# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0298/ # command:# Making conformation for sequence T0298 numbered 1 through 336 Created new target T0298 from T0298.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0298/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0298/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0298//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0298/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0298/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0298/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bkaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0298 read from 2bkaA/merged-good-all-a2m # 2bkaA read from 2bkaA/merged-good-all-a2m # found chain 2bkaA in training set T0298 4 :PLNVAVVGATGSVGEALVGLLDERD 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQG # choosing archetypes in rotamer library T0298 29 :FPLHRLHL 2bkaA 44 :FSKVTLIG T0298 46 :RMGFA 2bkaA 54 :KLTFD T0298 51 :ESSLRVGDVDSFD 2bkaA 64 :NVNQEVVDFEKLD T0298 64 :FSSVGLAFFAAAAE 2bkaA 82 :FQGHDVGFCCLGTT T0298 78 :VSRAHAERARAAGCSVIDLSGALE 2bkaA 111 :YVLKSAELAKAGGCKHFNLLSSKG T0298 118 :ASQAAP 2bkaA 136 :DKSSNF T0298 134 :AELCEVLAPLLATLDCRQLNLTA 2bkaA 144 :LQVKGEVEAKVEELKFDRYSVFR T0298 175 :TAELLNARPL 2bkaA 167 :PGVLLCDRQE T0298 185 :EPRLFDRQI 2bkaA 193 :DSWASGHSV T0298 199 :A 2bkaA 202 :P T0298 213 :ERRIFAEV 2bkaA 203 :VVTVVRAM T0298 221 :QALLGERIGPLNVT 2bkaA 212 :NNVVRPRDKQMELL T0298 257 :DLAAVTRV 2bkaA 226 :ENKAIHDL Number of specific fragments extracted= 14 number of extra gaps= 0 total=14 Number of alignments=1 # 2bkaA read from 2bkaA/merged-good-all-a2m # found chain 2bkaA in training set T0298 4 :PLNVAVVGATGSVGEALVGLLDERDF 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQGL T0298 30 :PLHRLHL 2bkaA 45 :SKVTLIG T0298 39 :SAE 2bkaA 52 :RRK T0298 42 :SAGQRMGFAESSLRVGDVDSFD 2bkaA 58 :DEEAYKNVNQEVVDFEKLDDYA T0298 64 :FSSVGLAFFAAAAEVS 2bkaA 82 :FQGHDVGFCCLGTTRG T0298 80 :RAHAERARAAGCSVIDLSGALEPS 2bkaA 113 :LKSAELAKAGGCKHFNLLSSKGAD T0298 104 :V 2bkaA 138 :S T0298 135 :ELCEVLAPLLATLDCRQLNLTA 2bkaA 145 :QVKGEVEAKVEELKFDRYSVFR T0298 175 :TAELLNAR 2bkaA 167 :PGVLLCDR T0298 205 :DAEG 2bkaA 175 :QESR T0298 211 :AIERRIFAEVQA 2bkaA 179 :PGEWLVRKFFGS T0298 224 :LGER 2bkaA 191 :LPDS T0298 228 :IGPLN 2bkaA 198 :GHSVP T0298 258 :LAAVTRVLDAT 2bkaA 203 :VVTVVRAMLNN T0298 269 :KGIEWVG 2bkaA 220 :KQMELLE Number of specific fragments extracted= 15 number of extra gaps= 0 total=29 Number of alignments=2 # 2bkaA read from 2bkaA/merged-good-all-a2m # found chain 2bkaA in training set T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLAS 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQGLFSKVTLIGRR T0298 46 :RMGFAES 2bkaA 54 :KLTFDEE T0298 53 :SLRVGDVDSFDFSS 2bkaA 64 :NVNQEVVDFEKLDD T0298 67 :VGLAFFAAA 2bkaA 85 :HDVGFCCLG T0298 76 :AEVSRAHAERARAAGCSVIDLSGALEPS 2bkaA 109 :RDYVLKSAELAKAGGCKHFNLLSSKGAD T0298 104 :VAPP 2bkaA 138 :SSNF T0298 115 :ERLA 2bkaA 142 :LYLQ T0298 135 :ELCEVLAPLLA 2bkaA 146 :VKGEVEAKVEE T0298 147 :LDCRQLNLTAC 2bkaA 157 :LKFDRYSVFRP T0298 163 :LGREG 2bkaA 176 :ESRPG T0298 171 :LARQTAEL 2bkaA 181 :EWLVRKFF T0298 182 :RPLEPRLFD 2bkaA 189 :GSLPDSWAS T0298 191 :RQIA 2bkaA 199 :HSVP T0298 213 :ERRIFAEVQALLG 2bkaA 203 :VVTVVRAMLNNVV T0298 226 :ERIGPLNVT 2bkaA 217 :PRDKQMELL T0298 257 :DLAAVTRV 2bkaA 226 :ENKAIHDL Number of specific fragments extracted= 16 number of extra gaps= 0 total=45 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hyeA expands to /projects/compbio/data/pdb/1hye.pdb.gz 1hyeA:# T0298 read from 1hyeA/merged-good-all-a2m # 1hyeA read from 1hyeA/merged-good-all-a2m # adding 1hyeA to template set # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)F189 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)E207 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLD 1hyeA 2 :KVTIIGASGRVGSATALLLA T0298 28 :DFPLH 1hyeA 22 :KEPFM T0298 33 :RLHLLASAESAGQRMGFA 1hyeA 28 :DLVLIGREHSINKLEGLR T0298 51 :ESSLRVGDVDSFD 1hyeA 58 :DANIYVESDENLR T0298 64 :FSSVGLAFFAAAA 1hyeA 72 :IDESDVVIITSGV T0298 77 :EVSRAHAERARAA 1hyeA 94 :DLAKTNAKIVGKY T0298 114 :AERLASQAAPFLLSS 1hyeA 107 :AKKIAEICDTKIFVI T0298 132 :VAA 1hyeA 122 :TNP T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1hyeA 125 :VDVMTYKALVDSKFERNQVFGLGTHLD T0298 168 :VKELARQTAELLNA 1hyeA 152 :SLRFKVAIAKFFGV T0298 183 :PL 1hyeA 166 :HI T0298 185 :EPRL 1hyeA 219 :EQII T0298 208 :GHSAIERRIFAE 1hyeA 231 :GPAAAILNVVRC T0298 223 :LLGERIGPLNVTC 1hyeA 243 :IVNNEKRLLTLSA T0298 237 :QA 1hyeA 256 :YV T0298 241 :FFGDSLSVTLQCAE 1hyeA 264 :IRDVCIGVPVKIGR T0298 255 :PVDLAA 1hyeA 287 :ELDKDE T0298 261 :VTRVLDATKG 1hyeA 303 :IKKYCEEVKN Number of specific fragments extracted= 18 number of extra gaps= 0 total=63 Number of alignments=4 # 1hyeA read from 1hyeA/merged-good-all-a2m # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)N180 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)E207 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLD 1hyeA 2 :KVTIIGASGRVGSATALLLA T0298 28 :DFPLH 1hyeA 22 :KEPFM T0298 33 :RLHLLASAESAGQRMGFAE 1hyeA 28 :DLVLIGREHSINKLEGLRE T0298 52 :SSLRVGDVDSFD 1hyeA 59 :ANIYVESDENLR T0298 64 :FSSVGLAFFAAAAEVS 1hyeA 72 :IDESDVVIITSGVPRK T0298 80 :RAHAERARAA 1hyeA 104 :GKYAKKIAEI T0298 90 :GCSVIDLSGA 1hyeA 115 :DTKIFVITNP T0298 121 :AAPFLLSSPCAVAA 1hyeA 138 :FERNQVFGLGTHLD T0298 136 :LCEVLAPLLATLDCR 1hyeA 152 :SLRFKVAIAKFFGVH T0298 151 :QLNLTACLSVSSL 1hyeA 169 :EVRTRIIGEHGDS T0298 164 :G 1hyeA 193 :G T0298 166 :E 1hyeA 203 :K T0298 168 :VKELARQTA 1hyeA 207 :IDEIIEDVK T0298 177 :ELL 1hyeA 220 :QII T0298 208 :GHSAIERRIF 1hyeA 231 :GPAAAILNVV T0298 221 :QALLGERIGPLNVTCIQ 1hyeA 241 :RCIVNNEKRLLTLSAYV T0298 238 :APVFF 1hyeA 261 :FDGIR T0298 243 :GDSLSVTLQ 1hyeA 268 :CIGVPVKIG T0298 252 :CAE 1hyeA 280 :IEE T0298 255 :PVDLAA 1hyeA 287 :ELDKDE T0298 261 :VTRVLDATKG 1hyeA 303 :IKKYCEEVKN Number of specific fragments extracted= 21 number of extra gaps= 0 total=84 Number of alignments=5 # 1hyeA read from 1hyeA/merged-good-all-a2m # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)P183 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)S210 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1hyeA 2 :KVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSIN T0298 44 :GQRM 1hyeA 54 :GTRS T0298 51 :ESSLRVGDV 1hyeA 58 :DANIYVESD T0298 60 :DSFDFSSVGLAFFAAA 1hyeA 68 :NLRIIDESDVVIITSG T0298 76 :AEVSRAHAERARAA 1hyeA 93 :MDLAKTNAKIVGKY T0298 115 :ERLASQAAPFLLSSPCAVAAELCEVLAP 1hyeA 108 :KKIAEICDTKIFVITNPVDVMTYKALVD T0298 147 :LDCRQLNLTACLS 1hyeA 136 :SKFERNQVFGLGT T0298 165 :REGVKELARQTAEL 1hyeA 149 :HLDSLRFKVAIAKF T0298 179 :LNAR 1hyeA 219 :EQII T0298 211 :AIERRIFAEVQALLGERIGPLNVTCIQ 1hyeA 231 :GPAAAILNVVRCIVNNEKRLLTLSAYV T0298 241 :FFGDSLSVTLQCAEP 1hyeA 264 :IRDVCIGVPVKIGRD T0298 256 :VD 1hyeA 288 :LD T0298 258 :LAAVTRVLDATKG 1hyeA 300 :AEIIKKYCEEVKN Number of specific fragments extracted= 13 number of extra gaps= 0 total=97 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b4rO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b4rO expands to /projects/compbio/data/pdb/2b4r.pdb.gz 2b4rO:# T0298 read from 2b4rO/merged-good-all-a2m # 2b4rO read from 2b4rO/merged-good-all-a2m # adding 2b4rO to template set # found chain 2b4rO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVG 2b4rO 4 :TKLGING T0298 13 :TGSVGEALVGLLDER 2b4rO 11 :FGRIGRLVFRAAFGR T0298 28 :DFPLHRLHL 2b4rO 27 :DIEVVAIND T0298 38 :ASAESAGQRMGFA 2b4rO 38 :MDLNHLCYLLKYD T0298 51 :ESSLRVGDVDSFDFS 2b4rO 74 :VSVFAEKDPSQIPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLAS 2b4rO 120 :IMSAPPKDDTPIYVMGINHHQYDT T0298 122 :APFLLSSP 2b4rO 144 :KQLIVSNA T0298 130 :CAVAA 2b4rO 153 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 2b4rO 158 :LAPLAKVINDRFGIVEGLMTTVHASTAN T0298 176 :AELLNARPL 2b4rO 186 :QLVVDGPSK T0298 185 :EPRLFDRQIAF 2b4rO 197 :KDWRAGRCALS T0298 198 :LA 2b4rO 210 :IP T0298 205 :DAEGHSAIERRIFAEVQA 2b4rO 212 :ASTGAAKAVGKVLPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 230 :KLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 2b4rO 272 :PLKGILGYTEDEVVSQDFVHDNRSSIFDMKAGLAL T0298 304 :PCQVNLWIVSDN 2b4rO 308 :DNFFKLVSWYDN T0298 317 :RKGAALNAVLLGELLI 2b4rO 320 :EWGYSNRVLDLAVHIT Number of specific fragments extracted= 18 number of extra gaps= 1 total=115 Number of alignments=7 # 2b4rO read from 2b4rO/merged-good-all-a2m # found chain 2b4rO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVGA 2b4rO 4 :TKLGINGF T0298 14 :GSVGEALVGLLD 2b4rO 12 :GRIGRLVFRAAF T0298 28 :DFPLHRLHLLASAE 2b4rO 24 :GRKDIEVVAINDPF T0298 42 :SAGQRMGFAE 2b4rO 39 :DLNHLCYLLK T0298 52 :SSLRVGDVDSFDFS 2b4rO 75 :SVFAEKDPSQIPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGGAKKVIMSAPPK T0298 103 :SVAPPVMVSVNAERLAS 2b4rO 127 :DDTPIYVMGINHHQYDT T0298 122 :APFLLSSP 2b4rO 144 :KQLIVSNA T0298 130 :CAVAA 2b4rO 153 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 2b4rO 158 :LAPLAKVINDRFGIVEGLMTTVHASTA T0298 177 :ELL 2b4rO 185 :NQL T0298 180 :NARPLEPRLFDRQIAF 2b4rO 192 :PSKGGKDWRAGRCALS T0298 198 :LA 2b4rO 210 :IP T0298 205 :DAEG 2b4rO 212 :ASTG T0298 213 :ERRIFAEV 2b4rO 216 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 224 :LPELNGKLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 2b4rO 272 :PLKGILGYTEDEVVSQDFVHDNRSSIFDMKAGL T0298 302 :ADPCQVNLWIVSDN 2b4rO 306 :LNDNFFKLVSWYDN T0298 317 :RKGAALNAVLLGELLI 2b4rO 320 :EWGYSNRVLDLAVHIT Number of specific fragments extracted= 19 number of extra gaps= 1 total=134 Number of alignments=8 # 2b4rO read from 2b4rO/merged-good-all-a2m # found chain 2b4rO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVGA 2b4rO 4 :TKLGINGF T0298 14 :GSVGEALVGLLDERDF 2b4rO 12 :GRIGRLVFRAAFGRKD T0298 32 :HRLHLLASAESA 2b4rO 28 :IEVVAINDPFMD T0298 44 :GQRMGFAES 2b4rO 57 :PCEVTHADG T0298 53 :SLRVGDVDSFDFSS 2b4rO 71 :EKKVSVFAEKDPSQ T0298 67 :VGLAFFAAA 2b4rO 92 :VDVVCESTG T0298 80 :RAHAERARAAGCSVIDLSGALE 2b4rO 105 :KELASSHLKGGAKKVIMSAPPK T0298 103 :SVAPPVMVSVNAERLA 2b4rO 127 :DDTPIYVMGINHHQYD T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 2b4rO 143 :TKQLIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHASTANQLV T0298 182 :RPLEPRLFDRQIAF 2b4rO 189 :VDGPSKGGKDWRAG T0298 198 :LAQVGA 2b4rO 210 :IPASTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 216 :AAKAVGKVLPELNGKLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEG 2b4rO 274 :KGILGYTED T0298 280 :PTVVGDALGQDETYVGRVRAGQ 2b4rO 283 :EVVSQDFVHDNRSSIFDMKAGL T0298 302 :ADPCQVNLWIVSDNV 2b4rO 306 :LNDNFFKLVSWYDNE T0298 318 :KGAALNAVLLGELLI 2b4rO 321 :WGYSNRVLDLAVHIT Number of specific fragments extracted= 16 number of extra gaps= 1 total=150 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vm6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vm6A expands to /projects/compbio/data/pdb/1vm6.pdb.gz 1vm6A:# T0298 read from 1vm6A/merged-good-all-a2m # 1vm6A read from 1vm6A/merged-good-all-a2m # adding 1vm6A to template set # found chain 1vm6A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHR 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGHELVL T0298 48 :GFAESSLRVGD 1vm6A 30 :KVDVNGVEELD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1vm6A 41 :SPDVVIDFSSPEALPKTVDLCKKYRAGLVLGTTALK T0298 103 :S 1vm6A 77 :E T0298 113 :NAERLASQAAPFLLSSP 1vm6A 79 :HLQMLRELSKEVPVVQA T0298 130 :CAVAA 1vm6A 97 :NFSIG T0298 136 :LCEVLAPLLATL 1vm6A 102 :INVLKRFLSELV T0298 149 :CR 1vm6A 119 :WD T0298 151 :QLNLTA 1vm6A 122 :EIVETH T0298 181 :ARPLEPRLFD 1vm6A 128 :HRFKKDAPSG T0298 216 :IFAEVQALLG 1vm6A 138 :TAILLESALG T0298 254 :EPV 1vm6A 148 :KSV T0298 270 :GIEWVGEGDYP 1vm6A 151 :PIHSLRVGGVP T0298 283 :VGDALGQDETYVGRVRAGQ 1vm6A 165 :VVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLIK 1vm6A 184 :RTVFAIGALKAAEFLVG Number of specific fragments extracted= 15 number of extra gaps= 0 total=165 Number of alignments=10 # 1vm6A read from 1vm6A/merged-good-all-a2m # found chain 1vm6A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDF 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGH T0298 33 :RLHLLASAESA 1vm6A 26 :ELVLKVDVNGV T0298 55 :RV 1vm6A 37 :EE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1vm6A 39 :LDSPDVVIDFSSPEALPKTVDLCKKYRAGLVLGTTALK T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1vm6A 79 :HLQMLRELSKEVPVVQAYNFSIGINVLKRFLSELV T0298 148 :DCR 1vm6A 118 :DWD T0298 151 :QLNLTAC 1vm6A 122 :EIVETHH T0298 159 :SVSS 1vm6A 134 :APSG T0298 213 :ERRIFAEV 1vm6A 138 :TAILLESA T0298 224 :LGE 1vm6A 146 :LGK T0298 255 :PV 1vm6A 149 :SV T0298 270 :GIEWVGEGDYP 1vm6A 151 :PIHSLRVGGVP T0298 282 :VVGDALGQDETYVGRVRAGQ 1vm6A 164 :HVVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLIKHY 1vm6A 184 :RTVFAIGALKAAEFLVGKD Number of specific fragments extracted= 14 number of extra gaps= 0 total=179 Number of alignments=11 # 1vm6A read from 1vm6A/merged-good-all-a2m # found chain 1vm6A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHRLHL 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGHELVLKVD T0298 51 :ESSLRVGD 1vm6A 33 :VNGVEELD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVID 1vm6A 41 :SPDVVIDFSSPEALPKTVDLCKKYRAGLVL T0298 108 :VMVSVNAERLAS 1vm6A 71 :GTTALKEEHLQM T0298 140 :LAPLLATL 1vm6A 83 :LRELSKEV T0298 153 :NLTACLSVS 1vm6A 91 :PVVQAYNFS T0298 169 :KELARQTAEL 1vm6A 100 :IGINVLKRFL T0298 218 :AEVQALLGERIGPLNVTCI 1vm6A 110 :SELVKVLEDWDVEIVETHH T0298 261 :VTRVLDATKGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQA 1vm6A 142 :LESALGKSVPIHSLRVGGVPGDHVVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLI 1vm6A 184 :RTVFAIGALKAAEFLV Number of specific fragments extracted= 10 number of extra gaps= 0 total=189 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b7gO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b7gO expands to /projects/compbio/data/pdb/1b7g.pdb.gz 1b7gO:# T0298 read from 1b7gO/merged-good-all-a2m # 1b7gO read from 1b7gO/merged-good-all-a2m # adding 1b7gO to template set # found chain 1b7gO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVG 1b7gO 2 :VNVAVNG T0298 13 :TGSVGEALVGLLDE 1b7gO 9 :YGTIGKRVADAIIK T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDV 1b7gO 24 :PDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQS T0298 60 :DSFDFSS 1b7gO 63 :SGIPVAG T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVI 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAI T0298 96 :LSGALEPSVAPPVMV 1b7gO 106 :FQGGEKAEVADISFS T0298 111 :SVN 1b7gO 122 :LCN T0298 117 :LASQAAPFLLSSP 1b7gO 125 :YNEALGKKYIRVV T0298 130 :CAVAA 1b7gO 139 :CNTTA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1b7gO 144 :LLRTICTVNKVSKVEKVRATIVRRAADQ T0298 180 :NARPLEPRLFDRQI 1b7gO 172 :KEVKKGPINSLVPD T0298 205 :DAEGHSAI 1b7gO 186 :PATVPSHH T0298 217 :FAEVQALL 1b7gO 194 :AKDVNSVI T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYP 1b7gO 202 :RNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDA T0298 283 :VGDALGQDETYVG 1b7gO 269 :KRDRNDIPEVMIF T0298 297 :VRAGQADPCQVNLWIVSDN 1b7gO 282 :SDSIYVKDDEVMLMYAVHQ T0298 317 :RKGAALNAVLLGELLIK 1b7gO 301 :ESIVVPENIDAIRASMK Number of specific fragments extracted= 17 number of extra gaps= 1 total=206 Number of alignments=13 # 1b7gO read from 1b7gO/merged-good-all-a2m # found chain 1b7gO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVGA 1b7gO 2 :VNVAVNGY T0298 14 :GSVGEALVGLLD 1b7gO 10 :GTIGKRVADAII T0298 28 :DFPLHRLHLLASAE 1b7gO 22 :KQPDMKLVGVAKTS T0298 42 :SAGQRMGFAESSLRVGDVDS 1b7gO 37 :NYEAFIAHRRGIRIYVPQQS T0298 62 :FDFSS 1b7gO 65 :IPVAG T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVI 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAI T0298 96 :LSGALEPSVA 1b7gO 106 :FQGGEKAEVA T0298 106 :PPVMVSVNAERLA 1b7gO 117 :ISFSALCNYNEAL T0298 122 :APFLLSSP 1b7gO 130 :GKKYIRVV T0298 130 :CAVAA 1b7gO 139 :CNTTA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLG 1b7gO 144 :LLRTICTVNKVSKVEKVRATIVRRAADQK T0298 166 :E 1b7gO 175 :K T0298 173 :RQTAELLNARPL 1b7gO 177 :GPINSLVPDPAT T0298 205 :DAEG 1b7gO 189 :VPSH T0298 213 :ERRIFAEV 1b7gO 193 :HAKDVNSV T0298 224 :LGE 1b7gO 201 :IRN T0298 229 :GPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1b7gO 204 :LDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYD T0298 283 :VGDALGQDETYVG 1b7gO 269 :KRDRNDIPEVMIF T0298 297 :VRAGQADPCQVNLWIVSDN 1b7gO 282 :SDSIYVKDDEVMLMYAVHQ T0298 317 :RKGAALNAVLLGELLIK 1b7gO 301 :ESIVVPENIDAIRASMK Number of specific fragments extracted= 20 number of extra gaps= 1 total=226 Number of alignments=14 # 1b7gO read from 1b7gO/merged-good-all-a2m # found chain 1b7gO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVGA 1b7gO 2 :VNVAVNGY T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1b7gO 10 :GTIGKRVADAIIKQPDMKLVGVAKTSPNYE T0298 44 :GQRMGFAES 1b7gO 47 :GIRIYVPQQ T0298 53 :SLRVGDVDSFDFSS 1b7gO 64 :GIPVAGTVEDLIKT T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVID 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAIF T0298 97 :SGALEPSVAPPVMV 1b7gO 107 :QGGEKAEVADISFS T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSL 1b7gO 124 :NYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQ T0298 180 :NARPLEPRLFDRQ 1b7gO 172 :KEVKKGPINSLVP T0298 204 :VDAEGHSA 1b7gO 185 :DPATVPSH T0298 220 :VQALLG 1b7gO 193 :HAKDVN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYPT 1b7gO 201 :IRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAE T0298 284 :GDALGQ 1b7gO 268 :LKRDRN T0298 291 :ETYVGRVRA 1b7gO 274 :DIPEVMIFS T0298 300 :GQADPCQVNLWIVSDNVRK 1b7gO 285 :IYVKDDEVMLMYAVHQESI T0298 320 :AALNAVLLGEL 1b7gO 304 :VVPENIDAIRA Number of specific fragments extracted= 15 number of extra gaps= 1 total=241 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gadO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gadO expands to /projects/compbio/data/pdb/1gad.pdb.gz 1gadO:Skipped atom 1733, because occupancy 0.4 <= existing 0.600 in 1gadO Skipped atom 1735, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1737, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1739, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1741, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1743, because occupancy 0.400 <= existing 0.600 in 1gadO # T0298 read from 1gadO/merged-good-all-a2m # 1gadO read from 1gadO/merged-good-all-a2m # adding 1gadO to template set # found chain 1gadO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVG 1gadO 1 :IKVGING T0298 13 :TGSVGEALVGLLDER 1gadO 8 :FGRIGRIVFRAAQKR T0298 28 :DFPLHRLHLLASAESAGQRMGFA 1gadO 24 :DIEIVAINDLLDADYMAYMLKYD T0298 51 :ESSLRVGDVDSFDFS 1gadO 71 :IRVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gadO 88 :GVDVVAEATGLFLTDETARKHITAGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLA 1gadO 117 :VMTGPSKDNTPMFVKGANFDKYA T0298 122 :APFLLSSP 1gadO 138A:GQDIVSNA T0298 130 :CAVAA 1gadO 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1gadO 154 :LAPLAKVINDNFGIIEGLMTTVHATTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1gadO 182 :QKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1gadO 206 :SSTGAAKAVGKVLPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 224 :KLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1gadO 266 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIAL T0298 304 :PCQVNLWIVSDN 1gadO 302 :DNFVKLVSWYDN T0298 317 :RKGAALNAVLLGELL 1gadO 314 :ETGYSNKVLDLIAHI Number of specific fragments extracted= 15 number of extra gaps= 0 total=256 Number of alignments=16 # 1gadO read from 1gadO/merged-good-all-a2m # found chain 1gadO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVGA 1gadO 1 :IKVGINGF T0298 14 :GSVGEALVGLLD 1gadO 9 :GRIGRIVFRAAQ T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1gadO 21 :KRSDIEIVAINDLLDADYMAYMLK T0298 52 :SSLRVGDVDSFDFS 1gadO 72 :RVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGAL 1gadO 88 :GVDVVAEATGLFLTDETARKHITAGAKKVVMTGPS T0298 103 :S 1gadO 122A:K T0298 104 :VAPPVMVSVNAERLA 1gadO 124 :NTPMFVKGANFDKYA T0298 122 :APFLLSSP 1gadO 138A:GQDIVSNA T0298 130 :CAVAA 1gadO 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gadO 154 :LAPLAKVINDNFGIIEGLMTTVHATTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gadO 181 :TQKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DAEG 1gadO 206 :SSTG T0298 213 :ERRIFAEV 1gadO 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 218 :LPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gadO 266 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1gadO 300 :LNDNFVKLVSWYDN T0298 317 :RKGAALNAVLLGEL 1gadO 314 :ETGYSNKVLDLIAH Number of specific fragments extracted= 17 number of extra gaps= 0 total=273 Number of alignments=17 # 1gadO read from 1gadO/merged-good-all-a2m # found chain 1gadO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVGA 1gadO 1 :IKVGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1gadO 9 :GRIGRIVFRAAQKRSDIEIVAINDLLDADY T0298 45 :QRMGFAES 1gadO 55 :GTVEVKDG T0298 53 :SLRVGDVDSFDFS 1gadO 70 :KIRVTAERDPANL T0298 66 :SVGLAFFAAA 1gadO 88 :GVDVVAEATG T0298 76 :AEVSR 1gadO 102 :DETAR T0298 85 :RARAAGCSVIDLSGALE 1gadO 107 :KHITAGAKKVVMTGPSK T0298 103 :SVAPPVMVSV 1gadO 123 :DNTPMFVKGA T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1gadO 133 :NFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGAVDAE 1gadO 186 :DGPSHKDWRGGRGASQNIIPSSTGAAKA T0298 220 :VQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 214 :VGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGD 1gadO 268 :KGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1gadO 278 :VVSTDFNGEVCTSVFD T0298 297 :VR 1gadO 297 :GI T0298 301 :QADPCQVNLWIVSDNVR 1gadO 299 :ALNDNFVKLVSWYDNET T0298 319 :GAALNAVLLGEL 1gadO 316 :GYSNKVLDLIAH Number of specific fragments extracted= 16 number of extra gaps= 0 total=289 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1crwG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1crwG expands to /projects/compbio/data/pdb/1crw.pdb.gz 1crwG:# T0298 read from 1crwG/merged-good-all-a2m # 1crwG read from 1crwG/merged-good-all-a2m # adding 1crwG to template set # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVG 1crwG 2 :KIGING T0298 13 :TGSVGEALVGLLDERDFPLHRLHL 1crwG 8 :FGRIGRLVLRAALEMGAQVVAVND T0298 37 :LASAESAGQRMGFA 1crwG 34 :FIALEYMVYMFKYD T0298 51 :ESSLRVGDVDSFDFS 1crwG 71 :ITVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1crwG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKV T0298 96 :LSGALE 1crwG 117 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1crwG 123 :ADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1crwG 140 :DMKVVSNA T0298 130 :CAVAA 1crwG 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1crwG 154 :LAPVAKVLHENFEIVEGLMTTVHAVTAT T0298 176 :AELLNARPLEPRLFDRQIA 1crwG 182 :QKTVDGPSAKDWRGGRGAA T0298 198 :LA 1crwG 204 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1crwG 206 :SSTGAAKAVGKVIPELDG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 224 :KLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1crwG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQL T0298 304 :PCQVNLWIVSDN 1crwG 302 :KTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1crwG 314 :EFGYSQRVIDLIKHMQKV Number of specific fragments extracted= 17 number of extra gaps= 1 total=306 Number of alignments=19 # 1crwG read from 1crwG/merged-good-all-a2m # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVGA 1crwG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFP 1crwG 9 :GRIGRLVLRAALEMGAQ T0298 34 :LHLLASAE 1crwG 27 :VVAVNDPF T0298 42 :SAGQRMGFAE 1crwG 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1crwG 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1crwG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1crwG 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1crwG 140 :DMKVVSNA T0298 130 :CAVAA 1crwG 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1crwG 154 :LAPVAKVLHENFEIVEGLMTTVHAVTA T0298 175 :TAELLNARPLEPRLFDRQIA 1crwG 181 :TQKTVDGPSAKDWRGGRGAA T0298 198 :LA 1crwG 204 :IP T0298 205 :DAEG 1crwG 206 :SSTG T0298 213 :ERRIFAEV 1crwG 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 218 :IPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1crwG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1crwG 300 :LSKTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1crwG 314 :EFGYSQRVIDLIKHMQKVD Number of specific fragments extracted= 18 number of extra gaps= 1 total=324 Number of alignments=20 # 1crwG read from 1crwG/merged-good-all-a2m # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVGA 1crwG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1crwG 9 :GRIGRLVLRAALEMGAQVVAVNDPFIALEY T0298 44 :GQRMGFAES 1crwG 54 :KGEVKAEDG T0298 53 :SLRVGDVD 1crwG 70 :KITVFNEM T0298 61 :SFDFSSVGLAFFAAA 1crwG 83 :PWSKAGAEYIVESTG T0298 76 :AEVSR 1crwG 102 :IEKAS T0298 87 :RAAGCSVIDLSGAL 1crwG 109 :FKGGAKKVIISAPS T0298 103 :SVAPPVMVSVNAERL 1crwG 123 :ADAPMFVCGVNLEKY T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1crwG 139 :KDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKT T0298 180 :NARPLEPRLFDRQIA 1crwG 186 :DGPSAKDWRGGRGAA T0298 198 :LAQVGA 1crwG 204 :IPSSTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 210 :AAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGD 1crwG 268 :QGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1crwG 278 :VVSCDFTGDNRSSIFD T0298 299 :AGQADPCQVNLWIVSDNV 1crwG 297 :GIQLSKTFVKVVSWYDNE T0298 318 :KGAALNAVLLGELLIKH 1crwG 315 :FGYSQRVIDLIKHMQKV Number of specific fragments extracted= 16 number of extra gaps= 1 total=340 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i32A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1i32A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1i32A/merged-good-all-a2m.gz for input Trying 1i32A/merged-good-all-a2m Error: Couldn't open file 1i32A/merged-good-all-a2m or 1i32A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t4bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0298 read from 1t4bA/merged-good-all-a2m # 1t4bA read from 1t4bA/merged-good-all-a2m # found chain 1t4bA in training set Warning: unaligning (T0298)P4 because first residue in template chain is (1t4bA)M1 T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1t4bA 27 :FDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEP 1t4bA 93 :YWIDAASSLRM T0298 103 :SVAPPVMVSVNAERLA 1t4bA 105 :DDAIIILDPVNQDVIT T0298 119 :SQ 1t4bA 125 :NG T0298 122 :APFLLSSPCAVAA 1t4bA 127 :IRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1t4bA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPL 1t4bA 190 :LATPSS T0298 185 :EPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 214 :PVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1t4bA 300 :PWAKVVPN T0298 283 :VGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 318 :PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 13 number of extra gaps= 0 total=353 Number of alignments=22 # 1t4bA read from 1t4bA/merged-good-all-a2m # found chain 1t4bA in training set T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLL 1t4bA 27 :FDAIRPVFF T0298 39 :SAESAGQRM 1t4bA 36 :STSQLGQAA T0298 48 :GFAESSLRVGDVDSFD 1t4bA 46 :SFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1t4bA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLA 1t4bA 106 :DAIIILDPVNQDVIT T0298 119 :SQAAPFLLSSPCAVAA 1t4bA 124 :NNGIRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1t4bA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMREL T0298 172 :ARQTAELLNARPLEPRL 1t4bA 183 :YGHVADELATPSSAILD T0298 189 :FDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 218 :FGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1t4bA 300 :PWAKVVPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 319 :AAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 14 number of extra gaps= 0 total=367 Number of alignments=23 # 1t4bA read from 1t4bA/merged-good-all-a2m # found chain 1t4bA in training set T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLH 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEERDFDA T0298 33 :RLHLLASAESAGQRMGFAESSLRVGDV 1t4bA 31 :RPVFFSTSQLGQAAPSFGGTTGTLQDA T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 59 :DLEALKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1t4bA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQ 1t4bA 106 :DAIIILDPVNQDVITDG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1t4bA 125 :NGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 208 :TRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 316 :LTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 9 number of extra gaps= 0 total=376 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ywgO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1ywgO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1ywgO/merged-good-all-a2m.gz for input Trying 1ywgO/merged-good-all-a2m Error: Couldn't open file 1ywgO/merged-good-all-a2m or 1ywgO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rm4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rm4A expands to /projects/compbio/data/pdb/1rm4.pdb.gz 1rm4A:Skipped atom 3025, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3027, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3029, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3031, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3182, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3184, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3186, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3188, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3190, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3192, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3194, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4114, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4116, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4745, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4747, because occupancy 0.500 <= existing 0.500 in 1rm4A # T0298 read from 1rm4A/merged-good-all-a2m # 1rm4A read from 1rm4A/merged-good-all-a2m # adding 1rm4A to template set # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVG 1rm4A 1 :LKVAING T0298 13 :TGSVGEALVGLLDERD 1rm4A 8 :FGRIGRNFLRCWHGRK T0298 29 :FPLHRLHLLASAESAGQRMGFA 1rm4A 25 :LDVVVINDTGGVKQASHLLKYD T0298 51 :ESSLRVGDVDSFDFS 1rm4A 71 :IKVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1rm4A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLAS 1rm4A 117 :LITAPGKGDIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm4A 140 :ADTIISNA T0298 130 :CAVAA 1rm4A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 176 :AELLNARP 1rm4A 182 :QRLLDASH T0298 185 :EPRLFDRQIAFNLLA 1rm4A 191 :RDLRRARAACLNIVP T0298 205 :DAEGHSAIERRIFAEVQA 1rm4A 206 :TSTGAAKAVALVLPNLKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm4A 224 :KLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1rm4A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTMVM T0298 304 :PCQVNLWIVSDN 1rm4A 302 :DDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1rm4A 314 :EWGYSQRVVDLADIVANKWQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=392 Number of alignments=25 # 1rm4A read from 1rm4A/merged-good-all-a2m # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVGA 1rm4A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAE 1rm4A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDTGGVKQASHLLK T0298 52 :SSLRVGDVDSFDFS 1rm4A 72 :KVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1rm4A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAPGK T0298 103 :SVAPPVMVSVNAERLAS 1rm4A 123 :GDIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm4A 140 :ADTIISNA T0298 130 :CAVAA 1rm4A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 176 :AELLNARPLEPRL 1rm4A 182 :QRLLDASHRDLRR T0298 190 :DRQIAFNLLA 1rm4A 196 :ARAACLNIVP T0298 205 :DAEG 1rm4A 206 :TSTG T0298 213 :ERRIFAEV 1rm4A 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm4A 218 :LPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1rm4A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDN 1rm4A 300 :MGDDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1rm4A 314 :EWGYSQRVVDLADIVANKW Number of specific fragments extracted= 16 number of extra gaps= 0 total=408 Number of alignments=26 # 1rm4A read from 1rm4A/merged-good-all-a2m # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVGA 1rm4A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1rm4A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDTGGV T0298 44 :GQRMGFAESSLRVGDVDSFDFSS 1rm4A 61 :DSAISVDGKVIKVVSDRNPVNLP T0298 67 :VGLAFFAAA 1rm4A 89 :IDLVIEGTG T0298 80 :RAHAERARAAGCSVIDLSGALE 1rm4A 102 :RDGAGKHLQAGAKKVLITAPGK T0298 104 :VAPPVMVSVNAERLA 1rm4A 124 :DIPTYVVGVNEEGYT T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 139 :HADTIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 181 :ARPLEPRLFDRQIA 1rm4A 182 :QRLLDASHRDLRRA T0298 195 :FNLLAQVGA 1rm4A 201 :LNIVPTSTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKG 1rm4A 210 :AAKAVALVLPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRESAD T0298 271 :IEWVGE 1rm4A 271 :LSVCDE T0298 280 :PTVVGDALGQDETYVGRVRAGQ 1rm4A 277 :PLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDNV 1rm4A 300 :MGDDMVKVIAWYDNE T0298 318 :KGAALNAVLLGELLIKHY 1rm4A 315 :WGYSQRVVDLADIVANKW Number of specific fragments extracted= 14 number of extra gaps= 0 total=422 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1drw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1drw expands to /projects/compbio/data/pdb/1drw.pdb.gz 1drw:Warning: there is no chain 1drw will retry with 1drwA # T0298 read from 1drw/merged-good-all-a2m # 1drw read from 1drw/merged-good-all-a2m # adding 1drw to template set # found chain 1drw in template set Warning: unaligning (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)Q45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L52 Warning: unaligning (T0298)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L52 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)D278 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)T292 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 3 :QPLNVAV 1drw 4 :ANIRVAI T0298 12 :ATGSVGEALVGLLD 1drw 13 :AGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAES 1drw 27 :ALEGVQLGAALEREG T0298 43 :AG 1drw 49 :AG T0298 47 :MGFAESSLRVGD 1drw 53 :AGAGKTGVTVQS T0298 64 :FSSVGLA 1drw 70 :KDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1drw 111 :KQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAA T0298 148 :DC 1drw 149 :DY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQT 1drw 166 :APSGTALAMGEAIAHAL T0298 177 :E 1drw 188 :D T0298 178 :LLNARPLE 1drw 190 :AVYSREGH T0298 205 :DAEGH 1drw 198 :TGERV T0298 227 :RI 1drw 203 :PG T0298 230 :PLNVTCIQ 1drw 205 :TIGFATVR T0298 243 :GDSLSVTLQ 1drw 217 :VGEHTAMFA T0298 275 :GEG 1drw 226 :DIG T0298 293 :YVGRVRAGQ 1drw 231 :LEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1drw 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 20 number of extra gaps= 5 total=442 Number of alignments=28 # 1drw read from 1drw/merged-good-all-a2m # found chain 1drw in template set Warning: unaligning (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D48 Warning: unaligning (T0298)F49 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D48 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)E291 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)T292 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 4 :PLNVAV 1drw 5 :NIRVAI T0298 12 :ATGSVGEALVGLLD 1drw 13 :AGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAESAGQRM 1drw 27 :ALEGVQLGAALEREGSSLLG T0298 50 :AE 1drw 49 :AG T0298 52 :SSLRVGDVDSF 1drw 59 :GVTVQSSLDAV T0298 64 :FSSVGLA 1drw 70 :KDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1drw 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDC 1drw 147 :MGDY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQ 1drw 166 :APSGTALAMGEAIAHA T0298 182 :RPLEPRL 1drw 182 :LDKDLKD T0298 196 :NLLAQVGAVDAEG 1drw 189 :CAVYSREGHTGER T0298 224 :L 1drw 202 :V T0298 228 :IGPLNVTCIQ 1drw 203 :PGTIGFATVR T0298 243 :GDSLSVTLQ 1drw 217 :VGEHTAMFA T0298 288 :GQD 1drw 226 :DIG T0298 293 :YVGRVRAGQ 1drw 231 :LEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1drw 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 19 number of extra gaps= 5 total=461 Number of alignments=29 # 1drw read from 1drw/merged-good-all-a2m # found chain 1drw in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1drw)D3 Warning: unaligning (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)Q45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L52 Warning: unaligning (T0298)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L52 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)Y279 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)P280 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 3 :QPLNVAV 1drw 4 :ANIRVAI T0298 12 :ATGSVGEALVGLLDERDFPLHRLHLLASAESA 1drw 13 :AGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 44 :G 1drw 50 :G T0298 47 :MGFAESSLRVGDVDSFDFSSVGLA 1drw 53 :AGAGKTGVTVQSSLDAVKDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1drw 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDC 1drw 147 :MGDY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 162 :SLGREGVKELARQTAEL 1drw 165 :DAPSGTALAMGEAIAHA T0298 179 :LNARPLEPRLF 1drw 192 :YSREGHTGERV T0298 228 :IGPLNVTCIQ 1drw 203 :PGTIGFATVR T0298 244 :DSLSVTLQ 1drw 218 :GEHTAMFA T0298 276 :EGD 1drw 226 :DIG T0298 281 :TV 1drw 231 :LE T0298 295 :GRV 1drw 233 :ITH T0298 299 :AGQA 1drw 236 :KASS T0298 317 :RKGAALNAVLLGELL 1drw 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 6 total=478 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1obfO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0298 read from 1obfO/merged-good-all-a2m # 1obfO read from 1obfO/merged-good-all-a2m # found chain 1obfO in training set Warning: unaligning (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVG 1obfO 2 :IRVAING T0298 13 :TGSVGEALVGLLDER 1obfO 9 :YGRIGRNILRAHYEG T0298 28 :DFPLHRLHLLASAESAGQRMGFA 1obfO 28 :DIEIVAINDLGDPKTNAHLTRYD T0298 51 :ESSLRVGDVDSFDFS 1obfO 74 :IRVDANRNPAQLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1obfO 91 :KVDVVLECTGFFTTKEKAGAHIKGGAKKV T0298 96 :LSGALEPSVA 1obfO 120 :IISAPGGADV T0298 106 :PP 1obfO 131 :AT T0298 110 :VSVNAERLAS 1obfO 135 :YGVNHGTLKS T0298 122 :APFLLSSP 1obfO 145 :TDTVISNA T0298 132 :VAA 1obfO 156 :TNC T0298 136 :LCEVLAPLLATLDCRQLN 1obfO 159 :LAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSSL 1obfO 182 :AYTNN T0298 176 :AELLNARP 1obfO 187 :QVLTDVYH T0298 185 :EPRLFDRQIAF 1obfO 195 :EDLRRARSATM T0298 198 :LA 1obfO 208 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1obfO 210 :TKTGAAAAVGDVLPELDG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 228 :KLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1obfO 270 :ELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDN T0298 317 :RKGAALNAVLLGELLIK 1obfO 317 :EWGFSNRMLDTTVALMS Number of specific fragments extracted= 20 number of extra gaps= 4 total=498 Number of alignments=31 # 1obfO read from 1obfO/merged-good-all-a2m # found chain 1obfO in training set Warning: unaligning (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVGA 1obfO 2 :IRVAINGY T0298 14 :GSVGEALVGLLDERDFP 1obfO 10 :GRIGRNILRAHYEGGKS T0298 31 :LHRLHLLASAESAGQRMGFAE 1obfO 28 :DIEIVAINDLGDPKTNAHLTR T0298 52 :SSLRVGDVDSFDFS 1obfO 75 :RVDANRNPAQLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1obfO 91 :KVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGAD T0298 104 :V 1obfO 130 :D T0298 106 :PP 1obfO 131 :AT T0298 110 :VSVNAERLAS 1obfO 135 :YGVNHGTLKS T0298 122 :APFLLSSP 1obfO 145 :TDTVISNA T0298 132 :VAA 1obfO 156 :TNC T0298 136 :LCEVLAPLLATLDCRQLN 1obfO 159 :LAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSS 1obfO 182 :AYTN T0298 177 :ELL 1obfO 186 :NQV T0298 180 :NARPLEPRL 1obfO 191 :DVYHEDLRR T0298 190 :DRQIAF 1obfO 200 :ARSATM T0298 198 :LA 1obfO 208 :IP T0298 205 :DAEG 1obfO 210 :TKTG T0298 213 :ERRIFAEV 1obfO 214 :AAAAVGDV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 222 :LPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1obfO 270 :ELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDN T0298 317 :RKGAALNAVLLGELLIK 1obfO 317 :EWGFSNRMLDTTVALMS Number of specific fragments extracted= 22 number of extra gaps= 4 total=520 Number of alignments=32 # 1obfO read from 1obfO/merged-good-all-a2m # found chain 1obfO in training set Warning: unaligning (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)C130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obfO)T155 Warning: unaligning (T0298)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVGA 1obfO 2 :IRVAINGY T0298 14 :GSVGEALVGLLDERDFPLHRLHLLA 1obfO 10 :GRIGRNILRAHYEGGKSHDIEIVAI T0298 39 :SAESA 1obfO 36 :DLGDP T0298 44 :GQRMGFAES 1obfO 57 :PGTVSVNGS T0298 53 :SLRVGDVDSFDFS 1obfO 73 :KIRVDANRNPAQL T0298 67 :VGLAFFAAA 1obfO 92 :VDVVLECTG T0298 80 :RAHAERARAAGCSVIDLSGALEPSVAPP 1obfO 105 :KEKAGAHIKGGAKKVIISAPGGADVDAT T0298 110 :VSVNAERLA 1obfO 135 :YGVNHGTLK T0298 121 :AAPFLLSSP 1obfO 144 :STDTVISNA T0298 133 :AAELCEVLAPLLATLDCRQLN 1obfO 156 :TNCLAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSSLGRE 1obfO 182 :AYTNNQVL T0298 180 :NARPLEPRLFDRQIAF 1obfO 190 :TDVYHEDLRRARSATM T0298 198 :LAQVGA 1obfO 208 :IPTKTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 214 :AAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEG 1obfO 272 :KGILDYNTE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNV 1obfO 281 :PLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNE T0298 318 :KGAALNAVLLGELLIK 1obfO 318 :WGFSNRMLDTTVALMS Number of specific fragments extracted= 18 number of extra gaps= 4 total=538 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nwhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1nwhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1nwhA/merged-good-all-a2m.gz for input Trying 1nwhA/merged-good-all-a2m Error: Couldn't open file 1nwhA/merged-good-all-a2m or 1nwhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nptO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1nptO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1nptO/merged-good-all-a2m.gz for input Trying 1nptO/merged-good-all-a2m Error: Couldn't open file 1nptO/merged-good-all-a2m or 1nptO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1arzC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1arzC expands to /projects/compbio/data/pdb/1arz.pdb.gz 1arzC:# T0298 read from 1arzC/merged-good-all-a2m # 1arzC read from 1arzC/merged-good-all-a2m # adding 1arzC to template set # found chain 1arzC in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLA 1arzC 27 :ALEGVQLGAAL T0298 39 :SAES 1arzC 41 :GSSL T0298 43 :AGQRMGFAESSLRVGD 1arzC 49 :AGELAGAGKTGVTVQS T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1arzC 70 :KDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1arzC 111 :KQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAA T0298 148 :DCR 1arzC 150 :YTD T0298 151 :QLNLTAC 1arzC 154 :EIIEAHH T0298 158 :LSVSSLGREGVKELARQTAE 1arzC 165 :DAPSGTALAMGEAIAHALDK T0298 178 :LLNARPLEPRLF 1arzC 190 :AVYSREGHTGER T0298 205 :DA 1arzC 202 :VP T0298 228 :I 1arzC 204 :G T0298 230 :PLNVTCIQ 1arzC 205 :TIGFATVR T0298 241 :FF 1arzC 216 :IV T0298 246 :LSVTLQCAE 1arzC 218 :GEHTAMFAD T0298 289 :QDETYVGRVRAGQ 1arzC 227 :IGERLEITHKASS T0298 317 :RKGAALNAVLLGELL 1arzC 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 0 total=555 Number of alignments=34 # 1arzC read from 1arzC/merged-good-all-a2m # found chain 1arzC in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAE 1arzC 27 :ALEGVQLGAALERE T0298 42 :SAGQRMGFAESSLR 1arzC 44 :LLGSDAGELAGAGK T0298 56 :VGDVDSFD 1arzC 63 :QSSLDAVK T0298 65 :SSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1arzC 71 :DDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1arzC 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDCR 1arzC 148 :GDYTD T0298 151 :QLNLTA 1arzC 154 :EIIEAH T0298 159 :SVSSLGREGVKELARQT 1arzC 166 :APSGTALAMGEAIAHAL T0298 183 :PLEPRL 1arzC 183 :DKDLKD T0298 196 :NLLAQVGAVDAEG 1arzC 189 :CAVYSREGHTGER T0298 224 :LGE 1arzC 202 :VPG T0298 230 :PLNVTCIQ 1arzC 205 :TIGFATVR T0298 277 :G 1arzC 214 :G T0298 290 :DETYVGRVRAGQ 1arzC 215 :DIVGEHTAMFAD T0298 303 :DPCQVNLWIVSDN 1arzC 227 :IGERLEITHKASS T0298 317 :RKGAALNAVLLGELL 1arzC 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 0 total=572 Number of alignments=35 # 1arzC read from 1arzC/merged-good-all-a2m # found chain 1arzC in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 44 :GQR 1arzC 46 :GSD T0298 47 :MGFAESSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDL 1arzC 53 :AGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIG T0298 109 :MVSVNAERLASQ 1arzC 103 :TTGFDEAGKQAI T0298 121 :AAPFLLSSPCAV 1arzC 119 :ADIAIVFAANFS T0298 134 :AELCEVLAPLLA 1arzC 131 :VGVNVMLKLLEK T0298 146 :TLDCRQLNLTACL 1arzC 147 :MGDYTDIEIIEAH T0298 159 :SV 1arzC 166 :AP T0298 165 :REGVKELARQTAELLNAR 1arzC 168 :SGTALAMGEAIAHALDKD T0298 183 :PLEPRLFDRQ 1arzC 196 :GHTGERVPGT T0298 231 :LNVTCIQ 1arzC 206 :IGFATVR T0298 244 :DSLSVTLQCA 1arzC 216 :IVGEHTAMFA T0298 288 :GQDETYVGRVRAGQ 1arzC 226 :DIGERLEITHKASS T0298 317 :RKGAALNAVLLGEL 1arzC 240 :RMTFANGAVRSALW Number of specific fragments extracted= 14 number of extra gaps= 0 total=586 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gd1O/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gd1O expands to /projects/compbio/data/pdb/1gd1.pdb.gz 1gd1O:# T0298 read from 1gd1O/merged-good-all-a2m # 1gd1O read from 1gd1O/merged-good-all-a2m # adding 1gd1O to template set # found chain 1gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)R55 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)I216 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)F217 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVG 1gd1O 1 :VKVGING T0298 13 :TGSVGEALVGLLD 1gd1O 8 :FGRIGRNVFRAAL T0298 28 :DF 1gd1O 21 :KN T0298 32 :HRLHLL 1gd1O 25 :IEVVAV T0298 38 :ASAESAGQRMGFA 1gd1O 34 :TDANTLAHLLKYD T0298 51 :ESSL 1gd1O 71 :IIVK T0298 57 :GDVDSFDFS 1gd1O 77 :RDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKV T0298 96 :LSGALEPSVAPPVM 1gd1O 117 :IISAPAKNEDITIV T0298 112 :VNAERLASQ 1gd1O 132 :VNQDKYDPK T0298 122 :APFLLSSP 1gd1O 140 :AHHVISNA T0298 130 :CAVAA 1gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTND T0298 176 :AELLNARP 1gd1O 182 :QRILDLPH T0298 185 :EPRLFDRQIAF 1gd1O 191 :KDLRRARAAAE T0298 198 :LA 1gd1O 204 :IP T0298 205 :DAEGHSAIERR 1gd1O 206 :TTTGAAKAVAL T0298 218 :AEVQA 1gd1O 219 :PELKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTMVI T0298 304 :PCQVNLWIVSDN 1gd1O 302 :GKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 22 number of extra gaps= 5 total=608 Number of alignments=37 # 1gd1O read from 1gd1O/merged-good-all-a2m # found chain 1gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)R55 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)L223 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)L224 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVGA 1gd1O 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 1gd1O 9 :GRIGRNVFRAAL T0298 28 :DF 1gd1O 21 :KN T0298 32 :HRLHLLASAESAGQRMGFAE 1gd1O 25 :IEVVAVNDLTDANTLAHLLK T0298 52 :SSL 1gd1O 72 :IVK T0298 57 :GDVDSFDFS 1gd1O 77 :RDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVM 1gd1O 126 :ITIV T0298 112 :VNAERLASQ 1gd1O 132 :VNQDKYDPK T0298 122 :APFLLSSP 1gd1O 140 :AHHVISNA T0298 130 :CAVAA 1gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 177 :ELL 1gd1O 181 :DQR T0298 180 :NARPLEPRL 1gd1O 186 :DLPHKDLRR T0298 190 :DRQIAF 1gd1O 196 :ARAAAE T0298 198 :LAQVGAVDAE 1gd1O 204 :IPTTTGAAKA T0298 220 :VQA 1gd1O 214 :VAL T0298 225 :GERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 219 :PELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 1gd1O 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 21 number of extra gaps= 5 total=629 Number of alignments=38 # 1gd1O read from 1gd1O/merged-good-all-a2m # found chain 1gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)D28 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)F29 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)D58 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V59 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)R187 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L188 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)V201 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)G202 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVGA 1gd1O 1 :VKVGINGF T0298 14 :GSVGEALVGLLDER 1gd1O 9 :GRIGRNVFRAALKN T0298 30 :PLHRLHLLASAESA 1gd1O 25 :IEVVAVNDLTDANT T0298 44 :GQRMGFAES 1gd1O 54 :DAEVSVNGN T0298 53 :SLRVG 1gd1O 70 :EIIVK T0298 60 :D 1gd1O 77 :R T0298 61 :SFD 1gd1O 79 :PEN T0298 64 :FS 1gd1O 84 :WG T0298 66 :SVGLAFFAAA 1gd1O 88 :GVDIVVESTG T0298 76 :AEVSR 1gd1O 102 :REDAA T0298 85 :RARAAGCSVIDLSGALEPSV 1gd1O 107 :KHLEAGAKKVIISAPAKNED T0298 106 :PPVM 1gd1O 126 :ITIV T0298 112 :VNAERLAS 1gd1O 132 :VNQDKYDP T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1gd1O 139 :KAHHVISNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRI T0298 179 :LNARPLEP 1gd1O 194 :RRARAAAE T0298 189 :FDRQI 1gd1O 204 :IPTTT T0298 194 :AFNLLAQ 1gd1O 210 :AAKAVAL T0298 203 :AVDAEG 1gd1O 219 :PELKGK T0298 231 :LNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 225 :LNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGE 1gd1O 269 :GILAYSEE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPC 1gd1O 277 :PLVSRDYNGSTVSSTIDALSTMVIDG T0298 306 :QVNLWIVSDNV 1gd1O 304 :MVKVVSWYDNE T0298 318 :KGAALNAVLLGELLIKHYL 1gd1O 315 :TGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 23 number of extra gaps= 5 total=652 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gpdG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1gpdG/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1gpdG/merged-good-all-a2m.gz for input Trying 1gpdG/merged-good-all-a2m Error: Couldn't open file 1gpdG/merged-good-all-a2m or 1gpdG/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mb4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mb4A expands to /projects/compbio/data/pdb/1mb4.pdb.gz 1mb4A:# T0298 read from 1mb4A/merged-good-all-a2m # 1mb4A read from 1mb4A/merged-good-all-a2m # adding 1mb4A to template set # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERD 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1mb4A 26 :FDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCS 1mb4A 62 :LKQLDAVITCQGGSYTEKVYPALRQAGWK T0298 93 :VIDLSGALEPS 1mb4A 93 :WIDAASTLRMD T0298 104 :VAPPVMVSVNAERLA 1mb4A 105 :EAIITLDPVNLKQIL T0298 119 :SQAAPFLLSSPCAVAA 1mb4A 123 :HHGTKTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPL 1mb4A 139 :MLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSS T0298 185 :EPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 213 :PTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATH T0298 269 :KGIEWVGE 1mb4A 300 :DWVKVIPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 319 :AKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 11 number of extra gaps= 0 total=663 Number of alignments=40 # 1mb4A read from 1mb4A/merged-good-all-a2m # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERD 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLL 1mb4A 26 :FDLIEPVFF T0298 39 :SAESAGQRMGFAESSLR 1mb4A 35 :STSQIGVPAPNFGKDAG T0298 56 :VGDVDSFD 1mb4A 53 :LHDAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCS 1mb4A 62 :LKQLDAVITCQGGSYTEKVYPALRQAGWK T0298 93 :VIDLSGALEPS 1mb4A 93 :WIDAASTLRMD T0298 104 :VAPPVMVSVNAERLAS 1mb4A 105 :EAIITLDPVNLKQILH T0298 120 :QAAPFLLSSPCAVAA 1mb4A 124 :HGTKTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1mb4A 139 :MLMALGGLYERGLVEWMSAMTYQAASGAGAQNMREL T0298 172 :ARQTAELLN 1mb4A 178 :MGVINDAVS T0298 181 :ARPLEPRL 1mb4A 191 :NPASSILD T0298 189 :FDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 217 :FGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATH T0298 269 :KGIEWVGE 1mb4A 300 :DWVKVIPN T0298 285 :DALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 320 :KVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 15 number of extra gaps= 0 total=678 Number of alignments=41 # 1mb4A read from 1mb4A/merged-good-all-a2m # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAES 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGK T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1mb4A 51 :GMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGW T0298 92 :SVIDLSGALEPS 1mb4A 92 :YWIDAASTLRMD T0298 104 :VAPPVMVSVNAERLASQ 1mb4A 105 :EAIITLDPVNLKQILHG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1mb4A 124 :HGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVI T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 207 :MRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 316 :LTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=686 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dih/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dih expands to /projects/compbio/data/pdb/1dih.pdb.gz 1dih:Warning: there is no chain 1dih will retry with 1dihA # T0298 read from 1dih/merged-good-all-a2m # 1dih read from 1dih/merged-good-all-a2m # adding 1dih to template set # found chain 1dih in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1dih)D3 Warning: unaligning (T0298)A43 because of BadResidue code BAD_PEPTIDE at template residue (1dih)A49 Warning: unaligning (T0298)Q45 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)L52 Warning: unaligning (T0298)R46 because of BadResidue code BAD_PEPTIDE at template residue (1dih)L52 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)D148 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1dih 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHL 1dih 27 :ALEGVQLGA T0298 37 :LASAES 1dih 37 :LEREGS T0298 44 :G 1dih 50 :G T0298 47 :MGFAESSLR 1dih 53 :AGAGKTGVT T0298 56 :VGDVDSF 1dih 63 :QSSLDAV T0298 64 :FSSVGLAFF 1dih 70 :KDDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSP 1dih 111 :KQAIRDAAADIAIVFA T0298 130 :CAVAA 1dih 128 :NFSVG T0298 136 :LCEVLAPLLATL 1dih 133 :VNVMLKLLEKAA T0298 151 :QLNLTACL 1dih 152 :DIEIIEAH T0298 159 :SVSSLGREGVKELARQTA 1dih 166 :APSGTALAMGEAIAHALD T0298 182 :RPLEPRLFD 1dih 184 :KDLKDCAVY T0298 205 :DAEGHSAI 1dih 193 :SREGHTGE T0298 226 :ERIG 1dih 201 :RVPG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 245 :SLSVTLQCA 1dih 217 :VGEHTAMFA T0298 275 :GEGD 1dih 226 :DIGE T0298 292 :TYVGRVRAGQ 1dih 230 :RLEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1dih 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 21 number of extra gaps= 6 total=707 Number of alignments=43 # 1dih read from 1dih/merged-good-all-a2m # found chain 1dih in template set Warning: unaligning (T0298)A50 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)G46 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1dih)G46 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)D148 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1dih 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRL 1dih 27 :ALEGVQL T0298 35 :HLLASAE 1dih 35 :AALEREG T0298 42 :S 1dih 43 :S T0298 49 :F 1dih 44 :L T0298 52 :SSLRVGDVDSFD 1dih 59 :GVTVQSSLDAVK T0298 65 :SSVGLAFF 1dih 71 :DDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQA 1dih 110 :GKQAIRDAA T0298 122 :APFLLSSPC 1dih 120 :DIAIVFAAN T0298 132 :VAAELCEVLAPLLATL 1dih 129 :FSVGVNVMLKLLEKAA T0298 150 :R 1dih 152 :D T0298 152 :LNLTACL 1dih 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQ 1dih 166 :APSGTALAMGEAIAHA T0298 182 :RPLEPRL 1dih 182 :LDKDLKD T0298 196 :NLLAQVGAVDAEG 1dih 189 :CAVYSREGHTGER T0298 224 :LGE 1dih 202 :VPG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 243 :GDSLSVTLQ 1dih 217 :VGEHTAMFA T0298 288 :GQDETYVGRVRAGQ 1dih 226 :DIGERLEITHKASS T0298 317 :RKGAALNAVLLGELLI 1dih 240 :RMTFANGAVRSALWLS Number of specific fragments extracted= 21 number of extra gaps= 4 total=728 Number of alignments=44 # 1dih read from 1dih/merged-good-all-a2m # found chain 1dih in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1dih)D3 Warning: unaligning (T0298)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)G46 Warning: unaligning (T0298)Q45 because of BadResidue code BAD_PEPTIDE at template residue (1dih)G46 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1dih 4 :ANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 46 :R 1dih 47 :S T0298 47 :MGFAESSLRVGDVDSFDFSSVGLAFF 1dih 53 :AGAGKTGVTVQSSLDAVKDDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQ 1dih 110 :GKQAIRDA T0298 121 :AAPFLLSSPCAV 1dih 119 :ADIAIVFAANFS T0298 134 :AELCEVLAPLLATLD 1dih 131 :VGVNVMLKLLEKAAK T0298 151 :QLNLTACL 1dih 152 :DIEIIEAH T0298 162 :SLGREGVKELARQTAELLNARPLEPRLFDRQ 1dih 165 :DAPSGTALAMGEAIAHALDKDLKDCAVYSRE T0298 203 :AVDAEGH 1dih 196 :GHTGERV T0298 228 :IG 1dih 203 :PG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 276 :EGDYP 1dih 213 :AGDIV T0298 292 :TYVGRVRAGQADPCQVN 1dih 218 :GEHTAMFADIGERLEIT T0298 317 :RKGAALNAVLLGELL 1dih 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 15 number of extra gaps= 5 total=743 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j0xO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1j0xO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1j0xO/merged-good-all-a2m.gz for input Trying 1j0xO/merged-good-all-a2m Error: Couldn't open file 1j0xO/merged-good-all-a2m or 1j0xO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k3tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1k3tA expands to /projects/compbio/data/pdb/1k3t.pdb.gz 1k3tA:# T0298 read from 1k3tA/merged-good-all-a2m # 1k3tA read from 1k3tA/merged-good-all-a2m # adding 1k3tA to template set # found chain 1k3tA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1k3tA)M1 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G82 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)A99 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVG 1k3tA 2 :PIKVGING T0298 13 :TGSVGEALVGLLDERDF 1k3tA 10 :FGRIGRMVFQALCEDGL T0298 30 :PLHRLHL 1k3tA 32 :DVVAVVD T0298 37 :LASAESAGQRMGFA 1k3tA 40 :NTDAEYFAYQMRYD T0298 52 :SSLR 1k3tA 83 :HRIL T0298 56 :VGDVDSFDFS 1k3tA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1k3tA 103 :GVEYVIESTGLFTAKAAAEGHLRGGARKV T0298 96 :LS 1k3tA 132 :VI T0298 100 :LEPSVAPPVMVSVNAERLASQ 1k3tA 136 :PASGGAKTLVMGVNHHEYNPS T0298 122 :APFLLSSP 1k3tA 157 :EHHVVSNA T0298 130 :CAVAA 1k3tA 166 :CTTNC T0298 136 :LCEVLAPLLAT 1k3tA 171 :LAPIVHVLVKE T0298 147 :LDCRQLNLTACLSVSSL 1k3tA 183 :FGVQTGLMTTIHSYTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1k3tA 200 :QKTVDGVSVKDWRGGRAAAVNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1k3tA 224 :STTGAAKAVGMVIPSTQG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 242 :KLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1k3tA 284 :YMKGILGYTDEELVSADFINDNRSSIYD T0298 298 :RAGQADPCQVNLWIVSDN 1k3tA 318 :NNLPKERRFFKIVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1k3tA 336 :EWGYSHRVVDLVRHMASK Number of specific fragments extracted= 19 number of extra gaps= 2 total=762 Number of alignments=46 # 1k3tA read from 1k3tA/merged-good-all-a2m # found chain 1k3tA in template set Warning: unaligning (T0298)S97 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVGA 1k3tA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1k3tA 11 :GRIGRMVFQALCEDGL T0298 30 :PLHRLHLLASAE 1k3tA 29 :TEIDVVAVVDMN T0298 42 :SAGQRMGFAE 1k3tA 42 :DAEYFAYQMR T0298 56 :VGDVDSFDFS 1k3tA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDL 1k3tA 103 :GVEYVIESTGLFTAKAAAEGHLRGGARKVVI T0298 99 :ALE 1k3tA 136 :PAS T0298 103 :SVAPPVMVSVNAERLASQ 1k3tA 139 :GGAKTLVMGVNHHEYNPS T0298 122 :APFLLSSP 1k3tA 157 :EHHVVSNA T0298 130 :CAVAA 1k3tA 166 :CTTNC T0298 136 :LCEVLAPLLA 1k3tA 171 :LAPIVHVLVK T0298 146 :TLDCRQLNLTACLSVSS 1k3tA 182 :GFGVQTGLMTTIHSYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1k3tA 199 :TQKTVDGVSVKDWRGGRAAAVNIIP T0298 205 :DAEG 1k3tA 224 :STTG T0298 213 :ERRIFAEV 1k3tA 228 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 236 :IPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1k3tA 284 :YMKGILGYTDEELVSADFINDNRSSIYD T0298 298 :RAGQADPCQVNLWIVSDN 1k3tA 318 :NNLPKERRFFKIVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1k3tA 336 :EWGYSHRVVDLVRHMASKD Number of specific fragments extracted= 19 number of extra gaps= 1 total=781 Number of alignments=47 # 1k3tA read from 1k3tA/merged-good-all-a2m # found chain 1k3tA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1k3tA)M1 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)G28 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G28 Warning: unaligning (T0298)A50 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)G82 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G82 Warning: unaligning (T0298)S97 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVGA 1k3tA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1k3tA 11 :GRIGRMVFQALCEDGL T0298 32 :HRLHLL 1k3tA 29 :TEIDVV T0298 38 :ASAESAGQR 1k3tA 68 :SSPSVAKDD T0298 47 :MGF 1k3tA 78 :LVV T0298 52 :SSLRVGDVDSFDFS 1k3tA 83 :HRILCVKAQRNPAD T0298 66 :SVGLAFFAAA 1k3tA 103 :GVEYVIESTG T0298 76 :AEVSR 1k3tA 117 :KAAAE T0298 85 :RARAAGCSVIDL 1k3tA 122 :GHLRGGARKVVI T0298 99 :ALE 1k3tA 136 :PAS T0298 104 :VAPPVMVSVNAERLA 1k3tA 140 :GAKTLVMGVNHHEYN T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLA 1k3tA 156 :SEHHVVSNASCTTNCLAPIVHVLVK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1k3tA 182 :GFGVQTGLMTTIHSYTATQKT T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGA 1k3tA 203 :VDGVSVKDWRGGRAAAVNIIPSTTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 228 :AAKAVGMVIPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEG 1k3tA 286 :KGILGYTDE T0298 280 :PTVVGDALGQDETYVGR 1k3tA 295 :ELVSADFINDNRSSIYD T0298 299 :AGQADPCQVNLWIVSDNV 1k3tA 319 :NLPKERRFFKIVSWYDNE T0298 318 :KGAALNAVLLGELLIKH 1k3tA 337 :WGYSHRVVDLVRHMASK Number of specific fragments extracted= 19 number of extra gaps= 3 total=800 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q2xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1q2xA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1q2xA/merged-good-all-a2m.gz for input Trying 1q2xA/merged-good-all-a2m Error: Couldn't open file 1q2xA/merged-good-all-a2m or 1q2xA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1ihxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1ihxA/merged-good-all-a2m.gz for input Trying 1ihxA/merged-good-all-a2m Error: Couldn't open file 1ihxA/merged-good-all-a2m or 1ihxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pquA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1pquA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1pquA/merged-good-all-a2m.gz for input Trying 1pquA/merged-good-all-a2m Error: Couldn't open file 1pquA/merged-good-all-a2m or 1pquA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/2cvoA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/2cvoA/merged-good-all-a2m.gz for input Trying 2cvoA/merged-good-all-a2m Error: Couldn't open file 2cvoA/merged-good-all-a2m or 2cvoA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pu2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1pu2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1pu2A/merged-good-all-a2m.gz for input Trying 1pu2A/merged-good-all-a2m Error: Couldn't open file 1pu2A/merged-good-all-a2m or 1pu2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gd1O/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gd1O expands to /projects/compbio/data/pdb/2gd1.pdb.gz 2gd1O:# T0298 read from 2gd1O/merged-good-all-a2m # 2gd1O read from 2gd1O/merged-good-all-a2m # adding 2gd1O to template set # found chain 2gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVG 2gd1O 4 :GING T0298 13 :TGSVGEALVGLLDE 2gd1O 8 :FGRIGRNVFRAALK T0298 27 :RDFPLHRLHLLASAESAGQRMGFA 2gd1O 23 :PDIEVVAVNDLTDANTLAHLLKYD T0298 51 :ESSLR 2gd1O 68 :GKEII T0298 56 :VGDVDSFDFS 2gd1O 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKV T0298 96 :LSGALEPSVAPP 2gd1O 117 :IISAPAKNEDIT T0298 110 :VSVNAERLASQ 2gd1O 130 :MGVNQDKYDPK T0298 122 :APF 2gd1O 140 :AHH T0298 127 :SSP 2gd1O 145 :SNA T0298 130 :CAVAA 2gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 2gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTND T0298 176 :AELLNARP 2gd1O 182 :QRILDLPH T0298 185 :EPRLFDRQIAFNLLA 2gd1O 191 :KDLRRARAAAESIIP T0298 205 :DAEGHSAIERRIFAEVQA 2gd1O 206 :TTTGAAKAVALVLPELKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 2gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTMVI T0298 304 :PCQ 2gd1O 302 :GKM T0298 309 :LWIVSDN 2gd1O 307 :VVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 2gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 22 number of extra gaps= 5 total=822 Number of alignments=49 # 2gd1O read from 2gd1O/merged-good-all-a2m # found chain 2gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVGA 2gd1O 4 :GINGF T0298 14 :GSVGEALVGLLD 2gd1O 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 2gd1O 21 :KNPDIEVVAVNDLTDANTLAHLLK T0298 53 :SLR 2gd1O 70 :EII T0298 56 :VGDVDSFDFS 2gd1O 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 2gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PP 2gd1O 126 :IT T0298 110 :VSVNAERLASQ 2gd1O 130 :MGVNQDKYDPK T0298 122 :APF 2gd1O 140 :AHH T0298 127 :SSP 2gd1O 145 :SNA T0298 130 :CAVAA 2gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 2gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 2gd1O 181 :DQ T0298 177 :ELLNARPLEPRL 2gd1O 183 :RILDLPHKDLRR T0298 190 :DRQIAFNLLA 2gd1O 196 :ARAAAESIIP T0298 205 :DAEG 2gd1O 206 :TTTG T0298 213 :ERRIFAEV 2gd1O 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 2gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQ 2gd1O 300 :IDGKM T0298 309 :LWIVSDN 2gd1O 307 :VVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 2gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 24 number of extra gaps= 5 total=846 Number of alignments=50 # 2gd1O read from 2gd1O/merged-good-all-a2m # found chain 2gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVGA 2gd1O 4 :GINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 2gd1O 9 :GRIGRNVFRAALKNPDIEVVAVNDLTDANT T0298 44 :GQRMGFAESSLRVGDV 2gd1O 61 :GNNLVVNGKEIIVKAE T0298 60 :DSFDFS 2gd1O 78 :DPENLA T0298 66 :SVGLAFFAAA 2gd1O 88 :GVDIVVESTG T0298 76 :AEVSR 2gd1O 102 :REDAA T0298 85 :RARAAGCSVIDLSGALEPSV 2gd1O 107 :KHLEAGAKKVIISAPAKNED T0298 106 :PP 2gd1O 126 :IT T0298 110 :VSVNAERLAS 2gd1O 130 :MGVNQDKYDP T0298 121 :AAPF 2gd1O 139 :KAHH T0298 127 :SSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 2gd1O 145 :SNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRI T0298 180 :NARPLEPRLFDRQIAFNLLAQVGA 2gd1O 185 :LDLPHKDLRRARAAAESIIPTTTG T0298 220 :VQALLG 2gd1O 210 :AAKAVA T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 220 :ELKGKLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 271 :IEWVGE 2gd1O 271 :LAYSEE T0298 280 :PTVVGDALGQDETYVGRVRAGQA 2gd1O 277 :PLVSRDYNGSTVSSTIDALSTMV T0298 303 :DPCQ 2gd1O 301 :DGKM T0298 309 :LWIVSDNV 2gd1O 307 :VVSWYDNE T0298 318 :KGAALNAVLLGELLIKHYL 2gd1O 315 :TGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 21 number of extra gaps= 5 total=867 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1s7cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1s7cA/merged-good-all-a2m.gz for input Trying 1s7cA/merged-good-all-a2m Error: Couldn't open file 1s7cA/merged-good-all-a2m or 1s7cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ggaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1ggaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1ggaA/merged-good-all-a2m.gz for input Trying 1ggaA/merged-good-all-a2m Error: Couldn't open file 1ggaA/merged-good-all-a2m or 1ggaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vc2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1vc2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1vc2A/merged-good-all-a2m.gz for input Trying 1vc2A/merged-good-all-a2m Error: Couldn't open file 1vc2A/merged-good-all-a2m or 1vc2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2czcA expands to /projects/compbio/data/pdb/2czc.pdb.gz 2czcA:# T0298 read from 2czcA/merged-good-all-a2m # 2czcA read from 2czcA/merged-good-all-a2m # adding 2czcA to template set # found chain 2czcA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (2czcA)M1 T0298 4 :PLNVAVVG 2czcA 2 :KVKVGVNG T0298 13 :TGSVGEALVGLLDE 2czcA 10 :YGTIGKRVAYAVTK T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDVD 2czcA 25 :DDMELIGITKTKPDFEAYRAKELGIPVYAASEEF T0298 61 :SFDFS 2czcA 66 :GFEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2czcA 79 :KVDIIVDATPGGIGAKNKPLYEKAGVKAI T0298 96 :LSGALEPS 2czcA 108 :FQGGEKAD T0298 104 :VAPPVMVSVNAERLA 2czcA 117 :AEVSFVAQANYEAAL T0298 122 :APFLLSSP 2czcA 132 :GKNYVRVV T0298 130 :CAVAA 2czcA 141 :CNTTG T0298 136 :LCEVLAPLLAT 2czcA 146 :LVRTLSAIREY T0298 149 :CRQLNLTACLSVSSL 2czcA 157 :ADYVYAVMIRRAADP T0298 180 :NARPLEPRLFDRQI 2czcA 172 :NDTKRGPINAIKPT T0298 205 :DAEGH 2czcA 186 :VEVPS T0298 215 :RIFAEVQAL 2czcA 191 :HHGPDVQTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 2czcA 200 :IPINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKE T0298 278 :DY 2czcA 252 :GF T0298 284 :GDALGQDETYVGRV 2czcA 266 :LHREWNNLYEIAVW T0298 298 :RAGQADPCQVNLWIVSDN 2czcA 281 :ESINIKGNRLFYIQAVHQ T0298 317 :RKGAALNAVLLGELLIK 2czcA 299 :ESDVIPENIDAIRAMFE Number of specific fragments extracted= 19 number of extra gaps= 0 total=886 Number of alignments=52 # 2czcA read from 2czcA/merged-good-all-a2m # found chain 2czcA in template set T0298 1 :M 2czcA 1 :M T0298 4 :PLNVAVVGA 2czcA 2 :KVKVGVNGY T0298 14 :GSVGEALVGLLD 2czcA 11 :GTIGKRVAYAVT T0298 28 :DFPLHRLHLLASAE 2czcA 23 :KQDDMELIGITKTK T0298 42 :SAGQRMGFAESSLRVGDVD 2czcA 40 :EAYRAKELGIPVYAASEEF T0298 61 :SFDFS 2czcA 66 :GFEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2czcA 79 :KVDIIVDATPGGIGAKNKPLYEKAGVKAI T0298 96 :LSGALEPS 2czcA 108 :FQGGEKAD T0298 104 :VAPPVMVSVNAERLA 2czcA 117 :AEVSFVAQANYEAAL T0298 122 :APFLLSSP 2czcA 132 :GKNYVRVV T0298 130 :CAVAA 2czcA 141 :CNTTG T0298 136 :LCEVLAPLLAT 2czcA 146 :LVRTLSAIREY T0298 149 :CRQLNLTACLSVSSLG 2czcA 157 :ADYVYAVMIRRAADPN T0298 177 :ELLNARPLEP 2czcA 173 :DTKRGPINAI T0298 198 :LAQVGAVDAEG 2czcA 183 :KPTVEVPSHHG T0298 218 :AEVQALL 2czcA 194 :PDVQTVI T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGD 2czcA 201 :PINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKEK T0298 279 :Y 2czcA 253 :F T0298 284 :GDALGQDETYVG 2czcA 266 :LHREWNNLYEIA T0298 297 :VRAGQ 2czcA 278 :VWKES T0298 302 :ADPCQVNLWIVSDN 2czcA 285 :IKGNRLFYIQAVHQ T0298 317 :RKGAALNAVLLGELLIK 2czcA 299 :ESDVIPENIDAIRAMFE Number of specific fragments extracted= 22 number of extra gaps= 0 total=908 Number of alignments=53 # 2czcA read from 2czcA/merged-good-all-a2m # found chain 2czcA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (2czcA)M1 T0298 4 :PLNVAVVG 2czcA 2 :KVKVGVNG T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAESA 2czcA 10 :YGTIGKRVAYAVTKQDDMELIGITKTKPDFE T0298 44 :GQRMGFAES 2czcA 48 :GIPVYAASE T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDL 2czcA 66 :GFEVAGTLNDLLEKVDIIVDATPGGIGAKNKPLYEKAGVKAIFQ T0298 98 :GALEPSVAPPVM 2czcA 110 :GGEKADVAEVSF T0298 112 :VNAERLASQAAPFLLSSPCAVAAELCEVLAPLLAT 2czcA 122 :VAQANYEAALGKNYVRVVSCNTTGLVRTLSAIREY T0298 149 :CRQLNLTACLSVSSL 2czcA 157 :ADYVYAVMIRRAADP T0298 180 :NARPLEPRLFD 2czcA 172 :NDTKRGPINAI T0298 202 :GAVDAEGH 2czcA 183 :KPTVEVPS T0298 219 :EVQALLG 2czcA 191 :HHGPDVQ T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 2czcA 199 :VIPINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKE T0298 278 :DYPT 2czcA 252 :GFDS T0298 284 :GDALGQDETYVGRVR 2czcA 266 :LHREWNNLYEIAVWK T0298 299 :AGQADPCQVNLWIVSDNVRK 2czcA 282 :SINIKGNRLFYIQAVHQESD T0298 320 :AALNAVLLGELLI 2czcA 302 :VIPENIDAIRAMF Number of specific fragments extracted= 15 number of extra gaps= 0 total=923 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1znqO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1znqO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1znqO/merged-good-all-a2m.gz for input Trying 1znqO/merged-good-all-a2m Error: Couldn't open file 1znqO/merged-good-all-a2m or 1znqO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xygA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1xygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1xygA/merged-good-all-a2m.gz for input Trying 1xygA/merged-good-all-a2m Error: Couldn't open file 1xygA/merged-good-all-a2m or 1xygA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nvmB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0298 read from 1nvmB/merged-good-all-a2m # 1nvmB read from 1nvmB/merged-good-all-a2m # found chain 1nvmB in training set Warning: unaligning (T0298)P239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0298)V240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0298 1 :MSQPLNVAVVG 1nvmB 1 :MNQKLKVAIIG T0298 13 :TGSVGEALVGLLDE 1nvmB 12 :SGNIGTDLMIKVLR T0298 28 :DFPLHRLHLL 1nvmB 26 :NAKYLEMGAM T0298 38 :ASAES 1nvmB 38 :IDAAS T0298 43 :AGQRMGFAESSLR 1nvmB 44 :GLARAQRMGVTTT T0298 59 :V 1nvmB 66 :L T0298 62 :FDFSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 67 :PEFADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVSV 1nvmB 109 :GPYCVPVV T0298 116 :RLASQAAPFLLSSP 1nvmB 117 :NLEEHLGKLNVNMV T0298 130 :CAVAA 1nvmB 132 :CGGQA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1nvmB 137 :TIPMVAAVSRVAKVHYAEIVASISSKSAGPGT T0298 207 :EGHSAIERRIFAEV 1nvmB 169 :RANIDEFTETTSKA T0298 221 :QALLGERIGPLNVTCIQA 1nvmB 184 :EVIGGAAKGKAIIIMNPA T0298 241 :FFGDSLSVTLQCA 1nvmB 204 :PLIMRDTVYVLSA T0298 255 :PVDLAAVTRVLDAT 1nvmB 217 :AADQAAVAASVAEM T0298 269 :KGIEWVGE 1nvmB 239 :PGYRLKQQ T0298 277 :GDYPT 1nvmB 254 :ESAPL T0298 285 :DALGQDETYVGRVRA 1nvmB 259 :NIPGLGRFSGLKTSV T0298 306 :QVNL 1nvmB 274 :FLEV T0298 315 :N 1nvmB 290 :N T0298 317 :RKGAALNAVLLGELLIKHY 1nvmB 291 :LDIMTSAALATAERMAQSM Number of specific fragments extracted= 22 number of extra gaps= 1 total=945 Number of alignments=55 # 1nvmB read from 1nvmB/merged-good-all-a2m # found chain 1nvmB in training set Warning: unaligning (T0298)P239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0298)V240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0298 1 :MSQPLNVAVVGA 1nvmB 1 :MNQKLKVAIIGS T0298 14 :GSVGEALVGLLD 1nvmB 13 :GNIGTDLMIKVL T0298 27 :RDFPLHRLHLL 1nvmB 25 :RNAKYLEMGAM T0298 38 :ASAESAGQRMGFAESSLRVGD 1nvmB 38 :IDAASDGLARAQRMGVTTTYA T0298 59 :VDS 1nvmB 66 :LPE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 69 :FADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVSVNAERLAS 1nvmB 109 :GPYCVPVVNLEEHLG T0298 122 :APFLLSSPCAVAA 1nvmB 124 :KLNVNMVTCGGQA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLG 1nvmB 137 :TIPMVAAVSRVAKVHYAEIVASISSKSAG T0298 165 :REGVKELARQ 1nvmB 169 :RANIDEFTET T0298 213 :ERRIFAEV 1nvmB 179 :TSKAIEVI T0298 224 :LGERIGPLNVTCIQA 1nvmB 187 :GGAAKGKAIIIMNPA T0298 241 :FFGDSLSVTLQCA 1nvmB 204 :PLIMRDTVYVLSA T0298 255 :PVDLAAVTRVLDAT 1nvmB 217 :AADQAAVAASVAEM T0298 269 :KGIEWV 1nvmB 239 :PGYRLK T0298 280 :PTVVGDALGQDETYVG 1nvmB 245 :QQVQFDVIPESAPLNI T0298 300 :GQADP 1nvmB 261 :PGLGR T0298 305 :CQVNLWIVSD 1nvmB 267 :SGLKTSVFLE T0298 315 :NVRKGAALNAVLLGELLIKH 1nvmB 289 :GNLDIMTSAALATAERMAQS Number of specific fragments extracted= 20 number of extra gaps= 1 total=965 Number of alignments=56 # 1nvmB read from 1nvmB/merged-good-all-a2m # found chain 1nvmB in training set T0298 1 :MSQPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1nvmB 1 :MNQKLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASD T0298 44 :GQRMGFAE 1nvmB 52 :GVTTTYAG T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 65 :KLPEFADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVS 1nvmB 109 :GPYCVPV T0298 115 :ERLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLS 1nvmB 116 :VNLEEHLGKLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASIS T0298 161 :SSLGREGVKELARQTAELL 1nvmB 161 :SKSAGPGTRANIDEFTETT T0298 217 :FAEVQALLGERIGPLNVTCI 1nvmB 180 :SKAIEVIGGAAKGKAIIIMN T0298 244 :DSLSVTLQCA 1nvmB 207 :MRDTVYVLSA T0298 255 :PVDLAAVTRVLDA 1nvmB 217 :AADQAAVAASVAE T0298 268 :TKG 1nvmB 238 :VPG T0298 271 :IEW 1nvmB 247 :VQF T0298 274 :VGEGDYPTVVGDALGQDETYVGRVRAGQADPC 1nvmB 251 :VIPESAPLNIPGLGRFSGLKTSVFLEVEGAAH T0298 313 :SDNVRK 1nvmB 288 :AGNLDI T0298 320 :AALNAVLLGELLIKH 1nvmB 294 :MTSAALATAERMAQS Number of specific fragments extracted= 15 number of extra gaps= 0 total=980 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xygD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xygD expands to /projects/compbio/data/pdb/1xyg.pdb.gz 1xygD:# T0298 read from 1xygD/merged-good-all-a2m # 1xygD read from 1xygD/merged-good-all-a2m # adding 1xygD to template set # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1xygD 16 :DIRIGLLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1xygD 38 :NHPHFQVTLMTADRKAGQSMESVFPHLR T0298 56 :VGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 72 :LVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPSV 1xygD 104 :TALKIVDLSADFRLRN T0298 105 :APPVMVSVNAERLA 1xygD 140 :VVYGLTEILREDIK T0298 122 :APFLLSSP 1xygD 154 :KARLVANP T0298 130 :CAVAA 1xygD 163 :CYPTT T0298 136 :LCEVLAPLLATLDCR 1xygD 168 :IQLPLVPLLKANLIK T0298 151 :QLNLTACLSVSSLGR 1xygD 185 :NIIIDAKSGVSGAGR T0298 181 :ARP 1xygD 200 :GAK T0298 186 :PRLFDRQIA 1xygD 203 :EANLYSEIA T0298 202 :GAVDAEGHSAIERRIFAEVQA 1xygD 217 :YGVTRHRHVPEIEQGLSDVAQ T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 238 :SKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KGIEWVGEGDYPTVV 1xygD 284 :EFVKVLDEGVVPRTH T0298 285 :DALGQDETYVGRVR 1xygD 299 :NVRGSNYCHMSVFP T0298 301 :QADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1xygD 313 :DRIPGRAIIISVIDNLVKGASGQALQNLNIMLG Number of specific fragments extracted= 16 number of extra gaps= 0 total=996 Number of alignments=58 # 1xygD read from 1xygD/merged-good-all-a2m # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1xygD 16 :DIRIGLLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1xygD 38 :NHPHFQVTLMTADRKAGQSMESVFPHLR T0298 56 :VGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 72 :LVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPSV 1xygD 104 :TALKIVDLSADFRLRN T0298 105 :APPVMVSVNAERLA 1xygD 140 :VVYGLTEILREDIK T0298 122 :APFLLSSP 1xygD 154 :KARLVANP T0298 130 :CAVAA 1xygD 163 :CYPTT T0298 136 :LCEVLAPLLATLDCR 1xygD 168 :IQLPLVPLLKANLIK T0298 151 :QLNLTACLSVSSLG 1xygD 185 :NIIIDAKSGVSGAG T0298 165 :REG 1xygD 203 :EAN T0298 168 :VKELAR 1xygD 207 :YSEIAE T0298 178 :LLNARPL 1xygD 213 :GISSYGV T0298 205 :DAEGHSAIERRIFAEV 1xygD 220 :TRHRHVPEIEQGLSDV T0298 225 :GERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 236 :AQSKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KGIEWVGEGDYPTVV 1xygD 284 :EFVKVLDEGVVPRTH T0298 285 :DALGQDETYVG 1xygD 299 :NVRGSNYCHMS T0298 297 :VRAGQ 1xygD 310 :VFPDR T0298 303 :DPCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1xygD 315 :IPGRAIIISVIDNLVKGASGQALQNLNIMLGYPE Number of specific fragments extracted= 18 number of extra gaps= 0 total=1014 Number of alignments=59 # 1xygD read from 1xygD/merged-good-all-a2m # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1xygD 16 :DIRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQ T0298 46 :R 1xygD 56 :S T0298 47 :MGFAESS 1xygD 62 :PHLRAQK T0298 54 :LRVGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 70 :PTLVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPS 1xygD 104 :TALKIVDLSADFRLR T0298 109 :MVSVNAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1xygD 141 :VYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1xygD 180 :LIKHENIIIDAKSGVSGAGRG T0298 184 :LEPRLFDRQIA 1xygD 201 :AKEANLYSEIA T0298 202 :GAVDAEGHSAIERRIFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 213 :GISSYGVTRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KG 1xygD 281 :ED T0298 271 :IEWVGEGDYPTVVGDALGQDETYVGR 1xygD 285 :FVKVLDEGVVPRTHNVRGSNYCHMSV T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLI 1xygD 311 :FPDRIPGRAIIISVIDNLVKGASGQALQNLNIML Number of specific fragments extracted= 12 number of extra gaps= 0 total=1026 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbvO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/2dbvO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/2dbvO/merged-good-all-a2m.gz for input Trying 2dbvO/merged-good-all-a2m Error: Couldn't open file 2dbvO/merged-good-all-a2m or 2dbvO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f06A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f06A expands to /projects/compbio/data/pdb/1f06.pdb.gz 1f06A:# T0298 read from 1f06A/merged-good-all-a2m # 1f06A read from 1f06A/merged-good-all-a2m # adding 1f06A to template set # found chain 1f06A in template set T0298 1 :MS 1f06A 1 :MT T0298 4 :PLNVAVVG 1f06A 3 :NIRVAIVG T0298 13 :TGSVGEALVGLLD 1f06A 11 :YGNLGRSVEKLIA T0298 28 :DFPLHRLHL 1f06A 24 :KQPDMDLVG T0298 37 :LASAE 1f06A 34 :FSRRA T0298 46 :RMGFAESSLRVGDVDSF 1f06A 39 :TLDTKTPVFDVADVDKH T0298 64 :FSSVGLAFFAAAAEVS 1f06A 56 :ADDVDVLFLCMGSATD T0298 80 :RAHAERA 1f06A 73 :PEQAPKF T0298 90 :GCSV 1f06A 82 :FACT T0298 96 :LSGALEPSV 1f06A 86 :VDTYDNHRD T0298 114 :AERLASQ 1f06A 103 :NEAATAA T0298 123 :PFLLSSPCAVAA 1f06A 110 :GNVALVSTGWDP T0298 136 :LCEVLAPLLATLDCRQLNLTACLS 1f06A 122 :GMFSINRVYAAAVLAEHQQHTFWG T0298 160 :VS 1f06A 148 :LS T0298 165 :REGVKELARQ 1f06A 150 :QGHSDALRRI T0298 182 :RPLE 1f06A 160 :PGVQ T0298 192 :QIAFNLLA 1f06A 164 :KAVQYTLP T0298 205 :D 1f06A 172 :S T0298 214 :RRIFAEVQA 1f06A 173 :EDALEKARR T0298 224 :LGERIGP 1f06A 182 :GEAGDLT T0298 244 :DSLSVTLQCAEP 1f06A 193 :HKRQCFVVADAA T0298 258 :LAAVTRVLDAT 1f06A 206 :HERIENDIRTM T0298 269 :KGIEWVGE 1f06A 221 :VGYEVEVN T0298 277 :GDYPT 1f06A 240 :TGMPH T0298 291 :ETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1f06A 245 :GGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 25 number of extra gaps= 0 total=1051 Number of alignments=61 # 1f06A read from 1f06A/merged-good-all-a2m # found chain 1f06A in template set T0298 1 :MSQ 1f06A 1 :MTN T0298 5 :LNVAVVGA 1f06A 4 :IRVAIVGY T0298 14 :GSVGEALVGLLD 1f06A 12 :GNLGRSVEKLIA T0298 28 :DFPLHRLHLL 1f06A 24 :KQPDMDLVGI T0298 38 :ASAESAGQ 1f06A 35 :SRRATLDT T0298 50 :AESSLRVGDVDSF 1f06A 43 :KTPVFDVADVDKH T0298 64 :FSSVGLAFFAAA 1f06A 56 :ADDVDVLFLCMG T0298 76 :AEVSRAHAERA 1f06A 69 :ATDIPEQAPKF T0298 90 :GCSVIDLSGA 1f06A 82 :FACTVDTYDN T0298 102 :PSV 1f06A 92 :HRD T0298 114 :AERLASQAAPFLLSSPCAVAA 1f06A 103 :NEAATAAGNVALVSTGWDPGM T0298 136 :LCEVLAP 1f06A 124 :FSINRVY T0298 143 :LLATLDCRQLNLTACLS 1f06A 156 :LRRIPGVQKAVQYTLPS T0298 165 :REGVKELARQ 1f06A 173 :EDALEKARRG T0298 180 :NARPLEPRL 1f06A 183 :EAGDLTGKQ T0298 201 :V 1f06A 201 :A T0298 205 :DAEG 1f06A 202 :DAAD T0298 213 :ERRIFAEVQA 1f06A 206 :HERIENDIRT T0298 224 :LGER 1f06A 216 :MPDY T0298 228 :IGPLNV 1f06A 224 :EVEVNF T0298 256 :VDLAAVTR 1f06A 230 :IDEATFDS T0298 285 :DALGQDETYVGRVRAGQ 1f06A 238 :EHTGMPHGGHVITTGDT T0298 302 :ADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1f06A 256 :GFNHTVEYILKLDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 23 number of extra gaps= 0 total=1074 Number of alignments=62 # 1f06A read from 1f06A/merged-good-all-a2m # found chain 1f06A in template set T0298 3 :QPLNVAVVG 1f06A 2 :TNIRVAIVG T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAE 1f06A 11 :YGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0298 50 :AESSLRVGDVDSFD 1f06A 40 :LDTKTPVFDVADVD T0298 64 :FSSVGLAFFAAAA 1f06A 56 :ADDVDVLFLCMGS T0298 77 :EVSRAHAERA 1f06A 70 :TDIPEQAPKF T0298 89 :AGCSVIDLSGALEPS 1f06A 81 :QFACTVDTYDNHRDI T0298 114 :AERLASQAAPFLLSS 1f06A 103 :NEAATAAGNVALVST T0298 129 :PCAVAAELCEV 1f06A 121 :PGMFSINRVYA T0298 142 :PLLATLDCRQLNLTACLS 1f06A 155 :ALRRIPGVQKAVQYTLPS T0298 165 :REGVKELARQ 1f06A 173 :EDALEKARRG T0298 204 :VDAEGHSAIE 1f06A 183 :EAGDLTGKQT T0298 244 :DSLSVTLQCAEP 1f06A 193 :HKRQCFVVADAA T0298 258 :LAAVTRVLDATKG 1f06A 206 :HERIENDIRTMPD T0298 271 :IEWVGEG 1f06A 225 :VEVNFID T0298 286 :ALGQDETYVGRVRAGQADPCQVNLWIV 1f06A 239 :HTGMPHGGHVITTGDTGGFNHTVEYIL T0298 313 :SDNVRKGAALNAVLLGELLIK 1f06A 267 :LDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 16 number of extra gaps= 0 total=1090 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dssG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dssG expands to /projects/compbio/data/pdb/1dss.pdb.gz 1dssG:Bad short name: OZ1 for alphabet: pdb_atoms Bad short name: OZ2 for alphabet: pdb_atoms # T0298 read from 1dssG/merged-good-all-a2m # 1dssG read from 1dssG/merged-good-all-a2m # adding 1dssG to template set # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)R317 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 T0298 6 :NVAVVG 1dssG 2 :KIGING T0298 13 :TGSVGEALVGLLDERDFPLHRLHL 1dssG 8 :FGRIGRLVLRAALEMGAQVVAVND T0298 37 :LASAESAGQRMGFA 1dssG 34 :FIALEYMVYMFKYD T0298 51 :ESSLRVGDVDSFDFS 1dssG 71 :ITVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1dssG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKV T0298 96 :LSGALE 1dssG 117 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1dssG 123 :ADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1dssG 140 :DMKVVSNA T0298 132 :VAA 1dssG 151 :TNC T0298 136 :LCEVLAPLLATLDCRQLNLTA 1dssG 154 :LAPVAKVLHENFEIVEGLMTT T0298 159 :SVSSL 1dssG 177 :AVTAT T0298 176 :AELLNARPLEPRLFDRQIA 1dssG 182 :QKTVDGPSAKDWRGGRGAA T0298 198 :LA 1dssG 204 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1dssG 206 :SSTGAAKAVGKVIPELDG T0298 230 :PLNVT 1dssG 224 :KLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1dssG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQL T0298 304 :PCQVNLWIVSDN 1dssG 302 :KTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKH 1dssG 316 :GYSQRVIDLIKHMQKV Number of specific fragments extracted= 19 number of extra gaps= 4 total=1109 Number of alignments=64 # 1dssG read from 1dssG/merged-good-all-a2m # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)R317 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 T0298 6 :NVAVVGA 1dssG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFP 1dssG 9 :GRIGRLVLRAALEMGAQ T0298 34 :LHLLASAE 1dssG 27 :VVAVNDPF T0298 42 :SAGQRMGFAE 1dssG 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1dssG 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1dssG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1dssG 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1dssG 140 :DMKVVSNA T0298 132 :VAA 1dssG 151 :TNC T0298 136 :LCEVLAPLLATLDCRQLNLTA 1dssG 154 :LAPVAKVLHENFEIVEGLMTT T0298 159 :SVSS 1dssG 177 :AVTA T0298 175 :TAELLNARPLEPRLFDRQIA 1dssG 181 :TQKTVDGPSAKDWRGGRGAA T0298 198 :LA 1dssG 204 :IP T0298 205 :DAEG 1dssG 206 :SSTG T0298 213 :ERRIFAEV 1dssG 210 :AAKAVGKV T0298 224 :LGERIGPLNVT 1dssG 218 :IPELDGKLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1dssG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1dssG 300 :LSKTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKHY 1dssG 316 :GYSQRVIDLIKHMQKVD Number of specific fragments extracted= 20 number of extra gaps= 4 total=1129 Number of alignments=65 # 1dssG read from 1dssG/merged-good-all-a2m # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)C130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dssG)T150 Warning: unaligning (T0298)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)V316 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 T0298 6 :NVAVVGA 1dssG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHL 1dssG 9 :GRIGRLVLRAALEMGAQVVAVND T0298 40 :AESA 1dssG 33 :PFIA T0298 44 :GQRMGFAES 1dssG 54 :KGEVKAEDG T0298 53 :SLRVGDVDSFDFSS 1dssG 68 :GKKITVFNEMKPEN T0298 67 :VGLAFFAAA 1dssG 89 :AEYIVESTG T0298 76 :AEVS 1dssG 102 :IEKA T0298 87 :RAAGCSVIDLSGAL 1dssG 109 :FKGGAKKVIISAPS T0298 103 :SVAPPVMVSVNAER 1dssG 123 :ADAPMFVCGVNLEK T0298 120 :Q 1dssG 137 :Y T0298 121 :AAPFLLSSP 1dssG 139 :KDMKVVSNA T0298 133 :AAELCEVLAPLLATLDCRQLNLTA 1dssG 151 :TNCLAPVAKVLHENFEIVEGLMTT T0298 159 :SVSSLGRE 1dssG 177 :AVTATQKT T0298 180 :NARPLEPRLFDRQIA 1dssG 186 :DGPSAKDWRGGRGAA T0298 198 :LAQVGA 1dssG 204 :IPSSTG T0298 216 :IFAEVQALLGERIGPLNVT 1dssG 210 :AAKAVGKVIPELDGKLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGD 1dssG 268 :QGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1dssG 278 :VVSCDFTGDNRSSIFD T0298 297 :V 1dssG 297 :G T0298 300 :GQADPCQVNLWIVSDN 1dssG 298 :IQLSKTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKH 1dssG 316 :GYSQRVIDLIKHMQKV Number of specific fragments extracted= 22 number of extra gaps= 4 total=1151 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1brmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1brmA expands to /projects/compbio/data/pdb/1brm.pdb.gz 1brmA:# T0298 read from 1brmA/merged-good-all-a2m # 1brmA read from 1brmA/merged-good-all-a2m # adding 1brmA to template set # found chain 1brmA in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1brmA)M1 Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1brmA 27 :FDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEP 1brmA 93 :YWIDAASSLRM T0298 103 :SVAPPVMVSVNAERLA 1brmA 105 :DDAIIILDPVNQDVIT T0298 119 :SQ 1brmA 125 :NG T0298 122 :APFLLSSPCAVAA 1brmA 127 :IRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1brmA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPL 1brmA 190 :LATPSS T0298 185 :EPRLFDRQIAFNLLAQV 1brmA 214 :PVDNFGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1brmA 300 :PWAKVVPN T0298 283 :VGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 318 :PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1165 Number of alignments=67 # 1brmA read from 1brmA/merged-good-all-a2m # found chain 1brmA in template set Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 1 :M 1brmA 1 :M T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLL 1brmA 27 :FDAIRPVFF T0298 39 :SAESAGQRMGFAESS 1brmA 36 :STSQLGQAAPSFGGT T0298 54 :LRVGDVDSFD 1brmA 52 :GTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1brmA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQA 1brmA 106 :DAIIILDPVNQDVITDGL T0298 122 :A 1brmA 126 :G T0298 123 :PFLLSSPCAVAA 1brmA 128 :RTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1brmA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMREL T0298 172 :ARQTAELLNARPLEPRL 1brmA 183 :YGHVADELATPSSAILD T0298 189 :FDRQIAFNLLAQV 1brmA 218 :FGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1brmA 300 :PWAKVVPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 319 :AAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1182 Number of alignments=68 # 1brmA read from 1brmA/merged-good-all-a2m # found chain 1brmA in template set Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESAGQRM 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAA T0298 48 :GFAESSLRVGDV 1brmA 46 :SFGGTTGTLQDA T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 59 :DLEALKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1brmA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQ 1brmA 106 :DAIIILDPVNQDVITDG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1brmA 125 :NGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPLEPRLFDRQIAFNLLAQV 1brmA 208 :TRSGELPVDNFGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 316 :LTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1192 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nwcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1nwcA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1nwcA/merged-good-all-a2m.gz for input Trying 1nwcA/merged-good-all-a2m Error: Couldn't open file 1nwcA/merged-good-all-a2m or 1nwcA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cf2O/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cf2O expands to /projects/compbio/data/pdb/1cf2.pdb.gz 1cf2O:# T0298 read from 1cf2O/merged-good-all-a2m # 1cf2O read from 1cf2O/merged-good-all-a2m # adding 1cf2O to template set # found chain 1cf2O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1cf2O)M1 T0298 5 :LNVAVVG 1cf2O 2 :KAVAING T0298 13 :TGSVGEALVGLLDE 1cf2O 9 :YGTVGKRVADAIAQ T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDVD 1cf2O 24 :DDMKVIGVSKTRPDFEARMALKKGYDLYVAIPER T0298 61 :SFDFS 1cf2O 65 :GIEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAI T0298 96 :LSGALE 1cf2O 107 :FQGGEK T0298 114 :AERLA 1cf2O 113 :HEDIG T0298 119 :SQAAPFLLSSP 1cf2O 128 :ESYGKDYTRVV T0298 130 :CAVAA 1cf2O 140 :CNTTG T0298 136 :LCEVLAPLLATLDCRQLNLTACLS 1cf2O 145 :LCRTLKPLHDSFGIKKVRAVIVRR T0298 176 :AELLNARPLEPRLFDRQI 1cf2O 169 :GADPAQVSKGPINAIIPN T0298 205 :DAEGHS 1cf2O 187 :PPKLPS T0298 215 :RIFAEVQALLG 1cf2O 193 :HHGPDVKTVLD T0298 229 :GPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1cf2O 204 :INIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDG T0298 285 :DALGQDETYVGRVR 1cf2O 269 :GRSRNDLFEIPVWR T0298 299 :AGQADPCQVNLWIVSDN 1cf2O 284 :SITVVDNEIYYMQAVHQ T0298 317 :RKGAALNAVLLGELLIK 1cf2O 301 :ESDIVPENVDAVRAILE Number of specific fragments extracted= 17 number of extra gaps= 0 total=1209 Number of alignments=70 # 1cf2O read from 1cf2O/merged-good-all-a2m # found chain 1cf2O in template set T0298 1 :M 1cf2O 1 :M T0298 5 :LNVAVVGA 1cf2O 2 :KAVAINGY T0298 14 :GSVGEALVGLLD 1cf2O 10 :GTVGKRVADAIA T0298 28 :DFPLHRLHLLASAE 1cf2O 22 :QQDDMKVIGVSKTR T0298 42 :SAGQRMGFAESS 1cf2O 37 :DFEARMALKKGY T0298 54 :LRVGDVDS 1cf2O 50 :LYVAIPER T0298 62 :FDFS 1cf2O 66 :IEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAI T0298 96 :LSGALEPSV 1cf2O 107 :FQGGEKHED T0298 105 :APPVMVSVNAERLA 1cf2O 117 :GLSFNSLSNYEESY T0298 122 :APFLLSSP 1cf2O 131 :GKDYTRVV T0298 130 :CAVAA 1cf2O 140 :CNTTG T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1cf2O 145 :LCRTLKPLHDSFGIKKVRAVIVRRGADPAQV T0298 173 :RQTAELLNARPL 1cf2O 178 :GPINAIIPNPPK T0298 205 :DAEGHSAI 1cf2O 190 :LPSHHGPD T0298 217 :FAEV 1cf2O 198 :VKTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1cf2O 202 :LDINIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDG T0298 285 :DALGQDETYVGRVRAG 1cf2O 269 :GRSRNDLFEIPVWRES T0298 302 :ADPCQVNLWIVSDN 1cf2O 287 :VVDNEIYYMQAVHQ T0298 317 :RKGAALNAVLLGELLIKHYL 1cf2O 301 :ESDIVPENVDAVRAILEMEE Number of specific fragments extracted= 20 number of extra gaps= 0 total=1229 Number of alignments=71 # 1cf2O read from 1cf2O/merged-good-all-a2m # found chain 1cf2O in template set T0298 5 :LNVAVVG 1cf2O 2 :KAVAING T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAESA 1cf2O 9 :YGTVGKRVADAIAQQDDMKVIGVSKTRPDFE T0298 44 :GQRMGFAES 1cf2O 47 :GYDLYVAIP T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSG 1cf2O 65 :GIEVAGTVDDMLDEADIVIDCTPEGIGAKNLKMYKEKGIKAIFQGG T0298 100 :LEPSVAPPVMVS 1cf2O 111 :EKHEDIGLSFNS T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLS 1cf2O 125 :NYEESYGKDYTRVVSCNTTGLCRTLKPLHDSFGIKKVRAVIVRR T0298 162 :SL 1cf2O 169 :GA T0298 182 :RPLEPRLFDRQ 1cf2O 171 :DPAQVSKGPIN T0298 201 :VGAVDAEGHSAI 1cf2O 183 :IIPNPPKLPSHH T0298 218 :AEVQALL 1cf2O 195 :GPDVKTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYPTVV 1cf2O 202 :LDINIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDGLTST T0298 284 :GDALGQDETYVGRVRA 1cf2O 268 :LGRSRNDLFEIPVWRE T0298 300 :GQADPCQVNLWIVSDNVRK 1cf2O 285 :ITVVDNEIYYMQAVHQESD T0298 320 :AALNAVLLGELLIK 1cf2O 304 :IVPENVDAVRAILE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1243 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gaeO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1gaeO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1gaeO/merged-good-all-a2m.gz for input Trying 1gaeO/merged-good-all-a2m Error: Couldn't open file 1gaeO/merged-good-all-a2m or 1gaeO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rm3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1rm3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1rm3A/merged-good-all-a2m.gz for input Trying 1rm3A/merged-good-all-a2m Error: Couldn't open file 1rm3A/merged-good-all-a2m or 1rm3A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gypA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gypA expands to /projects/compbio/data/pdb/1gyp.pdb.gz 1gypA:# T0298 read from 1gypA/merged-good-all-a2m # 1gypA read from 1gypA/merged-good-all-a2m # adding 1gypA to template set # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVG 1gypA 2 :PIKVGING T0298 13 :TGSVGEALVGLLDERDF 1gypA 10 :FGRIGRMVFQAICDQGL T0298 30 :PLHRLHL 1gypA 32 :DVVAVVD T0298 37 :LASAESAGQRMGFA 1gypA 40 :STNAEYFAYQMKHD T0298 51 :ESSLR 1gypA 82 :GHRIK T0298 56 :VGDVDSFDFS 1gypA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gypA 103 :GVDYVIESTGLFTDKLKAEGHIKGGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLASQ 1gypA 132 :VISAPASGGAKTIVMGVNQHEYSPA T0298 122 :APFLLSSP 1gypA 157 :SHHVVSNA T0298 130 :CAVAA 1gypA 166 :CTTNC T0298 136 :LCEVLAPLLAT 1gypA 171 :LAPIVHVLTKE T0298 147 :LDCRQLNLTACLSVSSL 1gypA 183 :FGIETGLMTTIHSYTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1gypA 200 :QKTVDGVSLKDWRGGRAAAVNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1gypA 224 :STTGAAKAVGMVIPSTKG T0298 230 :PLNVTCIQAPVF 1gypA 242 :KLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1gypA 284 :YMKGILGFTDEELVSADFINDNRSSVYD T0298 298 :RA 1gypA 318 :NN T0298 302 :ADPCQVNLWIVSDN 1gypA 322 :GEKRFFKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1gypA 336 :EWAYSHRVVDLVRYMAAK Number of specific fragments extracted= 20 number of extra gaps= 2 total=1263 Number of alignments=73 # 1gypA read from 1gypA/merged-good-all-a2m # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVGA 1gypA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1gypA 11 :GRIGRMVFQAICDQGL T0298 30 :PLHRLHLLASAE 1gypA 29 :TEIDVVAVVDMS T0298 42 :SAGQRMGFAE 1gypA 42 :NAEYFAYQMK T0298 52 :SSLR 1gypA 86 :KCVK T0298 56 :VGDVDSFDFS 1gypA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1gypA 103 :GVDYVIESTGLFTDKLKAEGHIKGGAKKVVISAPAS T0298 103 :SVAPPVMVSVNAERLASQ 1gypA 139 :GGAKTIVMGVNQHEYSPA T0298 122 :APFLLSSP 1gypA 157 :SHHVVSNA T0298 130 :CAVAA 1gypA 166 :CTTNC T0298 136 :LCEVLAPLLA 1gypA 171 :LAPIVHVLTK T0298 146 :TLDCRQLNLTACLSVSS 1gypA 182 :NFGIETGLMTTIHSYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gypA 199 :TQKTVDGVSLKDWRGGRAAAVNIIP T0298 205 :DAEG 1gypA 224 :STTG T0298 213 :ERRIFAEV 1gypA 228 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVF 1gypA 236 :IPSTKGKLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1gypA 284 :YMKGILGFTDEELVSADFINDNRSSVYD T0298 298 :RA 1gypA 318 :NN T0298 302 :ADPCQVNLWIVSDN 1gypA 322 :GEKRFFKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1gypA 336 :EWAYSHRVVDLVRYMAAKD Number of specific fragments extracted= 21 number of extra gaps= 2 total=1284 Number of alignments=74 # 1gypA read from 1gypA/merged-good-all-a2m # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVGA 1gypA 2 :PIKVGINGF T0298 14 :GSVGEALVGLL 1gypA 11 :GRIGRMVFQAI T0298 27 :RDFPLHRLHLLASAESAGQR 1gypA 56 :HGRPKYTVEAVKSSPSVETA T0298 47 :MGFAESSLRVGDVDSFDFS 1gypA 78 :LVVNGHRIKCVKAQRNPAD T0298 66 :SVGLAFFAAA 1gypA 103 :GVDYVIESTG T0298 80 :RAHAERARAAGCSVIDLSGALE 1gypA 117 :KLKAEGHIKGGAKKVVISAPAS T0298 104 :VAPPVMVSVNAERLAS 1gypA 140 :GAKTIVMGVNQHEYSP T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLA 1gypA 156 :ASHHVVSNASCTTNCLAPIVHVLTK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1gypA 182 :NFGIETGLMTTIHSYTATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGA 1gypA 204 :DGVSLKDWRGGRAAAVNIIPSTTG T0298 217 :FAEVQALLGER 1gypA 228 :AAKAVGMVIPS T0298 228 :IGPLNVTCIQAPVF 1gypA 240 :KGKLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVG 1gypA 287 :GILGFTD T0298 279 :YPTVVGDALGQDETYVG 1gypA 294 :EELVSADFINDNRSSVY T0298 299 :A 1gypA 319 :N T0298 302 :ADPCQVNLWIVSDNVRK 1gypA 322 :GEKRFFKVVSWYDNEWA T0298 320 :AALNAVLLGELLIKH 1gypA 339 :YSHRVVDLVRYMAAK Number of specific fragments extracted= 18 number of extra gaps= 2 total=1302 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gpdG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/3gpdG/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/3gpdG/merged-good-all-a2m.gz for input Trying 3gpdG/merged-good-all-a2m Error: Couldn't open file 3gpdG/merged-good-all-a2m or 3gpdG/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rm5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1rm5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1rm5A/merged-good-all-a2m.gz for input Trying 1rm5A/merged-good-all-a2m Error: Couldn't open file 1rm5A/merged-good-all-a2m or 1rm5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jn0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1jn0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1jn0A/merged-good-all-a2m.gz for input Trying 1jn0A/merged-good-all-a2m Error: Couldn't open file 1jn0A/merged-good-all-a2m or 1jn0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ys4A expands to /projects/compbio/data/pdb/1ys4.pdb.gz 1ys4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0298 read from 1ys4A/merged-good-all-a2m # 1ys4A read from 1ys4A/merged-good-all-a2m # adding 1ys4A to template set # found chain 1ys4A in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1ys4A)M7 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLA T0298 28 :DFPLHRLHLL 1ys4A 30 :DHPMFELTAL T0298 38 :ASAESAGQRMGFA 1ys4A 41 :ASERSAGKKYKDA T0298 51 :ESSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 68 :DMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLA 1ys4A 128 :PEVNADHLE T0298 120 :QAAPFLLSSP 1ys4A 146 :GWDGAIITNP T0298 130 :CAVAA 1ys4A 157 :CSTIC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 162 :AVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 181 :ARP 1ys4A 194 :VPS T0298 187 :RLFDRQ 1ys4A 197 :MAILDN T0298 205 :DAEGHSAIERRIFAEVQALLG 1ys4A 203 :LIPFIKNEEEKMQTESLKLLG T0298 226 :ER 1ys4A 227 :DG T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKF T0298 269 :KGIEWVGEGDYPTVV 1ys4A 287 :KPIVIREEIDRPQPR T0298 284 :GDALGQDETYVGRVRAGQADP 1ys4A 304 :RNEGNGMSIVVGRIRKDPIFD T0298 307 :VNLWIVSDNVRKGAALNAVLLGELLIKHYL 1ys4A 325 :VKYTALEHNTIRGAAGASVLNAEYFVKKYI Number of specific fragments extracted= 17 number of extra gaps= 1 total=1319 Number of alignments=76 # 1ys4A read from 1ys4A/merged-good-all-a2m # found chain 1ys4A in template set Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 1 :M 1ys4A 7 :M T0298 4 :PLNVAVVGATGSVGEALVGLLD 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLA T0298 28 :DFPLHRLHLL 1ys4A 30 :DHPMFELTAL T0298 38 :ASAESAGQRMGFAE 1ys4A 41 :ASERSAGKKYKDAC T0298 52 :SSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 69 :MVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLA 1ys4A 128 :PEVNADHLE T0298 119 :S 1ys4A 143 :E T0298 120 :QAAPFLLSSP 1ys4A 146 :GWDGAIITNP T0298 130 :CAVAA 1ys4A 157 :CSTIC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 162 :AVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 168 :VKELARQ 1ys4A 196 :SMAILDN T0298 178 :LLN 1ys4A 203 :LIP T0298 205 :DAEGH 1ys4A 206 :FIKNE T0298 213 :ERRIFAEVQALLGER 1ys4A 211 :EEKMQTESLKLLGTL T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKF T0298 269 :KGIEWVGEGDYPTVVGDAL 1ys4A 287 :KPIVIREEIDRPQPRLDRN T0298 288 :GQDETYVGRVRAGQADP 1ys4A 308 :NGMSIVVGRIRKDPIFD T0298 307 :VNLWIVSDNVRKGAALNAVLLGELLIKHY 1ys4A 325 :VKYTALEHNTIRGAAGASVLNAEYFVKKY Number of specific fragments extracted= 19 number of extra gaps= 1 total=1338 Number of alignments=77 # 1ys4A read from 1ys4A/merged-good-all-a2m # found chain 1ys4A in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1ys4A)M7 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHL 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLADHPMFELTALA T0298 38 :ASAESAGQR 1ys4A 41 :ASERSAGKK T0298 47 :MGFAES 1ys4A 56 :WFQDRD T0298 53 :SLRVGDVD 1ys4A 68 :DMVVIPTD T0298 61 :SFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 78 :HEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLASQ 1ys4A 128 :PEVNADHLELI T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 147 :WDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 184 :LEPRLFD 1ys4A 194 :VPSMAIL T0298 195 :FNLLAQV 1ys4A 201 :DNLIPFI T0298 210 :SAIERRIFAEVQALLG 1ys4A 208 :KNEEEKMQTESLKLLG T0298 226 :ER 1ys4A 227 :DG T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKG 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKFDP T0298 271 :IEWVGEGDYPTVV 1ys4A 289 :IVIREEIDRPQPR T0298 284 :GDALGQDETYVGRVRAGQ 1ys4A 304 :RNEGNGMSIVVGRIRKDP T0298 304 :PCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1ys4A 322 :IFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI Number of specific fragments extracted= 16 number of extra gaps= 1 total=1354 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4gpd1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/4gpd1/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/4gpd1/merged-good-all-a2m.gz for input Trying 4gpd1/merged-good-all-a2m Error: Couldn't open file 4gpd1/merged-good-all-a2m or 4gpd1/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dbvO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/3dbvO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/3dbvO/merged-good-all-a2m.gz for input Trying 3dbvO/merged-good-all-a2m Error: Couldn't open file 3dbvO/merged-good-all-a2m or 3dbvO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ozaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1ozaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1ozaA/merged-good-all-a2m.gz for input Trying 1ozaA/merged-good-all-a2m Error: Couldn't open file 1ozaA/merged-good-all-a2m or 1ozaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pqpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1pqpA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1pqpA/merged-good-all-a2m.gz for input Trying 1pqpA/merged-good-all-a2m Error: Couldn't open file 1pqpA/merged-good-all-a2m or 1pqpA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nqoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1nqoA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1nqoA/merged-good-all-a2m.gz for input Trying 1nqoA/merged-good-all-a2m Error: Couldn't open file 1nqoA/merged-good-all-a2m or 1nqoA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g17A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/2g17A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/2g17A/merged-good-all-a2m.gz for input Trying 2g17A/merged-good-all-a2m Error: Couldn't open file 2g17A/merged-good-all-a2m or 2g17A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cerA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1cerA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1cerA/merged-good-all-a2m.gz for input Trying 1cerA/merged-good-all-a2m Error: Couldn't open file 1cerA/merged-good-all-a2m or 1cerA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vknA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0298 read from 1vknA/merged-good-all-a2m # 1vknA read from 1vknA/merged-good-all-a2m # found chain 1vknA in training set Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1vknA 1 :MIRAGIIGATGYTGLELVRLLK T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLRVGD 1vknA 23 :NHPEAKITYLSSRTYAGKKLEEIFPSTLENS T0298 62 :FDFS 1vknA 56 :SEFD T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 89 :A 1vknA 84 :R T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 105 :APPVMVSVNAERLA 1vknA 122 :RVYGLPELHREEIK T0298 122 :APFLLSSP 1vknA 136 :NAQVVGNP T0298 130 :CAVAA 1vknA 145 :CYPTS T0298 136 :LCEVLAPLLAT 1vknA 150 :VILALAPALKH T0298 147 :LDCRQLNLTACLSVSSLGREG 1vknA 163 :VDPETILVDAKSGVSGAGRKE T0298 176 :AELLNARPLEPRLFDRQI 1vknA 184 :KVDYLFSEVNESLRPYNV T0298 205 :DAEGHSAIERRIFAEVQA 1vknA 202 :AKHRHVPEMEQELGKISG T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAE 1vknA 220 :KKVNVVFTPHLVPMTRGILSTIYVKTDK T0298 257 :DLAAVTRVLDAT 1vknA 248 :SLEEIHEAYLEF T0298 269 :KGIEWVGEGDYPTVV 1vknA 264 :PFVHVLPMGIYPSTK T0298 285 :DALGQDETYVGR 1vknA 279 :WCYGSNHVFIGM T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1vknA 291 :QMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFG Number of specific fragments extracted= 18 number of extra gaps= 0 total=1372 Number of alignments=79 # 1vknA read from 1vknA/merged-good-all-a2m # found chain 1vknA in training set Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1vknA 1 :MIRAGIIGATGYTGLELVRLLK T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1vknA 23 :NHPEAKITYLSSRTYAGKKLEEIFPSTL T0298 56 :VG 1vknA 55 :LS T0298 63 :DFS 1vknA 57 :EFD T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 105 :APPVMVSVNAERLA 1vknA 122 :RVYGLPELHREEIK T0298 122 :APFLLSSP 1vknA 136 :NAQVVGNP T0298 130 :CAVAA 1vknA 145 :CYPTS T0298 136 :LCEVLAPLLAT 1vknA 150 :VILALAPALKH T0298 147 :LDCRQLNLTACLSVSSLGRE 1vknA 163 :VDPETILVDAKSGVSGAGRK T0298 167 :GVKELARQTAELLNARPL 1vknA 184 :KVDYLFSEVNESLRPYNV T0298 205 :DAEGHSAIERRIFAE 1vknA 202 :AKHRHVPEMEQELGK T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAE 1vknA 217 :ISGKKVNVVFTPHLVPMTRGILSTIYVKTDK T0298 257 :DLAAVTRVLDAT 1vknA 248 :SLEEIHEAYLEF T0298 269 :KGIEWVGEGDYPTVVG 1vknA 264 :PFVHVLPMGIYPSTKW T0298 286 :ALGQDETYVG 1vknA 280 :CYGSNHVFIG T0298 297 :VRAG 1vknA 290 :MQME T0298 302 :ADPCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1vknA 294 :ERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1391 Number of alignments=80 # 1vknA read from 1vknA/merged-good-all-a2m # found chain 1vknA in training set Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLDERD 1vknA 1 :MIRAGIIGATGYTGLELVRLLKNHP T0298 31 :LHRLHLLASAESAGQR 1vknA 26 :EAKITYLSSRTYAGKK T0298 49 :FAES 1vknA 46 :FPST T0298 53 :SLRVGDVDSFDFS 1vknA 52 :NSILSEFDPEKVS T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 109 :MVSVNAERLASQAAPFLLSSPCAVAAELCEVLAPLL 1vknA 123 :VYGLPELHREEIKNAQVVGNPGCYPTSVILALAPAL T0298 145 :ATLDCRQLNLTACLSVSSLGRE 1vknA 161 :NLVDPETILVDAKSGVSGAGRK T0298 184 :LEPRLFDRQI 1vknA 183 :EKVDYLFSEV T0298 202 :GAVDAEGHSAIERRIFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQC 1vknA 195 :SLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKT T0298 255 :PVDLAAVTRVLDAT 1vknA 246 :DKSLEEIHEAYLEF T0298 270 :G 1vknA 261 :K T0298 271 :IEWVGEGDYPTVVGDALGQDETYVGR 1vknA 265 :FVHVLPMGIYPSTKWCYGSNHVFIGM T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLI 1vknA 291 :QMEERTNTLILMSAIDNLVKGASGQAVQNMNIMF Number of specific fragments extracted= 14 number of extra gaps= 0 total=1405 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u8fO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u8fO expands to /projects/compbio/data/pdb/1u8f.pdb.gz 1u8fO:Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 1u8fO # T0298 read from 1u8fO/merged-good-all-a2m # 1u8fO read from 1u8fO/merged-good-all-a2m # adding 1u8fO to template set # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 T0298 5 :LNVAVVG 1u8fO 4 :VKVGVNG T0298 13 :TGSVGEALVGLLDER 1u8fO 11 :FGRIGRLVTRAAFNS T0298 28 :DFPLHRLHL 1u8fO 27 :KVDIVAIND T0298 37 :LASAESAGQRMGFA 1u8fO 37 :FIDLNYMVYMFQYD T0298 51 :ESSLRVGDVDSFDFS 1u8fO 74 :ITIFQERDPSKIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1u8fO 91 :GAEYVVESTGVFTTMEKAGAHLQGGAKRV T0298 96 :LSGALE 1u8fO 120 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1u8fO 126 :ADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1u8fO 143 :SLKIISNA T0298 130 :CAVAA 1u8fO 152 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1u8fO 157 :LAPLAKVIHDNFGIVEGLMTTVHAITAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1u8fO 185 :QKTVDGPSGKLWRDGRGALQNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1u8fO 209 :ASTGAAKAVGKVIPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 227 :KLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1u8fO 269 :PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIAL T0298 304 :PCQVNLWIVSDN 1u8fO 305 :DHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1u8fO 317 :EFGYSNRVVDLMAHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1422 Number of alignments=82 # 1u8fO read from 1u8fO/merged-good-all-a2m # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 Warning: unaligning (T0298)Y335 because last residue in template chain is (1u8fO)E335 T0298 5 :LNVAVVGA 1u8fO 4 :VKVGVNGF T0298 14 :GSVGEALVGLLDERD 1u8fO 12 :GRIGRLVTRAAFNSG T0298 31 :LHRLHLLASAE 1u8fO 27 :KVDIVAINDPF T0298 42 :SAGQRMGFAE 1u8fO 39 :DLNYMVYMFQ T0298 52 :SSLRVGDVDSFDFS 1u8fO 75 :TIFQERDPSKIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1u8fO 91 :GAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1u8fO 125 :SADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1u8fO 143 :SLKIISNA T0298 130 :CAVAA 1u8fO 152 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1u8fO 157 :LAPLAKVIHDNFGIVEGLMTTVHAITA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1u8fO 184 :TQKTVDGPSGKLWRDGRGALQNIIP T0298 205 :DAEG 1u8fO 209 :ASTG T0298 213 :ERRIFAEV 1u8fO 213 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 221 :IPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1u8fO 269 :PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGI T0298 302 :ADPCQVNLWIVSDN 1u8fO 303 :LNDHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1u8fO 317 :EFGYSNRVVDLMAHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1439 Number of alignments=83 # 1u8fO read from 1u8fO/merged-good-all-a2m # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 T0298 5 :LNVAVVGA 1u8fO 4 :VKVGVNGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1u8fO 12 :GRIGRLVTRAAFNSGKVDIVAINDPFIDLN T0298 44 :GQRMGFAES 1u8fO 57 :HGTVKAENG T0298 53 :SLRVGDVDSFD 1u8fO 73 :PITIFQERDPS T0298 66 :S 1u8fO 84 :K T0298 67 :VGLAFFAAA 1u8fO 92 :AEYVVESTG T0298 76 :AEVSR 1u8fO 105 :MEKAG T0298 85 :RARAAGCSVIDLSGAL 1u8fO 110 :AHLQGGAKRVIISAPS T0298 103 :SVAPPVMVSVNAER 1u8fO 126 :ADAPMFVMGVNHEK T0298 120 :Q 1u8fO 140 :Y T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1u8fO 142 :NSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGAVDAE 1u8fO 189 :DGPSGKLWRDGRGALQNIIPASTGAAKA T0298 220 :VQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 217 :VGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEG 1u8fO 271 :KGILGYTEH T0298 281 :TVVGDALGQDETYVGR 1u8fO 280 :QVVSSDFNSDTHSSTF T0298 297 :V 1u8fO 300 :G T0298 300 :GQADPCQVNLWIVSDNV 1u8fO 301 :IALNDHFVKLISWYDNE T0298 318 :KGAALNAVLLGELLIKH 1u8fO 318 :FGYSNRVVDLMAHMASK Number of specific fragments extracted= 18 number of extra gaps= 0 total=1457 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ps8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1ps8A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1ps8A/merged-good-all-a2m.gz for input Trying 1ps8A/merged-good-all-a2m Error: Couldn't open file 1ps8A/merged-good-all-a2m or 1ps8A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdgO/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1hdgO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1hdgO/merged-good-all-a2m.gz for input Trying 1hdgO/merged-good-all-a2m Error: Couldn't open file 1hdgO/merged-good-all-a2m or 1hdgO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pr3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0298/1pr3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0298/1pr3A/merged-good-all-a2m.gz for input Trying 1pr3A/merged-good-all-a2m Error: Couldn't open file 1pr3A/merged-good-all-a2m or 1pr3A/merged-good-all-a2m.gz for input # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 84 Adding 5463 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -589.7804, CN propb: -589.7804 weights: 0.3317 constraints: 1238 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1238 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1238 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 4225 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 4225 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 5463 # command: