH T0375 270 :RSVQEALRFGCQVAGKKCGL 1lhpA 250 :NNLKVACEKTVSAMHHVLQR Number of specific fragments extracted= 21 number of extra gaps= 0 total=867 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lhpA/T0375-1lhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1lhpA/T0375-1lhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lhpA read from 1lhpA/T0375-1lhpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lhpA in template set T0375 1 :GSQILCVGLVV 1lhpA 4 :ECRVLSIQSHV T0375 33 :QRWQRGGNA 1lhpA 15 :VRGYVGNRA T0375 44 :SCTILSLLGAPCAFMGSMA 1lhpA 24 :ATFPLQVLGFEVDAVNSVQ T0375 81 :LRYTVFQTTGSVPI 1lhpA 43 :FSNHTGYSHWKGQV T0375 118 :VSATDF 1lhpA 57 :LNSDEL T0375 124 :EKVDLT 1lhpA 67 :DGLKLN T0375 130 :QFK 1lhpA 76 :QYD T0375 134 :IHIEGRNASEQVKMLQRIDAHN 1lhpA 79 :YVLTGYTRDKSFLAMVVDIVQE T0375 156 :TRQPPEQKIRVS 1lhpA 106 :PRLVYVCDPVMG T0375 172 :KPREELFQ 1lhpA 131 :DLLPVYRE T0375 180 :LFGYGDVVFVSKDVAKHLGFQ 1lhpA 140 :VVPVADIITPNQFEAELLTGR T0375 201 :S 1lhpA 164 :S T0375 202 :AEEALRGLYGRVRKGAVLVCAW 1lhpA 166 :EEALEVMDMLHSMGPDTVVITS T0375 224 :AEEG 1lhpA 195 :GSDY T0375 228 :ADALG 1lhpA 201 :ALGSQ T0375 238 :LHSDAFPPPRVV 1lhpA 218 :RIRMEMHKVDAV T0375 251 :TLGAGDTFNASVIFSLSQ 1lhpA 230 :FVGTGDLFAAMLLAWTHK T0375 269 :GRSVQEALRFGCQVAGKKCGL 1lhpA 249 :PNNLKVACEKTVSAMHHVLQR Number of specific fragments extracted= 18 number of extra gaps= 0 total=885 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jxhA/T0375-1jxhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jxhA expands to /projects/compbio/data/pdb/1jxh.pdb.gz 1jxhA:# T0375 read from 1jxhA/T0375-1jxhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jxhA read from 1jxhA/T0375-1jxhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jxhA to template set # found chain 1jxhA in template set Warning: unaligning (T0375)V168 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)L116 Warning: unaligning (T0375)W223 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)D187 Warning: unaligning (T0375)A228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)D187 Warning: unaligning (T0375)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)R202 Warning: unaligning (T0375)P245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)R202 T0375 1 :GSQILCVGL 1jxhA 3 :RINALTIAG T0375 17 :LVD 1jxhA 12 :TDP T0375 37 :RGGNASNSCT 1jxhA 15 :SGGAGIQADL T0375 47 :ILSLLGAPCAFMG 1jxhA 26 :TFSALGAYGCSVI T0375 83 :YTVFQT 1jxhA 39 :TALVAE T0375 101 :EASGSRTILYYDR 1jxhA 45 :NTCGVQSVYRIEP T0375 120 :ATDFEKVDLT 1jxhA 61 :AAQLDSVFSD T0375 130 :QFKWIHIEGRNA 1jxhA 72 :RIDTTKIGMLAE T0375 142 :SEQVKMLQRIDAHNTR 1jxhA 85 :DIVEAVAERLQRHHVR T0375 158 :QPPEQ 1jxhA 102 :VVLDT T0375 169 :EVEKPREELF 1jxhA 117 :LSPSAIETLR T0375 179 :QLFGYGDVVFVSKDVAKHL 1jxhA 128 :RLLPQVSLITPNLPEAAAL T0375 198 :GFQ 1jxhA 148 :DAP T0375 201 :SAEEALRGLYGRVRKGA 1jxhA 154 :TEQEMLAQGRALLAMGC T0375 218 :VLVCA 1jxhA 172 :AVLMK T0375 229 :DALGPDG 1jxhA 188 :WLFTREG T0375 237 :LLH 1jxhA 195 :EQR T0375 246 :PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGI 1jxhA 203 :VNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEV Number of specific fragments extracted= 18 number of extra gaps= 0 total=903 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jxhA/T0375-1jxhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1jxhA/T0375-1jxhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jxhA read from 1jxhA/T0375-1jxhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jxhA in template set Warning: unaligning (T0375)V168 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)L116 Warning: unaligning (T0375)W223 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)D187 Warning: unaligning (T0375)A228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)D187 Warning: unaligning (T0375)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)R202 Warning: unaligning (T0375)P245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)R202 T0375 1 :GSQILCVGLV 1jxhA 3 :RINALTIAGT T0375 35 :WQRGGNAS 1jxhA 13 :DPSGGAGI T0375 68 :DFVLDDLRRYSVDLRYTVF 1jxhA 21 :QADLKTFSALGAYGCSVIT T0375 96 :TVIINEASGSRTILYYDR 1jxhA 40 :ALVAENTCGVQSVYRIEP T0375 120 :ATDFEKVDLT 1jxhA 61 :AAQLDSVFSD T0375 130 :QFKWIHIEGRNASEQVKML 1jxhA 72 :RIDTTKIGMLAETDIVEAV T0375 149 :QRIDAHNTR 1jxhA 92 :ERLQRHHVR T0375 158 :QPPEQ 1jxhA 102 :VVLDT T0375 169 :EVEKPREELFQ 1jxhA 117 :LSPSAIETLRV T0375 180 :LFGYGDVVFVSKDVAKHL 1jxhA 129 :LLPQVSLITPNLPEAAAL T0375 198 :GF 1jxhA 148 :DA T0375 200 :QSAEEALRGLYGRV 1jxhA 156 :QEMLAQGRALLAMG T0375 216 :GAVLVCA 1jxhA 170 :CEAVLMK T0375 229 :DALG 1jxhA 188 :WLFT T0375 234 :DGKLLH 1jxhA 192 :REGEQR T0375 246 :PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDGI 1jxhA 203 :VNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEV Number of specific fragments extracted= 16 number of extra gaps= 0 total=919 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jxhA/T0375-1jxhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1jxhA/T0375-1jxhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jxhA read from 1jxhA/T0375-1jxhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jxhA in template set Warning: unaligning (T0375)S167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)L116 Warning: unaligning (T0375)W223 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)D187 Warning: unaligning (T0375)A228 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)D187 Warning: unaligning (T0375)D241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jxhA)R202 Warning: unaligning (T0375)P245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jxhA)R202 T0375 1 :GSQILCVGL 1jxhA 3 :RINALTIAG T0375 17 :LV 1jxhA 12 :TD T0375 36 :QRGGNASNSC 1jxhA 14 :PSGGAGIQAD T0375 46 :TILSLLGAPCAFMG 1jxhA 25 :KTFSALGAYGCSVI T0375 94 :IATVIINEASGSRTIL 1jxhA 39 :TALVAENTCGVQSVYR T0375 111 :YD 1jxhA 55 :IE T0375 115 :LPDVSATDFEKVDLTQFKWIHIE 1jxhA 57 :PDFVAAQLDSVFSDVRIDTTKIG T0375 139 :RNASEQVKMLQRIDAHNTRQP 1jxhA 80 :MLAETDIVEAVAERLQRHHVR T0375 160 :PEQKIRV 1jxhA 102 :VVLDTVM T0375 172 :KPREELFQLF 1jxhA 120 :SAIETLRVRL T0375 182 :GYGDVVFVSKDVAKHLGFQ 1jxhA 131 :PQVSLITPNLPEAAALLDA T0375 201 :SAEEALRGL 1jxhA 153 :RTEQEMLAQ T0375 210 :YGRVRKGAVLVCA 1jxhA 164 :ALLAMGCEAVLMK T0375 229 :DALGPDG 1jxhA 188 :WLFTREG T0375 238 :LHS 1jxhA 195 :EQR T0375 246 :PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQV 1jxhA 203 :VNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAW Number of specific fragments extracted= 16 number of extra gaps= 0 total=935 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1td2A/T0375-1td2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1td2A expands to /projects/compbio/data/pdb/1td2.pdb.gz 1td2A:# T0375 read from 1td2A/T0375-1td2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td2A read from 1td2A/T0375-1td2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1td2A to template set # found chain 1td2A in template set T0375 1 :GSQILCVGL 1td2A 2 :MKNILAIQS T0375 34 :RWQRGGNASNSCT 1td2A 11 :HVVYGHAGNSAAE T0375 47 :ILSLLGAPCAFMG 1td2A 25 :PMRRLGANVWPLN T0375 83 :YTVFQTT 1td2A 38 :TVQFSNH T0375 101 :EASGSRTILY 1td2A 45 :TQYGKWTGCV T0375 118 :VSATDFEKV 1td2A 55 :MPPSHLTEI T0375 128 :LTQFKWIHIEGRNAS 1td2A 73 :LHTCDAVLSGYLGSA T0375 143 :EQVKMLQRIDAH 1td2A 92 :HILGIVRQVKAA T0375 155 :NTRQPPEQ 1td2A 106 :QAKYFCDP T0375 163 :KIRVSVEVEKPREELF 1td2A 118 :PEKGCIVAPGVAEFHV T0375 179 :QLFGYGDVVFVSKDVAKHL 1td2A 135 :HGLPASDIIAPNLVELEIL T0375 198 :GFQ 1td2A 155 :EHA T0375 201 :SAEEALRGLYGRVRKGA 1td2A 160 :NVEEAVLAARELIAQGP T0375 218 :VLVCAWAEEG 1td2A 178 :IVLVKHLARA T0375 228 :ADALGPD 1td2A 196 :MLLVTAD T0375 236 :KLLHSDAF 1td2A 203 :EAWHISRP T0375 245 :PPRV 1td2A 211 :LVDF T0375 249 :VDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKC 1td2A 217 :RQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIM Number of specific fragments extracted= 18 number of extra gaps= 0 total=953 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1td2A/T0375-1td2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1td2A/T0375-1td2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td2A read from 1td2A/T0375-1td2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1td2A in template set T0375 2 :SQILCVG 1td2A 3 :KNILAIQ T0375 33 :QRWQRGGNASNSCT 1td2A 10 :SHVVYGHAGNSAAE T0375 47 :ILSLLGAPCAFMG 1td2A 25 :PMRRLGANVWPLN T0375 83 :YTVFQTT 1td2A 38 :TVQFSNH T0375 101 :EASGSRTILY 1td2A 45 :TQYGKWTGCV T0375 118 :VSATDFE 1td2A 55 :MPPSHLT T0375 125 :KVDLTQFKWIHIEGRNASEQ 1td2A 70 :IDKLHTCDAVLSGYLGSAEQ T0375 145 :VKMLQRIDAH 1td2A 94 :LGIVRQVKAA T0375 155 :NTRQPPEQKIRVSVEV 1td2A 106 :QAKYFCDPVMGHPEKG T0375 171 :EKPREELFQ 1td2A 126 :PGVAEFHVR T0375 180 :LFGYGDVVFVSKDVAKHL 1td2A 136 :GLPASDIIAPNLVELEIL T0375 198 :GF 1td2A 155 :EH T0375 200 :QSAEEALRGLYGRV 1td2A 162 :EEAVLAARELIAQG T0375 216 :GAVLVCAWAEEG 1td2A 176 :PQIVLVKHLARA T0375 228 :ADALG 1td2A 196 :MLLVT T0375 234 :DGKLLHSDA 1td2A 201 :ADEAWHISR T0375 244 :PPPRV 1td2A 210 :PLVDF T0375 249 :VDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1td2A 217 :RQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMV Number of specific fragments extracted= 18 number of extra gaps= 0 total=971 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1td2A/T0375-1td2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1td2A/T0375-1td2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td2A read from 1td2A/T0375-1td2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1td2A in template set T0375 1 :GSQILCVGL 1td2A 2 :MKNILAIQS T0375 34 :RWQRGGNASNSC 1td2A 11 :HVVYGHAGNSAA T0375 46 :TILSLLGAPCAFMGSM 1td2A 24 :FPMRRLGANVWPLNTV T0375 82 :RYTVFQTTGSVP 1td2A 42 :SNHTQYGKWTGC T0375 109 :LYYDRSLPDVSATDFEKVDLTQFKWIHIEGRNASE 1td2A 54 :VMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAE T0375 144 :QVKMLQRIDAHN 1td2A 91 :EHILGIVRQVKA T0375 156 :TRQPPEQKIRVSVEVE 1td2A 105 :PQAKYFCDPVMGHPEK T0375 172 :KPREELFQLF 1td2A 127 :GVAEFHVRHG T0375 182 :GYGDVVFVSKDVAKHLGFQ 1td2A 138 :PASDIIAPNLVELEILCEH T0375 202 :AEEALRGLYGRVRKGAVLVCAWAEE 1td2A 162 :EEAVLAARELIAQGPQIVLVKHLAR T0375 227 :GADALGPDGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKK 1td2A 195 :EMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEI Number of specific fragments extracted= 11 number of extra gaps= 0 total=982 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kyhA/T0375-1kyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kyhA expands to /projects/compbio/data/pdb/1kyh.pdb.gz 1kyhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 1kyhA/T0375-1kyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kyhA read from 1kyhA/T0375-1kyhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kyhA to template set # found chain 1kyhA in template set T0375 2 :SQILCVG 1kyhA 28 :GTALLLA T0375 18 :VDKYP 1kyhA 36 :SDDMP T0375 39 :GNASNSCTILSLLGAPCAFMGS 1kyhA 41 :GAALLAGLGAMRSGLGKLVIGT T0375 101 :EAS 1kyhA 63 :SEN T0375 112 :DRSLPDVS 1kyhA 71 :VPVLPEAT T0375 120 :ATDFEKVD 1kyhA 81 :RDGWKKAA T0375 128 :LT 1kyhA 92 :LE T0375 130 :QFKWIHIEGRNA 1kyhA 95 :TYRAIAIGPGLP T0375 142 :SEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKP 1kyhA 109 :ESVQQAVDHVLTADCPVILDAGALAKRTYPKR T0375 182 :GYGDVVFVSKDVAKHL 1kyhA 141 :EGPVILTPHPGEFFRM T0375 198 :GFQ 1kyhA 158 :GVP T0375 202 :AEEALRGLYGR 1kyhA 169 :AEYAKEWAAQL T0375 216 :GAVLVCA 1kyhA 180 :QTVIVLK T0375 225 :EEGADALGPDGKLLHSDAF 1kyhA 187 :GNQTVIAFPDGDCWLNPTG T0375 246 :PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 1kyhA 206 :NGALAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAEL T0375 290 :QGFDGIV 1kyhA 254 :HSAHTLL Number of specific fragments extracted= 16 number of extra gaps= 0 total=998 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kyhA/T0375-1kyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1kyhA/T0375-1kyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kyhA read from 1kyhA/T0375-1kyhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kyhA in template set T0375 2 :SQILCVG 1kyhA 28 :GTALLLA T0375 18 :VDKYP 1kyhA 36 :SDDMP T0375 39 :GNASNSCTILSLLGAPCAFMG 1kyhA 41 :GAALLAGLGAMRSGLGKLVIG T0375 61 :MAPG 1kyhA 62 :TSEN T0375 66 :VADFV 1kyhA 66 :VIPLI T0375 103 :SGS 1kyhA 75 :PEA T0375 109 :LYYDR 1kyhA 78 :TYWRD T0375 114 :SLPDVS 1kyhA 88 :ADAQLE T0375 129 :TQFKWIHIEG 1kyhA 94 :ETYRAIAIGP T0375 139 :RNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVEKP 1kyhA 106 :PQTESVQQAVDHVLTADCPVILDAGALAKRTYPKR T0375 182 :GYGDVVFVSKDVAKHL 1kyhA 141 :EGPVILTPHPGEFFRM T0375 198 :GF 1kyhA 158 :GV T0375 200 :QSAEEAL 1kyhA 166 :KKRAEYA T0375 207 :RGLYGRV 1kyhA 174 :EWAAQLQ T0375 216 :G 1kyhA 181 :T T0375 220 :VCAWAEEGADALGPDGKLLHSDAFP 1kyhA 182 :VIVLKGNQTVIAFPDGDCWLNPTGN T0375 249 :VDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 1kyhA 209 :LAKGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAEL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1015 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kyhA/T0375-1kyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1kyhA/T0375-1kyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kyhA read from 1kyhA/T0375-1kyhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kyhA in template set T0375 2 :SQILCVGL 1kyhA 28 :GTALLLAG T0375 18 :VDK 1kyhA 36 :SDD T0375 37 :RGGNASNSCTILSLLGAPCAFMGSMAP 1kyhA 39 :MPGAALLAGLGAMRSGLGKLVIGTSEN T0375 66 :VADFV 1kyhA 66 :VIPLI T0375 87 :QTT 1kyhA 74 :LPE T0375 108 :ILYYDRSLPDVSATDFE 1kyhA 77 :ATYWRDGWKKAADAQLE T0375 129 :TQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVSVEVE 1kyhA 94 :ETYRAIAIGPGLPQTESVQQAVDHVLTADCPVILDAGALAKRT T0375 182 :GYGDVVFVSKDVAKHLGFQSAEE 1kyhA 141 :EGPVILTPHPGEFFRMTGVPVNE T0375 205 :ALRGLYGRVRKG 1kyhA 170 :EYAKEWAAQLQT T0375 220 :VCAWAEEGADALGPDGKLLHSDAFP 1kyhA 182 :VIVLKGNQTVIAFPDGDCWLNPTGN T0375 251 :TLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1kyhA 211 :KGGTGDTLTGMILGMLCCHEDPKHAVLNAVYLHGACAE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1026 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8aA/T0375-1v8aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v8aA expands to /projects/compbio/data/pdb/1v8a.pdb.gz 1v8aA:Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 1v8aA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 1v8aA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 1v8aA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 1v8aA # T0375 read from 1v8aA/T0375-1v8aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8aA read from 1v8aA/T0375-1v8aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v8aA to template set # found chain 1v8aA in template set Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v8aA)G143 Warning: unaligning (T0375)A202 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1v8aA)E144 T0375 54 :PCAFMGSMAP 1v8aA 15 :RPLVHNITNF T0375 65 :HVADFVLDDLRRYSVDLRY 1v8aA 25 :VVMNTTANALLALGASPVM T0375 117 :DVSATDFEKV 1v8aA 44 :AHAEEELEEM T0375 128 :LTQFKWIHIEGRNA 1v8aA 54 :IRLADAVVINIGTL T0375 142 :S 1v8aA 69 :S T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1v8aA 74 :SMVKATEIANELGKPIVLDP T0375 163 :KIRVS 1v8aA 95 :GAGAT T0375 171 :EKPREELFQLF 1v8aA 100 :KFRTRVSLEIL T0375 182 :GYGDVVFVSKDVAKHL 1v8aA 112 :RGVDVLKGNFGEISAL T0375 198 :G 1v8aA 129 :G T0375 203 :EEALRGLYGRVRK 1v8aA 145 :EEAKKLTMNAARE T0375 216 :GAVLVCAW 1v8aA 159 :NTTVAVTG T0375 226 :EGADALGPD 1v8aA 167 :AVDYVSDGR T0375 236 :KLLHSDAF 1v8aA 176 :RTFAVYNG T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1v8aA 184 :HELLGRVTGTGCMVAALTGAFVAV T0375 270 :RSVQEALRFGCQVAGKKCG 1v8aA 208 :TEPLKATTSALVTFGIAAE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1042 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8aA/T0375-1v8aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1v8aA/T0375-1v8aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8aA read from 1v8aA/T0375-1v8aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8aA in template set T0375 44 :SCTILSLL 1v8aA 4 :IIEALKRV T0375 54 :PCAFMGSMA 1v8aA 15 :RPLVHNITN T0375 64 :GHVADFVLDDLRRYSVDL 1v8aA 24 :FVVMNTTANALLALGASP T0375 84 :TVF 1v8aA 42 :VMA T0375 118 :VSATDFEKV 1v8aA 45 :HAEEELEEM T0375 128 :LTQFKWIHIE 1v8aA 54 :IRLADAVVIN T0375 138 :GRNASEQ 1v8aA 65 :GTLDSGW T0375 145 :VKMLQRIDAHNTRQPPEQ 1v8aA 76 :VKATEIANELGKPIVLDP T0375 163 :KIRVS 1v8aA 95 :GAGAT T0375 171 :EKPREELFQLFGY 1v8aA 100 :KFRTRVSLEILSR T0375 184 :GDVVFVSKDVAKHL 1v8aA 114 :VDVLKGNFGEISAL T0375 198 :GF 1v8aA 129 :GE T0375 200 :QSAEEALRGLYGR 1v8aA 145 :EEAKKLTMNAARE T0375 214 :RKG 1v8aA 158 :FNT T0375 218 :VLVCAW 1v8aA 161 :TVAVTG T0375 226 :EGADALG 1v8aA 167 :AVDYVSD T0375 234 :DGKLLHSDAF 1v8aA 174 :GRRTFAVYNG T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQ 1v8aA 184 :HELLGRVTGTGCMVAALTGAFVAV T0375 270 :RSVQEALRFGCQVAGKKCG 1v8aA 208 :TEPLKATTSALVTFGIAAE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1061 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8aA/T0375-1v8aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1v8aA/T0375-1v8aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8aA read from 1v8aA/T0375-1v8aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8aA in template set Warning: unaligning (T0375)S201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v8aA)G143 Warning: unaligning (T0375)A202 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1v8aA)E144 T0375 44 :SCTILSLL 1v8aA 4 :IIEALKRV T0375 52 :GAPCAFMGS 1v8aA 15 :RPLVHNITN T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTT 1v8aA 24 :FVVMNTTANALLALGASPVMAHAEEE T0375 123 :F 1v8aA 50 :L T0375 125 :KVDLTQFKWIHIEGRNASE 1v8aA 51 :EEMIRLADAVVINIGTLDS T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLF 1v8aA 73 :RSMVKATEIANELGKPIVLDPVGAGATKFRTRVSLEIL T0375 182 :GYGDVVFVSKDVAKHLGFQ 1v8aA 112 :RGVDVLKGNFGEISALLGE T0375 203 :EEALRGLYGRVR 1v8aA 145 :EEAKKLTMNAAR T0375 215 :KG 1v8aA 159 :NT T0375 218 :VLVCA 1v8aA 161 :TVAVT T0375 225 :EEGADALGPDGK 1v8aA 166 :GAVDYVSDGRRT T0375 238 :LHSDAFPP 1v8aA 178 :FAVYNGHE T0375 251 :TLGAG 1v8aA 190 :VTGTG T0375 257 :TFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 1v8aA 195 :CMVAALTGAFVAVTEPLKATTSALVTFGIAAEK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1075 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ua4A/T0375-1ua4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ua4A expands to /projects/compbio/data/pdb/1ua4.pdb.gz 1ua4A:# T0375 read from 1ua4A/T0375-1ua4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ua4A read from 1ua4A/T0375-1ua4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ua4A to template set # found chain 1ua4A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1ua4A)Y29 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1ua4A)Y29 T0375 2 :SQILC 1ua4A 23 :KGVLL T0375 9 :LVVLDVISLVDK 1ua4A 30 :NTNIDAIKYLDS T0375 38 :GGNASNSCTILSLL 1ua4A 111 :GGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGHVA 1ua4A 126 :GVPVIVHVPQLSRLQA T0375 76 :RY 1ua4A 142 :NL T0375 80 :DLRYTVFQTTGSVPI 1ua4A 148 :PIYVPTLENGEVKLI T0375 95 :ATVIINEAS 1ua4A 176 :HYIYEFPRG T0375 105 :SRTILYYDRSLPDVS 1ua4A 196 :NRFIGSADDYNTTLF T0375 120 :ATDFE 1ua4A 212 :REEFR T0375 125 :KVD 1ua4A 218 :SFS T0375 128 :LTQFKWIHIEGRN 1ua4A 223 :IKNVQLAILSGLQ T0375 142 :S 1ua4A 240 :E T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVS 1ua4A 248 :IVKSNLEVLNEREIPVHLEFAFTPD T0375 171 :EKPREELFQLFGYGDVVFVSKDVA 1ua4A 273 :EKVREEILNVLGMFYSVGLNEVEL T0375 195 :KHLGFQ 1ua4A 301 :EILGEK T0375 201 :SAEEALRGLYGRVRK 1ua4A 319 :DPIAVTEAMLKLAKK T0375 216 :GA 1ua4A 335 :GV T0375 219 :LVCAWAEEGADALGP 1ua4A 338 :RIHFHTYGYYLALTE T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1ua4A 418 :GYQIAFIPTKIVAKPKSTVGIGDTISSSAFIGEF Number of specific fragments extracted= 19 number of extra gaps= 1 total=1094 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ua4A/T0375-1ua4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ua4A/T0375-1ua4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ua4A read from 1ua4A/T0375-1ua4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ua4A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1ua4A)Y29 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1ua4A)Y29 T0375 2 :SQILC 1ua4A 23 :KGVLL T0375 9 :LVVLDVISLVD 1ua4A 30 :NTNIDAIKYLD T0375 29 :RCLSQRWQRGGNASNSCTILSLL 1ua4A 102 :RWGWNELRMGGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGHVA 1ua4A 126 :GVPVIVHVPQLSRLQA T0375 76 :RY 1ua4A 142 :NL T0375 80 :DLRYTVFQTT 1ua4A 148 :PIYVPTLENG T0375 91 :SVPIATVIINE 1ua4A 172 :ENCIHYIYEFP T0375 103 :SG 1ua4A 183 :RG T0375 105 :SRTILYYDR 1ua4A 196 :NRFIGSADD T0375 114 :SLPDVSATDFEKVD 1ua4A 206 :NTTLFIREEFRESF T0375 128 :LTQFKWIHIEG 1ua4A 223 :IKNVQLAILSG T0375 139 :RNASEQ 1ua4A 241 :NYKEPF T0375 145 :VKMLQRIDAHNTRQPPEQKIRV 1ua4A 250 :KSNLEVLNEREIPVHLEFAFTP T0375 170 :VEKPREELFQLFGYGDVVFVSKDVA 1ua4A 272 :DEKVREEILNVLGMFYSVGLNEVEL T0375 195 :KHLGF 1ua4A 301 :EILGE T0375 200 :QSAE 1ua4A 318 :VDPI T0375 204 :EALRGLYGRV 1ua4A 325 :EAMLKLAKKT T0375 215 :KGAVLVCAWAEE 1ua4A 335 :GVKRIHFHTYGY T0375 228 :ADALGP 1ua4A 347 :YLALTE T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1ua4A 418 :GYQIAFIPTKIVAKPKSTVGIGDTISSSAFIGEF Number of specific fragments extracted= 20 number of extra gaps= 1 total=1114 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ua4A/T0375-1ua4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ua4A/T0375-1ua4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ua4A read from 1ua4A/T0375-1ua4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ua4A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1ua4A)Y29 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1ua4A)Y29 T0375 2 :SQILC 1ua4A 23 :KGVLL T0375 9 :LVVLDVISLVD 1ua4A 30 :NTNIDAIKYLD T0375 37 :RGGNASNSCTILSLL 1ua4A 110 :MGGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGHVA 1ua4A 126 :GVPVIVHVPQLSRLQA T0375 76 :RYSV 1ua4A 142 :NLFL T0375 80 :DLRYTVFQTT 1ua4A 148 :PIYVPTLENG T0375 90 :GSVPIATVIINEA 1ua4A 172 :ENCIHYIYEFPRG T0375 103 :SGSRTILYYDR 1ua4A 194 :RENRFIGSADD T0375 114 :SLPDVSATDF 1ua4A 206 :NTTLFIREEF T0375 124 :EKVDLTQFKWIHIEGRNASE 1ua4A 219 :FSEVIKNVQLAILSGLQALT T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVS 1ua4A 247 :EIVKSNLEVLNEREIPVHLEFAFT T0375 169 :EVEKPREELFQLFGYGDVVFVS 1ua4A 271 :PDEKVREEILNVLGMFYSVGLN T0375 191 :KDVAKHLGFQ 1ua4A 306 :KKLAKELLAH T0375 201 :SAEE 1ua4A 319 :DPIA T0375 205 :ALRGLYGRVRKGAVLVCAWA 1ua4A 325 :EAMLKLAKKTGVKRIHFHTY T0375 226 :EGADALGPDG 1ua4A 345 :GYYLALTEYK T0375 236 :KLLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1ua4A 420 :QIAFIPTKIVAKPKSTVGIGDTISSSAFIGEF Number of specific fragments extracted= 17 number of extra gaps= 1 total=1131 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ekqA/T0375-1ekqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ekqA expands to /projects/compbio/data/pdb/1ekq.pdb.gz 1ekqA:# T0375 read from 1ekqA/T0375-1ekqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ekqA read from 1ekqA/T0375-1ekqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ekqA to template set # found chain 1ekqA in template set Warning: unaligning (T0375)G198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)G147 Warning: unaligning (T0375)G255 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ekqA)L199 Warning: unaligning (T0375)T257 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)L199 T0375 41 :ASNSCTILSL 1ekqA 6 :AAKCLTAVRR T0375 54 :PCAFMGSMAP 1ekqA 17 :SPLVHSITNN T0375 65 :HVADFVLDDLRRYSVDLRY 1ekqA 27 :VVTNFTANGLLALGASPVM T0375 117 :DVSATDFEK 1ekqA 46 :AYAKEEVAD T0375 127 :DLTQFKWIHIEGRNA 1ekqA 55 :MAKIAGALVLNIGTL T0375 142 :S 1ekqA 71 :K T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1ekqA 76 :AMIIAGKSANEHGVPVILDP T0375 163 :KIRVS 1ekqA 97 :GAGAT T0375 171 :EKPREELFQLFGY 1ekqA 102 :PFRTESARDIIRE T0375 184 :GDVVFVSKDVAKHL 1ekqA 117 :LAAIRGNAAEIAHT T0375 203 :EEALRGLYGRVRK 1ekqA 148 :GDIIRLAQQAAQK T0375 216 :GAVLVCA 1ekqA 162 :NTVIAIT T0375 225 :EEGADALGPD 1ekqA 169 :GEVDVIADTS T0375 236 :KLLHSDAF 1ekqA 179 :HVYTLHNG T0375 245 :PPRVVDTLGA 1ekqA 187 :HKLLTKVTGA T0375 258 :FNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1ekqA 200 :LTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1147 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ekqA/T0375-1ekqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ekqA/T0375-1ekqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ekqA read from 1ekqA/T0375-1ekqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ekqA in template set Warning: unaligning (T0375)G198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)G147 Warning: unaligning (T0375)G255 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ekqA)L199 Warning: unaligning (T0375)T257 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)L199 T0375 41 :ASNSCTILSLL 1ekqA 6 :AAKCLTAVRRH T0375 54 :PCAFMGSMA 1ekqA 17 :SPLVHSITN T0375 64 :GHVADFVLDDLRRYSVDLRY 1ekqA 26 :NVVTNFTANGLLALGASPVM T0375 117 :DVSATDFEK 1ekqA 46 :AYAKEEVAD T0375 127 :DLTQFKWIHIE 1ekqA 55 :MAKIAGALVLN T0375 138 :GRNASEQ 1ekqA 67 :GTLSKES T0375 145 :VKMLQRIDAHNTRQPPEQ 1ekqA 78 :IIAGKSANEHGVPVILDP T0375 163 :KIRVS 1ekqA 97 :GAGAT T0375 171 :EKPREELFQLFGY 1ekqA 102 :PFRTESARDIIRE T0375 184 :GDVVFVSKDVAKHL 1ekqA 117 :LAAIRGNAAEIAHT T0375 200 :QSAEEALRGLYGRV 1ekqA 148 :GDIIRLAQQAAQKL T0375 215 :K 1ekqA 162 :N T0375 217 :AVLVCA 1ekqA 163 :TVIAIT T0375 225 :EEGADALG 1ekqA 169 :GEVDVIAD T0375 234 :DGKLLHSDAF 1ekqA 177 :TSHVYTLHNG T0375 245 :PPRVVDTLGA 1ekqA 187 :HKLLTKVTGA T0375 258 :FNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1ekqA 200 :LTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 17 number of extra gaps= 0 total=1164 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ekqA/T0375-1ekqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ekqA/T0375-1ekqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ekqA read from 1ekqA/T0375-1ekqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ekqA in template set Warning: unaligning (T0375)G198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ekqA)G147 Warning: unaligning (T0375)F199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)G147 Warning: unaligning (T0375)G255 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ekqA)L199 Warning: unaligning (T0375)T257 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ekqA)L199 T0375 41 :ASNSCTILSLLGAPCAFMG 1ekqA 6 :AAKCLTAVRRHSPLVHSIT T0375 63 :PGHVADFVLDDLRRYSVDLRYTVFQTT 1ekqA 25 :NNVVTNFTANGLLALGASPVMAYAKEE T0375 124 :EKVDLTQFKWIHIEGRNASE 1ekqA 52 :VADMAKIAGALVLNIGTLSK T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYG 1ekqA 75 :EAMIIAGKSANEHGVPVILDPVGAGATPFRTESARDIIREV T0375 185 :DVVFVSKDVAKHL 1ekqA 118 :AAIRGNAAEIAHT T0375 203 :EEALRGLYGRVR 1ekqA 148 :GDIIRLAQQAAQ T0375 215 :K 1ekqA 162 :N T0375 217 :AVLVCA 1ekqA 163 :TVIAIT T0375 225 :EEGADALGPDGK 1ekqA 169 :GEVDVIADTSHV T0375 238 :LHSDAFPP 1ekqA 181 :YTLHNGHK T0375 251 :TLGA 1ekqA 193 :VTGA T0375 258 :FNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1ekqA 200 :LTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=1176 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2xA/T0375-1u2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u2xA expands to /projects/compbio/data/pdb/1u2x.pdb.gz 1u2xA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 1u2xA/T0375-1u2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2xA read from 1u2xA/T0375-1u2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u2xA to template set # found chain 1u2xA in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)Y34 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)Y34 Warning: unaligning (T0375)V118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u2xA)T222 Warning: unaligning (T0375)S119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u2xA)T222 Warning: unaligning (T0375)G227 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)L362 Warning: unaligning (T0375)A228 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)L362 T0375 2 :SQILC 1u2xA 28 :LSIYT T0375 9 :LVVLDVISLVDK 1u2xA 35 :NANIDAIVKLNQ T0375 38 :GGNASNSCTILSLLGAP 1u2xA 117 :GGQAGIIANTLAGLKIR T0375 55 :CAFMGSMAP 1u2xA 135 :VIAYTPFLP T0375 68 :DFVL 1u2xA 144 :KRLA T0375 76 :RY 1u2xA 148 :EL T0375 78 :S 1u2xA 153 :G T0375 81 :LRYTVFQTTGSVPI 1u2xA 154 :VLYPVVENGELQFK T0375 95 :ATVII 1u2xA 183 :RIFEF T0375 101 :EAS 1u2xA 188 :RKG T0375 104 :GSRTILYY 1u2xA 205 :SGRFIVSA T0375 112 :DRSLPD 1u2xA 215 :ESISRI T0375 120 :ATDFEKVD 1u2xA 223 :REDIKPFL T0375 128 :LTQFKWIHIEGRN 1u2xA 234 :GKEVDGAIFSGYQ T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1u2xA 264 :RAKEDIIEFKEKDVKIHVEF T0375 166 :VSVEVEKPREELF 1u2xA 284 :ASVQDRKLRKKII T0375 179 :QLFGYGDVVFVSKDVAKHL 1u2xA 298 :NILPFVDSVGIDEAEIAQI T0375 198 :GFQ 1u2xA 321 :GYR T0375 201 :SAEEALRGLYGRVRK 1u2xA 334 :RLEDSILGGMIILDE T0375 216 :GAVLVCAWAEE 1u2xA 350 :NFEILQVHTTY T0375 229 :DALGP 1u2xA 363 :MYITH T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 1u2xA 433 :EYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLE Number of specific fragments extracted= 22 number of extra gaps= 3 total=1198 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2xA/T0375-1u2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1u2xA/T0375-1u2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2xA read from 1u2xA/T0375-1u2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u2xA in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)Y34 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)Y34 Warning: unaligning (T0375)R34 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)E114 Warning: unaligning (T0375)W35 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)E114 Warning: unaligning (T0375)V118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u2xA)T222 Warning: unaligning (T0375)S119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u2xA)T222 Warning: unaligning (T0375)E226 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)L362 Warning: unaligning (T0375)G227 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)L362 T0375 1 :GSQILC 1u2xA 27 :HLSIYT T0375 9 :LVVLDVISLVD 1u2xA 35 :NANIDAIVKLN T0375 29 :RCLSQ 1u2xA 108 :TFRYE T0375 36 :QRGGNASNSCTILSLLGAP 1u2xA 115 :RLGGQAGIIANTLAGLKIR T0375 55 :CAFMGSMAPGHVA 1u2xA 135 :VIAYTPFLPKRLA T0375 76 :RY 1u2xA 148 :EL T0375 78 :S 1u2xA 153 :G T0375 81 :LRYTVFQTTG 1u2xA 154 :VLYPVVENGE T0375 91 :SVPIATVIINE 1u2xA 178 :PLKINRIFEFR T0375 103 :SG 1u2xA 189 :KG T0375 105 :SRTILYY 1u2xA 206 :GRFIVSA T0375 112 :DRSLPD 1u2xA 215 :ESISRI T0375 120 :ATDFEKVD 1u2xA 223 :REDIKPFL T0375 128 :LTQFKWIHIEG 1u2xA 234 :GKEVDGAIFSG T0375 139 :RNASEQ 1u2xA 256 :KDANYY T0375 145 :VKMLQRIDAHNTRQPPEQ 1u2xA 266 :KEDIIEFKEKDVKIHVEF T0375 166 :VSVEVEKPREELFQ 1u2xA 284 :ASVQDRKLRKKIIT T0375 180 :LFGYGDVVFVSKDVAKHL 1u2xA 299 :ILPFVDSVGIDEAEIAQI T0375 198 :GF 1u2xA 321 :GY T0375 200 :QSAEEALR 1u2xA 333 :NRLEDSIL T0375 208 :GLYGRV 1u2xA 344 :IILDEL T0375 215 :KGAVLVCAWAE 1u2xA 350 :NFEILQVHTTY T0375 228 :ADALGP 1u2xA 363 :MYITHR T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 1u2xA 433 :EYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLE Number of specific fragments extracted= 24 number of extra gaps= 4 total=1222 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2xA/T0375-1u2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1u2xA/T0375-1u2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2xA read from 1u2xA/T0375-1u2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u2xA in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)Y34 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)Y34 Warning: unaligning (T0375)V118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1u2xA)T222 Warning: unaligning (T0375)S119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1u2xA)T222 Warning: unaligning (T0375)E226 because of BadResidue code BAD_PEPTIDE in next template residue (1u2xA)L362 Warning: unaligning (T0375)G227 because of BadResidue code BAD_PEPTIDE at template residue (1u2xA)L362 T0375 2 :SQILC 1u2xA 28 :LSIYT T0375 9 :LVVLDVISLVDK 1u2xA 35 :NANIDAIVKLNQ T0375 37 :RGGNASNSCTILSLLGAPCAFMGSMAPG 1u2xA 116 :LGGQAGIIANTLAGLKIRKVIAYTPFLP T0375 68 :D 1u2xA 144 :K T0375 73 :DLRRY 1u2xA 145 :RLAEL T0375 78 :SV 1u2xA 153 :GV T0375 80 :DLRYTVFQTTGSVPIATVIINEA 1u2xA 168 :PIQEAYREGDPLKINRIFEFRKG T0375 103 :SGSRTILYYDR 1u2xA 204 :NSGRFIVSARF T0375 114 :SLPD 1u2xA 217 :ISRI T0375 120 :ATDF 1u2xA 223 :REDI T0375 124 :EKVDLTQFKWIHIEGRNASE 1u2xA 230 :LGEIGKEVDGAIFSGYQGLR T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1u2xA 263 :RRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSV T0375 202 :AEEALRGLYGRVRKGAVLVCAWAE 1u2xA 337 :DSILGGMIILDELNFEILQVHTTY T0375 228 :ADALGPDG 1u2xA 363 :MYITHRDN T0375 236 :KLLHSDAFPPPRVVDTLGAGDTFNASVIFSLSQ 1u2xA 435 :KVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLE Number of specific fragments extracted= 15 number of extra gaps= 3 total=1237 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc5A/T0375-1gc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gc5A expands to /projects/compbio/data/pdb/1gc5.pdb.gz 1gc5A:# T0375 read from 1gc5A/T0375-1gc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc5A read from 1gc5A/T0375-1gc5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gc5A to template set # found chain 1gc5A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1gc5A)Y37 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1gc5A)Y37 T0375 2 :SQILC 1gc5A 31 :KGVLL T0375 9 :LVVLDVISLVDK 1gc5A 38 :NTNIDAIKYLDA T0375 38 :GGNASNSCTILSLL 1gc5A 119 :GGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGH 1gc5A 134 :RIPTIVHVPQNPKL T0375 74 :LRRYSVD 1gc5A 148 :QAELFVD T0375 81 :LRYTVFQTTGSVP 1gc5A 157 :IYVPVFEGNKLKL T0375 94 :IATVII 1gc5A 184 :HYIYEF T0375 102 :ASGSRTILYYDRSLPDVS 1gc5A 201 :PRENRFIANADDYNARVY T0375 121 :TDFEKVD 1gc5A 221 :REFREGF T0375 128 :LTQFKWIHIEG 1gc5A 231 :TRNVELAIISG T0375 139 :RNAS 1gc5A 248 :YYPD T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1gc5A 261 :RVESHLNILNRYNVKSHFEF T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVA 1gc5A 281 :AYTANRRVREALVELLPKFTSVGLNEVEL T0375 195 :KHLGFQ 1gc5A 314 :EIIGDE T0375 201 :SAEEALRGLYGRVRK 1gc5A 329 :HIFSVIDAMNVLMDE T0375 216 :GAVLVCAWAEEGADALGP 1gc5A 345 :GIERIHFHTYGYYLALTQ T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1gc5A 429 :DRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEF Number of specific fragments extracted= 17 number of extra gaps= 1 total=1254 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc5A/T0375-1gc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1gc5A/T0375-1gc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc5A read from 1gc5A/T0375-1gc5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gc5A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1gc5A)Y37 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1gc5A)Y37 T0375 2 :SQILC 1gc5A 31 :KGVLL T0375 9 :LVVLDVISLVD 1gc5A 38 :NTNIDAIKYLD T0375 31 :LSQRWQRGGNASNSCTILSLL 1gc5A 112 :GWDELRIGGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGHVA 1gc5A 134 :RIPTIVHVPQNPKLQA T0375 76 :RYSV 1gc5A 150 :ELFV T0375 80 :DLRYTVFQTTG 1gc5A 156 :PIYVPVFEGNK T0375 91 :SVPIATVIINE 1gc5A 181 :ELIHYIYEFPR T0375 102 :ASGSRTILYYDR 1gc5A 200 :APRENRFIANAD T0375 114 :SLPDVS 1gc5A 213 :YNARVY T0375 120 :ATDFE 1gc5A 220 :RREFR T0375 125 :KVDLTQFKWIHIEG 1gc5A 228 :EEITRNVELAIISG T0375 139 :RNASEQ 1gc5A 253 :TTYKDV T0375 145 :VKMLQRIDAHNTRQPPEQ 1gc5A 263 :ESHLNILNRYNVKSHFEF T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVA 1gc5A 281 :AYTANRRVREALVELLPKFTSVGLNEVEL T0375 195 :KHLGF 1gc5A 314 :EIIGD T0375 200 :QSAE 1gc5A 328 :GHIF T0375 204 :EALRGLYGRV 1gc5A 335 :DAMNVLMDET T0375 215 :KGAVLVCA 1gc5A 345 :GIERIHFH T0375 224 :AEEGADALGP 1gc5A 353 :TYGYYLALTQ T0375 234 :DGKLLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1gc5A 429 :DRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEF Number of specific fragments extracted= 20 number of extra gaps= 1 total=1274 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gc5A/T0375-1gc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1gc5A/T0375-1gc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gc5A read from 1gc5A/T0375-1gc5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gc5A in template set Warning: unaligning (T0375)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1gc5A)Y37 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE at template residue (1gc5A)Y37 T0375 2 :SQILC 1gc5A 31 :KGVLL T0375 9 :LVVLDVISLVD 1gc5A 38 :NTNIDAIKYLD T0375 37 :RGGNASNSCTILSLL 1gc5A 118 :IGGQAGIMANLLGGV T0375 52 :GAPCAFMGSMAPGH 1gc5A 134 :RIPTIVHVPQNPKL T0375 74 :LRRYSV 1gc5A 148 :QAELFV T0375 80 :DLRYTVFQTTGS 1gc5A 156 :PIYVPVFEGNKL T0375 92 :VPIATVIINEA 1gc5A 182 :LIHYIYEFPRG T0375 103 :SGSRTILYYDR 1gc5A 202 :RENRFIANADD T0375 114 :SLPDVSATDF 1gc5A 214 :NARVYMRREF T0375 124 :EKVDLTQFKWIHIEGRNASE 1gc5A 227 :FEEITRNVELAIISGLQVLK T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVS 1gc5A 260 :DRVESHLNILNRYNVKSHFEFAYT T0375 169 :EVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1gc5A 284 :ANRRVREALVELLPKFTSVGLNEVELASIMEI T0375 205 :ALRGLYGRVRKGAVLVCA 1gc5A 335 :DAMNVLMDETGIERIHFH T0375 224 :AEEGADALGPDG 1gc5A 353 :TYGYYLALTQYR T0375 237 :LLHSDAFPPPRVVDTLGAGDTFNASVIFSLS 1gc5A 432 :LAFVPTKIVASPKSTVGIGDTISSSAFVSEF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1289 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ax3A/T0375-2ax3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ax3A expands to /projects/compbio/data/pdb/2ax3.pdb.gz 2ax3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 802, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 2ax3A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1696, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1702, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1704, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1706, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1710, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1712, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 2ax3A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2139, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2143, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2145, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2147, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2149, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2282, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2286, because occupancy 0.400 <= existing 0.600 in 2ax3A Skipped atom 2288, because occupancy 0.400 <= existing 0.600 in 2ax3A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3191, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 3195, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 3197, because occupancy 0.500 <= existing 0.500 in 2ax3A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3535, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 3539, because occupancy 0.500 <= existing 0.500 in 2ax3A Skipped atom 3541, because occupancy 0.500 <= existing 0.500 in 2ax3A # T0375 read from 2ax3A/T0375-2ax3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ax3A read from 2ax3A/T0375-2ax3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ax3A to template set # found chain 2ax3A in template set Warning: unaligning (T0375)E161 because of BadResidue code BAD_PEPTIDE in next template residue (2ax3A)A343 Warning: unaligning (T0375)Q162 because of BadResidue code BAD_PEPTIDE at template residue (2ax3A)A343 Warning: unaligning (T0375)V189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ax3A)H366 Warning: unaligning (T0375)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ax3A)H366 T0375 2 :SQILCVGLV 2ax3A 233 :GKVLIIAGS T0375 35 :WQRGGNASNSCTILSLLGAP 2ax3A 242 :RLYSGAPVLSGMGSLKVGTG T0375 55 :CAFMGSMAPGHVA 2ax3A 263 :VKLAVPFPQNLIA T0375 75 :RRY 2ax3A 276 :TSR T0375 78 :S 2ax3A 281 :E T0375 81 :LRYTVFQTTG 2ax3A 282 :LISVPIDTEK T0375 116 :PDVSATDFEKVD 2ax3A 292 :GFFSLQNLQECL T0375 128 :LTQFKWIHIEGRNA 2ax3A 306 :SKDVDVVAIGPGLG T0375 142 :SEQVKMLQRIDAH 2ax3A 322 :EHVREFVNEFLKT T0375 155 :NTRQPP 2ax3A 336 :EKPAVI T0375 163 :KIRVSV 2ax3A 344 :DAINVL T0375 173 :PREELFQLFGYG 2ax3A 350 :DTSVLKERKSPA T0375 186 :VVF 2ax3A 362 :VLT T0375 191 :KDVAKHL 2ax3A 367 :PGEMARL T0375 198 :GFQ 2ax3A 375 :KKT T0375 201 :SAEEALRGLYGR 2ax3A 384 :NYELAEEFAKEN T0375 216 :GAVLVCA 2ax3A 396 :DCVLVLK T0375 225 :EEGADALGPD 2ax3A 403 :SATTIVTDGE T0375 236 :KLLHSDAF 2ax3A 413 :KTLFNITG T0375 246 :PRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFDG 2ax3A 421 :NTGLSKGGSGDVLTGMIAGFIAQGLSPLEASTVSVYLHGFAAELFEQDE Number of specific fragments extracted= 20 number of extra gaps= 2 total=1309 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ax3A/T0375-2ax3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2ax3A/T0375-2ax3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ax3A read from 2ax3A/T0375-2ax3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ax3A in template set T0375 1 :GSQILCVG 2ax3A 40 :DYRFLVLC T0375 38 :GGNASNSCTILSLL 2ax3A 49 :GGNNGGDGFVVARN T0375 52 :GAPCAFMGSMAPG 2ax3A 66 :VVKDVLVVFLGKK T0375 65 :HVADFVLDDLRRYSVDL 2ax3A 81 :PDCEYNYGLYKKFGGKV T0375 87 :QTT 2ax3A 98 :VEQ T0375 123 :FEKVDLTQFKWIHIEGRN 2ax3A 101 :FEPSILNEFDVVVDAIFG T0375 141 :ASEQVKMLQRIDAHNTRQ 2ax3A 126 :TGEYAEIINLVNKSGKVV T0375 159 :PPEQ 2ax3A 145 :SVDV T0375 163 :KIRVSVE 2ax3A 155 :NTGKVLR T0375 171 :E 2ax3A 199 :P T0375 175 :E 2ax3A 200 :V T0375 179 :QLFGYGDVVFVSKDVAKHL 2ax3A 201 :HLINSINRYVITREMVRSL T0375 198 :GF 2ax3A 222 :ER T0375 200 :QS 2ax3A 226 :DS T0375 212 :RVRKGAVLVCAWAE 2ax3A 229 :KGTYGKVLIIAGSR T0375 234 :DGKLLHSDA 2ax3A 411 :GEKTLFNIT T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGFD 2ax3A 420 :GNTGLSKGGSGDVLTGMIAGFIAQGLSPLEASTVSVYLHGFAAELFEQD Number of specific fragments extracted= 17 number of extra gaps= 0 total=1326 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ax3A/T0375-2ax3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2ax3A/T0375-2ax3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ax3A read from 2ax3A/T0375-2ax3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ax3A in template set Warning: unaligning (T0375)K163 because of BadResidue code BAD_PEPTIDE in next template residue (2ax3A)A343 Warning: unaligning (T0375)I164 because of BadResidue code BAD_PEPTIDE at template residue (2ax3A)A343 Warning: unaligning (T0375)V189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ax3A)H366 Warning: unaligning (T0375)S190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ax3A)H366 T0375 2 :SQILCVG 2ax3A 233 :GKVLIIA T0375 33 :QRWQRGGNASNSCTILSLLGA 2ax3A 240 :GSRLYSGAPVLSGMGSLKVGT T0375 54 :PCAFMGSMAPGH 2ax3A 262 :LVKLAVPFPQNL T0375 73 :DLRRY 2ax3A 274 :IATSR T0375 78 :SVDLRYTVFQTTGS 2ax3A 281 :ELISVPIDTEKGFF T0375 111 :Y 2ax3A 295 :S T0375 116 :PDVSATD 2ax3A 296 :LQNLQEC T0375 125 :KVDLTQFKWIHIEGRNASE 2ax3A 303 :LELSKDVDVVAIGPGLGNN T0375 144 :QVKMLQRIDAHNTRQPPEQ 2ax3A 323 :HVREFVNEFLKTLEKPAVI T0375 165 :RVSVEVE 2ax3A 344 :DAINVLD T0375 174 :REELFQ 2ax3A 351 :TSVLKE T0375 181 :FGYGDVVF 2ax3A 357 :RKSPAVLT T0375 191 :KDVAKHLGFQSAEE 2ax3A 367 :PGEMARLVKKTVGD T0375 205 :ALRGLYGRVRKG 2ax3A 386 :ELAEEFAKENDC T0375 220 :VCAWAEEGADALGPDG 2ax3A 398 :VLVLKSATTIVTDGEK T0375 238 :LHSDAF 2ax3A 414 :TLFNIT T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGL 2ax3A 420 :GNTGLSKGGSGDVLTGMIAGFIAQGLSPLEASTVSVYLHGFAAEL Number of specific fragments extracted= 17 number of extra gaps= 2 total=1343 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l2lA/T0375-1l2lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l2lA expands to /projects/compbio/data/pdb/1l2l.pdb.gz 1l2lA:# T0375 read from 1l2lA/T0375-1l2lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l2lA read from 1l2lA/T0375-1l2lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l2lA to template set # found chain 1l2lA in template set Warning: unaligning (T0375)Q87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)R163 Warning: unaligning (T0375)S91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)E175 Warning: unaligning (T0375)F243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)G440 Warning: unaligning (T0375)G253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)G440 T0375 4 :ILCVGLVVLDVISLVDK 1l2lA 28 :VLLAYNTNIDAIKYLKR T0375 38 :GGNASNSCTILSLL 1l2lA 114 :GGQVGIMANLLGGV T0375 52 :GAPCAFMGSMAPG 1l2lA 129 :GIPVIAHVPQLSE T0375 73 :DLRRYSVDLRYTVF 1l2lA 142 :LQASLFLDGPIYVP T0375 92 :VPIATVIINEAS 1l2lA 176 :DCIHYIYEFPRN T0375 104 :G 1l2lA 197 :R T0375 105 :SRTILYYDR 1l2lA 199 :NRFIGAADD T0375 114 :SLPDVSATDFEKVD 1l2lA 210 :PILYVREEWIERFE T0375 128 :LTQFKWIHIEGRNA 1l2lA 226 :AKRSELAIISGLHP T0375 142 :S 1l2lA 243 :E T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1l2lA 251 :LVREHLKILNDLGIRAHLEF T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKH 1l2lA 271 :AFTPDEVVRLEIVKLLKHFYSVGLNEVELAS T0375 197 :L 1l2lA 305 :V T0375 198 :GFQ 1l2lA 307 :GEK T0375 201 :SAEEALRGLYGRVRK 1l2lA 322 :DPIAVIEGLLKLIKE T0375 216 :GAVLVCAWAEEGADALGP 1l2lA 338 :GVKRIHFHTYGYYLALTR T0375 234 :DGKLLHSDA 1l2lA 421 :DYQLTFIPT T0375 254 :AGDTFNASVIFSLS 1l2lA 441 :IGDTISSSAFVSEF Number of specific fragments extracted= 18 number of extra gaps= 0 total=1361 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l2lA/T0375-1l2lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1l2lA/T0375-1l2lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l2lA read from 1l2lA/T0375-1l2lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l2lA in template set Warning: unaligning (T0375)Q87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)R163 Warning: unaligning (T0375)S91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)E175 Warning: unaligning (T0375)F243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)G440 Warning: unaligning (T0375)G253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)G440 T0375 3 :QILCVGLVVLDVISL 1l2lA 27 :GVLLAYNTNIDAIKY T0375 28 :I 1l2lA 42 :L T0375 30 :CLSQRWQRGGNASNSCTILSLL 1l2lA 106 :WGWDELRMGGQVGIMANLLGGV T0375 52 :GAPCAFMGSMAPGHVA 1l2lA 129 :GIPVIAHVPQLSELQA T0375 76 :RYSVDLRYTVF 1l2lA 145 :SLFLDGPIYVP T0375 92 :VPIATVIINE 1l2lA 176 :DCIHYIYEFP T0375 103 :SG 1l2lA 186 :RN T0375 105 :SRTILYYDR 1l2lA 199 :NRFIGAADD T0375 114 :SLPDVSATDFE 1l2lA 210 :PILYVREEWIE T0375 127 :D 1l2lA 223 :E T0375 128 :LTQFKWIHIEGRNA 1l2lA 226 :AKRSELAIISGLHP T0375 142 :SE 1l2lA 247 :KP T0375 145 :VKMLQRIDAHNTRQPPEQ 1l2lA 253 :REHLKILNDLGIRAHLEF T0375 166 :VSVEVEKPREELFQLFGYGDVVFVSKDVAKH 1l2lA 271 :AFTPDEVVRLEIVKLLKHFYSVGLNEVELAS T0375 198 :GF 1l2lA 307 :GE T0375 200 :QSAE 1l2lA 321 :ADPI T0375 204 :EALRGLYGRV 1l2lA 328 :EGLLKLIKET T0375 215 :KGAVLVCAW 1l2lA 338 :GVKRIHFHT T0375 226 :EGADALG 1l2lA 347 :YGYYLAL T0375 234 :DGKLLHSDA 1l2lA 421 :DYQLTFIPT T0375 254 :AGDTFNASVIFSLS 1l2lA 441 :IGDTISSSAFVSEF Number of specific fragments extracted= 21 number of extra gaps= 0 total=1382 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l2lA/T0375-1l2lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1l2lA/T0375-1l2lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l2lA read from 1l2lA/T0375-1l2lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l2lA in template set Warning: unaligning (T0375)Q87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)R163 Warning: unaligning (T0375)G90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)E175 Warning: unaligning (T0375)F243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1l2lA)G440 Warning: unaligning (T0375)G253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1l2lA)G440 T0375 2 :SQILCVGLVVLDVISLVDK 1l2lA 26 :RGVLLAYNTNIDAIKYLKR T0375 37 :RGGNASNSCTILSLL 1l2lA 113 :MGGQVGIMANLLGGV T0375 52 :GAPCAFMGSMAPGH 1l2lA 129 :GIPVIAHVPQLSEL T0375 74 :LRRYSVDLRYTVF 1l2lA 143 :QASLFLDGPIYVP T0375 91 :SVPIATVIINEA 1l2lA 176 :DCIHYIYEFPRN T0375 103 :SGSRTILYYDR 1l2lA 197 :RENRFIGAADD T0375 114 :SLPDVSATDF 1l2lA 209 :NPILYVREEW T0375 124 :EKVDLTQFKWIHIEGRNASE 1l2lA 222 :FEEIAKRSELAIISGLHPLT T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVS 1l2lA 250 :KLVREHLKILNDLGIRAHLEFAFT T0375 169 :EVEKPREELFQLFGYGDVVFVSKDVAKHLGFQ 1l2lA 274 :PDEVVRLEIVKLLKHFYSVGLNEVELASVVSV T0375 205 :ALRGLYGRVRKGAVLVCA 1l2lA 328 :EGLLKLIKETGVKRIHFH T0375 224 :AEEGADALGPDG 1l2lA 346 :TYGYYLALTREK T0375 236 :KLLHSDA 1l2lA 423 :QLTFIPT T0375 254 :AGDTFNASVIFSLS 1l2lA 441 :IGDTISSSAFVSEF Number of specific fragments extracted= 14 number of extra gaps= 0 total=1396 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lioA/T0375-1lioA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lioA expands to /projects/compbio/data/pdb/1lio.pdb.gz 1lioA:# T0375 read from 1lioA/T0375-1lioA-t06-local-adpstyle5.a2m # 1lioA read from 1lioA/T0375-1lioA-t06-local-adpstyle5.a2m # adding 1lioA to template set # found chain 1lioA in template set Warning: unaligning (T0375)E27 because of BadResidue code BAD_PEPTIDE in next template residue (1lioA)L39 Warning: unaligning (T0375)I28 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)L39 Warning: unaligning (T0375)R29 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)K40 Warning: unaligning (T0375)C30 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)R41 Warning: unaligning (T0375)S114 because of BadResidue code BAD_PEPTIDE in next template residue (1lioA)C145 Warning: unaligning (T0375)L115 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)C145 Warning: unaligning (T0375)E204 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lioA)G270 Warning: unaligning (T0375)G216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lioA)G270 Warning: unaligning (T0375)P233 because of BadResidue code BAD_PEPTIDE in next template residue (1lioA)T290 Warning: unaligning (T0375)D234 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)D292 Warning: unaligning (T0375)L237 because of BadResidue code BAD_PEPTIDE in next template residue (1lioA)V296 Warning: unaligning (T0375)L238 because of BadResidue code BAD_PEPTIDE at template residue (1lioA)V296 T0375 2 :SQILCVGLVVLDVISLVDKYPKEDS 1lioA 13 :MRVFAIGNPILDLVAEVPSSFLDEF T0375 31 :LSQRWQR 1lioA 42 :GDATLAT T0375 38 :GGNASNSCTILSLL 1lioA 68 :GGSALNSVRVVQKL T0375 52 :GAPCAFMGSMAPGHVADFVLDDLRRYSVDLRYTV 1lioA 85 :PGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMV T0375 87 :QTTGSVPIATVII 1lioA 119 :APGQSTGTCAVLI T0375 102 :ASGSRTILYYDR 1lioA 132 :NEKERTLCTHLG T0375 116 :PDVSATDFEKVDLTQFKWIHIEGRNA 1lioA 146 :GSFRIPEDWTTFASGALIFYATAYTL T0375 142 :SEQVKMLQRID 1lioA 173 :ATPKNALEVAG T0375 153 :AHNTR 1lioA 185 :AHGIP T0375 158 :QPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSKDVAKHL 1lioA 191 :AIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHL T0375 198 :GFQ 1lioA 232 :KVH T0375 202 :AE 1lioA 252 :AV T0375 217 :A 1lioA 271 :A T0375 218 :VLVCAWAEEGADALG 1lioA 274 :LVVMTRGHNPVIAAE T0375 235 :GK 1lioA 293 :GT T0375 239 :HSDAFPPPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCGLQGF 1lioA 301 :GVPVVAAEKIVDTNGAGDAFVGGFLYGLSQGKTVKQCIMCGNACAQDVIQHVGF Number of specific fragments extracted= 16 number of extra gaps= 5 total=1412 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gca/T0375-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gca expands to /projects/compbio/data/pdb/1gca.pdb.gz 1gca:Warning: there is no chain 1gca will retry with 1gcaA # T0375 read from 1gca/T0375-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0375-1gca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gca to template set # found chain 1gca in template set T0375 54 :PCAFMGSMAPGHVADFVLDDLRRY 1gca 4 :RIGVTIYKYDDNFMSVVRKAIEKD T0375 78 :S 1gca 33 :D T0375 81 :LRYTVFQTT 1gca 34 :VQLLMNDSQ T0375 104 :GS 1gca 43 :ND T0375 120 :ATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQ 1gca 49 :NDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFN T0375 171 :EKPREELFQLF 1gca 113 :KESGVIQGDLI T0375 184 :GDVVFVS 1gca 141 :IQYVLLK T0375 191 :KDVAKHLGFQ 1gca 163 :VKELNDKGIQ T0375 201 :SAEEALRGLYGRVRK 1gca 184 :DTAQAKDKMDAWLSG T0375 216 :GAVLVCAWA 1gca 203 :KIEVVIANN T0375 256 :DTFNASVIFSL 1gca 212 :DAMAMGAVEAL T0375 267 :SQGR 1gca 246 :KSGA T0375 271 :SVQEALRFGCQVAGKKCGLQGFDGI 1gca 257 :DANNQAKATFDLAKNLAEGKGAADG Number of specific fragments extracted= 13 number of extra gaps= 0 total=1425 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gca/T0375-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1gca/T0375-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0375-1gca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gca in template set T0375 55 :CAFMGSMA 1gca 3 :TRIGVTIY T0375 63 :PGHVADFVLDDLRRY 1gca 13 :DDNFMSVVRKAIEKD T0375 80 :DLRYTVFQT 1gca 33 :DVQLLMNDS T0375 103 :SGS 1gca 42 :QND T0375 120 :ATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQK 1gca 49 :NDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNK T0375 172 :KPREELFQLFGYGDVVFVSKDVAKHL 1gca 93 :EPSRKALDSYDKAYYVGTDSKESGVI T0375 203 :EEALRGLYGRVRK 1gca 120 :GDLIAKHWQANQG T0375 216 :GAVLVCAWAEE 1gca 141 :IQYVLLKGEPG T0375 245 :PPRVVDTLGAGDTFNASVIFSL 1gca 201 :ANKIEVVIANNDAMAMGAVEAL T0375 267 :SQG 1gca 224 :AHN T0375 270 :RSVQEALRFGCQVAGKKCGLQGFD 1gca 256 :NDANNQAKATFDLAKNLAEGKGAA T0375 294 :G 1gca 281 :G Number of specific fragments extracted= 12 number of extra gaps= 0 total=1437 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gca/T0375-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1gca/T0375-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gca read from 1gca/T0375-1gca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gca in template set T0375 54 :PCAFMGSMAPGHVADFVLDDLRRY 1gca 4 :RIGVTIYKYDDNFMSVVRKAIEKD T0375 78 :SVDLRYTVFQTT 1gca 33 :DVQLLMNDSQND T0375 116 :PDVSATDFEKVDLTQFKWIHIEGRNA 1gca 45 :QSKQNDQIDVLLAKGVKALAINLVDP T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVS 1gca 71 :AAAGTVIEKARGQNVPVVFFNKEP T0375 174 :REELFQLFGYGDVVFVSKDVAKHLGFQ 1gca 95 :SRKALDSYDKAYYVGTDSKESGVIQGD T0375 215 :KGAVLVCAWAEE 1gca 140 :KIQYVLLKGEPG T0375 235 :G 1gca 152 :H T0375 244 :PPPRVVDTL 1gca 202 :NKIEVVIAN T0375 255 :GDTFNASVIFSL 1gca 211 :NDAMAMGAVEAL T0375 270 :RSVQEALRFGCQVAGKKCGLQGF 1gca 256 :NDANNQAKATFDLAKNLAEGKGA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1447 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0375-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0375 read from 2d13A/T0375-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0375-2d13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0375)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0375)Q87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0375)E101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0375 2 :SQILCV 2d13A 5 :ADVAVL T0375 36 :QRGGNASNSCTI 2d13A 11 :YSGGKDSNYALY T0375 48 :LSLLGAPC 2d13A 24 :ALKSGLRV T0375 56 :AFMGSMAP 2d13A 33 :YLVSMVSE T0375 65 :HVADFVLDDL 2d13A 53 :ELTSLQARAL T0375 78 :SVDL 2d13A 63 :GIPI T0375 83 :YTVF 2d13A 67 :IKGF T0375 102 :ASG 2d13A 75 :KEK T0375 120 :ATDFEKVDLT 2d13A 79 :VEDLKNVLEG T0375 130 :QFKWIHIEGRNAS 2d13A 90 :KVDGIVAGALASR T0375 143 :EQVKMLQRIDAHNTRQPPEQ 2d13A 104 :QKERIENVARELGLKVYTPA T0375 169 :EVEKPREELFQLFGY 2d13A 124 :WEKDPYQYMLEIIKL T0375 189 :VSKD 2d13A 152 :LNES T0375 197 :L 2d13A 156 :W T0375 198 :GFQ 2d13A 158 :GRE T0375 201 :SAEEALR 2d13A 162 :NYKNLEE T0375 209 :LYGRVRK 2d13A 169 :LKKLSEK T0375 216 :GAV 2d13A 177 :GIH T0375 223 :WAEEG 2d13A 181 :AGEGG T0375 228 :ADALG 2d13A 189 :TFVLD T0375 233 :P 2d13A 195 :P Number of specific fragments extracted= 21 number of extra gaps= 0 total=1468 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0375-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2d13A/T0375-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0375-2d13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0375)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0375)F86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0375)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0375 2 :SQILCVG 2d13A 5 :ADVAVLY T0375 37 :RGGNASNSCTILSLL 2d13A 12 :SGGKDSNYALYWALK T0375 52 :GAPC 2d13A 28 :GLRV T0375 56 :AFMGSMAP 2d13A 33 :YLVSMVSE T0375 65 :HVADFVLDDL 2d13A 53 :ELTSLQARAL T0375 78 :SVDLRYTV 2d13A 63 :GIPIIKGF T0375 103 :SGS 2d13A 75 :KEK T0375 120 :ATDFEKVDLT 2d13A 79 :VEDLKNVLEG T0375 130 :QFKWIHIEGRNASEQVKML 2d13A 90 :KVDGIVAGALASRYQKERI T0375 149 :QRIDAHNTRQP 2d13A 110 :NVARELGLKVY T0375 166 :VSVEVEKPREELFQLFGY 2d13A 121 :TPAWEKDPYQYMLEIIKL T0375 189 :VSKDVAKHL 2d13A 161 :LNYKNLEEL T0375 207 :RGLYGRV 2d13A 171 :KLSEKYG T0375 216 :GA 2d13A 178 :IH T0375 223 :WAEEG 2d13A 181 :AGEGG T0375 228 :ADALG 2d13A 187 :FETFV T0375 238 :LHSDAF 2d13A 192 :LDMPFF T0375 245 :PPRVV 2d13A 198 :KAKIV Number of specific fragments extracted= 18 number of extra gaps= 0 total=1486 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/T0375-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2d13A/T0375-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d13A read from 2d13A/T0375-2d13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d13A in template set Warning: unaligning (T0375)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0375)Y111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 Warning: unaligning (T0375)S114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2d13A)E74 T0375 1 :GSQILCV 2d13A 4 :LADVAVL T0375 36 :QRGGNASNSCTILSLL 2d13A 11 :YSGGKDSNYALYWALK T0375 52 :GAPC 2d13A 28 :GLRV T0375 56 :AFMGSMAP 2d13A 33 :YLVSMVSE T0375 66 :VADFVLDDL 2d13A 54 :LTSLQARAL T0375 103 :SGSRTILY 2d13A 63 :GIPIIKGF T0375 115 :LPDVSATDFEKVDLTQFKWI 2d13A 75 :KEKEVEDLKNVLEGLKVDGI T0375 136 :IEGRNASEQVKMLQRIDAHNTRQPPE 2d13A 95 :VAGALASRYQKERIENVARELGLKVY T0375 167 :SVEVE 2d13A 121 :TPAWE T0375 172 :KPREELFQLFGY 2d13A 127 :DPYQYMLEIIKL T0375 189 :VSKD 2d13A 152 :LNES T0375 197 :LGFQ 2d13A 156 :WLGR T0375 201 :SAEEALRGLYGRV 2d13A 161 :LNYKNLEELKKLS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1499 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0375-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0375 read from 1zjjA/T0375-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0375-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zjjA to template set # found chain 1zjjA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1zjjA)M1 T0375 3 :QILCVG 1zjjA 2 :VAIIFD T0375 9 :LVV 1zjjA 10 :GVL T0375 30 :CLSQRWQRG 1zjjA 13 :YRGNRAIPG T0375 41 :ASNSCTILSLLGAPCAFMGSMAP 1zjjA 22 :VRELIEFLKERGIPFAFLTNNST T0375 65 :HVADFVLDDLRRYSVDL 1zjjA 45 :KTPEMYREKLLKMGIDV T0375 119 :SATDF 1zjjA 62 :SSSII T0375 128 :LTQFKWIHIE 1zjjA 81 :LDPGKIFVIG T0375 141 :ASEQVKMLQRI 1zjjA 91 :GEGLVKEMQAL T0375 155 :NTRQP 1zjjA 102 :GWGIV T0375 173 :PREELF 1zjjA 107 :TLDEAR T0375 179 :QLFGYGDVVFVS 1zjjA 114 :GSWKEVKHVVVG T0375 198 :GFQ 1zjjA 129 :DLT T0375 203 :EEALRGLYGRVRKGAVLVCAWAEE 1zjjA 132 :YEKLKYATLAIRNGATFIGTNPDA T0375 229 :DALGPD 1zjjA 156 :TLPGEE T0375 236 :KLLH 1zjjA 162 :GIYP T0375 253 :GAGDTFNASVIF 1zjjA 166 :GAGSIIAALKVA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1515 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0375-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1zjjA/T0375-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0375-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1zjjA)M1 T0375 3 :QILCVG 1zjjA 2 :VAIIFD T0375 9 :LVV 1zjjA 10 :GVL T0375 30 :CLSQRWQRG 1zjjA 13 :YRGNRAIPG T0375 41 :ASNSCTILSLLGAPCAFMGSMAPG 1zjjA 22 :VRELIEFLKERGIPFAFLTNNSTK T0375 66 :VADFVLDDLRRYSVDLR 1zjjA 46 :TPEMYREKLLKMGIDVS T0375 83 :YTVF 1zjjA 65 :IIIT T0375 102 :ASGSRTILYYDR 1zjjA 81 :LDPGKIFVIGGE T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEG 1zjjA 102 :GWGIVTLDEARQGSWKEVKHVVVGL T0375 139 :RNASEQVKMLQRIDAHNTRQPPEQ 1zjjA 129 :DLTYEKLKYATLAIRNGATFIGTN T0375 164 :IRVSVEVEK 1zjjA 153 :PDATLPGEE T0375 173 :PREELFQLFGYGDVVFV 1zjjA 170 :IIAALKVATNVEPIIIG T0375 190 :S 1zjjA 189 :N T0375 203 :EEALRGLYGRVRKGAVLVCAWAEE 1zjjA 190 :EPMYEVVREMFPGEELWMVGDRLD Number of specific fragments extracted= 13 number of extra gaps= 0 total=1528 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/T0375-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1zjjA/T0375-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0375-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0375 1 :GSQILCV 1zjjA 1 :MVAIIFD T0375 12 :LDVISLVDKYPKED 1zjjA 8 :MDGVLYRGNRAIPG T0375 41 :ASNSCTILSLLGAPCAFMGSMAPGH 1zjjA 22 :VRELIEFLKERGIPFAFLTNNSTKT T0375 67 :ADFVLDDLRRYSVDL 1zjjA 47 :PEMYREKLLKMGIDV T0375 82 :RYTVF 1zjjA 64 :SIIIT T0375 103 :SGSRTILYYDR 1zjjA 82 :DPGKIFVIGGE T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQKIRVS 1zjjA 102 :GWGIVTLDEARQGSWKEVKHVVVGLDPDLTYEKLKYATLAIRNGATFIGTNPDA T0375 172 :KPREELFQLFGYGDVVFVS 1zjjA 191 :PMYEVVREMFPGEELWMVG T0375 207 :RGLYGRVRKGAVLVCAWA 1zjjA 215 :DIAFAKKFGMKAIMVLTG Number of specific fragments extracted= 9 number of extra gaps= 0 total=1537 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/T0375-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qwgA expands to /projects/compbio/data/pdb/1qwg.pdb.gz 1qwgA:Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 1qwgA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1qwgA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qwgA # T0375 read from 1qwgA/T0375-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0375-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qwgA to template set # found chain 1qwgA in template set Warning: unaligning (T0375)F199 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0375)Q200 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0375 95 :A 1qwgA 16 :T T0375 108 :ILYYD 1qwgA 17 :VVLDK T0375 117 :DVSATDFEKV 1qwgA 22 :GLPPKFVEDY T0375 127 :DLTQFKWIHIEGRNAS 1qwgA 35 :CGDYIDFVKFGWGTSA T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEV 1qwgA 56 :VVKEKINYYKDWGIKVYPGGTLFEYAYS T0375 171 :EKPREELFQL 1qwgA 88 :DEFLNECEKL T0375 183 :YGDVVFV 1qwgA 98 :GFEAVEI T0375 190 :SKDV 1qwgA 112 :SLEE T0375 194 :AKHLG 1qwgA 123 :AKDNG T0375 201 :SAEEALRGLYGRVRKGA 1qwgA 146 :TIDDRIKLINFDLDAGA T0375 218 :VLVCAWAEEG 1qwgA 164 :YVIIEGRESG T0375 230 :ALGPDGKL 1qwgA 178 :LFDKEGKV Number of specific fragments extracted= 12 number of extra gaps= 1 total=1549 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/T0375-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1qwgA/T0375-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0375-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwgA in template set Warning: unaligning (T0375)F199 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 T0375 88 :TTGSVPIATVIINE 1qwgA 9 :EDFQRGLTVVLDKG T0375 118 :VSATDFE 1qwgA 23 :LPPKFVE T0375 125 :KVDLTQFKWIHIEG 1qwgA 33 :KVCGDYIDFVKFGW T0375 139 :RNASEQVKMLQRIDAHNTRQPPEQKIRVSVEV 1qwgA 52 :IDRDVVKEKINYYKDWGIKVYPGGTLFEYAYS T0375 171 :EKPREELFQL 1qwgA 88 :DEFLNECEKL T0375 183 :YGDVVFV 1qwgA 98 :GFEAVEI T0375 190 :SKDVAKH 1qwgA 112 :SLEERNN T0375 197 :LG 1qwgA 126 :NG T0375 200 :QSAEEALRGLYGRV 1qwgA 148 :DDRIKLINFDLDAG T0375 216 :GAVLVCAWAEEG 1qwgA 162 :ADYVIIEGRESG T0375 228 :ADALGPDGKL 1qwgA 176 :KGLFDKEGKV Number of specific fragments extracted= 11 number of extra gaps= 1 total=1560 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/T0375-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1qwgA/T0375-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0375-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwgA in template set Warning: unaligning (T0375)Q158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0375)P159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0375 54 :PCAFMG 1qwgA 40 :DFVKFG T0375 61 :MA 1qwgA 46 :WG T0375 63 :PGHVADFVLDDLRRYSVDLRY 1qwgA 53 :DRDVVKEKINYYKDWGIKVYP T0375 111 :YDR 1qwgA 74 :GGT T0375 114 :SLPDVSATDFEKVDLTQFKWIHIEGRNASE 1qwgA 82 :YSKGKFDEFLNECEKLGFEAVEISDGSSDI T0375 144 :QVKMLQRIDAHNTR 1qwgA 114 :EERNNAIKRAKDNG T0375 160 :PEQKIRVS 1qwgA 130 :VLTEVGKK T0375 173 :PREELFQ 1qwgA 138 :MPDKDKQ T0375 189 :VSKDVAKHL 1qwgA 145 :LTIDDRIKL T0375 208 :GLYGRVRKGAVLVCAWAEEG 1qwgA 154 :INFDLDAGADYVIIEGRESG T0375 231 :LGPDGKL 1qwgA 179 :FDKEGKV T0375 239 :H 1qwgA 186 :K T0375 263 :IFSLSQGRS 1qwgA 190 :LDVLAKNVD Number of specific fragments extracted= 13 number of extra gaps= 1 total=1573 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sviA/T0375-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sviA expands to /projects/compbio/data/pdb/1svi.pdb.gz 1sviA:# T0375 read from 1sviA/T0375-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0375-1sviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sviA to template set # found chain 1sviA in template set Warning: unaligning (T0375)Y77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0375)V92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0375 19 :DKYPKED 1sviA 16 :EQYPEGG T0375 53 :APCAFMGSMA 1sviA 23 :LPEIALAGRS T0375 64 :GHVADFVLDDLRR 1sviA 33 :NVGKSSFINSLIN T0375 93 :PIATVII 1sviA 61 :TLNFYII T0375 103 :SGSRTILYYDR 1sviA 68 :NDELHFVDVPG T0375 114 :SLPDVSATDFEKVD 1sviA 80 :GFAKVSKSEREAWG T0375 128 :LTQFKWIHIEGRN 1sviA 103 :REELKAVVQIVDL T0375 142 :SEQVKMLQRIDAHNTRQPPEQ 1sviA 121 :NDDVQMYEFLKYYGIPVIVIA T0375 164 :I 1sviA 146 :K T0375 166 :VS 1sviA 147 :IP T0375 170 :V 1sviA 149 :K T0375 171 :EKPREELFQLF 1sviA 153 :DKHAKVVRQTL T0375 182 :GYGDVVFVS 1sviA 167 :PEDELILFS T0375 202 :AEEALRGLYGRVR 1sviA 182 :KDEAWGAIKKMIN Number of specific fragments extracted= 14 number of extra gaps= 0 total=1587 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sviA/T0375-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1sviA/T0375-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0375-1sviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sviA in template set Warning: unaligning (T0375)Y77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0375)V92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0375 27 :EIRCLSQRWQRGG 1sviA 9 :VISAVKPEQYPEG T0375 52 :GAPCAFMGSMA 1sviA 22 :GLPEIALAGRS T0375 64 :GHVADFVLDDLRR 1sviA 33 :NVGKSSFINSLIN T0375 93 :PIATVII 1sviA 61 :TLNFYII T0375 103 :SGSRTILYYDR 1sviA 68 :NDELHFVDVPG T0375 114 :SLPDVSATDFEKVD 1sviA 80 :GFAKVSKSEREAWG T0375 128 :LTQFKWIHIEG 1sviA 103 :REELKAVVQIV T0375 139 :RNASEQVKMLQRIDAHNTRQPPEQKIRVSVEV 1sviA 118 :APSNDDVQMYEFLKYYGIPVIVIATKADKIPK T0375 171 :EKPREELFQLF 1sviA 153 :DKHAKVVRQTL T0375 182 :GYGDVVFVS 1sviA 167 :PEDELILFS T0375 197 :L 1sviA 176 :S T0375 198 :G 1sviA 178 :T T0375 200 :QSAEEALRGLYG 1sviA 183 :DEAWGAIKKMIN Number of specific fragments extracted= 13 number of extra gaps= 0 total=1600 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sviA/T0375-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1sviA/T0375-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sviA read from 1sviA/T0375-1sviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sviA in template set Warning: unaligning (T0375)Y77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sviA)Q60 Warning: unaligning (T0375)S91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sviA)Q60 T0375 18 :VDKYPKED 1sviA 15 :PEQYPEGG T0375 53 :APCAFMGSMAPG 1sviA 23 :LPEIALAGRSNV T0375 66 :VADFVLDDLRR 1sviA 35 :GKSSFINSLIN T0375 92 :VPIATVI 1sviA 61 :TLNFYII T0375 102 :ASGSRTILYYDRSLPDVSATDFEKV 1sviA 68 :NDELHFVDVPGYGFAKVSKSEREAW T0375 127 :DLTQFKWIHIEGRNASE 1sviA 102 :TREELKAVVQIVDLRHA T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1sviA 121 :NDDVQMYEFLKYYGIPVIVIATKADKIP T0375 172 :KPREELFQLF 1sviA 154 :KHAKVVRQTL T0375 182 :GYGDVVFVS 1sviA 167 :PEDELILFS T0375 198 :GFQ 1sviA 176 :SET T0375 202 :AEEALRGLYGRVR 1sviA 182 :KDEAWGAIKKMIN Number of specific fragments extracted= 11 number of extra gaps= 0 total=1611 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f0kA/T0375-1f0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f0kA expands to /projects/compbio/data/pdb/1f0k.pdb.gz 1f0kA:# T0375 read from 1f0kA/T0375-1f0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f0kA read from 1f0kA/T0375-1f0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f0kA to template set # found chain 1f0kA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1f0kA)K7 T0375 3 :QILCVGL 1f0kA 8 :RLMVMAG T0375 36 :QRGGN 1f0kA 15 :GTGGH T0375 41 :ASNSCTILSLLGAPCAFMGSMAP 1f0kA 23 :GLAVAHHLMAQGWQVRWLGTADR T0375 69 :FVLDDLRRYSVDLRYTVFQTTGSVP 1f0kA 46 :MEADLVPKHGIEIDFIRISGLRGKG T0375 119 :SATDFEKVD 1f0kA 77 :APLRIFNAW T0375 128 :LT 1f0kA 92 :MK T0375 130 :QFKWIHIEGRNA 1f0kA 96 :KPDVVLGMGGYV T0375 144 :QVKMLQRIDAHNTRQPPEQKI 1f0kA 108 :SGPGGLAAWSLGIPVVLHEQN T0375 171 :EKPREELFQLFGYGDVVFVS 1f0kA 129 :GIAGLTNKWLAKIATKVMQA T0375 197 :L 1f0kA 149 :F T0375 198 :G 1f0kA 151 :G T0375 199 :FQ 1f0kA 153 :FP T0375 201 :S 1f0kA 164 :R T0375 203 :EEALR 1f0kA 165 :TDVLA T0375 209 :LYGRVRK 1f0kA 173 :PQQRLAG T0375 216 :GA 1f0kA 182 :GP T0375 218 :VLVCAWAEEGA 1f0kA 185 :RVLVVGGSQGA T0375 248 :VVDTLGA 1f0kA 258 :VVCRSGA T0375 257 :TFNASVIFSL 1f0kA 265 :LTVSEIAAAG T0375 267 :SQGRSVQEALRFGCQVAG 1f0kA 319 :LAGWSRETLLTMAERARA Number of specific fragments extracted= 20 number of extra gaps= 0 total=1631 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f0kA/T0375-1f0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1f0kA/T0375-1f0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f0kA read from 1f0kA/T0375-1f0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f0kA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1f0kA)K7 T0375 3 :QILCVG 1f0kA 8 :RLMVMA T0375 36 :QRGGN 1f0kA 15 :GTGGH T0375 41 :ASNSCTILSLLGAPCAFMGS 1f0kA 23 :GLAVAHHLMAQGWQVRWLGT T0375 63 :PGHV 1f0kA 43 :ADRM T0375 70 :VLDDLRRYSVDLRYTVFQT 1f0kA 47 :EADLVPKHGIEIDFIRISG T0375 102 :ASGSR 1f0kA 66 :LRGKG T0375 119 :SATDFEKVD 1f0kA 77 :APLRIFNAW T0375 128 :LT 1f0kA 92 :MK T0375 130 :QFKWIHIEGRNASEQ 1f0kA 96 :KPDVVLGMGGYVSGP T0375 149 :QRIDAHNTRQPPEQ 1f0kA 113 :LAAWSLGIPVVLHE T0375 163 :K 1f0kA 128 :N T0375 171 :EKPREELFQLFGYGDVVFVS 1f0kA 129 :GIAGLTNKWLAKIATKVMQA T0375 197 :LGF 1f0kA 149 :FPG T0375 200 :QSAEEAL 1f0kA 171 :PLPQQRL T0375 211 :GRVRKGAVLVCAWAEEGA 1f0kA 178 :AGREGPVRVLVVGGSQGA T0375 233 :P 1f0kA 196 :R T0375 238 :LHSDAFP 1f0kA 305 :IEQPQLS T0375 263 :IFSLSQGRSVQEALRFGCQV 1f0kA 315 :VANTLAGWSRETLLTMAERA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1649 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f0kA/T0375-1f0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1f0kA/T0375-1f0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f0kA read from 1f0kA/T0375-1f0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f0kA in template set Warning: unaligning (T0375)S2 because first residue in template chain is (1f0kA)K7 T0375 3 :QILCVGL 1f0kA 8 :RLMVMAG T0375 36 :QRGGNASNSCTILSLL 1f0kA 15 :GTGGHVFPGLAVAHHL T0375 52 :GAPCAFMGSMAPG 1f0kA 34 :GWQVRWLGTADRM T0375 70 :VLDDLRRYSVDLRYTVFQTTGSVP 1f0kA 47 :EADLVPKHGIEIDFIRISGLRGKG T0375 114 :SLPDVSATDF 1f0kA 76 :AAPLRIFNAW T0375 124 :EKVDLTQFKWIHIEGRNA 1f0kA 90 :AIMKAYKPDVVLGMGGYV T0375 146 :KMLQRIDAHNTRQPPEQKIRVS 1f0kA 108 :SGPGGLAAWSLGIPVVLHEQNG T0375 172 :KPREELFQLFGYGDVVFVS 1f0kA 130 :IAGLTNKWLAKIATKVMQA T0375 197 :LGFQ 1f0kA 149 :FPGA T0375 202 :A 1f0kA 172 :L T0375 209 :LYGRVRKGA 1f0kA 173 :PQQRLAGRE T0375 218 :VLVCAWAEEGA 1f0kA 185 :RVLVVGGSQGA Number of specific fragments extracted= 12 number of extra gaps= 0 total=1661 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0375-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0375 read from 1wqaA/T0375-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0375-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0375 41 :ASNSCTILSLLGAP 1wqaA 27 :GMAFGTLLKREGRK T0375 55 :CAFMGSMAP 1wqaA 42 :PLVVVGRDT T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQT 1wqaA 55 :EMLKEALISGLLSVGCDVIDVGIAP T0375 91 :SVPIATVII 1wqaA 91 :NADGGAVIT T0375 100 :NEASGSRTILYYDRSLPDVSATDFEKV 1wqaA 102 :HNPPEYNGIKLLEPNGMGLKKEREAIV T0375 128 :LTQFK 1wqaA 134 :KEDFD T0375 140 :NAS 1wqaA 140 :AKW T0375 143 :EQVKMLQ 1wqaA 156 :PYIEAIK T0375 150 :RIDAHNTRQPPEQKIRVSVEV 1wqaA 169 :AIKKRKPFVVVDTSNGAGSLT T0375 173 :PREELFQL 1wqaA 190 :LPYLLREL T0375 183 :YGDVVFVS 1wqaA 198 :GCKVITVN T0375 198 :GFQ 1wqaA 211 :YFP T0375 201 :SAE 1wqaA 220 :NEE T0375 204 :EALRGLYGR 1wqaA 226 :EFMEIVKAL T0375 216 :GA 1wqaA 235 :GA T0375 218 :VLVCAWAE 1wqaA 238 :FGVAQDGD T0375 226 :EGADALGPDGKLL 1wqaA 247 :DRAVFIDENGRFI T0375 247 :R 1wqaA 260 :Q T0375 255 :GDTFNASVIFSLS 1wqaA 261 :GDKTFALVADAVL T0375 268 :QGRS 1wqaA 276 :KGGG Number of specific fragments extracted= 20 number of extra gaps= 0 total=1681 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0375-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1wqaA/T0375-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0375-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0375 41 :ASNSCTILSLLGAP 1wqaA 27 :GMAFGTLLKREGRK T0375 55 :CAFMGSMAP 1wqaA 43 :LVVVGRDTR T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQT 1wqaA 55 :EMLKEALISGLLSVGCDVIDVGIAP T0375 89 :T 1wqaA 91 :N T0375 91 :SVPIATVIIN 1wqaA 92 :ADGGAVITAS T0375 101 :E 1wqaA 104 :P T0375 103 :SGSRTILYYDRSLPDVSATDFE 1wqaA 105 :PEYNGIKLLEPNGMGLKKEREA T0375 125 :KVDLTQFK 1wqaA 134 :KEDFDRAK T0375 135 :HIEGRNASEQVKMLQ 1wqaA 148 :VRREDIIKPYIEAIK T0375 150 :RIDAHNTRQPPEQKIRVSVEV 1wqaA 169 :AIKKRKPFVVVDTSNGAGSLT T0375 174 :REELFQL 1wqaA 191 :PYLLREL T0375 183 :YGDVVFVS 1wqaA 198 :GCKVITVN T0375 198 :GF 1wqaA 207 :QP T0375 200 :QSAEEALRGLYGRV 1wqaA 222 :ENLKEFMEIVKALG T0375 216 :GAVLVCAWAE 1wqaA 236 :ADFGVAQDGD T0375 226 :EGADALGPDGKLL 1wqaA 247 :DRAVFIDENGRFI T0375 243 :F 1wqaA 260 :Q T0375 255 :GDTFNASVIFSLSQ 1wqaA 261 :GDKTFALVADAVLK T0375 269 :G 1wqaA 277 :G T0375 270 :RSVQEALR 1wqaA 381 :GDRHAIVN Number of specific fragments extracted= 20 number of extra gaps= 0 total=1701 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0375-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1wqaA/T0375-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0375-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0375 41 :ASNSCTILSLLGAP 1wqaA 27 :GMAFGTLLKREGRK T0375 55 :CAFMGSMAP 1wqaA 43 :LVVVGRDTR T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQ 1wqaA 55 :EMLKEALISGLLSVGCDVIDVGIA T0375 90 :GSVPIATV 1wqaA 91 :NADGGAVI T0375 99 :INEA 1wqaA 99 :TASH T0375 103 :SGSRTILYYDRSLPDVSATDFEKV 1wqaA 105 :PEYNGIKLLEPNGMGLKKEREAIV T0375 127 :DLTQFK 1wqaA 133 :FKEDFD T0375 144 :QVKMLQRI 1wqaA 155 :KPYIEAIK T0375 152 :DAHNTRQPPEQKIRVSVEVEKPREELFQL 1wqaA 169 :AIKKRKPFVVVDTSNGAGSLTLPYLLREL T0375 183 :YGDVVFVS 1wqaA 198 :GCKVITVN T0375 205 :ALRGLYGRVRKGAVLVCAWA 1wqaA 225 :KEFMEIVKALGADFGVAQDG T0375 225 :EEGADALGPDGKLLH 1wqaA 246 :ADRAVFIDENGRFIQ T0375 255 :GDTFNASVIFSLSQ 1wqaA 261 :GDKTFALVADAVLK T0375 269 :GR 1wqaA 277 :GG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1715 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/T0375-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1hdoA/T0375-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0375-1hdoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0375)R212 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0375)G216 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0375 2 :SQILCVG 1hdoA 4 :KKIAIFG T0375 38 :GGNASNSCTILSLLGAPCAFMGS 1hdoA 13 :GQTGLTTLAQAVQAGYEVTVLVR T0375 61 :MAPG 1hdoA 40 :LPSE T0375 78 :SVDLRYTVFQT 1hdoA 44 :GPRPAHVVVGD T0375 114 :SL 1hdoA 55 :VL T0375 119 :SATDFEKV 1hdoA 57 :QAADVDKT T0375 128 :LTQFKWIHIEGRNAS 1hdoA 65 :VAGQDAVIVLLGTRN T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEV 1hdoA 90 :GARNIVAAMKAHGVDKVVACTSAFLLWD T0375 171 :EKPREELFQLF 1hdoA 123 :PRLQAVTDDHI T0375 204 :EALRGLYG 1hdoA 134 :RMHKVLRE T0375 217 :AVLVCAWAE 1hdoA 144 :LKYVAVMPP T0375 226 :EGADALG 1hdoA 161 :GAYTVTL T0375 234 :DG 1hdoA 168 :DG T0375 241 :D 1hdoA 170 :R T0375 244 :PPPRVVD 1hdoA 171 :GPSRVIS T0375 276 :LRFGCQVAGKKCGLQGF 1hdoA 178 :KHDLGHFMLRCLTTDEY Number of specific fragments extracted= 16 number of extra gaps= 1 total=1731 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/T0375-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1hdoA/T0375-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0375-1hdoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0375)K172 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0375)P173 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0375)R212 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0375)V213 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0375 2 :SQILCVG 1hdoA 4 :KKIAIFG T0375 63 :PGHVADFVLDDLRRYSVDLRYTVFQTTGS 1hdoA 12 :TGQTGLTTLAQAVQAGYEVTVLVRDSSRL T0375 101 :EASGSRTILYYDR 1hdoA 41 :PSEGPRPAHVVVG T0375 114 :SL 1hdoA 55 :VL T0375 119 :SATDFEKV 1hdoA 57 :QAADVDKT T0375 128 :LTQFKWIHIEGRNASEQ 1hdoA 65 :VAGQDAVIVLLGTRNDL T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEV 1hdoA 92 :RNIVAAMKAHGVDKVVACTSAFLLWD T0375 171 :E 1hdoA 119 :T T0375 174 :REELFQLFG 1hdoA 122 :PPRLQAVTD T0375 201 :SAEEALRGLYG 1hdoA 131 :DHIRMHKVLRE T0375 216 :GAVLVCAWAE 1hdoA 144 :LKYVAVMPPH T0375 226 :EGADALG 1hdoA 161 :GAYTVTL T0375 234 :DGK 1hdoA 168 :DGR T0375 244 :PPPRVVDT 1hdoA 171 :GPSRVISK T0375 277 :RFGCQVAGKKCGLQ 1hdoA 179 :HDLGHFMLRCLTTD Number of specific fragments extracted= 15 number of extra gaps= 2 total=1746 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/T0375-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1hdoA/T0375-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hdoA read from 1hdoA/T0375-1hdoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hdoA in training set Warning: unaligning (T0375)R214 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0375)K215 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0375 2 :SQILCVGL 1hdoA 4 :KKIAIFGA T0375 37 :RGGNASNSCTILSLLGAPCAFMGSMA 1hdoA 12 :TGQTGLTTLAQAVQAGYEVTVLVRDS T0375 82 :RYT 1hdoA 38 :SRL T0375 100 :NEASGSRTILYYDRS 1hdoA 41 :PSEGPRPAHVVVGDV T0375 118 :VSATDFEK 1hdoA 56 :LQAADVDK T0375 127 :DLTQFKWIHIEGRNASE 1hdoA 64 :TVAGQDAVIVLLGTRND T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1hdoA 89 :EGARNIVAAMKAHGVDKVVACTSAFLLW T0375 172 :KPREELFQLF 1hdoA 124 :RLQAVTDDHI T0375 206 :LRGLYGRV 1hdoA 134 :RMHKVLRE T0375 216 :GAVLVCA 1hdoA 144 :LKYVAVM Number of specific fragments extracted= 10 number of extra gaps= 1 total=1756 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0375-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yx1A expands to /projects/compbio/data/pdb/1yx1.pdb.gz 1yx1A:Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 232, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 236, because occupancy 0.450 <= existing 0.450 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1128, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1130, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1134, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1401, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1463, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1465, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1467, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1469, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1471, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1475, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1694, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1yx1A # T0375 read from 1yx1A/T0375-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0375-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yx1A to template set # found chain 1yx1A in template set Warning: unaligning (T0375)P160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yx1A)T159 Warning: unaligning (T0375)E161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yx1A)T159 T0375 47 :ILSLLGAPCAFMG 1yx1A 29 :LLAMAGAQRVELR T0375 60 :SMAPGHVADFVLDDLRRYSVDL 1yx1A 44 :LFAGPPDTEALTAAIQLQGLEC T0375 82 :RYTVFQTTGSV 1yx1A 70 :PLELWREDGQL T0375 101 :EAS 1yx1A 81 :NPE T0375 105 :SRTILYYDRSLPDVSATDF 1yx1A 97 :GWLKVSLGLLPEQPDLAAL T0375 124 :EKVDLTQFKWIHIEGRNAS 1yx1A 117 :RRLARHGLQLLVENDQTPQ T0375 143 :EQVKMLQRIDAHNTRQP 1yx1A 141 :VLERFFRLAERQQLDLA T0375 162 :QKIRVSVEVEKPREELF 1yx1A 160 :FDIGNWRWQEQAADEAA T0375 179 :QLFGYGDVVFVS 1yx1A 178 :RLGRYVGYVHCK T0375 198 :GFQ 1yx1A 196 :DGK T0375 201 :SAEE 1yx1A 205 :SAAD T0375 206 :LRGLYGRVRK 1yx1A 209 :LQYWQRLLQH T0375 216 :GAVLVCAW 1yx1A 222 :GVARAIEY Number of specific fragments extracted= 13 number of extra gaps= 1 total=1769 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0375-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1yx1A/T0375-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0375-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx1A in template set Warning: unaligning (T0375)P160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yx1A)T159 Warning: unaligning (T0375)E161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yx1A)T159 T0375 47 :ILSLLGAPCAFMG 1yx1A 29 :LLAMAGAQRVELR T0375 60 :SMAPGHVADFVLDDLRRYSVDL 1yx1A 44 :LFAGPPDTEALTAAIQLQGLEC T0375 82 :RYTVFQTTGSVP 1yx1A 70 :PLELWREDGQLN T0375 107 :TILYYDRSLPDVSATDFEKVDLT 1yx1A 99 :LKVSLGLLPEQPDLAALGRRLAR T0375 130 :QFKWIHIEGRNASEQ 1yx1A 123 :GLQLLVENDQTPQGG T0375 145 :VKMLQRIDAHNTRQP 1yx1A 143 :ERFFRLAERQQLDLA T0375 162 :QKIRVSVEVEKPREELFQLF 1yx1A 160 :FDIGNWRWQEQAADEAALRL T0375 182 :GYGDVVFV 1yx1A 181 :RYVGYVHC T0375 190 :SKDVAKH 1yx1A 205 :SAADLQY T0375 206 :LRGLYGRVRKGAVLVCA 1yx1A 212 :WQRLLQHFPEGVARAIE Number of specific fragments extracted= 10 number of extra gaps= 1 total=1779 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0375-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1yx1A/T0375-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0375-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx1A in template set Warning: unaligning (T0375)Q162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yx1A)T159 Warning: unaligning (T0375)K163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yx1A)T159 T0375 47 :ILSLLGAPCAFMG 1yx1A 29 :LLAMAGAQRVELR T0375 60 :SMAPGHVADFVLDDLRRYSVDLRYTVFQT 1yx1A 44 :LFAGPPDTEALTAAIQLQGLECVFSSPLE T0375 98 :IINEASGSR 1yx1A 73 :LWREDGQLN T0375 117 :DVSATDFEKVDLTQFKWIHIEGRNASE 1yx1A 82 :PELEPTLRRAEACGAGWLKVSLGLLPE T0375 144 :QVKMLQRIDAHNTRQPPE 1yx1A 140 :EVLERFFRLAERQQLDLA T0375 164 :IRVSVEVE 1yx1A 160 :FDIGNWRW T0375 172 :KPREELFQLFGYGDVVFVS 1yx1A 171 :AADEAALRLGRYVGYVHCK T0375 201 :SAEEALRGLYGRVRKGA 1yx1A 204 :PSAADLQYWQRLLQHFP T0375 218 :VLVCAW 1yx1A 224 :ARAIEY Number of specific fragments extracted= 9 number of extra gaps= 1 total=1788 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3qA/T0375-1c3qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c3qA expands to /projects/compbio/data/pdb/1c3q.pdb.gz 1c3qA:# T0375 read from 1c3qA/T0375-1c3qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3qA read from 1c3qA/T0375-1c3qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c3qA to template set # found chain 1c3qA in template set T0375 40 :NASNSCTILSLL 1c3qA 5 :SAAKCLTAVRRH T0375 54 :PCAFMGSMAP 1c3qA 17 :SPLVHSITNN T0375 65 :HVADFVLDDLRRYSVDLRY 1c3qA 27 :VVTNFTANGLLALGASPVM T0375 117 :DVSATDFEK 1c3qA 46 :AYAKEEVAD T0375 127 :DLTQFKWIHIEGRNA 1c3qA 55 :MAKIAGALVLNIGTL T0375 142 :S 1c3qA 71 :K T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1c3qA 76 :AMIIAGKSANEHGVPVILDP T0375 163 :KIRVS 1c3qA 97 :GAGAT T0375 171 :EKPREELFQLFGY 1c3qA 102 :PFRTESARDIIRE T0375 184 :GDVVFVSKDVAKHL 1c3qA 117 :LAAIRGNAAEIAHT T0375 198 :GFQ 1c3qA 132 :GVT T0375 201 :S 1c3qA 147 :G T0375 203 :EEALRGLYGRVRK 1c3qA 148 :GDIIRLAQQAAQK T0375 216 :GAVLVCAW 1c3qA 162 :NTVIAITG T0375 226 :EGADALGPD 1c3qA 170 :EVDVIADTS T0375 236 :KLLHSDAF 1c3qA 179 :HVYTLHNG T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1c3qA 187 :HKLLTKVTGAGCLLTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 17 number of extra gaps= 0 total=1805 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3qA/T0375-1c3qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1c3qA/T0375-1c3qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3qA read from 1c3qA/T0375-1c3qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c3qA in template set T0375 41 :ASNSCTILSLL 1c3qA 6 :AAKCLTAVRRH T0375 54 :PCAFMGSMA 1c3qA 17 :SPLVHSITN T0375 64 :GHVADFVLDDLRRYSVDL 1c3qA 26 :NVVTNFTANGLLALGASP T0375 84 :TVF 1c3qA 44 :VMA T0375 118 :VSATDFEK 1c3qA 47 :YAKEEVAD T0375 127 :DLTQFKWIHIE 1c3qA 55 :MAKIAGALVLN T0375 138 :GRNASEQ 1c3qA 67 :GTLSKES T0375 145 :VKMLQRIDAHNTRQPPEQ 1c3qA 78 :IIAGKSANEHGVPVILDP T0375 163 :KIRV 1c3qA 97 :GAGA T0375 170 :VEKPREELFQLFGY 1c3qA 101 :TPFRTESARDIIRE T0375 184 :GDVVFVSKDVAKHL 1c3qA 117 :LAAIRGNAAEIAHT T0375 198 :GF 1c3qA 132 :GV T0375 200 :QSAEEALRGLYGRV 1c3qA 148 :GDIIRLAQQAAQKL T0375 215 :K 1c3qA 162 :N T0375 217 :AVLVCAW 1c3qA 163 :TVIAITG T0375 226 :EGADALG 1c3qA 170 :EVDVIAD T0375 234 :DGKLLHSDAF 1c3qA 177 :TSHVYTLHNG T0375 245 :PPRVVDTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1c3qA 187 :HKLLTKVTGAGCLLTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 18 number of extra gaps= 0 total=1823 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3qA/T0375-1c3qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1c3qA/T0375-1c3qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c3qA read from 1c3qA/T0375-1c3qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c3qA in template set T0375 40 :NASNSCTILSLLGAPCAFMGS 1c3qA 5 :SAAKCLTAVRRHSPLVHSITN T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTT 1c3qA 26 :NVVTNFTANGLLALGASPVMAYAKEE T0375 124 :EKVDLTQFKWIHIEGRNASE 1c3qA 52 :VADMAKIAGALVLNIGTLSK T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFG 1c3qA 75 :EAMIIAGKSANEHGVPVILDPVGAGATPFRTESARDIIR T0375 183 :YGDVVFVSKDVAKHLGFQ 1c3qA 116 :RLAAIRGNAAEIAHTVGV T0375 205 :ALRGLYGRVRKG 1c3qA 152 :RLAQQAAQKLNT T0375 218 :VLVCA 1c3qA 164 :VIAIT T0375 225 :EEGADALGPDGKLLHSDAFP 1c3qA 169 :GEVDVIADTSHVYTLHNGHK T0375 250 :DTLGAGDTFNASVIFSLSQGRSVQEALRFGCQVAGKKCG 1c3qA 192 :KVTGAGCLLTSVVGAFCAVEENPLFAAIAAISSYGVAAQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=1832 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0375-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1usgA expands to /projects/compbio/data/pdb/1usg.pdb.gz 1usgA:# T0375 read from 1usgA/T0375-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0375-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1usgA to template set # found chain 1usgA in template set T0375 1 :GS 1usgA 1 :DD T0375 3 :QILCVG 1usgA 4 :KVAVVG T0375 22 :PK 1usgA 11 :MS T0375 40 :NASNSCTILSL 1usgA 124 :QGPTAAKYILE T0375 51 :LGAPCAFMGSMAP 1usgA 136 :VKPQRIAIIHDKQ T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTG 1usgA 152 :EGLARSVQDGLKAANANVVFFDGITAG T0375 115 :LPDV 1usgA 179 :EKDF T0375 120 :ATDFEKVDLTQFKWIHIEGRN 1usgA 183 :SALIARLKKENIDFVYYGGYY T0375 142 :SEQVKMLQRIDAHNTR 1usgA 204 :PEMGQMLRQARSVGLK T0375 158 :QPPEQKIRVS 1usgA 221 :QFMGPEGVGN T0375 171 :EKPREELFQLFGYGDVVFVS 1usgA 231 :ASLSNIAGDAAEGMLVTMPK T0375 203 :EEALRGLYG 1usgA 259 :QGIVDALKA T0375 233 :PDG 1usgA 268 :DKK T0375 245 :PPRV 1usgA 271 :DPSG T0375 257 :TFNASVIFSLSQ 1usgA 280 :TYAAVQSLATAL T0375 269 :GRSVQEALRFGCQ 1usgA 296 :SDEPLALVKDLKA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1848 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0375-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1usgA/T0375-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0375-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set Warning: unaligning (T0375)H239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1usgA)A345 T0375 2 :SQILCVG 1usgA 3 :IKVAVVG T0375 23 :KEDSEI 1usgA 11 :MSGPIA T0375 29 :RCLSQRWQRGG 1usgA 109 :RGYQHIMRTAG T0375 40 :NASNSCTILSL 1usgA 124 :QGPTAAKYILE T0375 51 :LGAPCAFMGSMAP 1usgA 136 :VKPQRIAIIHDKQ T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTT 1usgA 152 :EGLARSVQDGLKAANANVVFFDGITA T0375 103 :S 1usgA 178 :G T0375 115 :LPDV 1usgA 179 :EKDF T0375 120 :ATDFEKVDLTQFKWIHIEGR 1usgA 183 :SALIARLKKENIDFVYYGGY T0375 141 :ASEQVKMLQRIDAHNTR 1usgA 203 :YPEMGQMLRQARSVGLK T0375 158 :QPPEQ 1usgA 221 :QFMGP T0375 166 :VSVEVEKPREELFQLFGYGDVVFVS 1usgA 226 :EGVGNASLSNIAGDAAEGMLVTMPK T0375 191 :KDVAKHLGF 1usgA 262 :VDALKADKK T0375 200 :QSAEEALRGLYGRV 1usgA 297 :DEPLALVKDLKANG T0375 216 :G 1usgA 311 :A T0375 223 :WAEEG 1usgA 320 :WDEKG T0375 228 :ADALGPDGKLL 1usgA 333 :VFQWHADGSST Number of specific fragments extracted= 17 number of extra gaps= 1 total=1865 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0375-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1usgA/T0375-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0375-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set T0375 10 :VVLDVISLVDKYPKEDSEIRCLSQRWQR 1usgA 95 :LMISPGATNPELTQRGYQHIMRTAGLDS T0375 39 :GNASNSCTILSLL 1usgA 123 :SQGPTAAKYILET T0375 52 :GAPCAFMGS 1usgA 138 :PQRIAIIHD T0375 62 :AP 1usgA 147 :KQ T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTGS 1usgA 152 :EGLARSVQDGLKAANANVVFFDGITAGE T0375 117 :DVSATDFEKVDLTQFKWIHIEGRN 1usgA 180 :KDFSALIARLKKENIDFVYYGGYY T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVSK 1usgA 204 :PEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPKR T0375 201 :SAEEALRGLYGRVRKG 1usgA 257 :ANQGIVDALKADKKDP T0375 242 :AF 1usgA 273 :SG T0375 257 :TFNASVIFSLSQ 1usgA 280 :TYAAVQSLATAL T0375 269 :GRSVQEALRFGCQ 1usgA 296 :SDEPLALVKDLKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1876 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cg2A/T0375-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cg2A expands to /projects/compbio/data/pdb/1cg2.pdb.gz 1cg2A:# T0375 read from 1cg2A/T0375-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0375-1cg2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cg2A to template set # found chain 1cg2A in template set T0375 65 :HVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVII 1cg2A 65 :AAGNFLEAELKNLGFTVTRSKSAGLVVGDNIVGKI T0375 101 :EASGSR 1cg2A 100 :KGRGGK T0375 132 :KWIHIEGRN 1cg2A 106 :NLLLMSHMD T0375 141 :A 1cg2A 118 :L T0375 142 :S 1cg2A 120 :G T0375 143 :EQVKMLQRIDAHNTR 1cg2A 148 :VILHTLKLLKEYGVR T0375 158 :QPPEQKIRVSV 1cg2A 169 :VLFNTDEEKGS T0375 171 :EKPREELFQLFGYGDVVFV 1cg2A 180 :FGSRDLIQEEAKLADYVLS T0375 197 :LGFQ 1cg2A 204 :AGDE T0375 201 :SAE 1cg2A 291 :RNE T0375 273 :QEALRFGCQVAGK 1cg2A 334 :KKLVDKAVAYYKE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1887 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cg2A/T0375-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1cg2A/T0375-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0375-1cg2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cg2A in template set T0375 44 :SCTILSLL 1cg2A 43 :VIKTLEKL T0375 52 :GAPC 1cg2A 52 :NIET T0375 62 :APG 1cg2A 56 :GTG T0375 65 :HVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIIN 1cg2A 65 :AAGNFLEAELKNLGFTVTRSKSAGLVVGDNIVGKIK T0375 102 :ASGSR 1cg2A 101 :GRGGK T0375 132 :KWIHIEG 1cg2A 106 :NLLLMSH T0375 139 :RNASEQ 1cg2A 117 :YLKGIL T0375 145 :VKMLQRIDAHNTR 1cg2A 150 :LHTLKLLKEYGVR T0375 158 :QPPEQKIRVSVEVE 1cg2A 169 :VLFNTDEEKGSFGS T0375 174 :REELFQLFGYGDVVFV 1cg2A 183 :RDLIQEEAKLADYVLS T0375 197 :LGF 1cg2A 204 :AGD T0375 200 :QSAEEALRGLYGRVRKGA 1cg2A 238 :VNALVEASDLVLRTMNID T0375 223 :WAEEGADALGP 1cg2A 256 :DKAKNLRFNWT T0375 245 :PPRVVDTLGAG 1cg2A 350 :TLGVEERTGGG T0375 262 :VIFSLSQG 1cg2A 363 :AAYAALSG T0375 272 :VQEALRFGCQVAGKKC 1cg2A 397 :IPRRLYMAARLIMDLG Number of specific fragments extracted= 16 number of extra gaps= 0 total=1903 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cg2A/T0375-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1cg2A/T0375-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cg2A read from 1cg2A/T0375-1cg2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cg2A in template set T0375 65 :HVADFVLDDLRRYSVDLRYTVFQTTGSVPIATVIINEASG 1cg2A 65 :AAGNFLEAELKNLGFTVTRSKSAGLVVGDNIVGKIKGRGG T0375 131 :FKWIHIEGRNA 1cg2A 105 :KNLLLMSHMDT T0375 143 :E 1cg2A 116 :V T0375 144 :QVKMLQRIDAHNTRQP 1cg2A 147 :AVILHTLKLLKEYGVR T0375 160 :PEQKIRVSVEVEKPREELFQLFGYGDVVFV 1cg2A 169 :VLFNTDEEKGSFGSRDLIQEEAKLADYVLS Number of specific fragments extracted= 5 number of extra gaps= 0 total=1908 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z15A/T0375-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z15A expands to /projects/compbio/data/pdb/1z15.pdb.gz 1z15A:# T0375 read from 1z15A/T0375-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0375-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z15A to template set # found chain 1z15A in template set T0375 2 :S 1z15A 2 :D T0375 3 :QILCVGL 1z15A 4 :KVAVVGA T0375 22 :PKE 1z15A 11 :MSG T0375 40 :NASNSCTILSL 1z15A 124 :QGPTAAKYILE T0375 51 :LGAPC 1z15A 136 :VKPQR T0375 57 :FMGSMAPG 1z15A 141 :IAIVHDKQ T0375 65 :HVADFVLDDLRRYSVDLRYTVFQTT 1z15A 153 :GLARAVQDGLKKGNANVVFFDGITA T0375 103 :SG 1z15A 178 :GE T0375 116 :PDV 1z15A 180 :KDF T0375 120 :ATDFEKVDLTQFKWIHIEGRNA 1z15A 183 :STLVARLKKENIDFVYYGGYHP T0375 143 :EQVKMLQRIDAHNTR 1z15A 205 :EMGQILRQARAAGLK T0375 158 :QPPEQKIRVS 1z15A 221 :QFMGPEGVAN T0375 171 :EKPREELFQLFGYGDVVFVS 1z15A 231 :VSLSNIAGESAEGLLVTKPK T0375 191 :KDVAKHLGFQ 1z15A 262 :VDAIKAKKQD T0375 201 :SAEEALRGLYG 1z15A 296 :DPAEIAKYLKA Number of specific fragments extracted= 15 number of extra gaps= 0 total=1923 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z15A/T0375-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1z15A/T0375-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0375-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z15A in template set T0375 1 :GSQILCVG 1z15A 2 :DIKVAVVG T0375 23 :KEDSEI 1z15A 11 :MSGPVA T0375 40 :NASNSCTILSL 1z15A 124 :QGPTAAKYILE T0375 51 :LGAPCAFMGSMAP 1z15A 136 :VKPQRIAIVHDKQ T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTT 1z15A 152 :EGLARAVQDGLKKGNANVVFFDGITA T0375 103 :SGS 1z15A 178 :GEK T0375 117 :DV 1z15A 181 :DF T0375 120 :ATDFEKVDLTQFKWIHIEGR 1z15A 183 :STLVARLKKENIDFVYYGGY T0375 141 :ASEQVKMLQRIDAHNTR 1z15A 203 :HPEMGQILRQARAAGLK T0375 158 :QPPEQK 1z15A 221 :QFMGPE T0375 167 :SVEVEKPREELFQLFGYGDVVFVS 1z15A 227 :GVANVSLSNIAGESAEGLLVTKPK T0375 191 :KDVAKHLGF 1z15A 262 :VDAIKAKKQ T0375 200 :QSAEEALRGLYGRV 1z15A 295 :DDPAEIAKYLKANS T0375 216 :GA 1z15A 309 :VD T0375 221 :CAWAEEG 1z15A 316 :LTWDEKG T0375 228 :ADALGPDGKLLHS 1z15A 331 :VFDWHANGTATDA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1939 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z15A/T0375-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1z15A/T0375-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0375-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z15A in template set T0375 10 :VVLDVISLVDKYPKEDSEIRCLSQRWQ 1z15A 95 :LMITPAATAPELTARGYQLILRTTGLD T0375 39 :GNASNSCTILSLL 1z15A 123 :DQGPTAAKYILEK T0375 53 :A 1z15A 138 :P T0375 54 :PCAFMGS 1z15A 140 :RIAIVHD T0375 62 :AP 1z15A 147 :KQ T0375 64 :GHVADFVLDDLRRYSVDLRYTVFQTTG 1z15A 152 :EGLARAVQDGLKKGNANVVFFDGITAG T0375 116 :PDVSATDFEKVDLTQFKWIHIEGRN 1z15A 179 :EKDFSTLVARLKKENIDFVYYGGYH T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLFGYGDVVFVS 1z15A 204 :PEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPK T0375 201 :SAEEALRGL 1z15A 257 :ANKPIVDAI T0375 212 :RVRKG 1z15A 266 :KAKKQ T0375 240 :SDAF 1z15A 271 :DPSG T0375 257 :TFNASVIFSL 1z15A 275 :AFVWTTYAAL T0375 267 :SQGRSVQEALRFGCQ 1z15A 292 :NQSDDPAEIAKYLKA Number of specific fragments extracted= 13 number of extra gaps= 0 total=1952 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rq2A/T0375-1rq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rq2A expands to /projects/compbio/data/pdb/1rq2.pdb.gz 1rq2A:Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 733, because occupancy 0.330 <= existing 0.330 in 1rq2A Skipped atom 734, because occupancy 0.330 <= existing 0.330 in 1rq2A Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1774, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1776, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1778, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1846, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2041, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2043, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2045, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2135, because occupancy 0.500 <= existing 0.500 in 1rq2A Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 1rq2A # T0375 read from 1rq2A/T0375-1rq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rq2A read from 1rq2A/T0375-1rq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rq2A to template set # found chain 1rq2A in template set Warning: unaligning (T0375)S105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0375)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0375 3 :QILCVG 1rq2A 10 :VIKVVG T0375 38 :GGNASNSCTILSLLGAP 1rq2A 17 :GGGGVNAVNRMIEQGLK T0375 55 :CAFMGSMAPGHVADF 1rq2A 35 :VEFIAINTDAQALLM T0375 79 :VDLRYTVFQTT 1rq2A 50 :SDADVKLDVGR T0375 103 :SG 1rq2A 61 :DS T0375 118 :VSATDFEKV 1rq2A 70 :ADPEVGRKA T0375 128 :LTQFKWIHIE 1rq2A 90 :LRGADMVFVT T0375 138 :GRN 1rq2A 103 :GGG T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLF 1rq2A 110 :GAPVVASIARKLGALTVGVVTRPFSFEGKRRSNQAENGI T0375 182 :GYGDVVFV 1rq2A 153 :ESCDTLIV T0375 190 :S 1rq2A 162 :P T0375 194 :AKHL 1rq2A 163 :NDRL T0375 198 :GFQ 1rq2A 168 :QMG T0375 201 :SAEEALRGLYGRVR 1rq2A 175 :SLMDAFRSADEVLL T0375 256 :DTFNASVIFSL 1rq2A 189 :NGVQGITDLIT T0375 267 :SQGRS 1rq2A 215 :MSGAG T0375 272 :VQEALRFGC 1rq2A 234 :SLKAAEIAI Number of specific fragments extracted= 17 number of extra gaps= 0 total=1969 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rq2A/T0375-1rq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rq2A/T0375-1rq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rq2A read from 1rq2A/T0375-1rq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rq2A in template set Warning: unaligning (T0375)S105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0375)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0375 3 :QILCVG 1rq2A 10 :VIKVVG T0375 38 :GGNASNSCTILSLLGAP 1rq2A 17 :GGGGVNAVNRMIEQGLK T0375 55 :CAFMGSMAPGHVADF 1rq2A 35 :VEFIAINTDAQALLM T0375 79 :VDLRYTVFQTT 1rq2A 50 :SDADVKLDVGR T0375 103 :SG 1rq2A 61 :DS T0375 118 :VSATDFE 1rq2A 70 :ADPEVGR T0375 125 :KVDLTQFKWIHIEGRNASEQ 1rq2A 87 :EELLRGADMVFVTAGEGGGT T0375 145 :VKMLQRIDAHNTRQPPEQKIRVSVEV 1rq2A 112 :PVVASIARKLGALTVGVVTRPFSFEG T0375 175 :EELFQL 1rq2A 138 :KRRSNQ T0375 202 :AEEALRGLYGR 1rq2A 144 :AENGIAALRES T0375 216 :GAVLVCA 1rq2A 155 :CDTLIVI T0375 234 :D 1rq2A 168 :Q T0375 235 :GK 1rq2A 170 :GD T0375 268 :QGRSVQEALRFGCQVAGKKCG 1rq2A 172 :AAVSLMDAFRSADEVLLNGVQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=1983 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rq2A/T0375-1rq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rq2A/T0375-1rq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rq2A read from 1rq2A/T0375-1rq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rq2A in template set Warning: unaligning (T0375)S2 because of BadResidue code BAD_PEPTIDE at template residue (1rq2A)A9 Warning: unaligning (T0375)G104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rq2A)G69 Warning: unaligning (T0375)Y110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rq2A)G69 T0375 3 :QILCVG 1rq2A 10 :VIKVVG T0375 37 :RGGNASNSCTILSLLGAP 1rq2A 16 :IGGGGVNAVNRMIEQGLK T0375 55 :CAFMGSMAPGHVADF 1rq2A 35 :VEFIAINTDAQALLM T0375 79 :VDLRYTVFQTT 1rq2A 50 :SDADVKLDVGR T0375 102 :AS 1rq2A 61 :DS T0375 111 :YDR 1rq2A 70 :ADP T0375 116 :PDVSAT 1rq2A 73 :EVGRKA T0375 122 :DFEKVDLTQFKWIHIEGRNASE 1rq2A 84 :DEIEELLRGADMVFVTAGEGGG T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1rq2A 109 :GGAPVVASIARKLGALTVGVVTRPFSFE T0375 172 :KPREELFQLF 1rq2A 142 :NQAENGIAAL T0375 182 :GYGDVVFV 1rq2A 153 :ESCDTLIV T0375 194 :AKHLGFQ 1rq2A 163 :NDRLLQM T0375 202 :AEEA 1rq2A 207 :DFAD T0375 209 :LYGRVRKGAVLVC 1rq2A 211 :VKGIMSGAGTALM T0375 227 :GADALGPDG 1rq2A 224 :GIGSARGEG Number of specific fragments extracted= 15 number of extra gaps= 1 total=1998 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gbp/T0375-2gbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gbp expands to /projects/compbio/data/pdb/2gbp.pdb.gz 2gbp:Warning: there is no chain 2gbp will retry with 2gbpA # T0375 read from 2gbp/T0375-2gbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gbp read from 2gbp/T0375-2gbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gbp to template set # found chain 2gbp in template set Warning: unaligning (T0375)A62 because of BadResidue code BAD_PEPTIDE in next template residue (2gbp)D13 Warning: unaligning (T0375)P63 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)D13 Warning: unaligning (T0375)D192 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2gbp)E165 Warning: unaligning (T0375)V193 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2gbp)E165 Warning: unaligning (T0375)Q290 because of BadResidue code BAD_PEPTIDE in next template residue (2gbp)G277 Warning: unaligning (T0375)G291 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)G277 T0375 54 :PCAFMGSM 2gbp 4 :RIGVTIYK T0375 64 :GHVADFVLDDLRRY 2gbp 14 :DNFMSVVRKAIEQD T0375 78 :S 2gbp 33 :D T0375 81 :LRYTVFQTT 2gbp 34 :VQLLMNDSQ T0375 104 :GS 2gbp 43 :ND T0375 120 :ATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQ 2gbp 49 :NDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFN T0375 171 :EKPREELFQLF 2gbp 113 :KESGIIQGDLI T0375 184 :GDVVFVS 2gbp 141 :IQFVLLK T0375 191 :K 2gbp 163 :I T0375 194 :AKHLGFQ 2gbp 166 :LNDKGIK T0375 201 :SAEEALRGLYGRVR 2gbp 184 :DTAQAKDKMDAWLS T0375 216 :GAVLVCAWA 2gbp 203 :KIEVVIANN T0375 256 :DTFNASVIFSL 2gbp 212 :DAMAMGAVEAL T0375 267 :SQGR 2gbp 246 :KSGA T0375 271 :SVQEALRFGCQVAGKKCGL 2gbp 257 :DANNQAKATFDLAKNLADG T0375 292 :FDGI 2gbp 278 :AADG Number of specific fragments extracted= 16 number of extra gaps= 3 total=2014 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gbp/T0375-2gbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2gbp/T0375-2gbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gbp read from 2gbp/T0375-2gbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gbp in template set Warning: unaligning (T0375)P63 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)D13 Warning: unaligning (T0375)Q290 because of BadResidue code BAD_PEPTIDE in next template residue (2gbp)G277 Warning: unaligning (T0375)G291 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)G277 T0375 56 :AFMGSMA 2gbp 5 :IGVTIYK T0375 64 :GHVADFVLDDLRRY 2gbp 14 :DNFMSVVRKAIEQD T0375 78 :S 2gbp 33 :D T0375 81 :LRYTVFQT 2gbp 34 :VQLLMNDS T0375 103 :SGS 2gbp 42 :QND T0375 120 :ATDFEKVDLTQFKWIHIEGRNASEQVKMLQRIDAHNTRQPPEQK 2gbp 49 :NDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNK T0375 172 :KPREELFQLFGYGDVVFV 2gbp 93 :EPSRKALDSYDKAYYVGT T0375 201 :SAEEALRGLYGR 2gbp 111 :DSKESGIIQGDL T0375 214 :RKGAVLVCAWAEE 2gbp 139 :GQIQFVLLKGEPG T0375 244 :PPPRVVDTL 2gbp 202 :NKIEVVIAN T0375 255 :GDTFNASVIFSL 2gbp 211 :NDAMAMGAVEAL T0375 267 :SQG 2gbp 224 :AHN T0375 270 :RSVQEALRFGCQVAGKKCGL 2gbp 256 :NDANNQAKATFDLAKNLADG T0375 292 :FD 2gbp 278 :AA T0375 294 :G 2gbp 281 :G Number of specific fragments extracted= 15 number of extra gaps= 2 total=2029 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gbp/T0375-2gbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2gbp/T0375-2gbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gbp read from 2gbp/T0375-2gbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gbp in template set Warning: unaligning (T0375)A62 because of BadResidue code BAD_PEPTIDE in next template residue (2gbp)D13 Warning: unaligning (T0375)P63 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)D13 Warning: unaligning (T0375)Q290 because of BadResidue code BAD_PEPTIDE in next template residue (2gbp)G277 Warning: unaligning (T0375)G291 because of BadResidue code BAD_PEPTIDE at template residue (2gbp)G277 T0375 54 :PCAFMGSM 2gbp 4 :RIGVTIYK T0375 64 :GHVADFVLDDLRRY 2gbp 14 :DNFMSVVRKAIEQD T0375 78 :SVDLRYTVFQTT 2gbp 33 :DVQLLMNDSQND T0375 116 :PDVSATDFEKVDLTQFKWIHIEGRNA 2gbp 45 :QSKQNDQIDVLLAKGVKALAINLVDP T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVS 2gbp 71 :AAAGTVIEKARGQNVPVVFFNKEP T0375 174 :REELFQLFGYGDVVFVSKDVAKHLGFQ 2gbp 95 :SRKALDSYDKAYYVGTDSKESGIIQGD T0375 201 :SAEEALRGLYGRVR 2gbp 184 :DTAQAKDKMDAWLS T0375 215 :KGAVLVCA 2gbp 203 :KIEVVIAN T0375 255 :GDTFNASVIFSL 2gbp 211 :NDAMAMGAVEAL T0375 269 :G 2gbp 248 :G T0375 270 :RSVQEALRFGCQVAGKKCGL 2gbp 256 :NDANNQAKATFDLAKNLADG T0375 292 :F 2gbp 278 :A Number of specific fragments extracted= 12 number of extra gaps= 2 total=2041 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofuA/T0375-1ofuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ofuA expands to /projects/compbio/data/pdb/1ofu.pdb.gz 1ofuA:# T0375 read from 1ofuA/T0375-1ofuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofuA read from 1ofuA/T0375-1ofuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ofuA to template set # found chain 1ofuA in template set T0375 1 :GSQILCVG 1ofuA 11 :TAVIKVIG T0375 38 :GGNASNSCTILSLLGAP 1ofuA 20 :GGGGGNAVNHMAKNNVE T0375 55 :CAFMGSMAPGHVA 1ofuA 38 :VEFICANTDAQAL T0375 78 :SVDLRYTVFQT 1ofuA 52 :NIAARTVLQLG T0375 112 :DRSLPDVSATDFEKV 1ofuA 67 :KGLGAGANPEVGRQA T0375 128 :LTQFKWIHIE 1ofuA 93 :LEGADMVFIT T0375 138 :GRNA 1ofuA 105 :MGGG T0375 143 :EQVKMLQRIDAHNTRQPPEQKIRVSVEVEKPREELFQLF 1ofuA 113 :AAPIIAEVAKEMGILTVAVVTRPFPFEGRKRMQIADEGI T0375 182 :GYGD 1ofuA 156 :ESVD T0375 186 :VVFVSKDVAKHL 1ofuA 161 :LITIPNEKLLTI T0375 198 :GFQ 1ofuA 174 :GKD T0375 201 :SAEEALRGLYGRV 1ofuA 178 :SLLAAFAKADDVL T0375 277 :RFGCQVAGKKCGLQGFDGI 1ofuA 191 :AGAVRGISDIIKRPGMINV Number of specific fragments extracted= 13 number of extra gaps= 0 total=2054 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofuA/T0375-1ofuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ofuA/T0375-1ofuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofuA read from 1ofuA/T0375-1ofuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ofuA in template set T0375 1 :GSQILCVG 1ofuA 11 :TAVIKVIG T0375 38 :GGNASNSCTILSLLGAP 1ofuA 20 :GGGGGNAVNHMAKNNVE T0375 55 :CAFMGSMAPGHVA 1ofuA 38 :VEFICANTDAQAL T0375 78 :SVDLRYTVFQT 1ofuA 52 :NIAARTVLQLG T0375 103 :SGSR 1ofuA 67 :KGLG T0375 114 :S 1ofuA 71 :A T0375 117 :DVSATDFE 1ofuA 72 :GANPEVGR T0375 125 :KVD 1ofuA 84 :EDR T0375 128 :LTQFKWIHI 1ofuA 93 :LEGADMVFI T0375 137 :EGRNASEQ 1ofuA 104 :GMGGGTGT T0375 145 :VKMLQRIDAHNTRQPP 1ofuA 115 :PIIAEVAKEMGILTVA T0375 186 :VVFV 1ofuA 131 :VVTR T0375 190 :SKDVAKH 1ofuA 140 :GRKRMQI T0375 202 :AEEALRGLYGR 1ofuA 147 :ADEGIRALAES T0375 216 :GAVLVCA 1ofuA 158 :VDSLITI T0375 261 :SVIFSLSQGRSVQEALRFGCQVAGKKCG 1ofuA 168 :KLLTILGKDASLLAAFAKADDVLAGAVR T0375 289 :LQGFDGI 1ofuA 203 :RPGMINV Number of specific fragments extracted= 17 number of extra gaps= 0 total=2071 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofuA/T0375-1ofuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1ofuA/T0375-1ofuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofuA read from 1ofuA/T0375-1ofuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ofuA in template set T0375 3 :QILCVG 1ofuA 13 :VIKVIG T0375 37 :RGGNASNSCTILSLLGAP 1ofuA 19 :VGGGGGNAVNHMAKNNVE T0375 55 :CAFMGSMAPGHV 1ofuA 38 :VEFICANTDAQA T0375 78 :SVDLRYTVFQ 1ofuA 52 :NIAARTVLQL T0375 88 :TT 1ofuA 67 :KG T0375 109 :LYYDRSLPDVSATDF 1ofuA 69 :LGAGANPEVGRQAAL T0375 124 :EKVDLTQFKWIHIEGRNASE 1ofuA 89 :ISEVLEGADMVFITTGMGGG T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1ofuA 112 :GAAPIIAEVAKEMGILTVAVVTRPFPFE T0375 172 :KPREELFQLF 1ofuA 145 :QIADEGIRAL T0375 182 :GYGD 1ofuA 156 :ESVD T0375 186 :VVFVSKDVAKHLGFQS 1ofuA 161 :LITIPNEKLLTILGKD T0375 202 :AEEALRGLY 1ofuA 178 :SLLAAFAKA T0375 256 :DTFNASVIFSLSQ 1ofuA 187 :DDVLAGAVRGISD T0375 269 :GRSVQEALR 1ofuA 208 :NVDFADVKT Number of specific fragments extracted= 14 number of extra gaps= 0 total=2085 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2liv/T0375-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2liv expands to /projects/compbio/data/pdb/2liv.pdb.gz 2liv:Warning: there is no chain 2liv will retry with 2livA # T0375 read from 2liv/T0375-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0375-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2liv to template set # found chain 2liv in template set Warning: unaligning (T0375)S2 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D2 Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)A10 Warning: unaligning (T0375)L9 because of BadResidue code BAD_PEPTIDE at template residue (2liv)A10 Warning: unaligning (T0375)V10 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S12 Warning: unaligning (T0375)K23 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S12 Warning: unaligning (T0375)S49 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N67 Warning: unaligning (T0375)L50 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N67 Warning: unaligning (T0375)G59 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)H76 Warning: unaligning (T0375)S60 because of BadResidue code BAD_PEPTIDE at template residue (2liv)H76 Warning: unaligning (T0375)V66 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T82 Warning: unaligning (T0375)A67 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T82 Warning: unaligning (T0375)Y111 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T118 Warning: unaligning (T0375)D112 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T118 Warning: unaligning (T0375)R113 because of BadResidue code BAD_PEPTIDE at template residue (2liv)G119 Warning: unaligning (T0375)H154 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0375)N155 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0375)T156 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0375)R157 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0375)P160 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0375)E161 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0375)F178 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0375)Q179 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0375)S267 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)Q293 Warning: unaligning (T0375)Q268 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q293 T0375 3 :QILCV 2liv 4 :KVAVV T0375 41 :ASNSCTIL 2liv 58 :AVAVANKV T0375 51 :LGAPC 2liv 68 :DGIKY T0375 57 :FM 2liv 73 :VI T0375 61 :MAP 2liv 77 :LCS T0375 65 :H 2liv 80 :S T0375 68 :DFVLDDLRRYSV 2liv 83 :QPASDIYEDEGI T0375 83 :YTVF 2liv 95 :LMIT T0375 87 :QTTG 2liv 103 :APEL T0375 101 :EASGSRTILY 2liv 107 :TARGYQLILR T0375 114 :SLPD 2liv 120 :LDSD T0375 122 :DFEKVD 2liv 124 :QGPTAA T0375 128 :LT 2liv 138 :PQ T0375 132 :KWIHIEGRNA 2liv 140 :RIAIVHDKQQ T0375 143 :EQVKMLQRIDA 2liv 154 :LARAVQDGLKK T0375 158 :QP 2liv 169 :VV T0375 162 :Q 2liv 173 :D T0375 163 :KIRVSV 2liv 177 :AGEKDF T0375 171 :EKPREEL 2liv 183 :STLVARL T0375 182 :GYGDVVFVS 2liv 192 :ENIDFVYYG T0375 200 :QSAEEALRGLYGRVRKGA 2liv 201 :GYHPEMGQILRQARAAGL T0375 218 :VLVCAWAE 2liv 221 :QFMGPEGV T0375 226 :EGADALGP 2liv 242 :EGLLVTKP T0375 251 :TLGA 2liv 272 :PSGA T0375 255 :GDTFNA 2liv 278 :WTTYAA T0375 261 :SVIFSL 2liv 286 :SLQAGL T0375 269 :GRSVQEALRFGCQ 2liv 294 :SDDPAEIAKYLKA Number of specific fragments extracted= 27 number of extra gaps= 10 total=2112 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2liv/T0375-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2liv/T0375-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0375-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2liv in template set Warning: unaligning (T0375)G8 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)A10 Warning: unaligning (T0375)K23 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S12 Warning: unaligning (T0375)E24 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S12 Warning: unaligning (T0375)L48 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)L133 Warning: unaligning (T0375)S49 because of BadResidue code BAD_PEPTIDE at template residue (2liv)L133 Warning: unaligning (T0375)Y77 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0375)S78 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0375)V79 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0375)D80 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0375)Y83 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0375)T84 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0375)D127 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0375)L128 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0375)E171 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S232 Warning: unaligning (T0375)K172 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S232 Warning: unaligning (T0375)F178 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)E239 Warning: unaligning (T0375)Q179 because of BadResidue code BAD_PEPTIDE at template residue (2liv)E239 Warning: unaligning (T0375)L197 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K266 Warning: unaligning (T0375)L237 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T341 Warning: unaligning (T0375)L238 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T341 T0375 1 :GSQILCV 2liv 2 :DIKVAVV T0375 25 :DSEI 2liv 13 :GPVA T0375 41 :ASNSCTI 2liv 125 :GPTAAKY T0375 52 :GAPCAFMGSMAP 2liv 137 :KPQRIAIVHDKQ T0375 64 :GHVADFVLDDLRR 2liv 152 :EGLARAVQDGLKK T0375 81 :LR 2liv 169 :VV T0375 85 :VFQTT 2liv 173 :DGITA T0375 103 :SGS 2liv 178 :GEK T0375 117 :DV 2liv 181 :DF T0375 120 :ATDFEKV 2liv 183 :STLVARL T0375 129 :TQFKWIHIEGR 2liv 192 :ENIDFVYYGGY T0375 141 :ASEQVKMLQRIDAHNTR 2liv 203 :HPEMGQILRQARAAGLK T0375 158 :QPPEQK 2liv 221 :QFMGPE T0375 167 :SVEV 2liv 227 :GVAN T0375 173 :PREEL 2liv 233 :LSNIA T0375 180 :LFGYGDVVFVS 2liv 240 :SAEGLLVTKPK T0375 191 :KDVAKH 2liv 259 :KPIVDA T0375 200 :QSAEEALRGLYGRV 2liv 295 :DDPAEIAKYLKANS T0375 216 :GA 2liv 309 :VD T0375 221 :CAWAEEG 2liv 316 :LTWDEKG T0375 228 :ADALGPDGK 2liv 331 :VFDWHANGT T0375 239 :HS 2liv 342 :DA Number of specific fragments extracted= 22 number of extra gaps= 10 total=2134 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2liv/T0375-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2liv/T0375-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0375-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2liv in template set Warning: unaligning (T0375)L48 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)L133 Warning: unaligning (T0375)S49 because of BadResidue code BAD_PEPTIDE at template residue (2liv)L133 Warning: unaligning (T0375)Y77 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0375)S78 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0375)V79 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0375)D80 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0375)Y83 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0375)T84 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0375)D127 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0375)L128 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0375)E171 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S232 Warning: unaligning (T0375)K172 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S232 Warning: unaligning (T0375)F178 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)E239 Warning: unaligning (T0375)Q179 because of BadResidue code BAD_PEPTIDE at template residue (2liv)E239 Warning: unaligning (T0375)G211 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K266 Warning: unaligning (T0375)R212 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K266 Warning: unaligning (T0375)S267 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)Q293 Warning: unaligning (T0375)Q268 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q293 T0375 40 :NASNSCTI 2liv 124 :QGPTAAKY T0375 50 :LL 2liv 134 :EK T0375 53 :APCAFMG 2liv 139 :QRIAIVH T0375 61 :MAP 2liv 146 :DKQ T0375 64 :GHVADFVLDDLRR 2liv 152 :EGLARAVQDGLKK T0375 81 :LR 2liv 169 :VV T0375 85 :VFQTTGS 2liv 173 :DGITAGE T0375 117 :DVSATDFEKV 2liv 180 :KDFSTLVARL T0375 129 :TQFKWIHIEGRN 2liv 192 :ENIDFVYYGGYH T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEV 2liv 204 :PEMGQILRQARAAGLKTQFMGPEGVAN T0375 173 :PREEL 2liv 233 :LSNIA T0375 180 :LFGYGDVVFVS 2liv 240 :SAEGLLVTKPK T0375 201 :SAEEA 2liv 257 :ANKPI T0375 208 :GLY 2liv 262 :VDA T0375 213 :VRKG 2liv 267 :AKKQ T0375 232 :GPDGK 2liv 271 :DPSGA T0375 257 :TFNA 2liv 280 :TYAA T0375 261 :SVIFSL 2liv 286 :SLQAGL T0375 269 :GRSVQEALRFGCQ 2liv 294 :SDDPAEIAKYLKA Number of specific fragments extracted= 19 number of extra gaps= 8 total=2153 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2lbp/T0375-2lbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2lbp expands to /projects/compbio/data/pdb/2lbp.pdb.gz 2lbp:Warning: there is no chain 2lbp will retry with 2lbpA # T0375 read from 2lbp/T0375-2lbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2lbp read from 2lbp/T0375-2lbp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2lbp to template set # found chain 2lbp in template set Warning: unaligning (T0375)Q3 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V5 Warning: unaligning (T0375)I4 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V5 Warning: unaligning (T0375)S60 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)K147 Warning: unaligning (T0375)M61 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)K147 Warning: unaligning (T0375)F69 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V158 Warning: unaligning (T0375)V70 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V158 Warning: unaligning (T0375)G138 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)Y202 Warning: unaligning (T0375)R139 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)Y202 Warning: unaligning (T0375)Q149 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)Q212 Warning: unaligning (T0375)R150 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)Q212 Warning: unaligning (T0375)P159 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)M223 Warning: unaligning (T0375)P160 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)M223 Warning: unaligning (T0375)S201 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)E298 Warning: unaligning (T0375)E204 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)L302 Warning: unaligning (T0375)A205 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)L302 Warning: unaligning (T0375)G211 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)N309 Warning: unaligning (T0375)K215 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)N309 Warning: unaligning (T0375)G216 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)G310 T0375 5 :LCVGLV 2lbp 6 :AVVGAM T0375 38 :GGNASNSCTILSLL 2lbp 118 :AGLDSSQGPTAAKY T0375 52 :GAPCAFMG 2lbp 138 :PQRIAIIH T0375 62 :AP 2lbp 148 :QQ T0375 64 :GHVAD 2lbp 152 :EGLAR T0375 71 :LDDLRRYSVDLRYTVFQT 2lbp 159 :QDGLKAANANVVFFDGIT T0375 102 :AS 2lbp 177 :AG T0375 115 :LPDV 2lbp 179 :EKDF T0375 120 :ATDFEKVDLTQFKWIHIE 2lbp 183 :SALIARLKKENIDFVYYG T0375 140 :N 2lbp 203 :Y T0375 142 :SEQVKML 2lbp 204 :PEMGQML T0375 151 :IDAHNTR 2lbp 213 :ARSVGLK T0375 158 :Q 2lbp 221 :Q T0375 161 :EQKIRVS 2lbp 224 :GPEGVGN T0375 171 :EKPREELFQLFGYGDVVFVS 2lbp 231 :ASLSNIAGDAAEGMLVTMPK T0375 191 :KDVAKHLGFQ 2lbp 262 :VDALKADKKD T0375 202 :AE 2lbp 299 :PL T0375 206 :LRGLY 2lbp 303 :VKDLK T0375 217 :A 2lbp 311 :A T0375 223 :WAEEG 2lbp 320 :WDEKG T0375 228 :ADALGPDGKLLHS 2lbp 333 :VFQWHADGSSTKA Number of specific fragments extracted= 21 number of extra gaps= 9 total=2174 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2lbp/T0375-2lbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2lbp/T0375-2lbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2lbp read from 2lbp/T0375-2lbp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2lbp in template set Warning: unaligning (T0375)Q3 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V5 Warning: unaligning (T0375)I4 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V5 Warning: unaligning (T0375)E24 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)G13 Warning: unaligning (T0375)D25 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)G13 Warning: unaligning (T0375)S60 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)K147 Warning: unaligning (T0375)M61 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)K147 Warning: unaligning (T0375)F69 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V158 Warning: unaligning (T0375)V70 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V158 Warning: unaligning (T0375)G138 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)Y202 Warning: unaligning (T0375)R139 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)Y202 Warning: unaligning (T0375)Q149 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)Q212 Warning: unaligning (T0375)R150 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)Q212 Warning: unaligning (T0375)P159 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)M223 Warning: unaligning (T0375)P160 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)M223 Warning: unaligning (T0375)Q200 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)D297 Warning: unaligning (T0375)S201 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)E298 Warning: unaligning (T0375)E204 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)L302 Warning: unaligning (T0375)A205 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)L302 Warning: unaligning (T0375)G211 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)N309 Warning: unaligning (T0375)R212 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)N309 Warning: unaligning (T0375)V213 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)G310 T0375 2 :S 2lbp 3 :I T0375 5 :LCVGL 2lbp 6 :AVVGA T0375 23 :K 2lbp 11 :M T0375 26 :SEI 2lbp 14 :PIA T0375 29 :RCLSQRWQRGGNASNSCTILSLL 2lbp 109 :RGYQHIMRTAGLDSSQGPTAAKY T0375 52 :GAPCAFMG 2lbp 138 :PQRIAIIH T0375 62 :AP 2lbp 148 :QQ T0375 64 :GHVAD 2lbp 152 :EGLAR T0375 71 :LDDLRRYSVDLRYTVFQT 2lbp 159 :QDGLKAANANVVFFDGIT T0375 102 :ASGS 2lbp 177 :AGEK T0375 117 :DV 2lbp 181 :DF T0375 120 :ATDFEKVDLTQFKWIHIE 2lbp 183 :SALIARLKKENIDFVYYG T0375 141 :ASEQVKML 2lbp 203 :YPEMGQML T0375 151 :IDAHNTR 2lbp 213 :ARSVGLK T0375 158 :Q 2lbp 221 :Q T0375 161 :EQ 2lbp 224 :GP T0375 166 :VSVEVEKPREELFQLFGYGDVVFVS 2lbp 226 :EGVGNASLSNIAGDAAEGMLVTMPK T0375 191 :KDVAKHL 2lbp 259 :QGIVDAL T0375 198 :GF 2lbp 269 :KK T0375 202 :AE 2lbp 299 :PL T0375 206 :LRGLY 2lbp 303 :VKDLK T0375 216 :GA 2lbp 311 :AN T0375 223 :WAEEG 2lbp 320 :WDEKG T0375 228 :ADALGPDGKLLHS 2lbp 333 :VFQWHADGSSTKA Number of specific fragments extracted= 24 number of extra gaps= 10 total=2198 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2lbp/T0375-2lbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 2lbp/T0375-2lbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2lbp read from 2lbp/T0375-2lbp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2lbp in template set Warning: unaligning (T0375)P54 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V5 Warning: unaligning (T0375)C55 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V5 Warning: unaligning (T0375)A62 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)G13 Warning: unaligning (T0375)P63 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)G13 Warning: unaligning (T0375)L74 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)N34 Warning: unaligning (T0375)R75 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)N34 Warning: unaligning (T0375)Y110 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)D50 Warning: unaligning (T0375)Y111 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)D50 Warning: unaligning (T0375)D112 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)D51 Warning: unaligning (T0375)S119 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V59 Warning: unaligning (T0375)A120 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)V59 Warning: unaligning (T0375)F131 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)K71 Warning: unaligning (T0375)K132 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)K71 Warning: unaligning (T0375)I136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2lbp)H76 Warning: unaligning (T0375)E137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2lbp)H76 Warning: unaligning (T0375)H154 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)D91 Warning: unaligning (T0375)N155 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)D91 Warning: unaligning (T0375)V189 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)K147 Warning: unaligning (T0375)S190 because of BadResidue code BAD_PEPTIDE at template residue (2lbp)K147 Warning: unaligning (T0375)Q200 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)V158 Warning: unaligning (T0375)W223 because of BadResidue code BAD_PEPTIDE in next template residue (2lbp)Y202 T0375 53 :A 2lbp 3 :I T0375 56 :AFMGSM 2lbp 6 :AVVGAM T0375 64 :GH 2lbp 14 :PI T0375 66 :VADFVLDD 2lbp 25 :GAEQAIKD T0375 76 :RYS 2lbp 35 :AKG T0375 101 :EASGSRTIL 2lbp 40 :KGDKLVGVE T0375 113 :RSLPDV 2lbp 52 :ACDPKQ T0375 121 :TDFEKVDLTQ 2lbp 60 :AVANKIVNDG T0375 133 :WIH 2lbp 72 :YVI T0375 138 :GRN 2lbp 77 :LCS T0375 144 :QVKMLQRIDA 2lbp 80 :SSTQPASDIY T0375 156 :TRQPPEQKIRVSVEVE 2lbp 92 :EGILMISPGATAPELT T0375 172 :KPREELFQLF 2lbp 123 :SQGPTAAKYI T0375 182 :GYGDVVF 2lbp 139 :QRIAIIH T0375 191 :KDVAKHLGF 2lbp 148 :QQYGEGLAR T0375 201 :SAEEALR 2lbp 181 :DFSALIA T0375 210 :YGRVRKGAVLVCA 2lbp 188 :RLKKENIDFVYYG Number of specific fragments extracted= 17 number of extra gaps= 11 total=2215 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcuA/T0375-1rcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rcuA expands to /projects/compbio/data/pdb/1rcu.pdb.gz 1rcuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0375 read from 1rcuA/T0375-1rcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcuA read from 1rcuA/T0375-1rcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rcuA to template set # found chain 1rcuA in template set T0375 1 :GSQILCVG 1rcuA 1 :MKKVVVVG T0375 18 :VDKYPKEDSE 1rcuA 10 :SGPVNKSPVS T0375 41 :ASNSCTILSLLGAPCAF 1rcuA 25 :CLELGRTLAKKGYLVFN T0375 61 :MAPGHVADFVLDDLRRYSVDLRYTVFQTTG 1rcuA 42 :GGRDGVMELVSQGVREAGGTVVGILPDEEA T0375 114 :SLPDV 1rcuA 72 :GNPYL T0375 119 :SATDFEKVD 1rcuA 83 :GLDFQMRSF T0375 128 :LTQFKWIHIEGRNA 1rcuA 94 :LRNADVVVSIGGEI T0375 143 :EQVKMLQRIDAHNTRQPPEQ 1rcuA 108 :GTAIEILGAYALGKPVILLR T0375 163 :KIRVSVEVEKP 1rcuA 135 :RISQVLIDGKY T0375 197 :L 1rcuA 146 :L T0375 198 :GFQ 1rcuA 148 :NRR T0375 201 :SAEEALRGLYG 1rcuA 159 :TVEEAVQIIEQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=2227 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcuA/T0375-1rcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rcuA/T0375-1rcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcuA read from 1rcuA/T0375-1rcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcuA in template set T0375 1 :GSQILCVG 1rcuA 1 :MKKVVVVG T0375 18 :VDKYPKED 1rcuA 10 :SGPVNKSP T0375 30 :CLSQR 1rcuA 18 :VSELR T0375 40 :NASNSCTILSLLGAPCA 1rcuA 24 :ICLELGRTLAKKGYLVF T0375 60 :SMAPGHVADFVLDDLRRYSVDLRYTVFQTTGSV 1rcuA 41 :NGGRDGVMELVSQGVREAGGTVVGILPDEEAGN T0375 103 :SGSRTILYY 1rcuA 74 :PYLSVAVKT T0375 119 :SATDFE 1rcuA 83 :GLDFQM T0375 125 :KVDLTQFKWIHIEG 1rcuA 91 :FVLLRNADVVVSIG T0375 140 :NASEQVKMLQRIDAHNTRQPPEQ 1rcuA 105 :GEIGTAIEILGAYALGKPVILLR T0375 163 :KIRVSVEVE 1rcuA 135 :RISQVLIDG T0375 182 :GY 1rcuA 144 :KY T0375 197 :L 1rcuA 146 :L T0375 198 :GF 1rcuA 148 :NR T0375 200 :QSAEEALRGLYG 1rcuA 158 :WTVEEAVQIIEQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=2241 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcuA/T0375-1rcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0375 read from 1rcuA/T0375-1rcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcuA read from 1rcuA/T0375-1rcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcuA in template set T0375 1 :GSQILCVG 1rcuA 1 :MKKVVVVG T0375 17 :LVDKYPKED 1rcuA 9 :YSGPVNKSP T0375 30 :CLSQ 1rcuA 18 :VSEL T0375 40 :NASNSCTILSLLGAPCAF 1rcuA 24 :ICLELGRTLAKKGYLVFN T0375 61 :MAPGHVADFVLDDLRRYSVDLRYTVFQTTGSV 1rcuA 42 :GGRDGVMELVSQGVREAGGTVVGILPDEEAGN T0375 101 :EA 1rcuA 74 :PY T0375 105 :SRTILYY 1rcuA 76 :LSVAVKT T0375 117 :DVSATDFEKVDLTQFKWIHIEGRN 1rcuA 83 :GLDFQMRSFVLLRNADVVVSIGGE T0375 144 :QVKMLQRIDAHNTRQPPEQKIRVSVEVE 1rcuA 107 :IGTAIEILGAYALGKPVILLRGTGGWTD T0375 172 :KPREELFQLFGY 1rcuA 158 :WTVEEAVQIIEQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=2251 Will force an alignment to be made, even if fragment is small Number of alignments=145 # command:CPU_time= 47.183 sec, elapsed time= 88.253 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 145 Adding 43660 constraints to all_contacts Done adding distance constraints # command:CPU_time= 47.437 sec, elapsed time= 88.536 sec. # command:Reading probabilities from T0375.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 52.843 Optimizing... Probability sum: -518.147, CN propb: -518.147 weights: 0.352 constraints: 1103 # command:CPU_time= 520.227 sec, elapsed time= 561.494 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1103 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1103 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 6040 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 6040 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 34185 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 34185 # command:CPU_time= 520.952 sec, elapsed time= 562.743 sec. # command: