# 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/T0355/ # command:# Making conformation for sequence T0355 numbered 1 through 288 Created new target T0355 from T0355.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0355/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0355//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0355/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0355//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0355/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0355/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0355/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c3zA expands to /projects/compbio/data/pdb/2c3z.pdb.gz 2c3zA:# T0355 read from 2c3zA/merged-good-all-a2m # 2c3zA read from 2c3zA/merged-good-all-a2m # adding 2c3zA to template set # found chain 2c3zA in template set T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKPDDIGP 2c3zA 33 :LNERILEFNKRNITAIIAEYKRKSPSGLDVERDP # choosing archetypes in rotamer library T0355 85 :SAFMSVVTDRIVRTAGVPV 2c3zA 67 :IEYSKFMERYAVGLSILTE T0355 104 :GINVLANAPIPAFAIA 2c3zA 95 :TLRKIASSVSIPILMK T0355 125 :KFIRVNQWANA 2c3zA 111 :DFIVKESQIDD T0355 137 :VANEGFMEGRAAEAMRYR 2c3zA 122 :AYNLGADTVLLIVKILTE T0355 155 :SLLRAEHIKVFADSH 2c3zA 147 :EYARSYGMEPLIEIN T0355 173 :GAHAIT 2c3zA 162 :DENDLD T0355 182 :SIDEL 2c3zA 168 :IALRI T0355 189 :DLAFFDADG 2c3zA 173 :GARFIGINS T0355 202 :GQRTGNSASLEEIEEIGAATH 2c3zA 182 :RDLETLEINKENQRKLISMIP T0355 223 :LPLLVGSGV 2c3zA 205 :VVKVAESGI T0355 232 :NEGNIVEILKR 2c3zA 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVWWNP 2c3zA 227 :VNAFLIGSSLMRNPEKIKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=13 Number of alignments=1 # 2c3zA read from 2c3zA/merged-good-all-a2m # found chain 2c3zA in template set T0355 8 :AANAIQEIFGRSKALIGMIHCPAFPGAPR 2c3zA 33 :LNERILEFNKRNITAIIAEYKRKSPSGLD T0355 38 :RNASMD 2c3zA 62 :VERDPI T0355 51 :RDAERLIEG 2c3zA 68 :EYSKFMERY T0355 61 :MHGLIV 2c3zA 77 :AVGLSI T0355 74 :FSKPDDI 2c3zA 83 :LTEEKYF T0355 97 :RTA 2c3zA 90 :NGS T0355 102 :PVGINVLANAPIPAFAI 2c3zA 93 :YETLRKIASSVSIPILM T0355 123 :GAKFIR 2c3zA 110 :KDFIVK T0355 130 :NQWANA 2c3zA 116 :ESQIDD T0355 137 :VANEGFMEGRA 2c3zA 122 :AYNLGADTVLL T0355 148 :AEAM 2c3zA 135 :KILT T0355 152 :RYRSLLRAEHIKVFADSHVKHG 2c3zA 140 :RELESLLEYARSYGMEPLIEIN T0355 179 :ADRSIDELTR 2c3zA 162 :DENDLDIALR T0355 193 :FDADGVIATG 2c3zA 172 :IGARFIGINS T0355 203 :QRTGNSASLEEIEEIGAAT 2c3zA 183 :DLETLEINKENQRKLISMI T0355 222 :HLPLLVGSGV 2c3zA 204 :NVVKVAESGI T0355 232 :NEGNIVEILKR 2c3zA 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVWWNP 2c3zA 227 :VNAFLIGSSLMRNPEKIKE Number of specific fragments extracted= 18 number of extra gaps= 0 total=31 Number of alignments=2 # 2c3zA read from 2c3zA/merged-good-all-a2m # found chain 2c3zA in template set T0355 8 :AANAIQEIFGRSKALIGMIHCPAFPGAPRYRN 2c3zA 33 :LNERILEFNKRNITAIIAEYKRKSPSGLDVER T0355 41 :S 2c3zA 65 :D T0355 49 :CMRDAERLIEG 2c3zA 66 :PIEYSKFMERY T0355 61 :MHGLIVENH 2c3zA 77 :AVGLSILTE T0355 79 :DIGPETSA 2c3zA 90 :NGSYETLR T0355 94 :RIVRTAGVPVGINVLANAPI 2c3zA 98 :KIASSVSIPILMKDFIVKES T0355 115 :AFAIAKAGGAKFIRVNQ 2c3zA 118 :QIDDAYNLGADTVLLIV T0355 140 :EGFMEGRAAEAMRYRSLLRAEH 2c3zA 135 :KILTERELESLLEYARSYGMEP T0355 165 :FADSHV 2c3zA 157 :LIEIND T0355 184 :DELTRDLAFFDADGVIATG 2c3zA 163 :ENDLDIALRIGARFIGINS T0355 203 :QRTGNSASLEEIEEIGA 2c3zA 183 :DLETLEINKENQRKLIS T0355 220 :ATHLPLLVGSGV 2c3zA 202 :PSNVVKVAESGI T0355 232 :NEGNIVEILKR 2c3zA 215 :ERNEIEELRKL T0355 243 :TSGVIVASSL 2c3zA 227 :VNAFLIGSSL Number of specific fragments extracted= 14 number of extra gaps= 0 total=45 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h5yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h5yA expands to /projects/compbio/data/pdb/1h5y.pdb.gz 1h5yA:Skipped atom 208, because occupancy 0.5 <= existing 0.500 in 1h5yA Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1h5yA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1h5yA # T0355 read from 1h5yA/merged-good-all-a2m # 1h5yA read from 1h5yA/merged-good-all-a2m # adding 1h5yA to template set # found chain 1h5yA in template set T0355 49 :CMRDAERLIEGGMH 1h5yA 35 :PVEMAVRYEEEGAD T0355 63 :GLIVE 1h5yA 50 :IAILD T0355 74 :FSKPDDIGPETSAFMSVVTDR 1h5yA 55 :ITAAPEGRATFIDSVKRVAEA T0355 112 :PIPA 1h5yA 76 :VSIP T0355 118 :IAKAGGAK 1h5yA 80 :VLVGGGVR T0355 128 :RVNQWA 1h5yA 88 :SLEDAT T0355 136 :YVANEGFMEGRA 1h5yA 94 :TLFRAGADKVSV T0355 149 :EAMRYR 1h5yA 106 :NTAAVR T0355 155 :SLL 1h5yA 114 :QLV T0355 158 :RAEHIK 1h5yA 121 :REFGSQ T0355 164 :VFADSHVKHG 1h5yA 128 :TVVAIDAKWN T0355 174 :AHAIT 1h5yA 157 :VKWAK T0355 182 :SIDEL 1h5yA 162 :EVEEL T0355 194 :DADGVIATGQ 1h5yA 167 :GAGEILLTSI T0355 204 :RTGNSASLEEIEEIGAATHLPLLVGSGV 1h5yA 180 :GTGLGYDVELIRRVADSVRIPVIASGGA T0355 232 :NEGNIVEILKR 1h5yA 209 :RVEHFYEAAAA T0355 243 :TSGVIVASSLKE 1h5yA 221 :ADAVLAASLFHF T0355 257 :VWWN 1h5yA 233 :RVLS T0355 267 :VRSFVAAARP 1h5yA 237 :IAQVKRYLKE Number of specific fragments extracted= 19 number of extra gaps= 0 total=64 Number of alignments=4 # 1h5yA read from 1h5yA/merged-good-all-a2m # found chain 1h5yA in template set T0355 18 :RSKALIGMIHCPAFPG 1h5yA 3 :MALRIIPCLDIDGGAK T0355 34 :APRY 1h5yA 21 :VKGV T0355 41 :SMDAIYD 1h5yA 25 :NFQGIRE T0355 48 :ACMRDAERLIEGGMHGLIV 1h5yA 34 :DPVEMAVRYEEEGADEIAI T0355 70 :GDVPFSKP 1h5yA 53 :LDITAAPE T0355 80 :IGPETS 1h5yA 61 :GRATFI T0355 103 :VGINVLANAPIPAFAIAKAGGAK 1h5yA 67 :DSVKRVAEAVSIPVLVGGGVRSL T0355 131 :QWANA 1h5yA 90 :EDATT T0355 137 :VANEGFMEGRAAEAM 1h5yA 95 :LFRAGADKVSVNTAA T0355 152 :RYRSLLRAEHIKVFADS 1h5yA 111 :RNPQLVALLAREFGSQS T0355 169 :HVKHGAHAIT 1h5yA 129 :VVAIDAKWNG T0355 179 :ADRSIDELTR 1h5yA 156 :AVKWAKEVEE T0355 193 :FDADGVIAT 1h5yA 166 :LGAGEILLT T0355 202 :GQRTGN 1h5yA 180 :GTGLGY T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1h5yA 186 :DVELIRRVADSVRIPVIASGGA T0355 232 :NEGNIVEILKR 1h5yA 209 :RVEHFYEAAAA T0355 243 :TSGVIVASSLKEGGVWW 1h5yA 221 :ADAVLAASLFHFRVLSI T0355 261 :PVELARVRS 1h5yA 238 :AQVKRYLKE Number of specific fragments extracted= 18 number of extra gaps= 0 total=82 Number of alignments=5 # 1h5yA read from 1h5yA/merged-good-all-a2m # found chain 1h5yA in template set T0355 21 :ALIGMIHCPA 1h5yA 6 :RIIPCLDIDG T0355 34 :APRYRNASM 1h5yA 21 :VKGVNFQGI T0355 49 :CMRDAERLIEGGMHGLIVENHGD 1h5yA 35 :PVEMAVRYEEEGADEIAILDITA T0355 81 :GPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAK 1h5yA 58 :APEGRATFIDSVKRVAEAVSIPVLVGGGVRSLEDATTLFR T0355 122 :GGAKFIRVNQWAN 1h5yA 98 :AGADKVSVNTAAV T0355 137 :V 1h5yA 111 :R T0355 143 :MEGR 1h5yA 112 :NPQL T0355 150 :AMRYRSLLRAEHIKVFADSHVKHGAH 1h5yA 116 :VALLAREFGSQSTVVAIDAKWNGEYY T0355 178 :TADRSIDELTRDLAFFDADGVIATGQ 1h5yA 151 :ATGLDAVKWAKEVEELGAGEILLTSI T0355 204 :RTGNSASLEEIEEIGAATHLPLLVGSGV 1h5yA 180 :GTGLGYDVELIRRVADSVRIPVIASGGA T0355 232 :NEGNIVEILKR 1h5yA 209 :RVEHFYEAAAA T0355 243 :TSGVIVASSLKEGGVW 1h5yA 221 :ADAVLAASLFHFRVLS T0355 267 :VRSFVAAARP 1h5yA 237 :IAQVKRYLKE Number of specific fragments extracted= 13 number of extra gaps= 0 total=95 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mzhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mzhA expands to /projects/compbio/data/pdb/1mzh.pdb.gz 1mzhA:# T0355 read from 1mzhA/merged-good-all-a2m # 1mzhA read from 1mzhA/merged-good-all-a2m # adding 1mzhA to template set # found chain 1mzhA in template set T0355 21 :ALIGMIHCPAFPG 1mzhA 106 :KYIDNAALKPHLS T0355 46 :YDACMRDAERLIEGGMHGLIV 1mzhA 119 :EKEIEEFVLKSEELGIYAVCV T0355 76 :KPD 1mzhA 140 :NPY T0355 104 :GINVLAN 1mzhA 143 :HVKLASS T0355 111 :APIPAFAIAKAGGAK 1mzhA 152 :KKVKVCCVIGFPLGL T0355 127 :IRVNQWAN 1mzhA 167 :NKTSVKVK T0355 136 :YVANE 1mzhA 175 :EAVEA T0355 141 :GFMEGRAA 1mzhA 183 :GAQELDIV T0355 155 :SLLRA 1mzhA 206 :EELKE T0355 160 :EHIKVFADSH 1mzhA 216 :PSAVHKVIVE T0355 170 :VKHGAHAIT 1mzhA 227 :PYLNEEEIK T0355 182 :SIDELTR 1mzhA 236 :KAVEICI T0355 189 :DLAF 1mzhA 245 :GADF T0355 198 :VIATGQRTGNSASLEEIEEIGAATH 1mzhA 249 :IKTSTGFAPRGTTLEEVRLIKSSAK T0355 223 :LPLLVGSGV 1mzhA 276 :IKVKASGGI T0355 232 :NEGNIVEILKR 1mzhA 286 :DLETAISMIEA T0355 243 :TSGVIVASSL 1mzhA 298 :ADRIGTSSGI T0355 269 :SFVAAARPGLEALEHHH 1mzhA 308 :SIAEEFLKRHLILEHHH Number of specific fragments extracted= 18 number of extra gaps= 0 total=113 Number of alignments=7 # 1mzhA read from 1mzhA/merged-good-all-a2m # found chain 1mzhA in template set Warning: unaligning (T0355)H286 because last residue in template chain is (1mzhA)H325 T0355 20 :KALIGMIHCPAFPG 1mzhA 105 :RKYIDNAALKPHLS T0355 46 :YDACMRDAERLIEGGMHGLIV 1mzhA 119 :EKEIEEFVLKSEELGIYAVCV T0355 76 :KPDDI 1mzhA 140 :NPYHV T0355 103 :VGINVLANAPIPAFAIAKAGGA 1mzhA 145 :KLASSIAKKVKVCCVIGFPLGL T0355 127 :IRVNQWANA 1mzhA 167 :NKTSVKVKE T0355 137 :VANE 1mzhA 176 :AVEA T0355 141 :GFMEGRAAEAMRYR 1mzhA 183 :GAQELDIVWNLSAF T0355 155 :SLLRAEHIKVFADS 1mzhA 202 :DFVVEELKEIFRET T0355 169 :HVKHGAHAITADRSIDELTRDLAFFDADGVIATGQRTGNSASLEEIEEIGAAT 1mzhA 220 :HKVIVETPYLNEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKSSA T0355 222 :HLPLLVGSGV 1mzhA 275 :RIKVKASGGI T0355 232 :NEGNIVEILKR 1mzhA 286 :DLETAISMIEA T0355 243 :TSGVIVASSL 1mzhA 298 :ADRIGTSSGI T0355 269 :SFVAAARPGLEALEHHH 1mzhA 308 :SIAEEFLKRHLILEHHH Number of specific fragments extracted= 13 number of extra gaps= 0 total=126 Number of alignments=8 # 1mzhA read from 1mzhA/merged-good-all-a2m # found chain 1mzhA in template set Warning: unaligning (T0355)H286 because last residue in template chain is (1mzhA)H325 T0355 23 :IGMIHCP 1mzhA 108 :IDNAALK T0355 38 :RNASMDAIYDACM 1mzhA 115 :PHLSEKEIEEFVL T0355 55 :RLIEGGMHGLIVENHG 1mzhA 128 :KSEELGIYAVCVNPYH T0355 92 :TDRIVRTA 1mzhA 144 :VKLASSIA T0355 100 :GVPVGINVLAN 1mzhA 153 :KVKVCCVIGFP T0355 111 :APIPAFA 1mzhA 172 :KVKEAVE T0355 119 :AKAGGAKFI 1mzhA 179 :AVRDGAQEL T0355 130 :NQWANAYVANEGFMEGRAAEAMRYRSLLR 1mzhA 188 :DIVWNLSAFKSEKYDFVVEELKEIFRETP T0355 161 :HIKVFADSHVKHG 1mzhA 217 :SAVHKVIVETPYL T0355 179 :ADRSIDELTRDLAFFDADGVIATGQRTGNSASLEEIEEIGA 1mzhA 230 :NEEEIKKAVEICIEAGADFIKTSTGFAPRGTTLEEVRLIKS T0355 220 :ATHLPLLVGSGV 1mzhA 273 :KGRIKVKASGGI T0355 232 :NEGNIVEILKR 1mzhA 286 :DLETAISMIEA T0355 243 :TSGVIVAS 1mzhA 298 :ADRIGTSS T0355 267 :VRSFVAAARPGLEALEHHH 1mzhA 306 :GISIAEEFLKRHLILEHHH Number of specific fragments extracted= 14 number of extra gaps= 0 total=140 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kfcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kfcA expands to /projects/compbio/data/pdb/1kfc.pdb.gz 1kfcA:# T0355 read from 1kfcA/merged-good-all-a2m # 1kfcA read from 1kfcA/merged-good-all-a2m # adding 1kfcA to template set # found chain 1kfcA in template set Warning: unaligning (T0355)D196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kfcA)L193 Warning: unaligning (T0355)L211 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kfcA)L193 T0355 12 :IQEIFGR 1kfcA 7 :LFAQLND T0355 28 :CPAFPGAPRYRNASMD 1kfcA 14 :RREGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1kfcA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1kfcA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIRE T0355 111 :APIPAFAIAKAGGAKF 1kfcA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWAN 1kfcA 109 :NGIDAFYA T0355 136 :YVANEGFMEGRAAEAM 1kfcA 117 :RCEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGAHAIT 1kfcA 138 :PFRQAALRHNIAPIFICPPNADDDLLR T0355 182 :SIDELTRDLAF 1kfcA 165 :QVASYGRGYTY T0355 194 :DA 1kfcA 176 :LL T0355 212 :E 1kfcA 194 :H T0355 213 :EIEEIGAATHLPLLVGSGV 1kfcA 196 :LIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1kfcA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKEGGVWW 1kfcA 228 :AAGAISGSAIVKIIEKN T0355 260 :NPVELARVRSFVAAARPG 1kfcA 248 :PKQMLAELRSFVSAMKAA Number of specific fragments extracted= 15 number of extra gaps= 0 total=155 Number of alignments=10 # 1kfcA read from 1kfcA/merged-good-all-a2m # found chain 1kfcA in template set Warning: unaligning (T0355)A9 because first residue in template chain is (1kfcA)M1 Warning: unaligning (T0355)D196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kfcA)L193 Warning: unaligning (T0355)L211 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kfcA)L193 T0355 10 :NAIQEIFG 1kfcA 2 :ERYENLFA T0355 18 :RSKALIGMIHCPAFP 1kfcA 15 :REGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1kfcA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1kfcA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIRE T0355 111 :APIPAFAIAKAGGAKF 1kfcA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWANA 1kfcA 109 :NGIDAFYAR T0355 137 :VANEGFMEGRAAEAM 1kfcA 118 :CEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1kfcA 134 :EESAPFRQAALRHNIAPIFICPP T0355 177 :ITADRSIDELTRDLAFFDA 1kfcA 157 :NADDDLLRQVASYGRGYTY T0355 212 :EEIEEIGAATHLPLLVGSGV 1kfcA 195 :HLIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1kfcA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKE 1kfcA 228 :AAGAISGSAIVK T0355 255 :GGVW 1kfcA 244 :NLAS T0355 260 :NPVELARVRSFVAAARPG 1kfcA 248 :PKQMLAELRSFVSAMKAA Number of specific fragments extracted= 14 number of extra gaps= 0 total=169 Number of alignments=11 # 1kfcA read from 1kfcA/merged-good-all-a2m # found chain 1kfcA in template set Warning: unaligning (T0355)S210 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kfcA)L193 T0355 7 :NAANAIQEIFGRSKALIGMIHCPAFP 1kfcA 3 :RYENLFAQLNDRREGAFVPFVTLGDP T0355 39 :N 1kfcA 29 :G T0355 46 :YDACMRDAERLIEGGMHGLIVENH 1kfcA 30 :IEQSLKIIDTLIDAGADALELGVP T0355 74 :FSKPDDIGPETSAFMS 1kfcA 54 :FSDPLADGPTIQNANL T0355 90 :VVTDRIVRTA 1kfcA 83 :EMLAIIREKH T0355 100 :GVPVGINVLANAPI 1kfcA 94 :TIPIGLLMYANLVF T0355 114 :PAFAIAKAGGAKFIRV 1kfcA 113 :AFYARCEQVGVDSVLV T0355 140 :EGFMEGRAAEAMRYRSLLRAEHIKVF 1kfcA 129 :ADVPVEESAPFRQAALRHNIAPIFIC T0355 178 :TADRSIDELTRDLAFFDADGVIA 1kfcA 155 :PPNADDDLLRQVASYGRGYTYLL T0355 211 :LEEIEEIGAATHLPLLVGSGV 1kfcA 194 :HHLIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1kfcA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSL 1kfcA 228 :AAGAISGSAI T0355 263 :ELA 1kfcA 247 :SPK T0355 269 :SFVAAARPGLEALE 1kfcA 250 :QMLAELRSFVSAMK Number of specific fragments extracted= 14 number of extra gaps= 0 total=183 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m5wA expands to /projects/compbio/data/pdb/1m5w.pdb.gz 1m5wA:# T0355 read from 1m5wA/merged-good-all-a2m # 1m5wA read from 1m5wA/merged-good-all-a2m # adding 1m5wA to template set # found chain 1m5wA in template set T0355 13 :QEIFGRSKA 1m5wA 15 :TLRNARGTA T0355 41 :SMD 1m5wA 24 :YPD T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFS 1m5wA 27 :PVQAAFIAEQAGADGITVHLREDRRHI T0355 102 :PV 1m5wA 54 :TD T0355 104 :GINVLANAPIPAFAIAKAGG 1m5wA 57 :DVRILRQTLDTRMNLEMAVT T0355 130 :NQWAN 1m5wA 77 :EEMLA T0355 136 :YVANEGFMEGRAAEAMRYR 1m5wA 82 :IAVETKPHFCCLVPEKRQE T0355 155 :SLLRAEHIKVFADSH 1m5wA 121 :KRLADAGIQVSLFID T0355 172 :HGAHAIT 1m5wA 136 :ADEEQIK T0355 182 :SIDEL 1m5wA 143 :AAAEV T0355 189 :DLAFF 1m5wA 148 :GAPFI T0355 198 :VIATG 1m5wA 153 :EIHTG T0355 203 :QRTGNSASLE 1m5wA 160 :ADAKTDAEQA T0355 213 :EIEEIGAA 1m5wA 171 :ELARIAKA T0355 221 :THLPLLVGSGVNEGNIVEILKR 1m5wA 185 :LGLKVNAGHGLTYHNVKAIAAI T0355 243 :TSGVIVASSLKEGGVWWN 1m5wA 209 :MHELNIGHAIIGRAVMTG T0355 263 :ELARVRSFVAAARPGL 1m5wA 227 :LKDAVAEMKRLMLEAR Number of specific fragments extracted= 17 number of extra gaps= 0 total=200 Number of alignments=13 # 1m5wA read from 1m5wA/merged-good-all-a2m # found chain 1m5wA in template set T0355 48 :ACMRDAERLIEGGMHGLIVENHGDVPFSK 1m5wA 26 :DPVQAAFIAEQAGADGITVHLREDRRHIT T0355 82 :P 1m5wA 55 :D T0355 103 :VGINVLANAPIPAFAIAKAGG 1m5wA 56 :RDVRILRQTLDTRMNLEMAVT T0355 130 :NQWANA 1m5wA 77 :EEMLAI T0355 137 :VANEGFMEGRAAEA 1m5wA 83 :AVETKPHFCCLVPE T0355 151 :M 1m5wA 109 :V T0355 152 :RYRSLLRAEHI 1m5wA 111 :GQRDKMRDACK T0355 163 :KVFADSHVKH 1m5wA 125 :DAGIQVSLFI T0355 177 :ITADRSIDELTR 1m5wA 135 :DADEEQIKAAAE T0355 193 :FDADGVIAT 1m5wA 147 :VGAPFIEIH T0355 202 :G 1m5wA 157 :G T0355 203 :QRTG 1m5wA 162 :AKTD T0355 209 :A 1m5wA 166 :A T0355 210 :SLEEIEEIGAAT 1m5wA 171 :ELARIAKAATFA T0355 222 :HLPLLVGSGVNEGNIVEILKR 1m5wA 186 :GLKVNAGHGLTYHNVKAIAAI T0355 243 :TSGVIVASSLKE 1m5wA 209 :MHELNIGHAIIG T0355 260 :NPVELARVRSFVAAARPGL 1m5wA 224 :MTGLKDAVAEMKRLMLEAR Number of specific fragments extracted= 17 number of extra gaps= 0 total=217 Number of alignments=14 # 1m5wA read from 1m5wA/merged-good-all-a2m # found chain 1m5wA in template set Warning: unaligning (T0355)S19 because first residue in template chain is (1m5wA)A2 T0355 20 :KALIGMI 1m5wA 3 :ELLLGVN T0355 33 :GAPRYRN 1m5wA 20 :RGTAYPD T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 1m5wA 27 :PVQAAFIAEQAGADGITVHLREDRRHITD T0355 90 :VVTDRIVRTAGVPVGINVLA 1m5wA 56 :RDVRILRQTLDTRMNLEMAV T0355 112 :PIPAFAIAKAGGAKFIRV 1m5wA 76 :TEEMLAIAVETKPHFCCL T0355 133 :ANA 1m5wA 103 :TEG T0355 137 :VANEGFMEGRAAEAMRYRSLLRA 1m5wA 106 :GLDVAGQRDKMRDACKRLADAGI T0355 161 :HIKVFADSH 1m5wA 129 :QVSLFIDAD T0355 184 :DELTRDLAFFDADGVIAT 1m5wA 138 :EEQIKAAAEVGAPFIEIH T0355 202 :GQRTGNSA 1m5wA 157 :GCYADAKT T0355 211 :LEEIEEIGA 1m5wA 172 :LARIAKAAT T0355 220 :ATHLPLLVGSGVNEGNIVEILK 1m5wA 184 :SLGLKVNAGHGLTYHNVKAIAA T0355 242 :RTSGVIVASSL 1m5wA 208 :EMHELNIGHAI T0355 264 :LARVRSFVAAARPGL 1m5wA 228 :KDAVAEMKRLMLEAR Number of specific fragments extracted= 14 number of extra gaps= 0 total=231 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nsj/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nsj expands to /projects/compbio/data/pdb/1nsj.pdb.gz 1nsj:Warning: there is no chain 1nsj will retry with 1nsjA # T0355 read from 1nsj/merged-good-all-a2m # 1nsj read from 1nsj/merged-good-all-a2m # adding 1nsj to template set # found chain 1nsj in template set Warning: unaligning (T0355)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1nsj)T138 Warning: unaligning (T0355)S208 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)T138 Warning: unaligning (T0355)A209 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)F139 T0355 35 :PRYRNASMD 1nsj 3 :RVKICGITN T0355 50 :MRDAERLIEGGMHGLIVENHGD 1nsj 12 :LEDALFSVESGADAVGFVFYPK T0355 75 :SKPDDIGPETSAFMSV 1nsj 34 :SKRYISPEDARRISVE T0355 111 :APIPAFAIAK 1nsj 51 :PPFVFRVGVF T0355 122 :GGA 1nsj 61 :VNE T0355 128 :RVNQWAN 1nsj 64 :EPEKILD T0355 136 :YVANEGFMEGRAAEAMR 1nsj 71 :VASYVQLNAVQLHGEEP T0355 154 :RSLLRA 1nsj 88 :IELCRK T0355 160 :EHIKVFADSHV 1nsj 96 :ERILVIKAVGV T0355 172 :HGAHAIT 1nsj 107 :SNERDME T0355 182 :SIDEL 1nsj 114 :RALNY T0355 188 :RDLAFFDA 1nsj 119 :REFPILLD T0355 197 :GVI 1nsj 127 :TKT T0355 203 :QRTG 1nsj 133 :GGSG T0355 210 :SLEEI 1nsj 140 :DWSLI T0355 219 :AATH 1nsj 146 :PYRD T0355 223 :LPLLVGSGVNEGNIVEILKR 1nsj 152 :RYLVLSGGLNPENVRSAIDV T0355 243 :TSGVIVASSLKEGGVWWN 1nsj 174 :PFAVDVSSGVEAFPGKKD T0355 264 :LARVRSFVAAAR 1nsj 192 :HDSIKMFIKNAK Number of specific fragments extracted= 19 number of extra gaps= 1 total=250 Number of alignments=16 # 1nsj read from 1nsj/merged-good-all-a2m # found chain 1nsj in template set Warning: unaligning (T0355)T205 because of BadResidue code BAD_PEPTIDE in next template residue (1nsj)T138 Warning: unaligning (T0355)S208 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)T138 Warning: unaligning (T0355)A209 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)F139 T0355 23 :IGMIHCPA 1nsj 4 :VKICGITN T0355 50 :MRDAERLIEGGMHGLIVENHGDV 1nsj 12 :LEDALFSVESGADAVGFVFYPKS T0355 77 :PDDIGP 1nsj 35 :KRYISP T0355 103 :VGINVLA 1nsj 41 :EDARRIS T0355 110 :NAPI 1nsj 52 :PFVF T0355 117 :AIAKAGGA 1nsj 56 :RVGVFVNE T0355 128 :RVNQWANA 1nsj 64 :EPEKILDV T0355 137 :VANEGFMEGRA 1nsj 72 :ASYVQLNAVQL T0355 148 :AEAM 1nsj 84 :GEEP T0355 152 :RYRSLLRAE 1nsj 89 :ELCRKIAER T0355 166 :ADSHVKHGA 1nsj 98 :ILVIKAVGV T0355 178 :TADRSIDELTR 1nsj 107 :SNERDMERALN T0355 192 :FFDADGVIAT 1nsj 118 :YREFPILLDT T0355 202 :GQR 1nsj 134 :GSG T0355 210 :SLEEI 1nsj 140 :DWSLI T0355 218 :GAATH 1nsj 148 :RDRFR T0355 224 :PLLVGSGVNEGNIVEILKR 1nsj 153 :YLVLSGGLNPENVRSAIDV T0355 243 :TSGVIVASSLKEGGVWWN 1nsj 174 :PFAVDVSSGVEAFPGKKD T0355 264 :LARVRSFVAAARP 1nsj 192 :HDSIKMFIKNAKG Number of specific fragments extracted= 19 number of extra gaps= 1 total=269 Number of alignments=17 # 1nsj read from 1nsj/merged-good-all-a2m # found chain 1nsj in template set Warning: unaligning (T0355)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1nsj)T138 Warning: unaligning (T0355)S208 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)T138 Warning: unaligning (T0355)A209 because of BadResidue code BAD_PEPTIDE at template residue (1nsj)F139 T0355 23 :IGMIHCP 1nsj 4 :VKICGIT T0355 41 :S 1nsj 11 :N T0355 50 :MRDAERLIEGGMHGLIVENHGDVPFS 1nsj 12 :LEDALFSVESGADAVGFVFYPKSKRY T0355 80 :IGPETSAFMSV 1nsj 38 :ISPEDARRISV T0355 98 :TA 1nsj 49 :EL T0355 100 :GVPVGINVLANA 1nsj 52 :PFVFRVGVFVNE T0355 112 :PIPAFAIAKAGGAKFIRVN 1nsj 65 :PEKILDVASYVQLNAVQLH T0355 140 :EGFMEGRAAEAM 1nsj 84 :GEEPIELCRKIA T0355 160 :EHIKVFADSHVK 1nsj 96 :ERILVIKAVGVS T0355 182 :SIDELTRDLAFFDADGVIAT 1nsj 108 :NERDMERALNYREFPILLDT T0355 205 :TG 1nsj 135 :SG T0355 210 :SLEEIEEIGAATHLPLLV 1nsj 140 :DWSLILPYRDRFRYLVLS T0355 229 :SGVNEGNIVEILKR 1nsj 158 :GGLNPENVRSAIDV T0355 243 :TSGVIVASSLKEGG 1nsj 174 :PFAVDVSSGVEAFP T0355 260 :NPVELARVRSFVAAAR 1nsj 188 :GKKDHDSIKMFIKNAK Number of specific fragments extracted= 15 number of extra gaps= 1 total=284 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1igs/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1igs expands to /projects/compbio/data/pdb/1igs.pdb.gz 1igs:Warning: there is no chain 1igs will retry with 1igsA # T0355 read from 1igs/merged-good-all-a2m # 1igs read from 1igs/merged-good-all-a2m # adding 1igs to template set # found chain 1igs in template set T0355 8 :AANAIQEIFGRSKA 1igs 33 :LNERILEFNKRNIT T0355 22 :LIGMIHCPAFPGAP 1igs 48 :IIAEYKRKSPSGLD T0355 38 :RNASM 1igs 62 :VERDP T0355 50 :MRDAERLIE 1igs 67 :IEYSKFMER T0355 60 :GMHGLIVE 1igs 76 :YAVGLSIL T0355 74 :FSKPDDIGP 1igs 84 :TEEKYFNGS T0355 102 :PVGINVLANAPIPAFAIA 1igs 93 :YETLRKIASSVSIPILMK T0355 125 :KFIRVNQWANA 1igs 111 :DFIVKESQIDD T0355 137 :VANEGFMEGRAAEAMRYR 1igs 122 :AYNLGADTVLLIVKILTE T0355 155 :SLLRAEHIKVFADSH 1igs 147 :EYARSYGMEPLIEIN T0355 173 :GAHAIT 1igs 162 :DENDLD T0355 182 :SIDEL 1igs 168 :IALRI T0355 189 :DLAFFDADG 1igs 173 :GARFIGINS T0355 202 :GQRTGNSASLEEIEEIGAATH 1igs 182 :RDLETLEINKENQRKLISMIP T0355 223 :LPLLVGSGV 1igs 205 :VVKVAESGI T0355 232 :NEGNIVEILKR 1igs 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVWWNP 1igs 227 :VNAFLIGSSLMRNPEKIKE T0355 270 :F 1igs 246 :F Number of specific fragments extracted= 18 number of extra gaps= 0 total=302 Number of alignments=19 # 1igs read from 1igs/merged-good-all-a2m # found chain 1igs in template set T0355 6 :DNAANAIQEIFGRSKALIGMIHCPAFPGA 1igs 31 :ISLNERILEFNKRNITAIIAEYKRKSPSG T0355 36 :RYRNAS 1igs 60 :LDVERD T0355 49 :CMRDAERLIEG 1igs 66 :PIEYSKFMERY T0355 61 :MHGLIVE 1igs 77 :AVGLSIL T0355 74 :FSKPDDIGP 1igs 84 :TEEKYFNGS T0355 102 :PVGINVLANAPIPAFAIAKAG 1igs 93 :YETLRKIASSVSIPILMKDFI T0355 127 :IR 1igs 114 :VK T0355 130 :NQWANA 1igs 116 :ESQIDD T0355 137 :VANEGFMEGRA 1igs 122 :AYNLGADTVLL T0355 148 :AEAM 1igs 134 :VKIL T0355 152 :RYRSLLRAEHIKVFADSHVKHG 1igs 140 :RELESLLEYARSYGMEPLIEIN T0355 179 :ADRSIDELTR 1igs 162 :DENDLDIALR T0355 193 :FDADGVIATG 1igs 172 :IGARFIGINS T0355 203 :QRTGNSASLEEIEEIGAAT 1igs 183 :DLETLEINKENQRKLISMI T0355 222 :HLPLLVGSGV 1igs 204 :NVVKVAESGI T0355 232 :NEGNIVEILKR 1igs 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVWW 1igs 227 :VNAFLIGSSLMRNPEKI T0355 268 :RSF 1igs 244 :KEF Number of specific fragments extracted= 18 number of extra gaps= 0 total=320 Number of alignments=20 # 1igs read from 1igs/merged-good-all-a2m # found chain 1igs in template set T0355 7 :NAANAIQEIFGRSKALIGMIHCPAFPGAPRYRN 1igs 32 :SLNERILEFNKRNITAIIAEYKRKSPSGLDVER T0355 41 :S 1igs 65 :D T0355 49 :CMRDAERLIEG 1igs 66 :PIEYSKFMERY T0355 61 :MHGLIVENHG 1igs 77 :AVGLSILTEE T0355 76 :KPDDIGPETSA 1igs 87 :KYFNGSYETLR T0355 94 :RIVRTAGVPVGINVLANA 1igs 98 :KIASSVSIPILMKDFIVK T0355 113 :IPAFAIAKAGGAKFIRVNQ 1igs 116 :ESQIDDAYNLGADTVLLIV T0355 140 :EGFMEGRAAEAMRYRSLLRAEH 1igs 135 :KILTERELESLLEYARSYGMEP T0355 165 :FADSHV 1igs 157 :LIEIND T0355 184 :DELTRDLAFFDADGVIATG 1igs 163 :ENDLDIALRIGARFIGINS T0355 203 :QRTGNSASLEEIEEIGA 1igs 183 :DLETLEINKENQRKLIS T0355 220 :ATHLPLLVGSGV 1igs 202 :PSNVVKVAESGI T0355 232 :NEGNIVEILKR 1igs 215 :ERNEIEELRKL T0355 243 :TSGVIVASSL 1igs 227 :VNAFLIGSSL T0355 263 :ELARVRSFV 1igs 239 :NPEKIKEFI Number of specific fragments extracted= 15 number of extra gaps= 0 total=335 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f6uA expands to /projects/compbio/data/pdb/2f6u.pdb.gz 2f6uA:Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 978, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 980, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 982, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 984, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1393, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1395, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1529, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1531, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1891, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1897, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1899, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1901, because occupancy 0.500 <= existing 0.500 in 2f6uA Skipped atom 1903, because occupancy 0.500 <= existing 0.500 in 2f6uA # T0355 read from 2f6uA/merged-good-all-a2m # 2f6uA read from 2f6uA/merged-good-all-a2m # adding 2f6uA to template set # found chain 2f6uA in template set T0355 30 :AFPGAPRYRNASM 2f6uA 1002 :RWRKWRHITKLDP T0355 43 :D 2f6uA 1020 :D T0355 51 :RDAERLIEGGMHGLIVE 2f6uA 1021 :EIIKAVADSGTDAVMIS T0355 75 :SKPDDIGPETSAF 2f6uA 1038 :GTQNVTYEKARTL T0355 105 :INVLANA 2f6uA 1051 :IEKVSQY T0355 113 :IPAFAIAKAGGAKF 2f6uA 1058 :GLPIVVEPSDPSNV T0355 127 :I 2f6uA 1073 :Y T0355 141 :GFMEGRAAEAMRYR 2f6uA 1074 :DVDYLFVPTVLNSA T0355 155 :SLLRAEHIKVFADS 2f6uA 1112 :EIIESEFIQIEGYI T0355 169 :HVKHGAH 2f6uA 1140 :LCNIDKE T0355 182 :SIDELTR 2f6uA 1147 :LAASYAL T0355 189 :DLAFFDADGV 2f6uA 1160 :NLPIIYIEYS T0355 206 :GNSASLEEIEEIGAATH 2f6uA 1170 :GTYGNPELVAEVKKVLD T0355 223 :LPLLVGSGV 2f6uA 1188 :ARLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGG 2f6uA 1198 :SREKAREMLRYADTIIVGNVIYEKG T0355 264 :LAR 2f6uA 1223 :IDA Number of specific fragments extracted= 16 number of extra gaps= 0 total=351 Number of alignments=22 # 2f6uA read from 2f6uA/merged-good-all-a2m # found chain 2f6uA in template set Warning: unaligning (T0355)P29 because first residue in template chain is (2f6uA)M1001 T0355 30 :AFPGAPRYRNASMD 2f6uA 1002 :RWRKWRHITKLDPD T0355 51 :RDAERLIEGGMHGLIVENHGDVP 2f6uA 1021 :EIIKAVADSGTDAVMISGTQNVT T0355 81 :GPETSAFMSVVTDRIVRTAGVPV 2f6uA 1044 :YEKARTLIEKVSQYGLPIVVEPS T0355 123 :GAK 2f6uA 1070 :NVV T0355 127 :IR 2f6uA 1073 :YD T0355 142 :FMEGRAAEAM 2f6uA 1075 :VDYLFVPTVL T0355 152 :RYRSLLRAEHIKVFADS 2f6uA 1090 :DWITGKHAQWVRMHYEN T0355 169 :HVKHGA 2f6uA 1124 :YIVLNP T0355 177 :IT 2f6uA 1130 :DS T0355 179 :ADRSIDELTRDLAFFDADGVIAT 2f6uA 1145 :KELAASYALVGEKLFNLPIIYIE T0355 204 :RTGNSASLEEIEEIGAAT 2f6uA 1168 :YSGTYGNPELVAEVKKVL T0355 222 :HLPLLVGSGV 2f6uA 1187 :KARLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGG 2f6uA 1198 :SREKAREMLRYADTIIVGNVIYEKG T0355 264 :LARV 2f6uA 1223 :IDAF Number of specific fragments extracted= 14 number of extra gaps= 0 total=365 Number of alignments=23 # 2f6uA read from 2f6uA/merged-good-all-a2m # found chain 2f6uA in template set T0355 24 :GMIHCPA 2f6uA 1008 :HITKLDP T0355 33 :G 2f6uA 1015 :D T0355 38 :RNASMD 2f6uA 1016 :RTNTDE T0355 45 :IY 2f6uA 1022 :II T0355 54 :ERLIEGGMHGLIVENH 2f6uA 1024 :KAVADSGTDAVMISGT T0355 78 :DDIGPETSA 2f6uA 1040 :QNVTYEKAR T0355 90 :VVTDRIV 2f6uA 1049 :TLIEKVS T0355 98 :TAGVPVGIN 2f6uA 1056 :QYGLPIVVE T0355 122 :GGAKFIRVNQWAN 2f6uA 1073 :YDVDYLFVPTVLN T0355 137 :VANEGFMEGRAAEAMR 2f6uA 1086 :SADGDWITGKHAQWVR T0355 153 :YRSLLRAEHIKVFADSHVKHGA 2f6uA 1110 :FTEIIESEFIQIEGYIVLNPDS T0355 175 :HAITADRSIDELTRDLAF 2f6uA 1137 :TKALCNIDKELAASYALV T0355 193 :FDADGVIAT 2f6uA 1159 :FNLPIIYIE T0355 204 :RTGNSASLEEIEEIGA 2f6uA 1168 :YSGTYGNPELVAEVKK T0355 220 :ATHLPLLVGSGV 2f6uA 1185 :LDKARLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVAS 2f6uA 1198 :SREKAREMLRYADTIIVGN Number of specific fragments extracted= 16 number of extra gaps= 0 total=381 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rpxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rpxA expands to /projects/compbio/data/pdb/1rpx.pdb.gz 1rpxA:# T0355 read from 1rpxA/merged-good-all-a2m # 1rpxA read from 1rpxA/merged-good-all-a2m # adding 1rpxA to template set # found chain 1rpxA in template set T0355 2 :QTIS 1rpxA 4 :DKFS T0355 28 :CPAFPGAPRYRNASMD 1rpxA 8 :KSDIIVSPSILSANFS T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 1rpxA 24 :KLGEQVKAIEQAGCDWIHVDVMDGR T0355 74 :FSKPDDIGPE 1rpxA 49 :FVPNITIGPL T0355 104 :GINVLANAPIPAFAIAKAG 1rpxA 59 :VVDSLRPITDLPLDVHLMI T0355 127 :IRVNQWANA 1rpxA 78 :VEPDQRVPD T0355 137 :VANEGFMEGRAA 1rpxA 87 :FIKAGADIVSVH T0355 149 :EAMRYRSLLRAEHIKVFADSHVKHGAHAIT 1rpxA 106 :HLHRTINQIKSLGAKAGVVLNPGTPLTAIE T0355 182 :SIDELTRDLAFFDADGVI 1rpxA 136 :YVLDAVDLVLIMSVNPGF T0355 202 :GQRTGNSASLEEIEEIGAATH 1rpxA 154 :GGQSFIESQVKKISDLRKICA T0355 223 :LPLLVGSGVNEGNIVEILKR 1rpxA 180 :PWIEVDGGVGPKNAYKVIEA T0355 243 :TSGVIVASSLKEGGV 1rpxA 201 :ANALVAGSAVFGAPD T0355 263 :ELARVRSFV 1rpxA 216 :YAEAIKGIK Number of specific fragments extracted= 13 number of extra gaps= 0 total=394 Number of alignments=25 # 1rpxA read from 1rpxA/merged-good-all-a2m # found chain 1rpxA in template set T0355 16 :FGRSKALIGM 1rpxA 6 :FSKSDIIVSP T0355 36 :RYRNASMDA 1rpxA 16 :SILSANFSK T0355 49 :CMRDAERLIEGGMHGLIVENHGDV 1rpxA 25 :LGEQVKAIEQAGCDWIHVDVMDGR T0355 74 :FSKPDDIGP 1rpxA 49 :FVPNITIGP T0355 103 :VGINVLANAPIPAFAIAKAGG 1rpxA 58 :LVVDSLRPITDLPLDVHLMIV T0355 128 :RVNQWANA 1rpxA 79 :EPDQRVPD T0355 137 :VANEGFMEGRAA 1rpxA 87 :FIKAGADIVSVH T0355 149 :EAMRYRSLLRAEHIKVFADSHVKHGA 1rpxA 102 :SSTIHLHRTINQIKSLGAKAGVVLNP T0355 177 :ITADRSIDELTRDLAFFDA 1rpxA 128 :GTPLTAIEYVLDAVDLVLI T0355 196 :DGVIATGQRTGNSASLEEIEEIGAAT 1rpxA 148 :SVNPGFGGQSFIESQVKKISDLRKIC T0355 222 :HLPLLVGSGVNEGNIVEILKR 1rpxA 179 :NPWIEVDGGVGPKNAYKVIEA T0355 243 :TSGVIVASSLKEGGV 1rpxA 201 :ANALVAGSAVFGAPD T0355 263 :ELARVR 1rpxA 216 :YAEAIK T0355 273 :AAR 1rpxA 222 :GIK Number of specific fragments extracted= 14 number of extra gaps= 0 total=408 Number of alignments=26 # 1rpxA read from 1rpxA/merged-good-all-a2m # found chain 1rpxA in template set T0355 16 :FGRSKALIGMIHCPA 1rpxA 6 :FSKSDIIVSPSILSA T0355 35 :P 1rpxA 21 :N T0355 37 :YRN 1rpxA 22 :FSK T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 1rpxA 25 :LGEQVKAIEQAGCDWIHVDVMDGRFVPNI T0355 79 :DIGPET 1rpxA 54 :TIGPLV T0355 92 :TDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKFIRVNQ 1rpxA 60 :VDSLRPITDLPLDVHLMIVEPDQRVPDFIKAGADIVSVHC T0355 139 :NEGFM 1rpxA 100 :EQSST T0355 145 :GRAAEAMRYRSLLRA 1rpxA 105 :IHLHRTINQIKSLGA T0355 163 :KVFADSHVKHGAHAITADRS 1rpxA 120 :KAGVVLNPGTPLTAIEYVLD T0355 194 :DADGVIATGQRTGNSAS 1rpxA 140 :AVDLVLIMSVNPGFGGQ T0355 211 :LEEIEEIGA 1rpxA 163 :VKKISDLRK T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1rpxA 177 :GLNPWIEVDGGVGPKNAYKVIEA T0355 243 :TSGVIVASSLKEGGV 1rpxA 201 :ANALVAGSAVFGAPD T0355 274 :ARPGLEALEHHHHH 1rpxA 216 :YAEAIKGIKTSKRP 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 2tpsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 2tpsA/merged-good-all-a2m # 2tpsA read from 2tpsA/merged-good-all-a2m # found chain 2tpsA in training set Warning: unaligning (T0355)P77 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2tpsA)A65 Warning: unaligning (T0355)D78 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2tpsA)A65 Warning: unaligning (T0355)Q131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2tpsA)D94 Warning: unaligning (T0355)W132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2tpsA)D94 Warning: unaligning (T0355)G206 because of BadResidue code BAD_PEPTIDE in next template residue (2tpsA)T162 Warning: unaligning (T0355)N207 because of BadResidue code BAD_PEPTIDE at template residue (2tpsA)T162 T0355 2 :QTISDN 2tpsA 11 :GIRMTR T0355 8 :AANAIQEIFG 2tpsA 18 :SREMMKELLS T0355 34 :APRY 2tpsA 28 :VYFI T0355 38 :RNASM 2tpsA 37 :TKADP T0355 50 :MRDAERLIEGGMHGLIVENHGD 2tpsA 42 :VTVVQKALKGGATLYQFREKGG T0355 79 :DIGPETSAFMSVVTDR 2tpsA 66 :LTGEARIKFAEKAQAA T0355 119 :AKAGGAKFI 2tpsA 82 :CREAGVPFI T0355 129 :VN 2tpsA 91 :VN T0355 133 :AN 2tpsA 95 :VE T0355 136 :YVANEGFMEGRAAEAMRYRSLLRA 2tpsA 97 :LALNLKADGIHIGQEDANAKEVRA T0355 160 :EHIKVFADS 2tpsA 123 :GDMILGVSA T0355 172 :HGAHAIT 2tpsA 132 :HTMSEVK T0355 182 :SIDEL 2tpsA 139 :QAEED T0355 189 :DLAFFDADGVIATGQRT 2tpsA 144 :GADYVGLGPIYPTETKK T0355 208 :SA 2tpsA 163 :RA T0355 210 :SLEEIEEIGAA 2tpsA 167 :GVSLIEAVRRQ T0355 221 :THLPLLVGSGVNEGNIVEILKR 2tpsA 179 :ISIPIVGIGGITIDNAAPVIQA T0355 243 :TSGVIVASSLKEGGV 2tpsA 202 :ADGVSMISAISQAED T0355 263 :ELARVRSFVAAARPGLEA 2tpsA 217 :PESAARKFREEIQTYKTG Number of specific fragments extracted= 19 number of extra gaps= 3 total=441 Number of alignments=28 # 2tpsA read from 2tpsA/merged-good-all-a2m # found chain 2tpsA in training set Warning: unaligning (T0355)D78 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2tpsA)A65 Warning: unaligning (T0355)D79 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2tpsA)A65 Warning: unaligning (T0355)I127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2tpsA)D94 Warning: unaligning (T0355)R128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2tpsA)D94 Warning: unaligning (T0355)G206 because of BadResidue code BAD_PEPTIDE in next template residue (2tpsA)T162 Warning: unaligning (T0355)N207 because of BadResidue code BAD_PEPTIDE at template residue (2tpsA)T162 T0355 3 :TISDN 2tpsA 12 :IRMTR T0355 8 :AANAIQEIFG 2tpsA 18 :SREMMKELLS T0355 23 :IGMIHCPAFP 2tpsA 28 :VYFIMGSNNT T0355 39 :NAS 2tpsA 38 :KAD T0355 49 :CMRDAERLIEGGMHGLIVE 2tpsA 41 :PVTVVQKALKGGATLYQFR T0355 74 :FSKP 2tpsA 60 :EKGG T0355 80 :I 2tpsA 66 :L T0355 81 :GPETSAFMSVVTDR 2tpsA 68 :GEARIKFAEKAQAA T0355 105 :INVL 2tpsA 82 :CREA T0355 113 :IPAFAI 2tpsA 86 :GVPFIV T0355 123 :G 2tpsA 92 :N T0355 129 :VNQ 2tpsA 95 :VEL T0355 137 :VANEGFMEGRAAEAM 2tpsA 98 :ALNLKADGIHIGQED T0355 152 :R 2tpsA 114 :N T0355 154 :RSLLRAEH 2tpsA 115 :AKEVRAAI T0355 166 :ADSHVKHGA 2tpsA 123 :GDMILGVSA T0355 178 :TADRSIDELTR 2tpsA 132 :HTMSEVKQAEE T0355 193 :FDADGVIATG 2tpsA 143 :DGADYVGLGP T0355 203 :QRT 2tpsA 158 :TKK T0355 208 :SA 2tpsA 163 :RA T0355 210 :SLEEIEEIGAAT 2tpsA 167 :GVSLIEAVRRQG T0355 222 :HLPLLVGSGVNEGNIVEILKR 2tpsA 180 :SIPIVGIGGITIDNAAPVIQA T0355 243 :TSGVIVASSLKEG 2tpsA 202 :ADGVSMISAISQA T0355 261 :PVELARVRSFVAAARPGLEA 2tpsA 215 :EDPESAARKFREEIQTYKTG Number of specific fragments extracted= 24 number of extra gaps= 3 total=465 Number of alignments=29 # 2tpsA read from 2tpsA/merged-good-all-a2m # found chain 2tpsA in training set Warning: unaligning (T0355)D78 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2tpsA)A65 Warning: unaligning (T0355)D79 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2tpsA)A65 Warning: unaligning (T0355)N110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2tpsA)D94 Warning: unaligning (T0355)A111 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2tpsA)D94 Warning: unaligning (T0355)R204 because of BadResidue code BAD_PEPTIDE in next template residue (2tpsA)T162 Warning: unaligning (T0355)T205 because of BadResidue code BAD_PEPTIDE at template residue (2tpsA)T162 T0355 8 :AANAIQEIFG 2tpsA 18 :SREMMKELLS T0355 22 :LIGMI 2tpsA 28 :VYFIM T0355 34 :APRYRNASM 2tpsA 33 :GSNNTKADP T0355 50 :MRDAERLIEGGMHGLIVENHGD 2tpsA 42 :VTVVQKALKGGATLYQFREKGG T0355 80 :IGPETSAFMS 2tpsA 66 :LTGEARIKFA T0355 90 :VVTDRIV 2tpsA 77 :KAQAACR T0355 98 :TAGVPVGIN 2tpsA 84 :EAGVPFIVN T0355 112 :PI 2tpsA 95 :VE T0355 118 :IAKAGGAKFIRVN 2tpsA 97 :LALNLKADGIHIG T0355 142 :FMEGRAAEA 2tpsA 110 :QEDANAKEV T0355 154 :RSLLR 2tpsA 119 :RAAIG T0355 161 :HIKVFADSHV 2tpsA 124 :DMILGVSAHT T0355 184 :DELTRDLAFFDADGVIA 2tpsA 134 :MSEVKQAEEDGADYVGL T0355 201 :TGQ 2tpsA 158 :TKK T0355 206 :GNSASLEEIEEIGA 2tpsA 163 :RAVQGVSLIEAVRR T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 2tpsA 178 :GISIPIVGIGGITIDNAAPVIQA T0355 243 :TSGVIVASSLKEGGV 2tpsA 202 :ADGVSMISAISQAED T0355 264 :LARVRSFVAAARPGLEA 2tpsA 218 :ESAARKFREEIQTYKTG Number of specific fragments extracted= 18 number of extra gaps= 3 total=483 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w8sA expands to /projects/compbio/data/pdb/1w8s.pdb.gz 1w8sA:Skipped atom 267, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 269, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 271, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 273, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 790, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 792, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1672, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1674, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1676, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1678, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1680, because occupancy 0.350 <= existing 0.650 in 1w8sA # T0355 read from 1w8sA/merged-good-all-a2m # 1w8sA read from 1w8sA/merged-good-all-a2m # adding 1w8sA to template set # found chain 1w8sA in template set Warning: unaligning (T0355)R275 because last residue in template chain is (1w8sA)Y252 T0355 9 :ANAIQEIFGRSKAL 1w8sA 5 :TEKFLRIFARRGKS T0355 36 :RYRNASM 1w8sA 19 :IILAYDH T0355 46 :YDACMRDAER 1w8sA 43 :PEYILRLARD T0355 59 :GGMHGLIVE 1w8sA 53 :AGFDGVVFQ T0355 102 :PVGINVLANAPIPAFAIAKAG 1w8sA 62 :RGIAEKYYDGSVPLILKLNGK T0355 124 :AKF 1w8sA 92 :SVA T0355 127 :IRVN 1w8sA 96 :CSVE T0355 136 :YVANEGFMEGRAAEAM 1w8sA 100 :EAVSLGASAVGYTIYP T0355 155 :SLLRAEHIKVFADSHVKHG 1w8sA 132 :RDAVKFDLPLVVESFPRGG T0355 175 :HAITADR 1w8sA 151 :KVVNETA T0355 182 :SIDELTR 1w8sA 160 :IVAYAAR T0355 189 :DLAFFDADGVI 1w8sA 172 :GADAMKIKYTG T0355 210 :SLEEIEEIGAATH 1w8sA 183 :DPKTFSWAVKVAG T0355 223 :LPLLVGSG 1w8sA 197 :VPVLMSGG T0355 231 :V 1w8sA 207 :T T0355 232 :NEG 1w8sA 209 :TEE T0355 235 :NIVEILKR 1w8sA 216 :QVEGVLEA T0355 243 :TSGVIVASSLKEGGV 1w8sA 225 :ALGIAVGRNVWQRRD T0355 263 :ELARVRSFVAAA 1w8sA 240 :ALKFARALAELV Number of specific fragments extracted= 19 number of extra gaps= 0 total=502 Number of alignments=31 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1w8sA)N3 Warning: unaligning (T0355)R275 because last residue in template chain is (1w8sA)Y252 T0355 8 :AANAIQEIF 1w8sA 4 :LTEKFLRIF T0355 17 :GRSKALIGMIH 1w8sA 14 :RRGKSIILAYD T0355 29 :PAFPG 1w8sA 30 :GPADF T0355 39 :NASMD 1w8sA 35 :MDNPD T0355 44 :AIYDACMRDAE 1w8sA 41 :ADPEYILRLAR T0355 58 :EGGMHGLIVE 1w8sA 52 :DAGFDGVVFQ T0355 102 :PVGINVLANAPIPAFAIAKA 1w8sA 62 :RGIAEKYYDGSVPLILKLNG T0355 126 :F 1w8sA 94 :A T0355 127 :IRVNQ 1w8sA 96 :CSVEE T0355 137 :VANEGFMEGRAAEA 1w8sA 101 :AVSLGASAVGYTIY T0355 151 :M 1w8sA 123 :M T0355 152 :RYRSLLRAEHIKVFADSHVKHGAH 1w8sA 125 :EELARIKRDAVKFDLPLVVESFPR T0355 178 :T 1w8sA 149 :G T0355 179 :ADRSIDELTRDLAFFDADGVIAT 1w8sA 157 :APEIVAYAARIALELGADAMKIK T0355 204 :RTG 1w8sA 180 :YTG T0355 210 :SLEEIEEIGAAT 1w8sA 183 :DPKTFSWAVKVA T0355 222 :HLPLLVGSG 1w8sA 196 :KVPVLMSGG T0355 231 :V 1w8sA 207 :T T0355 232 :NEGNIVE 1w8sA 209 :TEEDFLK T0355 239 :ILKR 1w8sA 220 :VLEA T0355 243 :TSGVIVASSLKEG 1w8sA 225 :ALGIAVGRNVWQR T0355 261 :PVELARVRSFVAAA 1w8sA 238 :RDALKFARALAELV Number of specific fragments extracted= 22 number of extra gaps= 0 total=524 Number of alignments=32 # 1w8sA read from 1w8sA/merged-good-all-a2m # found chain 1w8sA in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1w8sA)N3 T0355 8 :AANAIQEIF 1w8sA 4 :LTEKFLRIF T0355 17 :GRSKALIGMIH 1w8sA 14 :RRGKSIILAYD T0355 29 :PAFPGAPRYR 1w8sA 32 :ADFMDNPDSA T0355 41 :SMDAIYDACMR 1w8sA 42 :DPEYILRLARD T0355 59 :GGMHGLIVE 1w8sA 53 :AGFDGVVFQ T0355 92 :TDRIVRTA 1w8sA 62 :RGIAEKYY T0355 100 :GVPVGINV 1w8sA 72 :SVPLILKL T0355 109 :ANAPIP 1w8sA 95 :NCSVEE T0355 119 :AKAGGAKFIRVNQWAN 1w8sA 101 :AVSLGASAVGYTIYPG T0355 140 :EGFMEGRAAEAMRYRSLLRAEHIKVFADSHVKHGAHAITADRSI 1w8sA 117 :SGFEWKMFEELARIKRDAVKFDLPLVVESFPRGGKVVNETAPEI T0355 184 :DELTRDLAFFDADGVIATG 1w8sA 162 :AYAARIALELGADAMKIKY T0355 208 :SASLEEIEEIGA 1w8sA 181 :TGDPKTFSWAVK T0355 220 :ATHLPLLVGSG 1w8sA 194 :AGKVPVLMSGG T0355 232 :NEGNIVEILKR 1w8sA 209 :TEEDFLKQVEG T0355 243 :TSGVIVASSL 1w8sA 225 :ALGIAVGRNV T0355 253 :KEG 1w8sA 237 :RRD T0355 264 :LARVRSFVAAA 1w8sA 241 :LKFARALAELV Number of specific fragments extracted= 17 number of extra gaps= 0 total=541 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1gteA/merged-good-all-a2m # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0355)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0355)A148 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0355 6 :DNAANAIQEIFG 1gteA 615 :EKTAAYWCQSVT T0355 18 :R 1gteA 631 :D T0355 28 :CPAF 1gteA 632 :FPDN T0355 33 :GAPRYRNASMD 1gteA 636 :IVIASIMCSYN T0355 46 :YDACMRDAERLIEGGMHGLIVE 1gteA 647 :KNDWMELSRKAEASGADALELN T0355 70 :GDVPF 1gteA 669 :LSCPH T0355 75 :SKPDDIGPETSAF 1gteA 682 :LACGQDPELVRNI T0355 105 :INVLANAPIPAFAIAKAGGAK 1gteA 695 :CRWVRQAVQIPFFAKLTPNVT T0355 128 :RVNQWAN 1gteA 716 :DIVSIAR T0355 136 :YVANEGFMEGR 1gteA 723 :AAKEGGADGVT T0355 149 :EAM 1gteA 736 :NTV T0355 164 :VFADSHVKHGAHAITADRSI 1gteA 741 :LMGLKADGTPWPAVGAGKRT T0355 196 :DGVIATGQR 1gteA 761 :TYGGVSGTA T0355 208 :SASLEEIEEIGAATH 1gteA 772 :PIALRAVTTIARALP T0355 223 :LPLLVGSGV 1gteA 788 :FPILATGGI T0355 232 :NEGNIVEILKR 1gteA 798 :SAESGLQFLHS T0355 243 :TSGVIVASSLK 1gteA 810 :ASVLQVCSAVQ Number of specific fragments extracted= 17 number of extra gaps= 1 total=558 Number of alignments=34 # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0355)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0355)A148 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0355 6 :DNAANAIQEIFG 1gteA 619 :AYWCQSVTELKA T0355 18 :RSKALIGMIHCP 1gteA 633 :PDNIVIASIMCS T0355 40 :AS 1gteA 645 :YN T0355 46 :YDACMRDAERLIEGGMHGLIVE 1gteA 647 :KNDWMELSRKAEASGADALELN T0355 70 :GDVP 1gteA 669 :LSCP T0355 75 :SKPDDIGPETSAF 1gteA 682 :LACGQDPELVRNI T0355 105 :INVLANAPIPAFAIAKAGGAK 1gteA 695 :CRWVRQAVQIPFFAKLTPNVT T0355 128 :RVNQWANA 1gteA 716 :DIVSIARA T0355 137 :VANEGFMEGR 1gteA 724 :AKEGGADGVT T0355 149 :EAM 1gteA 736 :NTV T0355 167 :DSHVKHGAHAIT 1gteA 740 :GLMGLKADGTPW T0355 179 :AD 1gteA 755 :GA T0355 192 :FFDADGVIATGQRTG 1gteA 757 :GKRTTYGGVSGTAIR T0355 208 :SASLEEIEEIGAAT 1gteA 772 :PIALRAVTTIARAL T0355 222 :HLPLLVGSGV 1gteA 787 :GFPILATGGI T0355 232 :NEGNIVEILKR 1gteA 798 :SAESGLQFLHS T0355 243 :TSGVIVASSLKE 1gteA 810 :ASVLQVCSAVQN Number of specific fragments extracted= 17 number of extra gaps= 1 total=575 Number of alignments=35 # 1gteA read from 1gteA/merged-good-all-a2m # found chain 1gteA in training set Warning: unaligning (T0355)P73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gteA)M680 Warning: unaligning (T0355)F74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gteA)M680 Warning: unaligning (T0355)D167 because of BadResidue code BAD_PEPTIDE in next template residue (1gteA)T735 Warning: unaligning (T0355)S168 because of BadResidue code BAD_PEPTIDE at template residue (1gteA)T735 T0355 6 :DNAANAIQEIFG 1gteA 619 :AYWCQSVTELKA T0355 18 :RSKALIGMIHCP 1gteA 633 :PDNIVIASIMCS T0355 40 :ASMDAIY 1gteA 645 :YNKNDWM T0355 51 :RDAERLIEGGMHGLIVENHGDV 1gteA 652 :ELSRKAEASGADALELNLSCPH T0355 75 :S 1gteA 681 :G T0355 81 :GPETSA 1gteA 687 :DPELVR T0355 90 :VVTDRIVRTAGVPVGINVLANA 1gteA 693 :NICRWVRQAVQIPFFAKLTPNV T0355 145 :GRAAEAMRYRSLLRA 1gteA 715 :TDIVSIARAAKEGGA T0355 163 :KVFA 1gteA 730 :DGVT T0355 169 :HVKHGAHAITADRSI 1gteA 736 :NTVSGLMGLKADGTP T0355 202 :GQRTGNSAS 1gteA 753 :AVGAGKRTT T0355 211 :LEEIEEIGA 1gteA 771 :RPIALRAVT T0355 220 :ATHLPLLVGSGV 1gteA 785 :LPGFPILATGGI T0355 234 :GNIVEILKR 1gteA 800 :ESGLQFLHS T0355 243 :TSGVIVAS 1gteA 810 :ASVLQVCS Number of specific fragments extracted= 15 number of extra gaps= 2 total=590 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i4nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i4nA expands to /projects/compbio/data/pdb/1i4n.pdb.gz 1i4nA:# T0355 read from 1i4nA/merged-good-all-a2m # 1i4nA read from 1i4nA/merged-good-all-a2m # adding 1i4nA to template set # found chain 1i4nA in template set T0355 1 :MQTISDNAA 1i4nA 15 :ILEIDGENL T0355 10 :NAIQEIFGRSKA 1i4nA 30 :HRFLEVLSGKER T0355 22 :LIGMIHCPAFPGAPRYRNASMDAIYDACMRD 1i4nA 44 :IIAEFKKASPSAGDINADASLEDFIRMYDEL T0355 61 :MHGLIVENHGDV 1i4nA 75 :ADAISILTEKHY T0355 74 :FSKP 1i4nA 87 :FKGD T0355 102 :PVGINVLANAPIPAFAIAKAG 1i4nA 91 :PAFVRAARNLTCRPILAKDFY T0355 127 :IR 1i4nA 112 :ID T0355 130 :NQWAN 1i4nA 114 :TVQVK T0355 136 :YVANEGFMEGRAAEAMRYR 1i4nA 119 :LASSVGADAILIIARILTA T0355 155 :SLLRAEHIKVFADS 1i4nA 145 :EAAEELGMDSLVEV T0355 172 :HGAHAIT 1i4nA 159 :HSREDLE T0355 182 :SIDELT 1i4nA 166 :KVFSVI T0355 194 :DADGVIA 1i4nA 172 :RPKIIGI T0355 201 :TGQRTGNSASLEEIEEIGAATH 1i4nA 180 :TRDLDTFEIKKNVLWELLPLVP T0355 223 :LPLLVGSGV 1i4nA 204 :TVVVAESGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1i4nA 214 :DPRELKDLRGKVNAVLVGTSIMKAEN T0355 267 :VRSFVAAARPG 1i4nA 240 :PRRFLEEMRAW Number of specific fragments extracted= 17 number of extra gaps= 0 total=607 Number of alignments=37 # 1i4nA read from 1i4nA/merged-good-all-a2m # found chain 1i4nA in template set T0355 10 :NAIQEIFGRSKA 1i4nA 30 :HRFLEVLSGKER T0355 22 :LIGMIHCPAFPGAPRYRN 1i4nA 43 :KIIAEFKKASPSAGDINA T0355 40 :ASMDAIYDACMRD 1i4nA 62 :ASLEDFIRMYDEL T0355 61 :MHGLIVENHGDVPFSKP 1i4nA 75 :ADAISILTEKHYFKGDP T0355 103 :VGINVLANAPIPAFAI 1i4nA 92 :AFVRAARNLTCRPILA T0355 123 :GAKFIR 1i4nA 108 :KDFYID T0355 130 :NQWANA 1i4nA 114 :TVQVKL T0355 137 :VANEGFMEGRAAEAM 1i4nA 120 :ASSVGADAILIIARI T0355 152 :RYRSLLRAEHIKVFADSHVKHG 1i4nA 138 :EQIKEIYEAAEELGMDSLVEVH T0355 179 :ADRSIDELTRD 1i4nA 160 :SREDLEKVFSV T0355 193 :FDADGVIAT 1i4nA 171 :IRPKIIGIN T0355 202 :GQRTGNSASLEEIEEIGAAT 1i4nA 181 :RDLDTFEIKKNVLWELLPLV T0355 222 :HLPLLVGSGV 1i4nA 203 :DTVVVAESGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1i4nA 214 :DPRELKDLRGKVNAVLVGTSIMKAEN T0355 267 :VRSFVAAARPG 1i4nA 240 :PRRFLEEMRAW Number of specific fragments extracted= 15 number of extra gaps= 0 total=622 Number of alignments=38 # 1i4nA read from 1i4nA/merged-good-all-a2m # found chain 1i4nA in template set T0355 6 :DNAANAIQEIFGRSKALIGMIHCPAFPGAPRYR 1i4nA 27 :RRNHRFLEVLSGKERVKIIAEFKKASPSAGDIN T0355 39 :NASMDAIYDACMRD 1i4nA 61 :DASLEDFIRMYDEL T0355 61 :MHGLIVENHGDVPFSKP 1i4nA 75 :ADAISILTEKHYFKGDP T0355 90 :VVTDRIVRTAGVPVGINVLANAPIP 1i4nA 92 :AFVRAARNLTCRPILAKDFYIDTVQ T0355 116 :FAIAKAGGAKFIRVNQ 1i4nA 117 :VKLASSVGADAILIIA T0355 140 :EGFMEGRAAEAMRYRSLLR 1i4nA 133 :RILTAEQIKEIYEAAEELG T0355 162 :IKVFADSHV 1i4nA 152 :MDSLVEVHS T0355 184 :DELTRDLAFF 1i4nA 161 :REDLEKVFSV T0355 194 :DADGVIATG 1i4nA 172 :RPKIIGINT T0355 203 :QRTGNSASLEEIEEIGA 1i4nA 182 :DLDTFEIKKNVLWELLP T0355 220 :ATHLPLLVGSGV 1i4nA 201 :PDDTVVVAESGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGG 1i4nA 214 :DPRELKDLRGKVNAVLVGTSIMKAE T0355 267 :VRSFVAAARPG 1i4nA 240 :PRRFLEEMRAW Number of specific fragments extracted= 13 number of extra gaps= 0 total=635 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wq5A/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/T0355/1wq5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1wq5A/merged-good-all-a2m.gz for input Trying 1wq5A/merged-good-all-a2m Error: Couldn't open file 1wq5A/merged-good-all-a2m or 1wq5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ho1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ho1A expands to /projects/compbio/data/pdb/1ho1.pdb.gz 1ho1A:# T0355 read from 1ho1A/merged-good-all-a2m # 1ho1A read from 1ho1A/merged-good-all-a2m # adding 1ho1A to template set # found chain 1ho1A in template set Warning: unaligning (T0355)A150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ho1A)E104 T0355 41 :SMD 1ho1A 24 :YPD T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSK 1ho1A 27 :PVQAAFIAEQAGADGITVHLREDRRHIT T0355 80 :I 1ho1A 55 :D T0355 103 :VGINVLANAPIPAFAIAKAG 1ho1A 56 :RDVRILRQTLDTRMNLEMAV T0355 129 :VNQWAN 1ho1A 76 :TEEMLA T0355 136 :YVANEGFMEGRAAE 1ho1A 82 :IAVETKPHFCCLVP T0355 155 :SLLRAEHIKVFADSH 1ho1A 121 :KRLADAGIQVSLFID T0355 172 :HGAHAIT 1ho1A 136 :ADEEQIK T0355 182 :SIDEL 1ho1A 143 :AAAEV T0355 189 :DLAFFDA 1ho1A 148 :GAPFIEI T0355 200 :ATGQ 1ho1A 155 :HTGC T0355 204 :RTGNSA 1ho1A 161 :DAKTDA T0355 210 :SLEEIEEIGAA 1ho1A 171 :ELARIAKAATF T0355 221 :THLPLLVGSGVNEGNIVEILKR 1ho1A 185 :LGLKVNAGHGLTYHNVKAIAAI T0355 243 :TSGVIVASSLKEGGVWWN 1ho1A 209 :MHELNIGHAIIGRAVMTG T0355 263 :ELARVRSFVAAARPGL 1ho1A 227 :LKDAVAEMKRLMLEAR Number of specific fragments extracted= 16 number of extra gaps= 0 total=651 Number of alignments=40 # 1ho1A read from 1ho1A/merged-good-all-a2m # found chain 1ho1A in template set Warning: unaligning (T0355)A150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ho1A)E104 T0355 48 :ACMRDAERLIEGGMHGLIVENHGDVPFSKP 1ho1A 26 :DPVQAAFIAEQAGADGITVHLREDRRHITD T0355 103 :VGINVLANAPIPAFAIAKAGG 1ho1A 56 :RDVRILRQTLDTRMNLEMAVT T0355 130 :NQWANA 1ho1A 77 :EEMLAI T0355 137 :VANEGFMEGRA 1ho1A 83 :AVETKPHFCCL T0355 149 :E 1ho1A 95 :P T0355 151 :M 1ho1A 109 :V T0355 152 :RYRSLLRAEHI 1ho1A 111 :GQRDKMRDACK T0355 163 :KVFADSHVKH 1ho1A 125 :DAGIQVSLFI T0355 177 :ITADRSIDELTR 1ho1A 135 :DADEEQIKAAAE T0355 193 :FDADGVIAT 1ho1A 147 :VGAPFIEIH T0355 202 :GQRTGNSA 1ho1A 157 :GCYADAKT T0355 210 :SLEEIEEIGAAT 1ho1A 171 :ELARIAKAATFA T0355 222 :HLPLLVGSGVNEGNIVEILKR 1ho1A 186 :GLKVNAGHGLTYHNVKAIAAI T0355 243 :TSGVIVASSLKEGGV 1ho1A 209 :MHELNIGHAIIGRAV T0355 260 :NPVELARVRSFVAAARPGL 1ho1A 224 :MTGLKDAVAEMKRLMLEAR Number of specific fragments extracted= 15 number of extra gaps= 0 total=666 Number of alignments=41 # 1ho1A read from 1ho1A/merged-good-all-a2m # found chain 1ho1A in template set Warning: unaligning (T0355)W132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ho1A)E104 Warning: unaligning (T0355)E140 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ho1A)E104 T0355 20 :KALIGMI 1ho1A 3 :ELLLGVN T0355 32 :PGAP 1ho1A 20 :RGTA T0355 37 :YRN 1ho1A 24 :YPD T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 1ho1A 27 :PVQAAFIAEQAGADGITVHLREDRRHITD T0355 90 :VVTDRIVRTAGVPVGINVLA 1ho1A 56 :RDVRILRQTLDTRMNLEMAV T0355 112 :PIPAFAIAKAGGAKFIRVNQ 1ho1A 76 :TEEMLAIAVETKPHFCCLVP T0355 141 :GFME 1ho1A 105 :GGLD T0355 145 :GRAAEAMRYRSLLRA 1ho1A 114 :DKMRDACKRLADAGI T0355 161 :HIKVFADSH 1ho1A 129 :QVSLFIDAD T0355 184 :DELTRDLAFFDADGVIA 1ho1A 138 :EEQIKAAAEVGAPFIEI T0355 201 :TGQRTGNSAS 1ho1A 156 :TGCYADAKTD T0355 211 :LEEIEEIGA 1ho1A 172 :LARIAKAAT T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1ho1A 184 :SLGLKVNAGHGLTYHNVKAIAAI T0355 243 :TSGVIVASSL 1ho1A 209 :MHELNIGHAI T0355 264 :LARVRSFVAAARPGL 1ho1A 228 :KDAVAEMKRLMLEAR Number of specific fragments extracted= 15 number of extra gaps= 0 total=681 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w0mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w0mA expands to /projects/compbio/data/pdb/1w0m.pdb.gz 1w0mA:# T0355 read from 1w0mA/merged-good-all-a2m # 1w0mA read from 1w0mA/merged-good-all-a2m # adding 1w0mA to template set # found chain 1w0mA in template set Warning: unaligning (T0355)G277 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w0mA)R226 T0355 62 :HGLIVE 1w0mA 4 :PILIIN T0355 70 :GD 1w0mA 10 :FK T0355 75 :SKPDDIGPETSAFMSVV 1w0mA 12 :AYGEAAGKRAVELAKAA T0355 92 :TDR 1w0mA 32 :ARE T0355 95 :IVRTAGVPVG 1w0mA 36 :GVNIVVAPNH T0355 105 :INVLANAPIPAFAI 1w0mA 48 :LGLVSQSVDIPVYA T0355 122 :GGAKF 1w0mA 62 :QGADV T0355 127 :IR 1w0mA 68 :AG T0355 132 :WAN 1w0mA 77 :SLE T0355 136 :YVANEGFMEGRAAE 1w0mA 80 :NIKEAGGSGVILNH T0355 150 :AMRYRSLLRAEHIKVFADSH 1w0mA 103 :LARLVAKAKSLGLDVVVCAP T0355 179 :ADRSIDELTRD 1w0mA 123 :DPRTSLAAAAL T0355 194 :DADGVIATGQ 1w0mA 134 :GPHAVAVEPP T0355 204 :RTGNSA 1w0mA 147 :GTGRAV T0355 210 :SLEEIEEIGAAT 1w0mA 156 :KPEAIVETVGLV T0355 222 :HLPLLVGSGV 1w0mA 173 :EVSVITGAGI T0355 232 :NEGNIVEILKR 1w0mA 184 :SGDDVAAALRL T0355 243 :TSGVIVASSLKEGGV 1w0mA 196 :TRGVLLASAAVKAKD T0355 263 :ELARVRSFVAAARP 1w0mA 211 :PYAKIVELAKPLSE Number of specific fragments extracted= 19 number of extra gaps= 1 total=700 Number of alignments=43 # 1w0mA read from 1w0mA/merged-good-all-a2m # found chain 1w0mA in template set Warning: unaligning (T0355)G277 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w0mA)R226 T0355 62 :HGLIVE 1w0mA 4 :PILIIN T0355 70 :G 1w0mA 10 :F T0355 74 :FSKPDDIGPETSAFMSVVTDRI 1w0mA 11 :KAYGEAAGKRAVELAKAAERAA T0355 96 :VRTAGV 1w0mA 37 :VNIVVA T0355 102 :PVGINVLANAPIPAFAIAKA 1w0mA 45 :HLELGLVSQSVDIPVYAQGA T0355 123 :GAKFIRVNQ 1w0mA 72 :HTAHVSLEN T0355 137 :VANEGFMEGRA 1w0mA 81 :IKEAGGSGVIL T0355 148 :AEAM 1w0mA 96 :APLK T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1w0mA 101 :NDLARLVAKAKSLGLDVVVCAPD T0355 183 :IDELTRDLA 1w0mA 124 :PRTSLAAAA T0355 193 :FDADGVIATG 1w0mA 133 :LGPHAVAVEP T0355 203 :QRTGNSA 1w0mA 146 :IGTGRAV T0355 210 :SLEEIEEIGAAT 1w0mA 156 :KPEAIVETVGLV T0355 222 :HLPLLVGSGV 1w0mA 173 :EVSVITGAGI T0355 232 :NEGNIVEILKR 1w0mA 184 :SGDDVAAALRL T0355 243 :TSGVIVASSLKEG 1w0mA 196 :TRGVLLASAAVKA T0355 261 :PVELARVRSFVAAARP 1w0mA 209 :KDPYAKIVELAKPLSE Number of specific fragments extracted= 17 number of extra gaps= 1 total=717 Number of alignments=44 # 1w0mA read from 1w0mA/merged-good-all-a2m # found chain 1w0mA in template set T0355 19 :SKALIGMI 1w0mA 2 :RLPILIIN T0355 31 :FPGAPRYRNASMDAIYDACMRDAERL 1w0mA 10 :FKAYGEAAGKRAVELAKAAERAAREL T0355 60 :GMHGLIVENHGD 1w0mA 36 :GVNIVVAPNHLE T0355 92 :TDRIVRTAGVPVGIN 1w0mA 48 :LGLVSQSVDIPVYAQ T0355 116 :FAIAKAGGAKFIRV 1w0mA 78 :LENIKEAGGSGVIL T0355 134 :N 1w0mA 92 :N T0355 137 :VANEGFMEGRAAEAMRYRSLLR 1w0mA 93 :HSEAPLKLNDLARLVAKAKSLG T0355 162 :IKVFADSHVK 1w0mA 115 :LDVVVCAPDP T0355 184 :DELT 1w0mA 125 :RTSL T0355 189 :DLAFFDADGVIATGQRTGNSAS 1w0mA 129 :AAAALGPHAVAVEPPELIGTGR T0355 211 :LEEIEEIGA 1w0mA 157 :PEAIVETVG T0355 220 :ATHLPLLVGSGV 1w0mA 171 :FPEVSVITGAGI T0355 232 :NEGNIVEILKR 1w0mA 184 :SGDDVAAALRL T0355 243 :TSGVIVASSLKEGG 1w0mA 196 :TRGVLLASAAVKAK T0355 264 :LARVRSFVAAARP 1w0mA 212 :YAKIVELAKPLSE Number of specific fragments extracted= 15 number of extra gaps= 0 total=732 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q7zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1q7zA/merged-good-all-a2m # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0355 9 :ANAIQEIFGRSKALIGMIHCPAFPGA 1q7zA 90 :VRIARRAAGEKLVFGDIGPTGELPYP T0355 37 :YRNASMDAIYDACMRDAERLIEGGMHGLIVENHGDV 1q7zA 116 :LGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDI T0355 82 :PETSAFMSVVTDR 1q7zA 152 :LELKAAVLAAREV T0355 109 :A 1q7zA 165 :S T0355 111 :APIPAFAIAKA 1q7zA 166 :RDVFLIAHMTF T0355 122 :GGAKF 1q7zA 180 :GRSLT T0355 127 :IRVNQWAN 1q7zA 186 :TDPANFAI T0355 136 :YVANEGFMEGRAAEAMRYR 1q7zA 194 :TFDELDIDALGINCSLGPE T0355 155 :SLLR 1q7zA 344 :KEAK T0355 159 :AEHIK 1q7zA 351 :EKGAE T0355 165 :FADSHVKHGAHAIT 1q7zA 356 :VLDVNFGIESQIDV T0355 182 :SIDE 1q7zA 370 :RYVE T0355 186 :LTRDLAFFDAD 1q7zA 382 :VSNVPLSLDIQ T0355 210 :SLEEIEEIGAATH 1q7zA 393 :NVDLTERALRAYP T0355 223 :LPLLVGSGVNEGNIVEILKR 1q7zA 407 :RSLFNSAKVDEEELEMKINL T0355 243 :TSGVIV 1q7zA 431 :GGTLIV T0355 255 :GGVWWNP 1q7zA 439 :MGKDVPK T0355 263 :ELARVRSFVAAARPGLEAL 1q7zA 446 :SFEERKEYFEKALKILERH Number of specific fragments extracted= 18 number of extra gaps= 0 total=750 Number of alignments=46 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0355 7 :NAANAIQEIFG 1q7zA 88 :NAVRIARRAAG T0355 19 :SKALIGMIHCPAFPGAPR 1q7zA 99 :EKLVFGDIGPTGELPYPL T0355 38 :RNASMDAIYDACMRDAERLIEGGMHGLIVENHGD 1q7zA 117 :GSTLFEEFYENFRETVEIMVEEGVDGIIFETFSD T0355 84 :TSAFMSVV 1q7zA 151 :ILELKAAV T0355 103 :VGINVLANAPIP 1q7zA 159 :LAAREVSRDVFL T0355 116 :FAIAKA 1q7zA 171 :IAHMTF T0355 122 :GGAKF 1q7zA 180 :GRSLT T0355 127 :IRVNQWANA 1q7zA 186 :TDPANFAIT T0355 137 :VANEGFMEGRAAEAM 1q7zA 195 :FDELDIDALGINCSL T0355 152 :RYRSLLRAEHIKV 1q7zA 212 :EEILPIFQELSQY T0355 166 :ADSHVKHGA 1q7zA 225 :TDKFLVVEP T0355 177 :IT 1q7zA 234 :NA T0355 179 :ADRSIDELTRDLA 1q7zA 339 :EEIVIKEAKTQVE T0355 193 :FDADGVIAT 1q7zA 352 :KGAEVLDVN T0355 202 :GQRTGN 1q7zA 362 :GIESQI T0355 210 :SLEEIEEIGAAT 1q7zA 368 :DVRYVEKIVQTL T0355 222 :HLPLLVG 1q7zA 384 :NVPLSLD T0355 229 :SGVNEGNIVEILKR 1q7zA 413 :AKVDEEELEMKINL T0355 243 :TSGVIV 1q7zA 431 :GGTLIV T0355 256 :GVWWNP 1q7zA 440 :GKDVPK T0355 263 :ELARVRSFVAAARPGLEA 1q7zA 446 :SFEERKEYFEKALKILER Number of specific fragments extracted= 21 number of extra gaps= 0 total=771 Number of alignments=47 # 1q7zA read from 1q7zA/merged-good-all-a2m # found chain 1q7zA in training set T0355 6 :DNAANAIQEIFG 1q7zA 87 :RNAVRIARRAAG T0355 19 :SKALIGMIHCP 1q7zA 99 :EKLVFGDIGPT T0355 32 :PG 1q7zA 110 :GE T0355 34 :APRYRNASMDAIYDACMRDAERLIEGGMHGLIVENHGD 1q7zA 113 :PYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSD T0355 85 :SAFMSVVTDRIVRTAGVPVGINVLA 1q7zA 151 :ILELKAAVLAAREVSRDVFLIAHMT T0355 110 :NAPIPAFAIAKAGGAKFIRV 1q7zA 186 :TDPANFAITFDELDIDALGI T0355 131 :QWA 1q7zA 228 :FLV T0355 134 :NAYVANEGFMEGRAAEAM 1q7zA 267 :NIFGGCCGTTPEHVKLFR T0355 155 :SLLR 1q7zA 285 :KVLG T0355 159 :AEHIKVFADSHVKHGA 1q7zA 312 :FDHFVVIGERINPAGR T0355 177 :ITADR 1q7zA 337 :GNEEI T0355 183 :IDELTRDLAFFDADGVIATGQRTG 1q7zA 342 :VIKEAKTQVEKGAEVLDVNFGIES T0355 208 :SASLEEIEEIGA 1q7zA 366 :QIDVRYVEKIVQ T0355 220 :ATHLPLLVG 1q7zA 382 :VSNVPLSLD T0355 229 :SGVNEGNIVEILKR 1q7zA 413 :AKVDEEELEMKINL T0355 243 :TSGVIVASS 1q7zA 431 :GGTLIVLLM T0355 254 :EGGVWW 1q7zA 440 :GKDVPK T0355 263 :ELARVRSFVAAARPGLEALEHH 1q7zA 446 :SFEERKEYFEKALKILERHDFS Number of specific fragments extracted= 18 number of extra gaps= 0 total=789 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jvnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jvnA expands to /projects/compbio/data/pdb/1jvn.pdb.gz 1jvnA:Bad short name: CI for alphabet: pdb_atoms Bad short name: NI for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: OJ1 for alphabet: pdb_atoms Bad short name: OJ2 for alphabet: pdb_atoms Bad short name: CF for alphabet: pdb_atoms Bad short name: OF for alphabet: pdb_atoms Bad short name: NX for alphabet: pdb_atoms # T0355 read from 1jvnA/merged-good-all-a2m # 1jvnA read from 1jvnA/merged-good-all-a2m # adding 1jvnA to template set # found chain 1jvnA in template set Warning: unaligning (T0355)Y46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)D304 Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)D304 Warning: unaligning (T0355)P77 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)P306 Warning: unaligning (T0355)I127 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)I344 T0355 2 :QTISDNAANAIQEI 1jvnA 214 :PPIPNYSAEEKELL T0355 17 :GRSKA 1jvnA 228 :MNDYS T0355 22 :LIGMIHCPAFPGAP 1jvnA 243 :CLDVRTNDQGDLVV T0355 47 :DACMRDAERLIEGGMHGLIVENH 1jvnA 277 :GKPVQLAQKYYQQGADEVTFLNI T0355 78 :DDIGPET 1jvnA 307 :LKDTPML T0355 103 :VGINVLANAPIPAFAIAKAGGAKF 1jvnA 314 :EVLKQAAKTVFVPLTVGGGIKDIV T0355 128 :RVNQWAN 1jvnA 345 :PALEVAS T0355 136 :YVANEGFMEGRAAEAMRYR 1jvnA 352 :LYFRSGADKVSIGTDAVYA T0355 155 :SLLRAE 1jvnA 389 :TISKAY T0355 164 :VFADSHVK 1jvnA 399 :VVISVDPK T0355 172 :HGAHAITADR 1jvnA 411 :NSQADTKNKV T0355 183 :IDELTR 1jvnA 451 :VWELTR T0355 189 :DLAFFDADGVI 1jvnA 462 :GAGEILLNCID T0355 202 :GQRTGNSASLEEIEEIGAATHLPLLVGSGV 1jvnA 473 :KDGSNSGYDLELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1jvnA 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKE 1jvnA 517 :ADACLGAGMFHR T0355 257 :VWWN 1jvnA 529 :GEFT T0355 267 :VRSFVAAARP 1jvnA 533 :VNDVKEYLLE Number of specific fragments extracted= 18 number of extra gaps= 2 total=807 Number of alignments=49 # 1jvnA read from 1jvnA/merged-good-all-a2m # found chain 1jvnA in template set Warning: unaligning (T0355)Y46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)D304 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)D304 Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jvnA)P306 Warning: unaligning (T0355)P77 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)P306 Warning: unaligning (T0355)I127 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)I344 T0355 1 :MQTISDNAANAIQ 1jvnA 216 :IPNYSAEEKELLM T0355 14 :EIFGRSKALIGMIHCPAFPGAPRYRN 1jvnA 232 :SNYGLTRRIIACLDVRTNDQGDLVVT T0355 47 :DACMRDAERLIEGGMHGLIVENH 1jvnA 277 :GKPVQLAQKYYQQGADEVTFLNI T0355 78 :DDIGPE 1jvnA 307 :LKDTPM T0355 102 :PVGINVLANAPIPAFAIAKAGGAKF 1jvnA 313 :LEVLKQAAKTVFVPLTVGGGIKDIV T0355 128 :RVNQWANA 1jvnA 345 :PALEVASL T0355 137 :VANEGFMEGRAAEAM 1jvnA 353 :YFRSGADKVSIGTDA T0355 155 :SLLRAEHIKVFADS 1jvnA 368 :VYAAEKYYELGNRG T0355 169 :HVKHGAHAIT 1jvnA 407 :RVYVNSQADT T0355 183 :IDELTRDLAFFDADGVIAT 1jvnA 451 :VWELTRACEALGAGEILLN T0355 202 :GQRTGN 1jvnA 475 :GSNSGY T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1jvnA 481 :DLELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1jvnA 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKE 1jvnA 517 :ADACLGAGMFHR T0355 256 :GVWW 1jvnA 529 :GEFT T0355 267 :VRSFVAAARP 1jvnA 533 :VNDVKEYLLE Number of specific fragments extracted= 16 number of extra gaps= 1 total=823 Number of alignments=50 # 1jvnA read from 1jvnA/merged-good-all-a2m # found chain 1jvnA in template set Warning: unaligning (T0355)S41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1jvnA)D304 Warning: unaligning (T0355)F74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jvnA)D304 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jvnA)P306 Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jvnA)P306 T0355 1 :MQTISDNAANAI 1jvnA 216 :IPNYSAEEKELL T0355 14 :EIFGRSKALIGMIHCPAFP 1jvnA 232 :SNYGLTRRIIACLDVRTND T0355 33 :GAPRYRNA 1jvnA 252 :GDLVVTKG T0355 48 :ACMRDAERLIEGGMHGLIVENH 1jvnA 278 :KPVQLAQKYYQQGADEVTFLNI T0355 77 :PDDI 1jvnA 307 :LKDT T0355 87 :FMSVVTDRIVRTAGVPVGIN 1jvnA 311 :PMLEVLKQAAKTVFVPLTVG T0355 111 :APIPAFAIAKAGGAKFIRVN 1jvnA 345 :PALEVASLYFRSGADKVSIG T0355 145 :GRAAEAMRYRSLLR 1jvnA 365 :TDAVYAAEKYYELG T0355 164 :VFADSHVKH 1jvnA 399 :VVISVDPKR T0355 174 :AHAITADRS 1jvnA 418 :NKVFETEYP T0355 183 :IDELTRDLAFFDADGVIATGQRTGNSAS 1jvnA 451 :VWELTRACEALGAGEILLNCIDKDGSNS T0355 211 :LEEIEEIGAATHLPLLVGSGV 1jvnA 482 :LELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1jvnA 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKEGGVW 1jvnA 517 :ADACLGAGMFHRGEFT T0355 267 :VRSFVAAARP 1jvnA 533 :VNDVKEYLLE Number of specific fragments extracted= 15 number of extra gaps= 0 total=838 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tjpA/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/T0355/1tjpA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1tjpA/merged-good-all-a2m.gz for input Trying 1tjpA/merged-good-all-a2m Error: Couldn't open file 1tjpA/merged-good-all-a2m or 1tjpA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2tysA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2tysA expands to /projects/compbio/data/pdb/2tys.pdb.gz 2tysA:# T0355 read from 2tysA/merged-good-all-a2m # 2tysA read from 2tysA/merged-good-all-a2m # adding 2tysA to template set # found chain 2tysA in template set Warning: unaligning (T0355)D196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2tysA)P192 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2tysA)P192 T0355 10 :NAIQEIFGRS 2tysA 5 :ENLFAQLNDR T0355 29 :PAFPGAPRYRNASMD 2tysA 15 :REGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 2tysA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 2tysA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIRE T0355 111 :APIPAFAIAKAGGAKF 2tysA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWAN 2tysA 109 :NGIDAFYA T0355 136 :YVANEGFMEGRAAEAM 2tysA 117 :RCEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGAHAIT 2tysA 138 :PFRQAALRHNIAPIFICPPNADDDLLR T0355 182 :SIDELTRDLAF 2tysA 165 :QVASYGRGYTY T0355 194 :DA 2tysA 176 :LL T0355 211 :LE 2tysA 193 :LH T0355 213 :EIEEIGAATHLPLLVGSGV 2tysA 196 :LIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 2tysA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKEGGVWW 2tysA 228 :AAGAISGSAIVKIIEKN T0355 260 :NPVELARVRSFVAAARPGL 2tysA 248 :PKQMLAELRSFVSAMKAAS Number of specific fragments extracted= 15 number of extra gaps= 0 total=853 Number of alignments=52 # 2tysA read from 2tysA/merged-good-all-a2m # found chain 2tysA in template set Warning: unaligning (T0355)A9 because first residue in template chain is (2tysA)M1 Warning: unaligning (T0355)D196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2tysA)P192 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2tysA)P192 T0355 10 :NAIQEIF 2tysA 2 :ERYENLF T0355 17 :GRSKALIG 2tysA 14 :RREGAFVP T0355 36 :RYRNASMD 2tysA 22 :FVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 2tysA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 2tysA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIRE T0355 111 :APIPAFAIAKAGGAKF 2tysA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWANA 2tysA 109 :NGIDAFYAR T0355 137 :VANEGFMEGRAAEAM 2tysA 118 :CEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 2tysA 134 :EESAPFRQAALRHNIAPIFICPP T0355 177 :ITADRSIDELTRDLAFFDA 2tysA 157 :NADDDLLRQVASYGRGYTY T0355 211 :L 2tysA 193 :L T0355 212 :EEIEEIGAATHLPLLVGSGV 2tysA 195 :HLIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 2tysA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKE 2tysA 228 :AAGAISGSAIVK T0355 255 :GG 2tysA 244 :NL T0355 258 :WWNPVELARVRSFVAAARPGLE 2tysA 246 :ASPKQMLAELRSFVSAMKAASR Number of specific fragments extracted= 16 number of extra gaps= 0 total=869 Number of alignments=53 # 2tysA read from 2tysA/merged-good-all-a2m # found chain 2tysA in template set Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2tysA)P192 T0355 6 :DNAANAIQEIFGRSKALIGMIHCPAFP 2tysA 2 :ERYENLFAQLNDRREGAFVPFVTLGDP T0355 39 :N 2tysA 29 :G T0355 46 :YDACMRDAERLIEGGMHGLIVEN 2tysA 30 :IEQSLKIIDTLIDAGADALELGV T0355 73 :PFSKPDDIGPETSAFMS 2tysA 53 :PFSDPLADGPTIQNANL T0355 90 :VVTDRIVRTA 2tysA 83 :EMLALIREKH T0355 100 :GVPVGINVLANAPI 2tysA 94 :TIPIGLLMYANLVF T0355 114 :PAFAIAKAGGAKFIRVN 2tysA 113 :AFYARCEQVGVDSVLVA T0355 141 :GFMEGRAAEAMRYRSLLRAEHIKVF 2tysA 130 :DVPVEESAPFRQAALRHNIAPIFIC T0355 178 :TADRSIDELTRDLAFFDADGVI 2tysA 155 :PPNADDDLLRQVASYGRGYTYL T0355 211 :L 2tysA 193 :L T0355 212 :EEIEEIGAATHLPLLVGSGV 2tysA 195 :HLIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 2tysA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSL 2tysA 228 :AAGAISGSAI T0355 263 :ELA 2tysA 247 :SPK T0355 269 :SFVAAARPGLEALEHH 2tysA 250 :QMLAELRSFVSAMKAA Number of specific fragments extracted= 15 number of extra gaps= 0 total=884 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1geqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1geqA expands to /projects/compbio/data/pdb/1geq.pdb.gz 1geqA:# T0355 read from 1geqA/merged-good-all-a2m # 1geqA read from 1geqA/merged-good-all-a2m # adding 1geqA to template set # found chain 1geqA in template set Warning: unaligning (T0355)V198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1geqA)E174 Warning: unaligning (T0355)G206 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1geqA)E174 T0355 28 :CPAFPGAPRYRNASMD 1geqA 2 :FKDGSLIPYLTAGDPD T0355 46 :YDACMRDAERL 1geqA 18 :KQSTLNFLLAL T0355 61 :MHGLIVE 1geqA 32 :AGAIELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKF 1geqA 39 :IPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIY T0355 127 :IRVNQWAN 1geqA 95 :AGVRNFLA T0355 136 :YVANEGFMEGRAAEAMRYR 1geqA 103 :EAKASGVDGILVVDLPVFH T0355 155 :SLLRAEHIKVFADSHVKHGAHAIT 1geqA 127 :EIAREEGIKTVFLAAPNTPDERLK T0355 182 :SIDELTRDLAF 1geqA 151 :VIDDMTTGFVY T0355 194 :DADG 1geqA 162 :LVSL T0355 207 :NSASL 1geqA 175 :IPKTA T0355 212 :EEIEEIGAATHLPLLVGSGV 1geqA 181 :DLLRRAKRICRNKVAVGFGV T0355 232 :NEGNIVEILKR 1geqA 202 :KREHVVSLLKE T0355 243 :TSGVIVASSLKEGGVWWNPVELARVRSFVAAA 1geqA 214 :ANGVVVGSALVKIIGEKGREATEFLKKKVEEL Number of specific fragments extracted= 13 number of extra gaps= 0 total=897 Number of alignments=55 # 1geqA read from 1geqA/merged-good-all-a2m # found chain 1geqA in template set Warning: unaligning (T0355)V198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1geqA)E174 Warning: unaligning (T0355)G206 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1geqA)E174 T0355 28 :CPAFPGAPRYRNASMD 1geqA 2 :FKDGSLIPYLTAGDPD T0355 46 :YDACMRDAERLIEG 1geqA 18 :KQSTLNFLLALDEY T0355 61 :MHGLIVE 1geqA 32 :AGAIELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKF 1geqA 39 :IPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIY T0355 127 :IRVNQWANA 1geqA 95 :AGVRNFLAE T0355 137 :VANEGFMEGRAAEAM 1geqA 104 :AKASGVDGILVVDLP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1geqA 120 :FHAKEFTEIAREEGIKTVFLAAP T0355 177 :ITADRSIDELTRDLAFFDA 1geqA 143 :NTPDERLKVIDDMTTGFVY T0355 196 :DG 1geqA 164 :SL T0355 207 :NSASL 1geqA 175 :IPKTA T0355 212 :EEIEEIGAATHLPLLVGSGV 1geqA 181 :DLLRRAKRICRNKVAVGFGV T0355 232 :NEGNIVEILKR 1geqA 202 :KREHVVSLLKE T0355 243 :TSGVIVASSLKE 1geqA 214 :ANGVVVGSALVK T0355 255 :GGVWWNPVELARVRSFV 1geqA 230 :KGREATEFLKKKVEELL Number of specific fragments extracted= 14 number of extra gaps= 0 total=911 Number of alignments=56 # 1geqA read from 1geqA/merged-good-all-a2m # found chain 1geqA in template set Warning: unaligning (T0355)Q203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1geqA)E174 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1geqA)E174 T0355 6 :DNAANAIQEIFGRSKALIGMIHC 1geqA 19 :QSTLNFLLALDEYAGAIELGIPF T0355 32 :PGAPRYRN 1geqA 42 :SDPIADGK T0355 48 :ACMRDAERLIEGG 1geqA 50 :TIQESHYRALKNG T0355 80 :IGPETSA 1geqA 63 :FKLREAF T0355 90 :VVTDRIVRTAGVPVGINVLANAPIPA 1geqA 70 :WIVKEFRRHSSTPIVLMTYYNPIYRA T0355 116 :FAIAKAGGAKFIRV 1geqA 101 :LAEAKASGVDGILV T0355 140 :EGFMEGRAAEAMRYRSLLR 1geqA 115 :VDLPVFHAKEFTEIAREEG T0355 162 :IKVFADSH 1geqA 134 :IKTVFLAA T0355 179 :ADRSIDELTRDLAFFDADGVIATG 1geqA 142 :PNTPDERLKVIDDMTTGFVYLVSL T0355 211 :LEEIEEIGAATHLPLLVGSGV 1geqA 180 :YDLLRRAKRICRNKVAVGFGV T0355 232 :NEGNIVEILKR 1geqA 202 :KREHVVSLLKE T0355 243 :TSGVIVASSL 1geqA 214 :ANGVVVGSAL T0355 267 :VRSFVAA 1geqA 224 :VKIIGEK T0355 274 :ARPGLEAL 1geqA 238 :LKKKVEEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=925 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1thfD/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1thfD/merged-good-all-a2m # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0355 39 :NAS 1thfD 29 :SGD T0355 49 :CMRDAERLIEGGMH 1thfD 32 :PVELGKFYSEIGID T0355 63 :GLIVE 1thfD 47 :LVFLD T0355 70 :G 1thfD 52 :I T0355 75 :SKPDDIGPETSAF 1thfD 53 :TASVEKRKTMLEL T0355 105 :INVLANAPIPAFAIAKAGG 1thfD 66 :VEKVAEQIDIPFTVGGGIH T0355 128 :RVNQ 1thfD 85 :DFET T0355 133 :AN 1thfD 89 :AS T0355 136 :YVANEGFMEGRAAEA 1thfD 91 :ELILRGADKVSINTA T0355 152 :RYR 1thfD 106 :AVE T0355 155 :SLLRAEHIKVFADS 1thfD 115 :QIAQTFGSQAVVVA T0355 174 :AHAIT 1thfD 154 :RDWVV T0355 182 :SIDEL 1thfD 159 :EVEKR T0355 189 :DLAFFDADGVI 1thfD 164 :GAGEILLTSID T0355 202 :GQRTGNSASLEEIEEIGAATHLPLLVGSGV 1thfD 175 :RDGTKSGYDTEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1thfD 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLKEGG 1thfD 218 :ADAALAASVFHFRE T0355 259 :WN 1thfD 232 :ID T0355 267 :VRSFVAAARP 1thfD 234 :VRELKEYLKK Number of specific fragments extracted= 19 number of extra gaps= 0 total=944 Number of alignments=58 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set Warning: unaligning (T0355)G17 because first residue in template chain is (1thfD)M1 T0355 18 :RSKALIGMIHCPAFPGAPRYRN 1thfD 2 :LAKRIIACLDVKDGRVVKGSNF T0355 40 :AS 1thfD 27 :RD T0355 46 :YDACMRDAERLIEGGMHGLIV 1thfD 29 :SGDPVELGKFYSEIGIDELVF T0355 70 :GDVPFSKP 1thfD 50 :LDITASVE T0355 97 :RTAGVPVGINVLANAPIPAFAIAKAGGA 1thfD 58 :KRKTMLELVEKVAEQIDIPFTVGGGIHD T0355 130 :NQWANA 1thfD 86 :FETASE T0355 137 :VANEGFMEGRAAEAM 1thfD 92 :LILRGADKVSINTAA T0355 152 :RYRSLLRAEHIKVFADS 1thfD 108 :ENPSLITQIAQTFGSQA T0355 183 :IDELTRDLAFFDADGVIAT 1thfD 153 :LRDWVVEVEKRGAGEILLT T0355 202 :GQRTGN 1thfD 177 :GTKSGY T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1thfD 183 :DTEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1thfD 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLKEGGVW 1thfD 218 :ADAALAASVFHFREID T0355 267 :VRSFVAAARPG 1thfD 234 :VRELKEYLKKH Number of specific fragments extracted= 14 number of extra gaps= 0 total=958 Number of alignments=59 # 1thfD read from 1thfD/merged-good-all-a2m # found chain 1thfD in training set T0355 18 :RSKALIGMIHC 1thfD 2 :LAKRIIACLDV T0355 29 :PAFPGAPRYRN 1thfD 21 :SNFENLRDSGD T0355 49 :CMRDAERLIEGGMHGLIVENHG 1thfD 32 :PVELGKFYSEIGIDELVFLDIT T0355 80 :IGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAK 1thfD 54 :ASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELIL T0355 122 :GGAKFIRVNQWAN 1thfD 95 :RGADKVSINTAAV T0355 145 :GRAAEAMRYRSLLRAEHIKVFADSHVKHGAH 1thfD 108 :ENPSLITQIAQTFGSQAVVVAIDAKRVDGEF T0355 178 :TADRSIDELTRDLAFFDADGVIATGQRTGNSAS 1thfD 148 :NTGILLRDWVVEVEKRGAGEILLTSIDRDGTKS T0355 211 :LEEIEEIGAATHLPLLVGSGV 1thfD 184 :TEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1thfD 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLKEG 1thfD 218 :ADAALAASVFHFR T0355 261 :PVE 1thfD 231 :EID T0355 267 :VRSFVAAARP 1thfD 234 :VRELKEYLKK Number of specific fragments extracted= 12 number of extra gaps= 0 total=970 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tjrA/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/T0355/1tjrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1tjrA/merged-good-all-a2m.gz for input Trying 1tjrA/merged-good-all-a2m Error: Couldn't open file 1tjrA/merged-good-all-a2m or 1tjrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1beuA/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/T0355/1beuA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1beuA/merged-good-all-a2m.gz for input Trying 1beuA/merged-good-all-a2m Error: Couldn't open file 1beuA/merged-good-all-a2m or 1beuA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qopA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1qopA/merged-good-all-a2m # 1qopA read from 1qopA/merged-good-all-a2m # found chain 1qopA in training set Warning: unaligning (T0355)N207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qopA)P192 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qopA)P192 Warning: unaligning (T0355)G228 because of BadResidue code BAD_PEPTIDE in next template residue (1qopA)F212 Warning: unaligning (T0355)S229 because of BadResidue code BAD_PEPTIDE at template residue (1qopA)F212 T0355 10 :NAIQEIFGR 1qopA 5 :ENLFAQLND T0355 28 :CPAFPGAPRYRNASMD 1qopA 14 :RREGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1qopA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1qopA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIRE T0355 111 :APIPAFAIAKAGGAKF 1qopA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWAN 1qopA 109 :NGIDAFYA T0355 136 :YVANEGFMEGRAAEAMRYR 1qopA 117 :RCEQVGVDSVLVADVPVEE T0355 155 :SLLRAEHIKVFADSHVKHGAHAIT 1qopA 141 :QAALRHNIAPIFICPPNADDDLLR T0355 182 :SIDELTRDLAF 1qopA 165 :QVASYGRGYTY T0355 194 :DADGVIATGQRTG 1qopA 176 :LLSRSGVTGAENR T0355 211 :L 1qopA 193 :L T0355 212 :EEIEEIGAATHLPLLV 1qopA 195 :HLIEKLKEYHAAPALQ T0355 230 :GV 1qopA 213 :GI T0355 232 :NEGNIVEILKR 1qopA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKEGGVWW 1qopA 228 :AAGAISGSAIVKIIEKN T0355 260 :NPVELARVRSFVAAARPG 1qopA 248 :PKQMLAELRSFVSAMKAA Number of specific fragments extracted= 16 number of extra gaps= 1 total=986 Number of alignments=61 # 1qopA read from 1qopA/merged-good-all-a2m # found chain 1qopA in training set Warning: unaligning (T0355)A9 because first residue in template chain is (1qopA)M1 Warning: unaligning (T0355)N207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qopA)P192 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qopA)P192 Warning: unaligning (T0355)G228 because of BadResidue code BAD_PEPTIDE in next template residue (1qopA)F212 Warning: unaligning (T0355)S229 because of BadResidue code BAD_PEPTIDE at template residue (1qopA)F212 T0355 10 :NAIQEIFG 1qopA 2 :ERYENLFA T0355 18 :RSKALIGMIHCPAFP 1qopA 15 :REGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1qopA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1qopA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIRE T0355 111 :APIPAFAIAKAGGAKF 1qopA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWANA 1qopA 109 :NGIDAFYAR T0355 137 :VANEGFMEGRAAEAM 1qopA 118 :CEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1qopA 134 :EESAPFRQAALRHNIAPIFICPP T0355 177 :ITADRSIDELTRDLAFFDA 1qopA 157 :NADDDLLRQVASYGRGYTY T0355 196 :DGVIATGQRTG 1qopA 178 :SRSGVTGAENR T0355 211 :L 1qopA 193 :L T0355 212 :EEIEEIGAATHLPLLV 1qopA 195 :HLIEKLKEYHAAPALQ T0355 230 :GV 1qopA 213 :GI T0355 232 :NEGNIVEILKR 1qopA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSLKE 1qopA 228 :AAGAISGSAIVK T0355 255 :GGVW 1qopA 244 :NLAS T0355 260 :NPVELARVRSFVAAARPG 1qopA 248 :PKQMLAELRSFVSAMKAA Number of specific fragments extracted= 17 number of extra gaps= 1 total=1003 Number of alignments=62 # 1qopA read from 1qopA/merged-good-all-a2m # found chain 1qopA in training set Warning: unaligning (T0355)G228 because of BadResidue code BAD_PEPTIDE in next template residue (1qopA)F212 Warning: unaligning (T0355)S229 because of BadResidue code BAD_PEPTIDE at template residue (1qopA)F212 T0355 7 :NAANAIQEIFGRSKALIGMIHCPAFPG 1qopA 3 :RYENLFAQLNDRREGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVENHGDVP 1qopA 30 :IEQSLKIIDTLIDAGADALELGVPFSDP T0355 78 :DDIGPETSAFMS 1qopA 58 :LADGPTIQNANL T0355 90 :VVTDRIVRTA 1qopA 83 :EMLAIIREKH T0355 100 :GVPVGINVLANAPI 1qopA 94 :TIPIGLLMYANLVF T0355 114 :PAFAIAKAGGAKFIRV 1qopA 113 :AFYARCEQVGVDSVLV T0355 140 :EGFMEGRAAEAMRYRSLLRAEHIKVF 1qopA 129 :ADVPVEESAPFRQAALRHNIAPIFIC T0355 178 :TADRSIDELTRDLAFFDADGVIATGQ 1qopA 155 :PPNADDDLLRQVASYGRGYTYLLSRS T0355 204 :RTGNSAS 1qopA 182 :VTGAENR T0355 211 :LEEIEEIGAATHLPLLV 1qopA 194 :HHLIEKLKEYHAAPALQ T0355 230 :GV 1qopA 213 :GI T0355 232 :NEGNIVEILKR 1qopA 216 :SPEQVSAAVRA T0355 243 :TSGVIVASSL 1qopA 228 :AAGAISGSAI T0355 263 :ELA 1qopA 247 :SPK T0355 269 :SFVAAARPGLEALEH 1qopA 250 :QMLAELRSFVSAMKA Number of specific fragments extracted= 15 number of extra gaps= 1 total=1018 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bksA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bksA expands to /projects/compbio/data/pdb/1bks.pdb.gz 1bksA:Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1bksA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1bksA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1bksA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1bksA # T0355 read from 1bksA/merged-good-all-a2m # 1bksA read from 1bksA/merged-good-all-a2m # adding 1bksA to template set # found chain 1bksA in template set Warning: unaligning (T0355)A195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bksA)A190 Warning: unaligning (T0355)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bksA)A190 Warning: unaligning (T0355)V248 because of BadResidue code BAD_PEPTIDE in next template residue (1bksA)G234 Warning: unaligning (T0355)A249 because of BadResidue code BAD_PEPTIDE at template residue (1bksA)G234 T0355 10 :NAIQEIFGRS 1bksA 5 :ENLFAQLNDR T0355 29 :PAFPGAPRYRNASMD 1bksA 15 :REGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1bksA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1bksA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIRE T0355 111 :APIPAFAIAKAGGAKF 1bksA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWAN 1bksA 109 :NGIDAFYA T0355 136 :YVANEGFMEGRAAEAM 1bksA 117 :RCEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGAHAIT 1bksA 138 :PFRQAALRHNIAPIFICPPNADDDLLR T0355 182 :SIDELTRDLAF 1bksA 165 :QVASYGRGYTY T0355 194 :D 1bksA 176 :L T0355 209 :ASLE 1bksA 191 :LPLH T0355 213 :EIEEIGAATHLPLLVGSGV 1bksA 196 :LIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1bksA 216 :SPEQVSAAVRA T0355 243 :TSGVI 1bksA 228 :AAGAI T0355 250 :SSLKEGGVWW 1bksA 235 :SAIVKIIEKN T0355 260 :NPVELARVRSFVAAARPG 1bksA 248 :PKQMLAELRSFVSAMKAA Number of specific fragments extracted= 16 number of extra gaps= 1 total=1034 Number of alignments=64 # 1bksA read from 1bksA/merged-good-all-a2m # found chain 1bksA in template set Warning: unaligning (T0355)A9 because first residue in template chain is (1bksA)M1 Warning: unaligning (T0355)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bksA)A190 Warning: unaligning (T0355)V248 because of BadResidue code BAD_PEPTIDE in next template residue (1bksA)G234 Warning: unaligning (T0355)A249 because of BadResidue code BAD_PEPTIDE at template residue (1bksA)G234 T0355 10 :NAIQEIFG 1bksA 2 :ERYENLFA T0355 18 :RSKALIGMIHCPAFP 1bksA 15 :REGAFVPFVTLGDPG T0355 46 :YDACMRDAERLIEGGMHGLIVE 1bksA 30 :IEQSLKIIDTLIDAGADALELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLAN 1bksA 52 :VPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIRE T0355 111 :APIPAFAIAKAGGAKF 1bksA 92 :HPTIPIGLLMYANLVF T0355 127 :IRVNQWANA 1bksA 109 :NGIDAFYAR T0355 137 :VANEGFMEGRAAEAM 1bksA 118 :CEQVGVDSVLVADVP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1bksA 134 :EESAPFRQAALRHNIAPIFICPP T0355 177 :ITADRSIDELTRDLAFFDA 1bksA 157 :NADDDLLRQVASYGRGYTY T0355 209 :ASL 1bksA 191 :LPL T0355 212 :EEIEEIGAATHLPLLVGSGV 1bksA 195 :HLIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1bksA 216 :SPEQVSAAVRA T0355 243 :TSGVI 1bksA 228 :AAGAI T0355 250 :SSLKE 1bksA 235 :SAIVK T0355 255 :GGV 1bksA 244 :NLA T0355 259 :WNPVELARVRSFVAAARPG 1bksA 247 :SPKQMLAELRSFVSAMKAA Number of specific fragments extracted= 16 number of extra gaps= 1 total=1050 Number of alignments=65 # 1bksA read from 1bksA/merged-good-all-a2m # found chain 1bksA in template set Warning: unaligning (T0355)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bksA)A190 Warning: unaligning (T0355)V248 because of BadResidue code BAD_PEPTIDE in next template residue (1bksA)G234 Warning: unaligning (T0355)A249 because of BadResidue code BAD_PEPTIDE at template residue (1bksA)G234 T0355 6 :DNAANAIQEIFGRSK 1bksA 2 :ERYENLFAQLNDRRE T0355 21 :ALIGMIHCP 1bksA 18 :AFVPFVTLG T0355 39 :NASMDA 1bksA 27 :DPGIEQ T0355 49 :CMRDAERLIEGGMHGLIVEN 1bksA 33 :SLKIIDTLIDAGADALELGV T0355 73 :PFSKPDDIGPETSAFMS 1bksA 53 :PFSDPLADGPTIQNANL T0355 90 :VVTDRIVRTA 1bksA 83 :EMLALIREKH T0355 100 :GVPVGINVLANAPI 1bksA 94 :TIPIGLLMYANLVF T0355 114 :PAFAIAKAGGAKFIRV 1bksA 113 :AFYARCEQVGVDSVLV T0355 140 :EGFMEGRAAEAMRYRSLLRAEHIKVF 1bksA 129 :ADVPVEESAPFRQAALRHNIAPIFIC T0355 178 :TADRSIDELTRDLAFFDADGVI 1bksA 155 :PPNADDDLLRQVASYGRGYTYL T0355 209 :ASLE 1bksA 191 :LPLH T0355 213 :EIEEIGAATHLPLLVGSGV 1bksA 196 :LIEKLKEYHAAPALQGFGI T0355 232 :NEGNIVEILKR 1bksA 216 :SPEQVSAAVRA T0355 243 :TSGVI 1bksA 228 :AAGAI T0355 250 :SSL 1bksA 235 :SAI T0355 263 :ELA 1bksA 247 :SPK T0355 266 :RVR 1bksA 251 :MLA T0355 273 :AARPGLEALE 1bksA 254 :ELRSFVSAMK Number of specific fragments extracted= 18 number of extra gaps= 1 total=1068 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tx2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tx2A expands to /projects/compbio/data/pdb/1tx2.pdb.gz 1tx2A:# T0355 read from 1tx2A/merged-good-all-a2m # 1tx2A read from 1tx2A/merged-good-all-a2m # adding 1tx2A to template set # found chain 1tx2A in template set Warning: unaligning (T0355)N39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0355)A40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0355 24 :GMIHCPAFPGAPRYR 1tx2A 12 :YTLNLNEKTLIMGIL T0355 41 :SM 1tx2A 29 :TP T0355 43 :DAIYDACMRDAERLIEGGMHGLIVENH 1tx2A 39 :YNEVDAAVRHAKEMRDEGAHIIDIGGE T0355 76 :KPDDI 1tx2A 72 :AKVSV T0355 82 :PETSAFMS 1tx2A 77 :EEEIKRVV T0355 103 :VGINVLANAPIPAFAI 1tx2A 85 :PMIQAVSKEVKLPISI T0355 119 :AKAGGAKF 1tx2A 111 :AIEAGAHI T0355 127 :IR 1tx2A 120 :ND T0355 129 :VNQWAN 1tx2A 128 :EPKIAE T0355 136 :YVANEGFMEGRAAEAM 1tx2A 134 :VAAHYDVPIILMHNRD T0355 155 :SLLRAEHIK 1tx2A 169 :KIAKDAGVR T0355 164 :VFADSH 1tx2A 181 :IILDPG T0355 170 :VKHGAHAIT 1tx2A 189 :FAKTPEQNL T0355 182 :SIDELTRDLAFFDADGVIATGQRT 1tx2A 198 :EAMRNLEQLNVLGYPVLLGTSRKS T0355 206 :GNSASLEEIEEI 1tx2A 230 :PVEERLEGTGAT T0355 236 :IVEILKR 1tx2A 242 :VCLGIEK T0355 243 :TSGVIV 1tx2A 250 :CEFVRV T0355 267 :VRSFVAAARPGLEAL 1tx2A 258 :VKEMSRMAKMMDAMI Number of specific fragments extracted= 18 number of extra gaps= 1 total=1086 Number of alignments=67 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0355)H27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0355)C28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0355)P35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)G36 Warning: unaligning (T0355)R36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)G36 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0355 17 :GRSKALIGMI 1tx2A 17 :NEKTLIMGIL T0355 29 :PAFPGA 1tx2A 29 :TPDSFS T0355 40 :ASMDA 1tx2A 37 :GSYNE T0355 46 :YDACMRDAERLIEGGMHGLIVENH 1tx2A 42 :VDAAVRHAKEMRDEGAHIIDIGGE T0355 76 :KPDDIGPETSAFM 1tx2A 72 :AKVSVEEEIKRVV T0355 103 :VGINVLANAPIPAFAIAKA 1tx2A 85 :PMIQAVSKEVKLPISIDTY T0355 128 :R 1tx2A 104 :K T0355 130 :NQWANA 1tx2A 105 :AEVAKQ T0355 137 :VANEGFMEGRA 1tx2A 111 :AIEAGAHIIND T0355 148 :AEAM 1tx2A 126 :KAEP T0355 156 :LLRAEHIKVFADSHVKHGAHAIT 1tx2A 130 :KIAEVAAHYDVPIILMHNRDNMN T0355 180 :DRSIDELTRDLAFFDA 1tx2A 161 :IADLYDSIKIAKDAGV T0355 196 :DGVIAT 1tx2A 179 :ENIILD T0355 203 :QRTGNSASLEEIEEIGAAT 1tx2A 185 :PGIGFAKTPEQNLEAMRNL T0355 222 :HLPLLVG 1tx2A 210 :GYPVLLG T0355 233 :EGNIVEILKR 1tx2A 239 :GATVCLGIEK T0355 243 :TSGVIV 1tx2A 250 :CEFVRV T0355 255 :G 1tx2A 257 :D T0355 267 :VRSFVAAARPGLEAL 1tx2A 258 :VKEMSRMAKMMDAMI Number of specific fragments extracted= 19 number of extra gaps= 2 total=1105 Number of alignments=68 # 1tx2A read from 1tx2A/merged-good-all-a2m # found chain 1tx2A in template set Warning: unaligning (T0355)H27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)V28 Warning: unaligning (T0355)C28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)V28 Warning: unaligning (T0355)R38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tx2A)G36 Warning: unaligning (T0355)N39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tx2A)G36 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tx2A)F71 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tx2A)F71 T0355 17 :GRSKALIGMI 1tx2A 17 :NEKTLIMGIL T0355 29 :PA 1tx2A 29 :TP T0355 34 :APRY 1tx2A 31 :DSFS T0355 41 :SMDAIYDACMRDAERLIEGGMHGLIVENH 1tx2A 37 :GSYNEVDAAVRHAKEMRDEGAHIIDIGGE T0355 76 :KP 1tx2A 72 :AK T0355 80 :IGPETSAFMS 1tx2A 74 :VSVEEEIKRV T0355 90 :VVTDRIVRTAGVPVGINVLA 1tx2A 85 :PMIQAVSKEVKLPISIDTYK T0355 113 :IPAFAIAKAGGAKFIRV 1tx2A 105 :AEVAKQAIEAGAHIIND T0355 139 :NEGFMEGRAAEAMRYR 1tx2A 123 :WGAKAEPKIAEVAAHY T0355 161 :HIKVFADSHVKHGAH 1tx2A 139 :DVPIILMHNRDNMNY T0355 179 :AD 1tx2A 154 :RN T0355 183 :IDELTRDLAFFDA 1tx2A 164 :LYDSIKIAKDAGV T0355 196 :DGVIATG 1tx2A 180 :NIILDPG T0355 205 :TGNSASLEEIEEIGA 1tx2A 187 :IGFAKTPEQNLEAMR T0355 220 :ATHLPLLVGS 1tx2A 208 :VLGYPVLLGT T0355 233 :EGNIVEILKR 1tx2A 235 :LEGTGATVCL T0355 243 :TSGVIVAS 1tx2A 250 :CEFVRVHD T0355 267 :VRSFVAAARPGLEALE 1tx2A 258 :VKEMSRMAKMMDAMIG Number of specific fragments extracted= 18 number of extra gaps= 2 total=1123 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xcfA/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/T0355/1xcfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1xcfA/merged-good-all-a2m.gz for input Trying 1xcfA/merged-good-all-a2m Error: Couldn't open file 1xcfA/merged-good-all-a2m or 1xcfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ojxA expands to /projects/compbio/data/pdb/1ojx.pdb.gz 1ojxA:# T0355 read from 1ojxA/merged-good-all-a2m # 1ojxA read from 1ojxA/merged-good-all-a2m # adding 1ojxA to template set # found chain 1ojxA in template set Warning: unaligning (T0355)R275 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0355)P276 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0355 8 :AANAIQEIFGRSK 1ojxA 4 :LTEKFLRIFARRG T0355 34 :APRYRNASM 1ojxA 17 :KSIILAYDH T0355 46 :YDACMRDAER 1ojxA 43 :PEYILRLARD T0355 59 :GGMHGLIVE 1ojxA 53 :AGFDGVVFQ T0355 102 :PVGINVLANAPIPAFAIAKAG 1ojxA 62 :RGIAEKYYDGSVPLILKLNGK T0355 124 :AKF 1ojxA 92 :SVA T0355 127 :IRVN 1ojxA 96 :CSVE T0355 136 :YVANEGFMEGRAAEAM 1ojxA 100 :EAVSLGASAVGYTIYP T0355 155 :SLLRAEHIKVFADSHVKHG 1ojxA 132 :RDAVKFDLPLVVWSYPRGG T0355 175 :HAITADR 1ojxA 151 :KVVNETA T0355 182 :SIDELTR 1ojxA 160 :IVAYAAR T0355 189 :DLAFFDADGVI 1ojxA 172 :GADAMKIKYTG T0355 210 :SLEEIEEIGAATH 1ojxA 183 :DPKTFSWAVKVAG T0355 223 :LPLLVGSG 1ojxA 197 :VPVLMSGG T0355 231 :V 1ojxA 207 :T T0355 232 :NEG 1ojxA 209 :TEE T0355 235 :NIVEILKR 1ojxA 216 :QVEGVLEA T0355 243 :TSGVIVASSLKEGGV 1ojxA 225 :ALGIAVGRNVWQRRD T0355 263 :ELARVRSFVAAA 1ojxA 240 :ALKFARALAELV Number of specific fragments extracted= 19 number of extra gaps= 1 total=1142 Number of alignments=70 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1ojxA)N3 Warning: unaligning (T0355)R275 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ojxA)G253 Warning: unaligning (T0355)P276 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ojxA)G253 T0355 8 :AANAIQEIF 1ojxA 4 :LTEKFLRIF T0355 17 :GRSKALIGMIH 1ojxA 14 :RRGKSIILAYD T0355 29 :PAFPG 1ojxA 30 :GPADF T0355 39 :NASMD 1ojxA 35 :MDNPD T0355 44 :AIYDACMRDAE 1ojxA 41 :ADPEYILRLAR T0355 58 :EGGMHGLIVE 1ojxA 52 :DAGFDGVVFQ T0355 102 :PVGINVLANAPIPAFAIAKA 1ojxA 62 :RGIAEKYYDGSVPLILKLNG T0355 124 :AKF 1ojxA 92 :SVA T0355 127 :IRVNQ 1ojxA 96 :CSVEE T0355 137 :VANEGFMEGRAAEA 1ojxA 101 :AVSLGASAVGYTIY T0355 151 :M 1ojxA 123 :M T0355 152 :RYRSLLRAEHIKVFADSHVKHGAH 1ojxA 125 :EELARIKRDAVKFDLPLVVWSYPR T0355 178 :T 1ojxA 149 :G T0355 179 :ADRSIDELTRDLAFFDADGVIAT 1ojxA 157 :APEIVAYAARIALELGADAMKIK T0355 204 :RTG 1ojxA 180 :YTG T0355 210 :SLEEIEEIGAAT 1ojxA 183 :DPKTFSWAVKVA T0355 222 :HLPLLVGSG 1ojxA 196 :KVPVLMSGG T0355 231 :V 1ojxA 207 :T T0355 232 :NEGNIVE 1ojxA 209 :TEEDFLK T0355 239 :ILKR 1ojxA 220 :VLEA T0355 243 :TSGVIVASSLKEG 1ojxA 225 :ALGIAVGRNVWQR T0355 261 :PVELARVRSFVAAA 1ojxA 238 :RDALKFARALAELV Number of specific fragments extracted= 22 number of extra gaps= 1 total=1164 Number of alignments=71 # 1ojxA read from 1ojxA/merged-good-all-a2m # found chain 1ojxA in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1ojxA)N3 T0355 8 :AANAIQEIF 1ojxA 4 :LTEKFLRIF T0355 17 :GRSKALIGMIH 1ojxA 14 :RRGKSIILAYD T0355 29 :PAFPGAPRYR 1ojxA 32 :ADFMDNPDSA T0355 41 :SMDAIYDACMR 1ojxA 42 :DPEYILRLARD T0355 59 :GGMHGLIVE 1ojxA 53 :AGFDGVVFQ T0355 92 :TDRIVRTA 1ojxA 62 :RGIAEKYY T0355 100 :GVPVGINV 1ojxA 72 :SVPLILKL T0355 109 :ANAPI 1ojxA 95 :NCSVE T0355 119 :AKAGGAKFIRVNQWA 1ojxA 101 :AVSLGASAVGYTIYP T0355 139 :NEGFMEGRAAEAMRYRSLLRAEHIKVFADSHVKHGAHAITADRS 1ojxA 116 :GSGFEWKMFEELARIKRDAVKFDLPLVVWSYPRGGKVVNETAPE T0355 183 :IDELTRDLAFFDADGVIAT 1ojxA 161 :VAYAARIALELGADAMKIK T0355 207 :NSASLEEIEEIGA 1ojxA 180 :YTGDPKTFSWAVK T0355 220 :ATHLPLLVGSG 1ojxA 194 :AGKVPVLMSGG T0355 232 :NEGNIVEILKR 1ojxA 209 :TEEDFLKQVEG T0355 243 :TSGVIVASSL 1ojxA 225 :ALGIAVGRNV T0355 253 :KEG 1ojxA 237 :RRD T0355 264 :LARVRSFVAAA 1ojxA 241 :LKFARALAELV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1181 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y0eA expands to /projects/compbio/data/pdb/1y0e.pdb.gz 1y0eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0355 read from 1y0eA/merged-good-all-a2m # 1y0eA read from 1y0eA/merged-good-all-a2m # adding 1y0eA to template set # found chain 1y0eA in template set Warning: unaligning (T0355)A150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0355)M151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 T0355 20 :KALIGMIHCPAFPGAP 1y0eA 5 :GLIVSCQALPDEPLHS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1y0eA 21 :SFIMSKMALAAYEGGAVGIRAN T0355 101 :VPVGINVLANAPIPAFAIAKAG 1y0eA 43 :TKEDILAIKETVDLPVIGIVKR T0355 123 :GAKFIRVNQWAN 1y0eA 70 :DVFITATSKEVD T0355 136 :YVANEGF 1y0eA 82 :ELIESQC T0355 144 :EGRAAE 1y0eA 89 :EVIALD T0355 152 :RYR 1y0eA 97 :LQQ T0355 155 :SLLRAE 1y0eA 110 :SYIRTH T0355 161 :HIKVFADSHV 1y0eA 118 :NVEIMADIAT T0355 174 :AHAIT 1y0eA 128 :VEEAK T0355 182 :SIDEL 1y0eA 133 :NAARL T0355 189 :DLAFFDADGVIATGQRTGNSA 1y0eA 138 :GFDYIGTTLHGYTSYTQGQLL T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1y0eA 162 :DFQFLKDVLQSVDAKVIAEGNV T0355 232 :NEGNIVEILKR 1y0eA 185 :TPDMYKRVMDL T0355 243 :TSGVIVASSLKE 1y0eA 197 :VHCSVVGGAITR T0355 261 :PVELA 1y0eA 209 :PKEIT T0355 280 :ALEHHHH 1y0eA 214 :KRFVQVM Number of specific fragments extracted= 17 number of extra gaps= 1 total=1198 Number of alignments=73 # 1y0eA read from 1y0eA/merged-good-all-a2m # found chain 1y0eA in template set Warning: unaligning (T0355)F165 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y0eA)P117 Warning: unaligning (T0355)A166 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y0eA)P117 T0355 19 :SKALI 1y0eA 3 :PHGLI T0355 24 :GMIHCPAFPGAP 1y0eA 9 :SCQALPDEPLHS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1y0eA 21 :SFIMSKMALAAYEGGAVGIRAN T0355 101 :VPVGINVLANAPIPAFA 1y0eA 43 :TKEDILAIKETVDLPVI T0355 120 :KAGGAKF 1y0eA 60 :GIVKRDY T0355 127 :IRV 1y0eA 69 :SDV T0355 130 :NQWANA 1y0eA 77 :SKEVDE T0355 137 :VANEGFMEGRA 1y0eA 83 :LIESQCEVIAL T0355 148 :AEAM 1y0eA 98 :QQRP T0355 152 :RYRSLLRAEHIKV 1y0eA 103 :ETLDELVSYIRTH T0355 167 :DSHVKHG 1y0eA 118 :NVEIMAD T0355 177 :ITADRSIDELTR 1y0eA 125 :IATVEEAKNAAR T0355 193 :FDADGVIAT 1y0eA 137 :LGFDYIGTT T0355 202 :G 1y0eA 148 :G T0355 203 :QRTGNSA 1y0eA 152 :YTQGQLL T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1y0eA 162 :DFQFLKDVLQSVDAKVIAEGNV T0355 232 :NEGNIVEILKR 1y0eA 185 :TPDMYKRVMDL T0355 243 :TSGVIVASSLKE 1y0eA 197 :VHCSVVGGAITR T0355 261 :PVELAR 1y0eA 209 :PKEITK T0355 281 :L 1y0eA 215 :R Number of specific fragments extracted= 20 number of extra gaps= 1 total=1218 Number of alignments=74 # 1y0eA read from 1y0eA/merged-good-all-a2m # found chain 1y0eA in template set Warning: unaligning (T0355)V137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0355)A138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 Warning: unaligning (T0355)A159 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1y0eA)P117 Warning: unaligning (T0355)E160 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1y0eA)P117 T0355 19 :SKAL 1y0eA 3 :PHGL T0355 25 :MIHCPAFPGAPRYRN 1y0eA 7 :IVSCQALPDEPLHSS T0355 43 :D 1y0eA 22 :F T0355 48 :ACMRDAERLIEGGMHGLIVE 1y0eA 23 :IMSKMALAAYEGGAVGIRAN T0355 81 :GPET 1y0eA 43 :TKED T0355 92 :TDRIVRTAGVPVGIN 1y0eA 47 :ILAIKETVDLPVIGI T0355 108 :LANAPIPAFAIAKAGGAKFIRVN 1y0eA 72 :FITATSKEVDELIESQCEVIALD T0355 139 :NEGFMEGRAAEAMRYRSL 1y0eA 97 :LQQRPKETLDELVSYIRT T0355 158 :R 1y0eA 115 :H T0355 161 :HIKVFADSHV 1y0eA 118 :NVEIMADIAT T0355 184 :DELTRDLAFFDADGVIAT 1y0eA 128 :VEEAKNAARLGFDYIGTT T0355 202 :GQRTGNSASLE 1y0eA 151 :SYTQGQLLYQN T0355 213 :EIEEIGAATHLPLLVGSGV 1y0eA 165 :FLKDVLQSVDAKVIAEGNV T0355 232 :NEGNIVEILKR 1y0eA 185 :TPDMYKRVMDL T0355 243 :TSGVIVA 1y0eA 197 :VHCSVVG Number of specific fragments extracted= 15 number of extra gaps= 2 total=1233 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1twdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1twdA/merged-good-all-a2m # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set Warning: unaligning (T0355)A280 because last residue in template chain is (1twdA)K248 T0355 35 :PRYRNASMD 1twdA 4 :LEICCYSME T0355 52 :DAERLIEGGMHGLIV 1twdA 13 :CALTAQQNGADRVEL T0355 74 :FSKPDDI 1twdA 28 :CAAPKEG T0355 95 :IVRTA 1twdA 35 :GLTPS T0355 102 :PVGINVLANAPIPAFAIAKAGG 1twdA 40 :LGVLKSVRQRVTIPVHPIIRPR T0355 124 :AKF 1twdA 63 :GDF T0355 127 :IR 1twdA 67 :YS T0355 129 :VNQWAN 1twdA 75 :ILEDVR T0355 136 :YVANEGFMEGRAA 1twdA 81 :TVRELGFPGLVTG T0355 149 :EAMRYR 1twdA 102 :DMPRME T0355 155 :SLLR 1twdA 111 :AAAG T0355 161 :HIKVFAD 1twdA 115 :PLAVTFH T0355 172 :HGAHAITADRSIDELTR 1twdA 122 :RAFDMCANPLYTLNNLA T0355 194 :DADGVIATGQRTGNSASLEEIEEIGAATH 1twdA 141 :GIARVLTSGQKSDALQGLSKIMELIAHRD T0355 223 :LPLLVGSGVNEGNIVEILKR 1twdA 171 :PIIMAGAGVRAENLHHFLDA T0355 243 :TSGVIVA 1twdA 192 :VLEVHSS T0355 257 :VWW 1twdA 208 :RYR T0355 264 :LARVRSFVAAARPGLE 1twdA 232 :GAAVAEMKGIIERHQA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1251 Number of alignments=76 # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set Warning: unaligning (T0355)P261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1twdA)Y225 Warning: unaligning (T0355)A280 because last residue in template chain is (1twdA)K248 T0355 23 :IGMIHCP 1twdA 4 :LEICCYS T0355 50 :MRDAERLIEGGMHGLIV 1twdA 11 :MECALTAQQNGADRVEL T0355 74 :FSKPDDIG 1twdA 28 :CAAPKEGG T0355 96 :VRTA 1twdA 36 :LTPS T0355 102 :PVGINVLANAPIPAFAIAKAGGAKF 1twdA 40 :LGVLKSVRQRVTIPVHPIIRPRGGD T0355 127 :I 1twdA 67 :Y T0355 128 :RVNQWANA 1twdA 74 :AILEDVRT T0355 137 :VANEGFMEGRA 1twdA 82 :VRELGFPGLVT T0355 148 :AEAM 1twdA 99 :GNVD T0355 152 :RYRSLLRAEH 1twdA 104 :PRMEKIMAAA T0355 165 :FADSHVKHGAHAITA 1twdA 114 :GPLAVTFHRAFDMCA T0355 181 :R 1twdA 129 :N T0355 183 :IDELTRDLAFFDADGVIATGQRTGNSASLEEIEEIGAATHLP 1twdA 130 :PLYTLNNLAELGIARVLTSGQKSDALQGLSKIMELIAHRDAP T0355 225 :LLVGSGVNEGNIVEILKR 1twdA 173 :IMAGAGVRAENLHHFLDA T0355 243 :TSGVIVASSLKE 1twdA 192 :VLEVHSSAGAWQ T0355 255 :GGVWWN 1twdA 205 :SPMRYR T0355 264 :LARVRSFVAAARPGLE 1twdA 232 :GAAVAEMKGIIERHQA Number of specific fragments extracted= 17 number of extra gaps= 0 total=1268 Number of alignments=77 # 1twdA read from 1twdA/merged-good-all-a2m # found chain 1twdA in training set Warning: unaligning (T0355)A21 because first residue in template chain is (1twdA)A2 Warning: unaligning (T0355)V257 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1twdA)Y225 Warning: unaligning (T0355)A280 because last residue in template chain is (1twdA)K248 T0355 22 :LIGMIHCP 1twdA 3 :LLEICCYS T0355 50 :MRDAERLIEGGMHGLIVENHGDVPFSK 1twdA 11 :MECALTAQQNGADRVELCAAPKEGGLT T0355 80 :IGPET 1twdA 38 :PSLGV T0355 92 :TDRIVRTAGVPVGINVLA 1twdA 43 :LKSVRQRVTIPVHPIIRP T0355 112 :PIPAFAIAKAGGAK 1twdA 75 :ILEDVRTVRELGFP T0355 130 :NQWANAYVANEGFMEGRAAEAMRYR 1twdA 89 :GLVTGVLDVDGNVDMPRMEKIMAAA T0355 160 :EHIKVFADSHVKHGA 1twdA 114 :GPLAVTFHRAFDMCA T0355 182 :SIDELTRDLAFFDADGVIATGQRTGNSA 1twdA 129 :NPLYTLNNLAELGIARVLTSGQKSDALQ T0355 211 :LEEIEEIGAATHLP 1twdA 158 :LSKIMELIAHRDAP T0355 225 :LLVGSGVNEGNIVEILKR 1twdA 173 :IMAGAGVRAENLHHFLDA T0355 243 :TSGVIVA 1twdA 192 :VLEVHSS T0355 258 :WWNPVELARVRSFVAAARPGLE 1twdA 226 :SRYIVDGAAVAEMKGIIERHQA Number of specific fragments extracted= 12 number of extra gaps= 0 total=1280 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ox6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ox6A expands to /projects/compbio/data/pdb/1ox6.pdb.gz 1ox6A:# T0355 read from 1ox6A/merged-good-all-a2m # 1ox6A read from 1ox6A/merged-good-all-a2m # adding 1ox6A to template set # found chain 1ox6A in template set Warning: unaligning (T0355)Y37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ox6A)L276 Warning: unaligning (T0355)Y46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ox6A)D304 Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)D304 T0355 2 :QTISDNAANAIQEI 1ox6A 214 :PPIPNYSAEEKELL T0355 17 :GRSKA 1ox6A 228 :MNDYS T0355 22 :LIGMIHCPAFPG 1ox6A 243 :CLDVRTNDQGDL T0355 36 :R 1ox6A 255 :V T0355 47 :DACMRDAERLIEGGMHGLIVENH 1ox6A 277 :GKPVQLAQKYYQQGADEVTFLNI T0355 77 :PDDIGPET 1ox6A 306 :PLKDTPML T0355 103 :VGINVLANAPIPAFAIAKAGGAKF 1ox6A 314 :EVLKQAAKTVFVPLTVGGGIKDIV T0355 127 :IRVNQWAN 1ox6A 344 :IPALEVAS T0355 136 :YVANEGFMEGRAAEAMRYR 1ox6A 352 :LYFRSGADKVSIGTDAVYA T0355 155 :SLLRAEHI 1ox6A 389 :TISKAYGA T0355 164 :VFADSHVK 1ox6A 399 :VVISVDPK T0355 172 :HGAHAITADR 1ox6A 411 :NSQADTKNKV T0355 183 :IDELTR 1ox6A 451 :VWELTR T0355 189 :DLAFFDADGVI 1ox6A 462 :GAGEILLNCID T0355 202 :GQRTGNSASLEEIEEIGAATHLPLLVGSGV 1ox6A 473 :KDGSNSGYDLELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1ox6A 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKE 1ox6A 517 :ADACLGAGMFHR T0355 257 :VWWN 1ox6A 529 :GEFT T0355 267 :VRSFVAAARP 1ox6A 533 :VNDVKEYLLE Number of specific fragments extracted= 19 number of extra gaps= 0 total=1299 Number of alignments=79 # 1ox6A read from 1ox6A/merged-good-all-a2m # found chain 1ox6A in template set Warning: unaligning (T0355)Y37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ox6A)L276 Warning: unaligning (T0355)Y46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ox6A)D304 Warning: unaligning (T0355)S75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)D304 T0355 1 :MQTISDNAANAIQ 1ox6A 216 :IPNYSAEEKELLM T0355 14 :EIFGRSKALIGMIHCPAFPGAP 1ox6A 232 :SNYGLTRRIIACLDVRTNDQGD T0355 36 :R 1ox6A 255 :V T0355 47 :DACMRDAERLIEGGMHGLIVENH 1ox6A 277 :GKPVQLAQKYYQQGADEVTFLNI T0355 76 :KPDDIGPE 1ox6A 305 :CPLKDTPM T0355 102 :PVGINVLANAPIPAFAIAKAGGAKF 1ox6A 313 :LEVLKQAAKTVFVPLTVGGGIKDIV T0355 127 :IRVNQWANA 1ox6A 344 :IPALEVASL T0355 137 :VANEGFMEGRAAEAM 1ox6A 353 :YFRSGADKVSIGTDA T0355 152 :RYRSLL 1ox6A 369 :YAAEKY T0355 162 :IKVFADS 1ox6A 375 :YELGNRG T0355 169 :HVKHGAHAIT 1ox6A 407 :RVYVNSQADT T0355 183 :IDELTRDLAFFDADGVIAT 1ox6A 451 :VWELTRACEALGAGEILLN T0355 202 :GQRTGN 1ox6A 475 :GSNSGY T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1ox6A 481 :DLELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1ox6A 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKE 1ox6A 517 :ADACLGAGMFHR T0355 256 :GVWW 1ox6A 529 :GEFT T0355 267 :VRSFVAAARP 1ox6A 533 :VNDVKEYLLE Number of specific fragments extracted= 18 number of extra gaps= 0 total=1317 Number of alignments=80 # 1ox6A read from 1ox6A/merged-good-all-a2m # found chain 1ox6A in template set Warning: unaligning (T0355)M42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)L276 Warning: unaligning (T0355)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ox6A)D304 Warning: unaligning (T0355)F74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ox6A)D304 T0355 1 :MQTISDNAANAI 1ox6A 216 :IPNYSAEEKELL T0355 14 :EIFGRSKALIGMIHCPAFPGA 1ox6A 232 :SNYGLTRRIIACLDVRTNDQG T0355 43 :DA 1ox6A 277 :GK T0355 49 :CMRDAERLIEGGMHGLIVENH 1ox6A 279 :PVQLAQKYYQQGADEVTFLNI T0355 75 :SKPDDI 1ox6A 305 :CPLKDT T0355 87 :FMSVVTDRIVRTAGVPVGIN 1ox6A 311 :PMLEVLKQAAKTVFVPLTVG T0355 111 :APIPAFAIAKAGGAKFIRVN 1ox6A 345 :PALEVASLYFRSGADKVSIG T0355 145 :GRAAEAMRYRSLLR 1ox6A 365 :TDAVYAAEKYYELG T0355 160 :EHIK 1ox6A 379 :NRGD T0355 164 :VFADSHVKHGAHAITADRS 1ox6A 399 :VVISVDPKRVYVNSQADTK T0355 183 :IDELTRDLAFFDADGVIATGQR 1ox6A 451 :VWELTRACEALGAGEILLNCID T0355 205 :TG 1ox6A 474 :DG T0355 207 :NSASLEEIEEIGAATHLPLLVGSGV 1ox6A 478 :SGYDLELIEHVKDAVKIPVIASSGA T0355 232 :NEGNIVEILKR 1ox6A 504 :VPEHFEEAFLK T0355 243 :TSGVIVASSLKEGGVW 1ox6A 517 :ADACLGAGMFHRGEFT T0355 267 :VRSFVAAARP 1ox6A 533 :VNDVKEYLLE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1333 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a53/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a53 expands to /projects/compbio/data/pdb/1a53.pdb.gz 1a53:Warning: there is no chain 1a53 will retry with 1a53A # T0355 read from 1a53/merged-good-all-a2m # 1a53 read from 1a53/merged-good-all-a2m # adding 1a53 to template set # found chain 1a53 in template set T0355 8 :AANAIQEIFGRSKA 1a53 33 :LNERILEFNKRNIT T0355 22 :LIGMIHCPAFPGAP 1a53 48 :IIAEYKRKSPSGLD T0355 38 :RNASMD 1a53 62 :VERDPI T0355 51 :RDAERLI 1a53 68 :EYSKFME T0355 59 :GGMHGLIVE 1a53 75 :RYAVGLSIL T0355 74 :FSKPDDIGP 1a53 84 :TEEKYFNGS T0355 102 :PVGINVLANAPIPAFAIA 1a53 93 :YETLRKIASSVSIPILMK T0355 125 :KFIRVNQWANA 1a53 111 :DFIVKESQIDD T0355 137 :VANEGFMEGRAAEAMRYR 1a53 122 :AYNLGADTVLLIVKILTE T0355 155 :SLLRAEHIKVFADSH 1a53 147 :EYARSYGMEPLIEIN T0355 173 :GAHAIT 1a53 162 :DENDLD T0355 182 :SIDEL 1a53 168 :IALRI T0355 189 :DLAFFDADG 1a53 173 :GARFIGINS T0355 202 :GQRTGNSASLEEIEEIGAATH 1a53 182 :RDLETLEINKENQRKLISMIP T0355 223 :LPLLVGSGV 1a53 205 :VVKVAESGI T0355 232 :NEGNIVEILKR 1a53 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVW 1a53 227 :VNAFLIGSSLMRNPEK T0355 267 :VRS 1a53 243 :IKE Number of specific fragments extracted= 18 number of extra gaps= 0 total=1351 Number of alignments=82 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0355 2 :QTISDNAANAIQEIFGRSKALIGMIHCPAFPGA 1a53 27 :QRPIISLNERILEFNKRNITAIIAEYKRKSPSG T0355 36 :RYRNASM 1a53 60 :LDVERDP T0355 50 :MRDAERLIEG 1a53 67 :IEYSKFMERY T0355 61 :MHGLIVE 1a53 77 :AVGLSIL T0355 74 :FSKPDDIGP 1a53 84 :TEEKYFNGS T0355 102 :PVGINVLANAPIPAFAIAKAGG 1a53 93 :YETLRKIASSVSIPILMKDFIV T0355 128 :R 1a53 115 :K T0355 130 :NQWANA 1a53 116 :ESQIDD T0355 137 :VANEGFMEGRA 1a53 122 :AYNLGADTVLL T0355 148 :AEAM 1a53 134 :VKIL T0355 152 :RYRSLLRAEHIKVFADSHVKHG 1a53 140 :RELESLLEYARSYGMEPLIEIN T0355 179 :ADRSIDELTR 1a53 162 :DENDLDIALR T0355 193 :FDADGVIATG 1a53 172 :IGARFIGINS T0355 203 :QRTGNSASLEEIEEIGAAT 1a53 183 :DLETLEINKENQRKLISMI T0355 222 :HLPLLVGSGV 1a53 204 :NVVKVAESGI T0355 232 :NEGNIVEILKR 1a53 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKEGGVW 1a53 227 :VNAFLIGSSLMRNPEK T0355 267 :VRSF 1a53 243 :IKEF Number of specific fragments extracted= 18 number of extra gaps= 0 total=1369 Number of alignments=83 # 1a53 read from 1a53/merged-good-all-a2m # found chain 1a53 in template set T0355 7 :NAANAIQEIFGRSKALIGMIHCPAFPGAPRYRN 1a53 32 :SLNERILEFNKRNITAIIAEYKRKSPSGLDVER T0355 41 :S 1a53 65 :D T0355 49 :CMRDAERLIEG 1a53 66 :PIEYSKFMERY T0355 61 :MHGLIVENHG 1a53 77 :AVGLSILTEE T0355 76 :KPDDIGPETSA 1a53 87 :KYFNGSYETLR T0355 94 :RIVRTAGVPVGINVLAN 1a53 98 :KIASSVSIPILMKDFIV T0355 112 :PIPAFAIAKAGGAKFIRVNQ 1a53 115 :KESQIDDAYNLGADTVLLIV T0355 140 :EGFMEGRAAEAMRYRSLLRAEH 1a53 135 :KILTERELESLLEYARSYGMEP T0355 165 :FADSHV 1a53 157 :LIEIND T0355 184 :DELTRDLAFFDADGVIATG 1a53 163 :ENDLDIALRIGARFIGINS T0355 203 :QRTGNSASLEEIEEIGA 1a53 183 :DLETLEINKENQRKLIS T0355 220 :ATHLPLLVGSGV 1a53 202 :PSNVVKVAESGI T0355 232 :NEGNIVEILKR 1a53 215 :ERNEIEELRKL T0355 243 :TSGVIVASSLKE 1a53 227 :VNAFLIGSSLMR T0355 263 :ELARVRSF 1a53 239 :NPEKIKEF Number of specific fragments extracted= 15 number of extra gaps= 0 total=1384 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ujpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1ujpA/merged-good-all-a2m # 1ujpA read from 1ujpA/merged-good-all-a2m # found chain 1ujpA in training set Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujpA)G59 Warning: unaligning (T0355)G81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)G59 Warning: unaligning (T0355)G197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujpA)E189 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)E189 T0355 10 :NAIQE 1ujpA 8 :AKARS T0355 28 :CPAFPGAPRYRNASMD 1ujpA 13 :EGRAALIPYLTAGFPS T0355 46 :YDACMRDAERL 1ujpA 29 :REGFLQAVEEV T0355 61 :MHGLIVE 1ujpA 43 :ADLLEIG T0355 72 :VPFS 1ujpA 50 :LPYS T0355 82 :PETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKF 1ujpA 60 :PVIQRASELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVL T0355 127 :IRVNQWAN 1ujpA 106 :WGPERFFG T0355 136 :YVANEGFMEGRAAEAMRYR 1ujpA 114 :LFKQAGATGVILPDLPPDE T0355 155 :SLLRAEHIKVFADSHVKHGAHAIT 1ujpA 138 :RLAQEIGLETVFLLAPTSTDARIA T0355 182 :SIDELTRDLAF 1ujpA 162 :TVVRHATGFVY T0355 194 :DAD 1ujpA 173 :AVS T0355 211 :L 1ujpA 190 :V T0355 212 :EEIEEIGAATHLPLLVGSGV 1ujpA 192 :DLVRRIKARTALPVAVGFGV T0355 232 :NEGNIVEIL 1ujpA 213 :GKATAAQAA T0355 242 :RTSGVIVASSLKEGGVWW 1ujpA 222 :VADGVVVGSALVRALEEG T0355 260 :N 1ujpA 241 :S T0355 267 :VRSFVAAARPGL 1ujpA 242 :LAPLLQEIRQGL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1401 Number of alignments=85 # 1ujpA read from 1ujpA/merged-good-all-a2m # found chain 1ujpA in training set Warning: unaligning (T0355)K76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujpA)G59 Warning: unaligning (T0355)G81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)G59 Warning: unaligning (T0355)G197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujpA)E189 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)E189 T0355 9 :ANAIQEIFG 1ujpA 4 :LEAFAKARS T0355 18 :RSKALIGMIHCPAFP 1ujpA 14 :GRAALIPYLTAGFPS T0355 46 :YDACMRDAER 1ujpA 29 :REGFLQAVEE T0355 61 :MHGLIVE 1ujpA 43 :ADLLEIG T0355 72 :VPFS 1ujpA 50 :LPYS T0355 82 :PETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKF 1ujpA 60 :PVIQRASELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVL T0355 127 :IRVNQWANA 1ujpA 106 :WGPERFFGL T0355 137 :VANEGFMEGRAAEAM 1ujpA 115 :FKQAGATGVILPDLP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1ujpA 131 :DEDPGLVRLAQEIGLETVFLLAP T0355 177 :ITADRSIDELTRDLAFFDA 1ujpA 154 :TSTDARIATVVRHATGFVY T0355 196 :D 1ujpA 175 :S T0355 211 :L 1ujpA 190 :V T0355 212 :EEIEEIGAATHLPLLVGSGV 1ujpA 192 :DLVRRIKARTALPVAVGFGV T0355 232 :NEGNIVEIL 1ujpA 213 :GKATAAQAA T0355 243 :TSGVIVASSLKE 1ujpA 223 :ADGVVVGSALVR T0355 255 :GGVW 1ujpA 238 :EGRS T0355 267 :VRSFVAAARPGL 1ujpA 242 :LAPLLQEIRQGL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1418 Number of alignments=86 # 1ujpA read from 1ujpA/merged-good-all-a2m # found chain 1ujpA in training set Warning: unaligning (T0355)V72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ujpA)G59 Warning: unaligning (T0355)P77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)G59 Warning: unaligning (T0355)S210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ujpA)E189 T0355 8 :AANAIQEIFGRSK 1ujpA 3 :TLEAFAKARSEGR T0355 21 :ALIGMIHCP 1ujpA 17 :ALIPYLTAG T0355 39 :NASMDAIY 1ujpA 26 :FPSREGFL T0355 51 :RDAERLIEG 1ujpA 34 :QAVEEVLPY T0355 61 :MHGLIVENHGD 1ujpA 43 :ADLLEIGLPYS T0355 82 :PETSAFMS 1ujpA 60 :PVIQRASE T0355 90 :VVTDRIVRTAGVPVGIN 1ujpA 81 :ELVREVRALTEKPLFLM T0355 107 :VLANAPIPAFAIAKAGGAKFIR 1ujpA 103 :VLAWGPERFFGLFKQAGATGVI T0355 135 :AYVANEGFMEGR 1ujpA 125 :LPDLPPDEDPGL T0355 151 :MRYRSLLRAEHIKVF 1ujpA 137 :VRLAQEIGLETVFLL T0355 178 :TADRSIDELTRDLAFFDADGVIA 1ujpA 152 :APTSTDARIATVVRHATGFVYAV T0355 211 :LEEIEEIGAATHLPLLVGSGV 1ujpA 191 :KDLVRRIKARTALPVAVGFGV T0355 232 :NEGNIVEIL 1ujpA 213 :GKATAAQAA T0355 242 :RTSGVIVAS 1ujpA 222 :VADGVVVGS T0355 251 :SLKEGGV 1ujpA 235 :ALEEGRS T0355 267 :VRSFVAAARPGL 1ujpA 242 :LAPLLQEIRQGL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1434 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fliA expands to /projects/compbio/data/pdb/2fli.pdb.gz 2fliA:# T0355 read from 2fliA/merged-good-all-a2m # 2fliA read from 2fliA/merged-good-all-a2m # adding 2fliA to template set # found chain 2fliA in template set Warning: unaligning (T0355)A30 because first residue in template chain is (2fliA)T3 T0355 31 :FPGAPRYRNASMD 2fliA 4 :LKIAPSILAADYA T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 2fliA 17 :NFASELARIEETDAEYVHIDIMDGQ T0355 74 :FSKPDDIG 2fliA 42 :FVPNISFG T0355 102 :PVGINVLANAPIPAFAIAKAG 2fliA 50 :ADVVASMRKHSKLVFDCHLMV T0355 127 :IRVNQWAN 2fliA 71 :VDPERYVE T0355 136 :YVANEGFMEGRAA 2fliA 79 :AFAQAGADIMTIH T0355 149 :EAMRYRSLLRAEHIKVFADSHVKHGAHAIT 2fliA 97 :HIHGALQKIKAAGMKAGVVINPGTPATALE T0355 182 :SIDELTRDLAFFDADGVI 2fliA 127 :PLLDLVDQVLIMTVNPGF T0355 202 :GQRTGNSASLEEIEEIGAA 2fliA 145 :GGQAFIPECLEKVATVAKW T0355 221 :THLPLLVGSGVNEGNIVEILKR 2fliA 169 :LSFDIEVDGGVDNKTIRACYEA T0355 243 :TSGVIVASSLKEGGV 2fliA 192 :ANVFVAGSYLFKASD T0355 263 :ELARVRSFVAAA 2fliA 207 :LVSQVQTLRTAL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1446 Number of alignments=88 # 2fliA read from 2fliA/merged-good-all-a2m # found chain 2fliA in template set Warning: unaligning (T0355)S19 because first residue in template chain is (2fliA)T3 Warning: unaligning (T0355)R275 because last residue in template chain is (2fliA)N219 T0355 20 :KALIGM 2fliA 4 :LKIAPS T0355 37 :YRNASMD 2fliA 10 :ILAADYA T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 2fliA 17 :NFASELARIEETDAEYVHIDIMDGQ T0355 74 :FSKPDDIGP 2fliA 42 :FVPNISFGA T0355 103 :VGINVLANAPIPAFAIAKAGG 2fliA 51 :DVVASMRKHSKLVFDCHLMVV T0355 128 :RVNQWANA 2fliA 72 :DPERYVEA T0355 137 :VANEGFMEGRAAEAM 2fliA 80 :FAQAGADIMTIHTES T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 2fliA 96 :RHIHGALQKIKAAGMKAGVVINP T0355 177 :ITADRS 2fliA 119 :GTPATA T0355 190 :LAFFDA 2fliA 125 :LEPLLD T0355 196 :DGVIAT 2fliA 134 :QVLIMT T0355 202 :GQRTGNSASLEEIEEIGAAT 2fliA 145 :GGQAFIPECLEKVATVAKWR T0355 222 :HLPLLVGSGVNEGNIVEILKR 2fliA 170 :SFDIEVDGGVDNKTIRACYEA T0355 243 :TSGVIVASSLKEG 2fliA 192 :ANVFVAGSYLFKA T0355 261 :PVELARVRSFVAAA 2fliA 205 :SDLVSQVQTLRTAL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1461 Number of alignments=89 # 2fliA read from 2fliA/merged-good-all-a2m # found chain 2fliA in template set T0355 21 :ALIG 2fliA 5 :KIAP T0355 31 :FPGAPRYRN 2fliA 9 :SILAADYAN T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 2fliA 18 :FASELARIEETDAEYVHIDIMDGQFVPNI T0355 79 :DIGPETSAFM 2fliA 47 :SFGADVVASM T0355 96 :VRTAGVPVGINVLANAPIPAFAIAKAGGAKFIRVNQ 2fliA 57 :RKHSKLVFDCHLMVVDPERYVEAFAQAGADIMTIHT T0355 142 :FMEGRAAEAMRYRSLLRA 2fliA 93 :ESTRHIHGALQKIKAAGM T0355 163 :KVFADSHVKHGAHAITAD 2fliA 111 :KAGVVINPGTPATALEPL T0355 192 :FFDADGVIATG 2fliA 129 :LDLVDQVLIMT T0355 203 :QRTGNSAS 2fliA 143 :GFGGQAFI T0355 211 :LEEIEEIGA 2fliA 154 :LEKVATVAK T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 2fliA 168 :GLSFDIEVDGGVDNKTIRACYEA T0355 243 :TSGVIVASSLKEGGV 2fliA 192 :ANVFVAGSYLFKASD T0355 264 :LARVRSFVAAA 2fliA 208 :VSQVQTLRTAL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1474 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1ub3A/merged-good-all-a2m # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0355 21 :ALIGMIHCPAFPG 1ub3A 5 :AHIDHTLLKPTAT T0355 46 :YDACMRDAERLIEGGMHGLIV 1ub3A 18 :LEEVAKAAEEALEYGFYGLCI T0355 76 :KPDDI 1ub3A 39 :PPSYV T0355 89 :SVVTDR 1ub3A 44 :AWVRAR T0355 98 :TAG 1ub3A 50 :YPH T0355 111 :APIPAFAIAKAGGAKF 1ub3A 53 :APFRLVTVVGFPLGYQ T0355 128 :R 1ub3A 69 :E T0355 129 :VNQWAN 1ub3A 73 :KALEAA T0355 136 :YVANEGFMEGRAA 1ub3A 79 :LACARGADEVDMV T0355 149 :EAMRYRSLLRA 1ub3A 101 :DLDYLEAEVRA T0355 160 :EHIKVFADSHVK 1ub3A 117 :PQAVLKVILETG T0355 172 :HGAHAIT 1ub3A 130 :FSPEEIA T0355 182 :SIDELTR 1ub3A 137 :RLAEAAI T0355 189 :DLAFFDADGVI 1ub3A 146 :GADFLKTSTGF T0355 205 :TGNSASLEEIEEIGAATH 1ub3A 157 :GPRGASLEDVALLVRVAQ T0355 223 :LPLLVGSGV 1ub3A 177 :AQVKAAGGI T0355 232 :NEGNIVEILKR 1ub3A 187 :DRETALRMLKA T0355 243 :TSGVIV 1ub3A 199 :ASRLGT T0355 249 :ASSLK 1ub3A 207 :GVALV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1493 Number of alignments=91 # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0355 20 :KALIGMIHCPAFPG 1ub3A 4 :AAHIDHTLLKPTAT T0355 46 :YDACMRDAERLIEGGMHGLIV 1ub3A 18 :LEEVAKAAEEALEYGFYGLCI T0355 76 :KPDDI 1ub3A 39 :PPSYV T0355 103 :VGINVLANAPIPAFAIAKAGGAKFIRV 1ub3A 44 :AWVRARYPHAPFRLVTVVGFPLGYQEK T0355 130 :NQWANA 1ub3A 74 :ALEAAL T0355 137 :VANEGFMEGRAAEAMRYR 1ub3A 80 :ACARGADEVDMVLHLGRA T0355 155 :SLLRA 1ub3A 103 :DYLEA T0355 160 :EHIKVFADSHVKH 1ub3A 111 :AVREAVPQAVLKV T0355 173 :GAHAITADRSIDELTRDLAFFDADGVIAT 1ub3A 125 :LETGYFSPEEIARLAEAAIRGGADFLKTS T0355 202 :GQRTG 1ub3A 155 :GFGPR T0355 208 :SASLEEIEEIGAAT 1ub3A 160 :GASLEDVALLVRVA T0355 223 :LPLLVGSGV 1ub3A 177 :AQVKAAGGI T0355 232 :NEGNIVEILKR 1ub3A 187 :DRETALRMLKA T0355 243 :TSGVIVAS 1ub3A 199 :ASRLGTSS Number of specific fragments extracted= 14 number of extra gaps= 0 total=1507 Number of alignments=92 # 1ub3A read from 1ub3A/merged-good-all-a2m # found chain 1ub3A in training set T0355 23 :IGMIHCP 1ub3A 7 :IDHTLLK T0355 38 :RNASMDAI 1ub3A 14 :PTATLEEV T0355 50 :MRDAERLIEGGMHGLI 1ub3A 22 :AKAAEEALEYGFYGLC T0355 80 :IGPETSA 1ub3A 38 :IPPSYVA T0355 94 :RIVRTA 1ub3A 45 :WVRARY T0355 100 :GVPV 1ub3A 54 :PFRL T0355 105 :INVLAN 1ub3A 58 :VTVVGF T0355 111 :API 1ub3A 73 :KAL T0355 115 :AFAIAKAGGAK 1ub3A 76 :EAALACARGAD T0355 128 :RVNQWANAYVANEGFMEGRAAEAMRYRSLLRAEHIKVF 1ub3A 87 :EVDMVLHLGRAKAGDLDYLEAEVRAVREAVPQAVLKVI T0355 168 :SHVKH 1ub3A 125 :LETGY T0355 177 :ITA 1ub3A 130 :FSP T0355 181 :RSIDELTRDLAFFDADGVIATGQRTGNSASLEEIEEIGA 1ub3A 133 :EEIARLAEAAIRGGADFLKTSTGFGPRGASLEDVALLVR T0355 220 :ATHLPLLVGSGV 1ub3A 174 :QGRAQVKAAGGI T0355 232 :NEGNIVEILKR 1ub3A 187 :DRETALRMLKA T0355 243 :TSGVIV 1ub3A 199 :ASRLGT Number of specific fragments extracted= 16 number of extra gaps= 0 total=1523 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tqjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1tqjA/merged-good-all-a2m # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0355)P29 because first residue in template chain is (1tqjA)K3 Warning: unaligning (T0355)A195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0355)D196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0355)G197 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 Warning: unaligning (T0355)R204 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tqjA)Q150 T0355 30 :AFPGAPRYRNASMD 1tqjA 4 :NIVVAPSILSADFS T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 1tqjA 18 :RLGEEIKAVDEAGADWIHVDVMDGR T0355 74 :FSKPDDIGPET 1tqjA 43 :FVPNITIGPLI T0355 105 :INVLANAPIPAFAIAKAG 1tqjA 54 :VDAIRPLTKKTLDVHLMI T0355 127 :IRVNQWANA 1tqjA 72 :VEPEKYVED T0355 137 :VANEGFMEGRAA 1tqjA 81 :FAKAGADIISVH T0355 149 :EAMRYRSLLRAEHIKVFADSHVKHGAHAIT 1tqjA 100 :HLHRTLCQIRELGKKAGAVLNPSTPLDFLE T0355 182 :SIDELTRDLAFFD 1tqjA 130 :YVLPVCDLILIMS T0355 205 :TGNSASLEEIEEIGAATH 1tqjA 151 :SFIPEVLPKIRALRQMCD T0355 223 :LPLLVGSGVNEGNIVEILKR 1tqjA 174 :PWIEVDGGLKPNNTWQVLEA T0355 243 :TSGVIVASSLKEGGV 1tqjA 195 :ANAIVAGSAVFNAPN T0355 263 :ELARVRSFV 1tqjA 210 :YAEAIAGVR Number of specific fragments extracted= 12 number of extra gaps= 1 total=1535 Number of alignments=94 # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0355)R18 because first residue in template chain is (1tqjA)K3 Warning: unaligning (T0355)G197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0355)V198 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0355)I199 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 Warning: unaligning (T0355)R204 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tqjA)Q150 T0355 19 :SKALIG 1tqjA 4 :NIVVAP T0355 36 :RYRNASMDA 1tqjA 10 :SILSADFSR T0355 49 :CMRDAERLIEGGMHGLIVENHGDV 1tqjA 19 :LGEEIKAVDEAGADWIHVDVMDGR T0355 74 :FSKPDDIGP 1tqjA 43 :FVPNITIGP T0355 103 :VGINVLANAPIPAFAIAKAGG 1tqjA 52 :LIVDAIRPLTKKTLDVHLMIV T0355 128 :RVNQWANA 1tqjA 73 :EPEKYVED T0355 137 :VANEGFMEGRA 1tqjA 81 :FAKAGADIISV T0355 148 :AEAMRYRSLLRAEHIKVFADSHVKHGA 1tqjA 95 :HNASPHLHRTLCQIRELGKKAGAVLNP T0355 177 :ITADRSIDELTRDLAFFDA 1tqjA 122 :STPLDFLEYVLPVCDLILI T0355 196 :D 1tqjA 142 :S T0355 205 :TGNSASLEEIEEIGAAT 1tqjA 151 :SFIPEVLPKIRALRQMC T0355 222 :HLPLLVGSGVNEGNIVEILKR 1tqjA 173 :DPWIEVDGGLKPNNTWQVLEA T0355 243 :TSGVIVASSLKEGGV 1tqjA 195 :ANAIVAGSAVFNAPN T0355 267 :VRSFVAAARP 1tqjA 210 :YAEAIAGVRN Number of specific fragments extracted= 14 number of extra gaps= 1 total=1549 Number of alignments=95 # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0355)S19 because first residue in template chain is (1tqjA)K3 Warning: unaligning (T0355)Q203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0355)R204 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0355)T205 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 Warning: unaligning (T0355)S210 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tqjA)Q150 T0355 20 :KALIGM 1tqjA 4 :NIVVAP T0355 30 :AFPGAPRYR 1tqjA 10 :SILSADFSR T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 1tqjA 19 :LGEEIKAVDEAGADWIHVDVMDGRFVPNI T0355 79 :DIGPET 1tqjA 48 :TIGPLI T0355 92 :TDRIVRTAGVPVGINVLANAPI 1tqjA 54 :VDAIRPLTKKTLDVHLMIVEPE T0355 115 :AFAIAK 1tqjA 78 :VEDFAK T0355 122 :GGAKFIRVNQ 1tqjA 84 :AGADIISVHV T0355 139 :NEG 1tqjA 94 :EHN T0355 143 :MEGRAAEAMRYRSLLRA 1tqjA 97 :ASPHLHRTLCQIRELGK T0355 163 :KVFADSHVKHGAHAITADRS 1tqjA 114 :KAGAVLNPSTPLDFLEYVLP T0355 194 :DADGVIATG 1tqjA 134 :VCDLILIMS T0355 211 :LEEIEEIGA 1tqjA 157 :LPKIRALRQ T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1tqjA 171 :GLDPWIEVDGGLKPNNTWQVLEA T0355 243 :TSGVIVASSLKEGGV 1tqjA 195 :ANAIVAGSAVFNAPN T0355 270 :FVAAARPGL 1tqjA 210 :YAEAIAGVR Number of specific fragments extracted= 15 number of extra gaps= 1 total=1564 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pii/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pii expands to /projects/compbio/data/pdb/1pii.pdb.gz 1pii:Warning: there is no chain 1pii will retry with 1piiA Skipped atom 428, because occupancy 0.540 <= existing 0.540 in 1pii Skipped atom 436, because occupancy 0.530 <= existing 0.700 in 1pii Skipped atom 438, because occupancy 0.390 <= existing 0.640 in 1pii Skipped atom 1193, because occupancy 0.710 <= existing 0.710 in 1pii Skipped atom 1195, because occupancy 0.650 <= existing 0.670 in 1pii Skipped atom 1197, because occupancy 0.680 <= existing 0.680 in 1pii Skipped atom 1199, because occupancy 0.820 <= existing 0.860 in 1pii Skipped atom 1201, because occupancy 0.650 <= existing 0.750 in 1pii Skipped atom 1203, because occupancy 0.620 <= existing 0.830 in 1pii Skipped atom 1205, because occupancy 0.750 <= existing 0.800 in 1pii Skipped atom 1207, because occupancy 0.540 <= existing 0.630 in 1pii Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 2537, because occupancy 0.510 <= existing 0.520 in 1pii Skipped atom 2539, because occupancy 0.450 <= existing 0.450 in 1pii Skipped atom 2541, because occupancy 0.470 <= existing 0.470 in 1pii Skipped atom 2543, because occupancy 0.550 <= existing 0.550 in 1pii Skipped atom 2545, because occupancy 0.500 <= existing 0.500 in 1pii Skipped atom 2547, because occupancy 0.490 <= existing 0.540 in 1pii Skipped atom 2549, because occupancy 0.440 <= existing 0.510 in 1pii Skipped atom 2902, because occupancy 0.620 <= existing 0.620 in 1pii Skipped atom 2906, because occupancy 0.600 <= existing 0.600 in 1pii Skipped atom 2908, because occupancy 0.480 <= existing 0.480 in 1pii Skipped atom 2910, because occupancy 0.510 <= existing 0.520 in 1pii Skipped atom 2912, because occupancy 0.410 <= existing 0.480 in 1pii Skipped atom 2914, because occupancy 0.350 <= existing 0.470 in 1pii Skipped atom 2918, because occupancy 0.380 <= existing 0.420 in 1pii Skipped atom 2922, because occupancy 0.560 <= existing 0.670 in 1pii # T0355 read from 1pii/merged-good-all-a2m # 1pii read from 1pii/merged-good-all-a2m # adding 1pii to template set # found chain 1pii in template set Warning: unaligning (T0355)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)R47 Warning: unaligning (T0355)K20 because of BadResidue code BAD_PEPTIDE at template residue (1pii)R47 Warning: unaligning (T0355)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)S60 Warning: unaligning (T0355)R38 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)D67 Warning: unaligning (T0355)N39 because of BadResidue code BAD_PEPTIDE at template residue (1pii)D67 Warning: unaligning (T0355)T221 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)G206 Warning: unaligning (T0355)H222 because of BadResidue code BAD_PEPTIDE at template residue (1pii)G206 T0355 11 :AIQEIFGR 1pii 38 :HFYDALQG T0355 21 :ALIGMIHCPAF 1pii 48 :TAFILECKKAS T0355 33 :GAPRY 1pii 61 :KGVIR T0355 40 :ASMD 1pii 68 :FDPA T0355 51 :RDAERL 1pii 72 :RIAAIY T0355 58 :EGGMHGLIVE 1pii 78 :KHYASAISVL T0355 75 :SKPDDI 1pii 88 :TDEKYF T0355 96 :VRTA 1pii 94 :QGSF T0355 103 :VGINVLANAPIPAFAIAKA 1pii 98 :NFLPIVSQIAPQPILCKDF T0355 126 :FIR 1pii 117 :IID T0355 130 :NQWAN 1pii 120 :PYQIY T0355 136 :YVANEGFMEGRAA 1pii 125 :LARYYQADACLLM T0355 149 :EAMRYR 1pii 142 :DDDQYR T0355 155 :SLLRAEHIKVFADSHV 1pii 151 :AVAHSLEMGVLTEVSN T0355 174 :AHAIT 1pii 167 :EEEQE T0355 182 :SIDEL 1pii 172 :RAIAL T0355 194 :DADGVIATGQR 1pii 177 :GAKVVGINNRD T0355 205 :TGNSASLEEIEEIGAA 1pii 189 :RDLSIDLNRTRELAPK T0355 223 :LPLLVGSGV 1pii 209 :VTVISESGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1pii 219 :TYAQVRELSHFANGFLIGSALMAHDD T0355 259 :W 1pii 245 :L Number of specific fragments extracted= 21 number of extra gaps= 4 total=1585 Number of alignments=97 # 1pii read from 1pii/merged-good-all-a2m # found chain 1pii in template set Warning: unaligning (T0355)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)R47 Warning: unaligning (T0355)K20 because of BadResidue code BAD_PEPTIDE at template residue (1pii)R47 Warning: unaligning (T0355)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)S60 Warning: unaligning (T0355)G33 because of BadResidue code BAD_PEPTIDE at template residue (1pii)S60 Warning: unaligning (T0355)R38 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)D67 Warning: unaligning (T0355)N39 because of BadResidue code BAD_PEPTIDE at template residue (1pii)D67 Warning: unaligning (T0355)T221 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)G206 T0355 12 :IQEIFGR 1pii 39 :FYDALQG T0355 21 :ALIGMIHCPAF 1pii 48 :TAFILECKKAS T0355 34 :AP 1pii 61 :KG T0355 36 :RY 1pii 64 :IR T0355 40 :ASMD 1pii 68 :FDPA T0355 51 :RDAERL 1pii 72 :RIAAIY T0355 58 :EGGMHGLIVE 1pii 78 :KHYASAISVL T0355 74 :FSKPDDIGP 1pii 88 :TDEKYFQGS T0355 102 :PVGINVLANAPIPAFAI 1pii 97 :FNFLPIVSQIAPQPILC T0355 123 :GAKFIR 1pii 114 :KDFIID T0355 130 :NQWANA 1pii 120 :PYQIYL T0355 137 :VANEGFMEGRAAEAM 1pii 126 :ARYYQADACLLMLSV T0355 152 :RYRSLLRAEHIKVFADSHVKHG 1pii 144 :DQYRQLAAVAHSLEMGVLTEVS T0355 179 :ADRSIDELTR 1pii 166 :NEEEQERAIA T0355 193 :FDADGVIATG 1pii 176 :LGAKVVGINN T0355 203 :QRTGNSASLEEIEEIGAA 1pii 187 :DLRDLSIDLNRTRELAPK T0355 222 :HLPLLVGSGV 1pii 208 :NVTVISESGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEG 1pii 219 :TYAQVRELSHFANGFLIGSALMAH T0355 261 :PVELARVRS 1pii 243 :DDLHAAVRR Number of specific fragments extracted= 19 number of extra gaps= 4 total=1604 Number of alignments=98 # 1pii read from 1pii/merged-good-all-a2m # found chain 1pii in template set Warning: unaligning (T0355)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)R47 Warning: unaligning (T0355)K20 because of BadResidue code BAD_PEPTIDE at template residue (1pii)R47 Warning: unaligning (T0355)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)S60 Warning: unaligning (T0355)G33 because of BadResidue code BAD_PEPTIDE at template residue (1pii)S60 Warning: unaligning (T0355)R38 because of BadResidue code BAD_PEPTIDE in next template residue (1pii)D67 Warning: unaligning (T0355)N39 because of BadResidue code BAD_PEPTIDE at template residue (1pii)D67 Warning: unaligning (T0355)A220 because of BadResidue code BAD_PEPTIDE at template residue (1pii)G206 T0355 12 :IQEIFGR 1pii 39 :FYDALQG T0355 21 :ALIGMIHCPAF 1pii 48 :TAFILECKKAS T0355 34 :AP 1pii 61 :KG T0355 36 :RY 1pii 64 :IR T0355 40 :ASMD 1pii 68 :FDPA T0355 51 :RDAERLIE 1pii 72 :RIAAIYKH T0355 60 :GMHGLIVENHGDVPFSKPD 1pii 80 :YASAISVLTDEKYFQGSFN T0355 91 :VTDRIVRTAGVPVGINVLANAPIPA 1pii 99 :FLPIVSQIAPQPILCKDFIIDPYQI T0355 117 :AIAKAGGAKFIRVNQ 1pii 124 :YLARYYQADACLLML T0355 136 :YV 1pii 139 :SV T0355 142 :FMEGRAAEAMRYRSLLR 1pii 141 :LDDDQYRQLAAVAHSLE T0355 162 :IKVFADSHV 1pii 158 :MGVLTEVSN T0355 184 :DELTRDLAFFDADGVIATGQ 1pii 167 :EEEQERAIALGAKVVGINNR T0355 204 :RTGNSASLEEIEEIGA 1pii 188 :LRDLSIDLNRTRELAP T0355 221 :THLPLLVGSGVN 1pii 207 :HNVTVISESGIN T0355 234 :GNIVEILKRTSGVIVASSLKEGGV 1pii 221 :AQVRELSHFANGFLIGSALMAHDD T0355 263 :ELARVRSFVA 1pii 264 :RGQDAKAAYD Number of specific fragments extracted= 17 number of extra gaps= 4 total=1621 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kfbA/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/T0355/1kfbA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1kfbA/merged-good-all-a2m.gz for input Trying 1kfbA/merged-good-all-a2m Error: Couldn't open file 1kfbA/merged-good-all-a2m or 1kfbA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xi3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1xi3A/merged-good-all-a2m # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0355)Q131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xi3A)R70 Warning: unaligning (T0355)W132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xi3A)R70 Warning: unaligning (T0355)D196 because of BadResidue code BAD_PEPTIDE in next template residue (1xi3A)S128 Warning: unaligning (T0355)G197 because of BadResidue code BAD_PEPTIDE at template residue (1xi3A)S128 Warning: unaligning (T0355)T201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xi3A)D137 Warning: unaligning (T0355)G206 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xi3A)D137 T0355 37 :YRNASMD 1xi3A 10 :YVITDRR T0355 49 :CMRDAERLIEGGMHGLIVE 1xi3A 20 :EVESVREALEGGATAIQMR T0355 75 :SKP 1xi3A 39 :IKN T0355 79 :DIGPETSAFMSVVTD 1xi3A 42 :APTREMYEIGKTLRQ T0355 118 :IAKAGGAKFI 1xi3A 57 :LTREYDALFF T0355 129 :VN 1xi3A 67 :VD T0355 133 :AN 1xi3A 71 :VD T0355 136 :YVANEGFMEGRAAEAMRYRSLLRA 1xi3A 73 :VALAVDADGVQLGPEDMPIEVAKE T0355 160 :EHIKVFADS 1xi3A 99 :PNLIIGASV T0355 172 :HGAHAIT 1xi3A 108 :YSLEEAL T0355 182 :SIDEL 1xi3A 115 :EAEKK T0355 189 :DLAFFDA 1xi3A 120 :GADYLGA T0355 198 :VIA 1xi3A 129 :VFP T0355 207 :NSA 1xi3A 138 :ARV T0355 210 :SLEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1xi3A 142 :GLEGLRKIVESVKIPVVAIGGINKDNAREVLKT T0355 243 :TSGVIVASSLKEGGV 1xi3A 176 :VDGIAVISAVMGAED T0355 263 :ELARVRSFVAAARPGL 1xi3A 191 :VRKATEELRKIVEEVL Number of specific fragments extracted= 17 number of extra gaps= 2 total=1638 Number of alignments=100 # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0355)I127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xi3A)R70 Warning: unaligning (T0355)R128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xi3A)R70 Warning: unaligning (T0355)D196 because of BadResidue code BAD_PEPTIDE at template residue (1xi3A)S128 Warning: unaligning (T0355)A200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xi3A)D137 Warning: unaligning (T0355)G206 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xi3A)D137 T0355 21 :A 1xi3A 8 :K T0355 23 :IGMIHCPAFPG 1xi3A 9 :LYVITDRRLKP T0355 49 :CMRDAERLIEGGMHGLIVE 1xi3A 20 :EVESVREALEGGATAIQMR T0355 75 :SKP 1xi3A 39 :IKN T0355 79 :DIGPETSAFMSVVTDR 1xi3A 42 :APTREMYEIGKTLRQL T0355 108 :LAN 1xi3A 58 :TRE T0355 112 :PIPAFAI 1xi3A 61 :YDALFFV T0355 129 :VNQ 1xi3A 71 :VDV T0355 137 :VANEGFMEGRAAEAM 1xi3A 74 :ALAVDADGVQLGPED T0355 152 :R 1xi3A 90 :P T0355 158 :RAEHIKVFADSHVKHGA 1xi3A 91 :IEVAKEIAPNLIIGASV T0355 178 :TADRSIDELTRD 1xi3A 108 :YSLEEALEAEKK T0355 190 :LAFFDA 1xi3A 121 :ADYLGA T0355 197 :GVI 1xi3A 129 :VFP T0355 207 :NSA 1xi3A 138 :ARV T0355 210 :SLEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1xi3A 142 :GLEGLRKIVESVKIPVVAIGGINKDNAREVLKT T0355 243 :TSGVIVASSLKEG 1xi3A 176 :VDGIAVISAVMGA T0355 261 :PVELARVRSFVAAARPGL 1xi3A 189 :EDVRKATEELRKIVEEVL Number of specific fragments extracted= 18 number of extra gaps= 2 total=1656 Number of alignments=101 # 1xi3A read from 1xi3A/merged-good-all-a2m # found chain 1xi3A in training set Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE in next template residue (1xi3A)S128 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE at template residue (1xi3A)S128 Warning: unaligning (T0355)T205 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xi3A)D137 T0355 23 :IGMI 1xi3A 9 :LYVI T0355 33 :GAPRYRN 1xi3A 13 :TDRRLKP T0355 49 :CMRDAERLIEGGMHGLIVEN 1xi3A 20 :EVESVREALEGGATAIQMRI T0355 76 :KP 1xi3A 40 :KN T0355 80 :IGPETSAFMSVVTDRIVRTAGVPVGIN 1xi3A 42 :APTREMYEIGKTLRQLTREYDALFFVD T0355 116 :FAIAKAGGAKFIRV 1xi3A 71 :VDVALAVDADGVQL T0355 138 :ANEGFMEGRAAEA 1xi3A 85 :GPEDMPIEVAKEI T0355 159 :AEHIKVFADSHV 1xi3A 98 :APNLIIGASVYS T0355 184 :DELTRDLAFFDADGVIA 1xi3A 110 :LEEALEAEKKGADYLGA T0355 206 :GNSASLEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1xi3A 138 :ARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKT T0355 243 :TSGVIVASSLKEGGV 1xi3A 176 :VDGIAVISAVMGAED T0355 264 :LARVRSFVAAARPGL 1xi3A 192 :RKATEELRKIVEEVL Number of specific fragments extracted= 12 number of extra gaps= 1 total=1668 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wa3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wa3A expands to /projects/compbio/data/pdb/1wa3.pdb.gz 1wa3A:# T0355 read from 1wa3A/merged-good-all-a2m # 1wa3A read from 1wa3A/merged-good-all-a2m # adding 1wa3A to template set # found chain 1wa3A in template set Warning: unaligning (T0355)L252 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1wa3A)V182 Warning: unaligning (T0355)K253 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1wa3A)V182 Warning: unaligning (T0355)G277 because last residue in template chain is (1wa3A)C203 T0355 9 :ANAIQEI 1wa3A 4 :EELFKKH T0355 21 :ALIGMIHCPA 1wa3A 11 :KIVAVLRANS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1wa3A 21 :VEEAKEKALAVFEGGVHLIEIT T0355 70 :GDVP 1wa3A 43 :FTVP T0355 79 :DIGPETSA 1wa3A 47 :DADTVIKE T0355 105 :INVLANAPIPAFAI 1wa3A 55 :LSFLKEKGAIIGAG T0355 128 :RVN 1wa3A 69 :TVT T0355 131 :QWAN 1wa3A 74 :EQCR T0355 136 :YVANEGFMEGRAAEAMRYR 1wa3A 78 :KAVESGAEFIVSPHLDEEI T0355 155 :SLLRAEHIKVFADSHV 1wa3A 98 :QFCKEKGVFYMPGVMT T0355 174 :AHAIT 1wa3A 114 :PTELV T0355 182 :SIDEL 1wa3A 119 :KAMKL T0355 194 :DADGVIAT 1wa3A 124 :GHTILKLF T0355 209 :ASLEEIEEIGAATH 1wa3A 136 :VGPQFVKAMKGPFP T0355 223 :LPLLVGSGVNEGNIVEILKR 1wa3A 151 :VKFVPTGGVNLDNVCEWFKA T0355 243 :TSGVIVASS 1wa3A 172 :VLAVGVGSA T0355 254 :EG 1wa3A 183 :KG T0355 259 :WNPVELARVRSFVAAARP 1wa3A 185 :TPDEVREKAKAFVEKIRG Number of specific fragments extracted= 18 number of extra gaps= 1 total=1686 Number of alignments=103 # 1wa3A read from 1wa3A/merged-good-all-a2m # found chain 1wa3A in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1wa3A)K2 Warning: unaligning (T0355)L252 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1wa3A)V182 Warning: unaligning (T0355)K253 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1wa3A)V182 Warning: unaligning (T0355)G277 because last residue in template chain is (1wa3A)C203 T0355 8 :AANAIQEI 1wa3A 3 :MEELFKKH T0355 21 :ALIGMIHCPA 1wa3A 11 :KIVAVLRANS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1wa3A 21 :VEEAKEKALAVFEGGVHLIEIT T0355 70 :GDVP 1wa3A 43 :FTVP T0355 100 :GVPVGINV 1wa3A 47 :DADTVIKE T0355 108 :LANAPIP 1wa3A 58 :LKEKGAI T0355 116 :FAIAK 1wa3A 65 :IGAGT T0355 122 :G 1wa3A 70 :V T0355 128 :RVNQWANA 1wa3A 71 :TSVEQCRK T0355 137 :VANEGFMEGRAAEA 1wa3A 79 :AVESGAEFIVSPHL T0355 154 :RSLLRAEHIKVFADSHVK 1wa3A 93 :DEEISQFCKEKGVFYMPG T0355 177 :ITADRSIDELTR 1wa3A 111 :VMTPTELVKAMK T0355 193 :FDADGVIAT 1wa3A 123 :LGHTILKLF T0355 208 :SASLEEIEEIGAAT 1wa3A 135 :VVGPQFVKAMKGPF T0355 222 :HLPLLVGSGVNEGNIVEILKR 1wa3A 150 :NVKFVPTGGVNLDNVCEWFKA T0355 243 :TSGVIVASS 1wa3A 172 :VLAVGVGSA T0355 254 :EG 1wa3A 183 :KG T0355 259 :WNPVELARVRSFVAAARP 1wa3A 185 :TPDEVREKAKAFVEKIRG Number of specific fragments extracted= 18 number of extra gaps= 1 total=1704 Number of alignments=104 # 1wa3A read from 1wa3A/merged-good-all-a2m # found chain 1wa3A in template set Warning: unaligning (T0355)N7 because first residue in template chain is (1wa3A)K2 Warning: unaligning (T0355)L252 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1wa3A)V182 Warning: unaligning (T0355)K253 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1wa3A)V182 T0355 8 :AANAIQEI 1wa3A 3 :MEELFKKH T0355 21 :ALIGMIHCP 1wa3A 11 :KIVAVLRAN T0355 41 :SMDA 1wa3A 20 :SVEE T0355 49 :CMRDAERLIEGGMHGLIVENHG 1wa3A 24 :AKEKALAVFEGGVHLIEITFTV T0355 81 :GP 1wa3A 46 :PD T0355 88 :MSVVTDRIVRTA 1wa3A 48 :ADTVIKELSFLK T0355 100 :GVPVGIN 1wa3A 62 :GAIIGAG T0355 111 :APIPAFAIAKAGGAKFIRV 1wa3A 71 :TSVEQCRKAVESGAEFIVS T0355 139 :N 1wa3A 90 :P T0355 142 :FMEG 1wa3A 91 :HLDE T0355 149 :EAMRYRSLLR 1wa3A 95 :EISQFCKEKG T0355 162 :IKVFADSHV 1wa3A 105 :VFYMPGVMT T0355 184 :DELTRDLAFFDADGVIA 1wa3A 114 :PTELVKAMKLGHTILKL T0355 210 :SLEEIEEIGA 1wa3A 137 :GPQFVKAMKG T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1wa3A 148 :FPNVKFVPTGGVNLDNVCEWFKA T0355 243 :TSGVIVASS 1wa3A 172 :VLAVGVGSA T0355 254 :E 1wa3A 183 :K T0355 262 :VELARVRSFVAAARPGLEA 1wa3A 184 :GTPDEVREKAKAFVEKIRG Number of specific fragments extracted= 18 number of extra gaps= 1 total=1722 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vc4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1vc4A/merged-good-all-a2m # 1vc4A read from 1vc4A/merged-good-all-a2m # found chain 1vc4A in training set T0355 3 :TISDNAA 1vc4A 27 :PLPEPPS T0355 10 :NAIQEIFGRSKALIGMIHCPAFPGAPRYRNASMD 1vc4A 35 :PSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPV T0355 51 :RDAERLIEGGMHGLIVENHGDV 1vc4A 69 :EAALAYARGGARAVSVLTEPHR T0355 74 :FS 1vc4A 91 :FG T0355 96 :VR 1vc4A 93 :GS T0355 102 :PVGINVLANAPIPAFAIAKAG 1vc4A 95 :LLDLKRVREAVDLPLLRKDFV T0355 127 :I 1vc4A 116 :V T0355 129 :VNQWAN 1vc4A 117 :DPFMLE T0355 136 :YVANEGFMEGRAA 1vc4A 123 :EARAFGASAALLI T0355 149 :E 1vc4A 141 :E T0355 155 :SLLRAEHIKVFADSH 1vc4A 148 :EEARRLGLEALVEVH T0355 173 :GAHAIT 1vc4A 163 :TERELE T0355 182 :SIDEL 1vc4A 169 :IALEA T0355 189 :DLAFFDADG 1vc4A 174 :GAEVLGINN T0355 202 :GQRTGNSASLEEIEEIGAA 1vc4A 183 :RDLATLHINLETAPRLGRL T0355 221 :THLPLLVGSGV 1vc4A 207 :FGGVLVAESGY T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1vc4A 219 :RKEELKALEGLFDAVLIGTSLMRAPD T0355 263 :ELARVRSFV 1vc4A 245 :LEAALRELV Number of specific fragments extracted= 18 number of extra gaps= 0 total=1740 Number of alignments=106 # 1vc4A read from 1vc4A/merged-good-all-a2m # found chain 1vc4A in training set T0355 9 :ANAIQEIFGRSKALIGMIHCPAFPGAPRYRNASMD 1vc4A 34 :VPSFKEALLRPGLSVIAEVKRQSPSEGLIREVDPV T0355 51 :RDAERLIEGGMHGLIVE 1vc4A 69 :EAALAYARGGARAVSVL T0355 74 :FSKPDDIGP 1vc4A 86 :TEPHRFGGS T0355 102 :PVGINVLANAPIPAFAI 1vc4A 95 :LLDLKRVREAVDLPLLR T0355 124 :AKF 1vc4A 112 :KDF T0355 127 :IR 1vc4A 116 :VD T0355 130 :NQWANA 1vc4A 118 :PFMLEE T0355 137 :VANEGFMEGRA 1vc4A 124 :ARAFGASAALL T0355 148 :AEAM 1vc4A 136 :VALL T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1vc4A 141 :ELTGAYLEEARRLGLEALVEVHT T0355 180 :DRSIDELTR 1vc4A 164 :ERELEIALE T0355 193 :FDADGVIATG 1vc4A 173 :AGAEVLGINN T0355 203 :QRTGNSASLEEIEE 1vc4A 184 :DLATLHINLETAPR T0355 217 :IGAAT 1vc4A 202 :ARKRG T0355 222 :HLPLLVGSGV 1vc4A 208 :GGVLVAESGY T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1vc4A 219 :RKEELKALEGLFDAVLIGTSLMRAPD T0355 263 :ELARVRSFV 1vc4A 245 :LEAALRELV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1757 Number of alignments=107 # 1vc4A read from 1vc4A/merged-good-all-a2m # found chain 1vc4A in training set T0355 5 :SD 1vc4A 35 :PS T0355 12 :IQEIFGRSKALIGMIHCPAFPGAPRYRNAS 1vc4A 37 :FKEALLRPGLSVIAEVKRQSPSEGLIREVD T0355 49 :CMRDAERLIEGGMHGLIVENHGDVP 1vc4A 67 :PVEAALAYARGGARAVSVLTEPHRF T0355 79 :DIGPET 1vc4A 92 :GGSLLD T0355 92 :TDRIVRTAGVPVGINVLANAPI 1vc4A 98 :LKRVREAVDLPLLRKDFVVDPF T0355 115 :AFAIAKAGGAKFIRV 1vc4A 120 :MLEEARAFGASAALL T0355 134 :NAYV 1vc4A 135 :IVAL T0355 143 :MEGRAAEAMRYRSLLR 1vc4A 139 :LGELTGAYLEEARRLG T0355 162 :IKVFADSHV 1vc4A 155 :LEALVEVHT T0355 184 :DELTRDLAFFDADGVIATG 1vc4A 164 :ERELEIALEAGAEVLGINN T0355 203 :QRTGNSASLEEIEEIGA 1vc4A 184 :DLATLHINLETAPRLGR T0355 220 :ATHLPLLVGSGV 1vc4A 206 :GFGGVLVAESGY T0355 232 :NEGNIVEILKRTSGVIVASSLKEGGV 1vc4A 219 :RKEELKALEGLFDAVLIGTSLMRAPD T0355 264 :LARVRSFV 1vc4A 246 :EAALRELV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1771 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gjlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gjlA expands to /projects/compbio/data/pdb/2gjl.pdb.gz 2gjlA:# T0355 read from 2gjlA/merged-good-all-a2m # 2gjlA read from 2gjlA/merged-good-all-a2m # adding 2gjlA to template set # found chain 2gjlA in template set T0355 11 :AIQEIFGRSKALIGMIHCP 2gjlA 7 :RFTETFGVEHPIMQGGMQW T0355 39 :NAS 2gjlA 26 :VGR T0355 50 :MRDAERLIEGGM 2gjlA 29 :AEMAAAVANAGG T0355 65 :IVENHGD 2gjlA 43 :TLSALTQ T0355 79 :DIGPETSAFMSVVTDR 2gjlA 50 :PSPEALAAEIARCREL T0355 111 :APIPAFAIAKAGGAKF 2gjlA 66 :TDRPFGVNLTLLPTQK T0355 127 :IRVNQWAN 2gjlA 83 :VPYAEYRA T0355 136 :YVANEGFMEGRAAEAMRYR 2gjlA 91 :AIIEAGIRVVETAGNDPGE T0355 155 :SLLRAEHIKVFADS 2gjlA 112 :AEFRRHGVKVIHKC T0355 172 :HGAHAIT 2gjlA 126 :TAVRHAL T0355 182 :SIDEL 2gjlA 133 :KAERL T0355 189 :DLAFFDADGVIATGQRTGNSASLE 2gjlA 138 :GVDAVSIDGFECAGHPGEDDIPGL T0355 213 :EIEEIGAATHLPLLVGSGV 2gjlA 163 :LLPAAANRLRVPIIASGGF T0355 232 :NEGNIVEILKR 2gjlA 183 :DGRGLVAALAL T0355 243 :TSGVIVASSLKE 2gjlA 195 :ADAINMGTRFLA T0355 256 :GVWW 2gjlA 207 :TREC T0355 260 :NPVELARVRS 2gjlA 213 :HPAVKAAIRA Number of specific fragments extracted= 17 number of extra gaps= 0 total=1788 Number of alignments=109 # 2gjlA read from 2gjlA/merged-good-all-a2m # found chain 2gjlA in template set T0355 11 :AIQEIFGRSKALIGM 2gjlA 7 :RFTETFGVEHPIMQG T0355 30 :AFPGAPR 2gjlA 22 :GMQWVGR T0355 50 :MRDAERLIEGG 2gjlA 29 :AEMAAAVANAG T0355 61 :M 2gjlA 42 :A T0355 65 :IVE 2gjlA 43 :TLS T0355 69 :HGDVP 2gjlA 46 :ALTQP T0355 80 :IGPETSAFMSVVTD 2gjlA 51 :SPEALAAEIARCRE T0355 108 :LANAPIPAFA 2gjlA 65 :LTDRPFGVNL T0355 120 :KAGGAKF 2gjlA 75 :TLLPTQK T0355 127 :IRVNQWANA 2gjlA 83 :VPYAEYRAA T0355 137 :VANEGFMEGRA 2gjlA 92 :IIEAGIRVVET T0355 148 :AEAM 2gjlA 104 :GNDP T0355 152 :RYRSLL 2gjlA 109 :EHIAEF T0355 162 :IKVFADSHVKHGA 2gjlA 115 :RRHGVKVIHKCTA T0355 180 :DRSIDELTR 2gjlA 128 :VRHALKAER T0355 193 :FDADGVIATG 2gjlA 137 :LGVDAVSIDG T0355 203 :QRTGNSASL 2gjlA 152 :HPGEDDIPG T0355 212 :EEIEEIGAATHLPLLVGSGV 2gjlA 162 :VLLPAAANRLRVPIIASGGF T0355 232 :NEGNIVEILKR 2gjlA 183 :DGRGLVAALAL T0355 243 :TSGVIVASSLKE 2gjlA 195 :ADAINMGTRFLA T0355 255 :GGVWWNPVELARVRS 2gjlA 208 :RECPIHPAVKAAIRA Number of specific fragments extracted= 21 number of extra gaps= 0 total=1809 Number of alignments=110 # 2gjlA read from 2gjlA/merged-good-all-a2m # found chain 2gjlA in template set T0355 11 :AIQEIFGRSKALIGM 2gjlA 7 :RFTETFGVEHPIMQG T0355 33 :GAPRYRN 2gjlA 22 :GMQWVGR T0355 50 :MRDAERLIEGGM 2gjlA 29 :AEMAAAVANAGG T0355 65 :IVENHGD 2gjlA 43 :TLSALTQ T0355 80 :IGPETSA 2gjlA 50 :PSPEALA T0355 90 :VVTDRIVRTAGVPVGINVLAN 2gjlA 57 :AEIARCRELTDRPFGVNLTLL T0355 112 :PIPAFAIAKAGGAKFIRVNQ 2gjlA 85 :YAEYRAAIIEAGIRVVETAG T0355 141 :GFMEGRAAEAMR 2gjlA 105 :NDPGEHIAEFRR T0355 160 :EHIKVFADSHV 2gjlA 117 :HGVKVIHKCTA T0355 184 :DELTRDLAFFDADGVIATGQRT 2gjlA 128 :VRHALKAERLGVDAVSIDGFEC T0355 206 :GNSAS 2gjlA 151 :GHPGE T0355 211 :LEEIEEIGAATHLPLLVGSGV 2gjlA 161 :LVLLPAAANRLRVPIIASGGF T0355 232 :NEGNIVEILKR 2gjlA 183 :DGRGLVAALAL T0355 243 :TSGVIVASSL 2gjlA 195 :ADAINMGTRF T0355 258 :WWNPVEL 2gjlA 208 :RECPIHP T0355 269 :SFVAAARP 2gjlA 215 :AVKAAIRA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1825 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vizA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vizA expands to /projects/compbio/data/pdb/1viz.pdb.gz 1vizA:Skipped atom 384, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 386, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 388, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 390, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 411, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 413, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 415, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 473, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 475, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 953, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 955, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 957, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 959, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 1474, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 1476, because occupancy 0.350 <= existing 0.650 in 1vizA Skipped atom 1478, because occupancy 0.350 <= existing 0.650 in 1vizA # T0355 read from 1vizA/merged-good-all-a2m # 1vizA read from 1vizA/merged-good-all-a2m # adding 1vizA to template set # found chain 1vizA in template set Warning: unaligning (T0355)N68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vizA)T44 Warning: unaligning (T0355)I80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vizA)T44 Warning: unaligning (T0355)A119 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)S83 Warning: unaligning (T0355)K120 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)S83 Warning: unaligning (T0355)A195 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)E160 Warning: unaligning (T0355)D196 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)E160 T0355 28 :CPAFPGAPRYRNASM 1vizA 1 :LYDVTEWKHVFKLDP T0355 43 :D 1vizA 21 :D T0355 51 :RDAERLIEGGMHGLIVE 1vizA 22 :EQLEILCESGTDAVIIG T0355 81 :GPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFA 1vizA 45 :EDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFI T0355 121 :AGGAK 1vizA 84 :VLNSK T0355 126 :F 1vizA 92 :W T0355 127 :IRVNQWANA 1vizA 94 :VGMHQKAMK T0355 136 :YVANEGFMEGRAAEAMRYRSLLRAEH 1vizA 107 :LMSMEEIVAEGYCIANPDCKAAALTE T0355 168 :SHVKHGAHAIT 1vizA 133 :ADADLNMDDIV T0355 182 :SIDELTR 1vizA 144 :AYARVSE T0355 189 :DLAFFD 1vizA 153 :QLPIFY T0355 197 :G 1vizA 161 :Y T0355 205 :TGNSASLEEIEEIGAATH 1vizA 162 :SGVLGDIEAVKKTKAVLE T0355 223 :LPLLVGSGV 1vizA 181 :STLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEG 1vizA 191 :DAETAKQYAEHADVIVVGNAVYED T0355 264 :LARVRSFVAAAR 1vizA 215 :FDRALKTVAAVK Number of specific fragments extracted= 16 number of extra gaps= 2 total=1841 Number of alignments=112 # 1vizA read from 1vizA/merged-good-all-a2m # found chain 1vizA in template set Warning: unaligning (T0355)N68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vizA)T44 Warning: unaligning (T0355)P73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vizA)T44 Warning: unaligning (T0355)I118 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)S83 Warning: unaligning (T0355)A119 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)S83 Warning: unaligning (T0355)A200 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)E160 Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)E160 T0355 28 :CPAFPGAPRYRNASMD 1vizA 1 :LYDVTEWKHVFKLDPN T0355 51 :RDAERLIEGGMHGLIVE 1vizA 22 :EQLEILCESGTDAVIIG T0355 81 :GPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFA 1vizA 45 :EDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFI T0355 120 :KAG 1vizA 84 :VLN T0355 123 :GAKF 1vizA 89 :NADW T0355 127 :IRVNQWANAY 1vizA 94 :VGMHQKAMKE T0355 137 :VANEGFMEGRAAEAM 1vizA 108 :MSMEEIVAEGYCIAN T0355 152 :RY 1vizA 124 :DC T0355 159 :AEHIKVFADS 1vizA 126 :KAAALTEADA T0355 177 :ITADRSIDELTRDLAFFDADGVI 1vizA 136 :DLNMDDIVAYARVSELLQLPIFY T0355 204 :RTGNSASLEEIEEIGAAT 1vizA 161 :YSGVLGDIEAVKKTKAVL T0355 222 :HLPLLVGSGV 1vizA 180 :TSTLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVASSLKEG 1vizA 191 :DAETAKQYAEHADVIVVGNAVYED T0355 264 :LARVRSFVAAARP 1vizA 215 :FDRALKTVAAVKG Number of specific fragments extracted= 14 number of extra gaps= 2 total=1855 Number of alignments=113 # 1vizA read from 1vizA/merged-good-all-a2m # found chain 1vizA in template set Warning: unaligning (T0355)N68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vizA)T44 Warning: unaligning (T0355)G81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vizA)T44 Warning: unaligning (T0355)N130 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)S83 Warning: unaligning (T0355)Q131 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)S83 Warning: unaligning (T0355)A200 because of BadResidue code BAD_PEPTIDE in next template residue (1vizA)E160 Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE at template residue (1vizA)E160 T0355 24 :GMIHCPA 1vizA 9 :HVFKLDP T0355 37 :YRNASMD 1vizA 16 :NKDLPDE T0355 52 :DAERLIEGGMHGLIVE 1vizA 23 :QLEILCESGTDAVIIG T0355 82 :PETSA 1vizA 45 :EDNVL T0355 90 :VVTDRIVRT 1vizA 50 :RMMSKVRRF T0355 100 :GVPVGINV 1vizA 59 :LVPCVLEV T0355 123 :GAKFIRV 1vizA 75 :GFDLYFI T0355 132 :WANA 1vizA 84 :VLNS T0355 138 :ANEGFMEGRAAEAMRYRS 1vizA 88 :KNADWIVGMHQKAMKEYG T0355 156 :LLRAEHIKVFADSHVKHGA 1vizA 107 :LMSMEEIVAEGYCIANPDC T0355 175 :HAITADRSIDELTR 1vizA 131 :TEADADLNMDDIVA T0355 189 :DLAFFDADGVI 1vizA 148 :VSELLQLPIFY T0355 204 :RTGNSASLEEIEEIGA 1vizA 161 :YSGVLGDIEAVKKTKA T0355 220 :ATHLPLLVGSGV 1vizA 178 :LETSTLFYGGGI T0355 232 :NEGNIVEILKRTSGVIVASSL 1vizA 191 :DAETAKQYAEHADVIVVGNAV T0355 263 :ELARVRSFVAAAR 1vizA 214 :DFDRALKTVAAVK Number of specific fragments extracted= 16 number of extra gaps= 2 total=1871 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rd5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rd5A expands to /projects/compbio/data/pdb/1rd5.pdb.gz 1rd5A:Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1742, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1744, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1rd5A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1rd5A # T0355 read from 1rd5A/merged-good-all-a2m # 1rd5A read from 1rd5A/merged-good-all-a2m # adding 1rd5A to template set # found chain 1rd5A in template set Warning: unaligning (T0355)F126 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)F108 Warning: unaligning (T0355)I127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)S110 Warning: unaligning (T0355)R128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)S110 Warning: unaligning (T0355)D167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0355)S168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE in next template residue (1rd5A)G180 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE at template residue (1rd5A)G180 T0355 9 :ANAIQEIFGR 1rd5A 6 :SDTMAALMAK T0355 29 :PAFPGAPRYRNASMD 1rd5A 16 :GKTAFIPYITAGDPD T0355 46 :YDACMRDAERLIEGGMHGLIVE 1rd5A 31 :LATTAEALRLLDGCGADVIELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAK 1rd5A 53 :VPCSDPYIDGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPI T0355 129 :VN 1rd5A 111 :LA T0355 136 :YVANEGFMEGRAAEAMRYR 1rd5A 113 :KMKEAGVHGLIVPDLPYVA T0355 155 :SLLRAEHIKVFA 1rd5A 137 :SEAKNNNLELVL T0355 169 :HVKHGAHAIT 1rd5A 151 :TPAIPEDRMK T0355 182 :SIDELTRDLAF 1rd5A 161 :EITKASEGFVY T0355 194 :DADGVIA 1rd5A 172 :LVSVNGV T0355 203 :QRTGNSASL 1rd5A 181 :PRANVNPRV T0355 212 :EEIEEIGAATHLPLLVGSGV 1rd5A 191 :SLIQEVKKVTNKPVAVGFGI T0355 232 :NEGNIVEILKR 1rd5A 212 :KPEHVKQIAQW T0355 243 :TSGVIVASSLKEGGVWW 1rd5A 224 :ADGVIIGSAMVRQLGEA T0355 260 :NPVELARVRSFVAAARPGL 1rd5A 243 :PKQGLRRLEEYARGMKNAL Number of specific fragments extracted= 15 number of extra gaps= 4 total=1886 Number of alignments=115 # 1rd5A read from 1rd5A/merged-good-all-a2m # found chain 1rd5A in template set Warning: unaligning (T0355)F126 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)F108 Warning: unaligning (T0355)I127 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)S110 Warning: unaligning (T0355)R128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)S110 Warning: unaligning (T0355)K171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0355)H172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE in next template residue (1rd5A)G180 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE at template residue (1rd5A)G180 T0355 8 :AANAIQEIFGRSKA 1rd5A 5 :VSDTMAALMAKGKT T0355 22 :LIGMIHC 1rd5A 20 :FIPYITA T0355 40 :ASMD 1rd5A 27 :GDPD T0355 46 :YDACMRDAERLIEGGMHGLIVE 1rd5A 31 :LATTAEALRLLDGCGADVIELG T0355 72 :VPFSKPDDIGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKAGGAK 1rd5A 53 :VPCSDPYIDGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPI T0355 129 :VNQ 1rd5A 111 :LAK T0355 137 :VANEGFMEGRAAEAM 1rd5A 114 :MKEAGVHGLIVPDLP T0355 152 :RYRSLLRAEHIKVFADSHV 1rd5A 130 :VAAHSLWSEAKNNNLELVL T0355 173 :GA 1rd5A 151 :TP T0355 177 :ITADRSIDELTRDLAFFDA 1rd5A 153 :AIPEDRMKEITKASEGFVY T0355 196 :DGVIA 1rd5A 174 :SVNGV T0355 203 :QRTGNSASL 1rd5A 181 :PRANVNPRV T0355 212 :EEIEEIGAATHLPLLVGSGV 1rd5A 191 :SLIQEVKKVTNKPVAVGFGI T0355 232 :NEGNIVEILKR 1rd5A 212 :KPEHVKQIAQW T0355 243 :TSGVIVASSLKEGGVWW 1rd5A 224 :ADGVIIGSAMVRQLGEA T0355 260 :NPVELARVRSFVAAARPGL 1rd5A 243 :PKQGLRRLEEYARGMKNAL Number of specific fragments extracted= 16 number of extra gaps= 4 total=1902 Number of alignments=116 # 1rd5A read from 1rd5A/merged-good-all-a2m # found chain 1rd5A in template set Warning: unaligning (T0355)I113 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)F108 Warning: unaligning (T0355)V164 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rd5A)T150 Warning: unaligning (T0355)F165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rd5A)T150 Warning: unaligning (T0355)T205 because of BadResidue code BAD_PEPTIDE in next template residue (1rd5A)G180 Warning: unaligning (T0355)G206 because of BadResidue code BAD_PEPTIDE at template residue (1rd5A)G180 T0355 8 :AANAIQEIFGRSKALIGMIHCP 1rd5A 5 :VSDTMAALMAKGKTAFIPYITA T0355 33 :GAP 1rd5A 27 :GDP T0355 41 :S 1rd5A 30 :D T0355 46 :YDACMRDAERLIEGGMHGLIVENHGDVP 1rd5A 31 :LATTAEALRLLDGCGADVIELGVPCSDP T0355 78 :DDIGPETSAFMS 1rd5A 59 :YIDGPIIQASVA T0355 90 :VVTDRIVRTA 1rd5A 81 :AVLEMLREVT T0355 100 :GVPVGINVLANAP 1rd5A 94 :SCPVVLLSYYKPI T0355 119 :AKAGGAKFIRV 1rd5A 114 :MKEAGVHGLIV T0355 140 :EGFMEGRAAEAMRYRSLLRAEHIK 1rd5A 125 :PDLPYVAAHSLWSEAKNNNLELVL T0355 178 :TADRSIDELTRDLAFFDADGVIATGQR 1rd5A 151 :TPAIPEDRMKEITKASEGFVYLVSVNG T0355 207 :NSAS 1rd5A 181 :PRAN T0355 211 :LEEIEEIGAATHLPLLVGSGV 1rd5A 190 :ESLIQEVKKVTNKPVAVGFGI T0355 232 :NEGNIVEILKR 1rd5A 212 :KPEHVKQIAQW T0355 243 :TSGVIVASSL 1rd5A 224 :ADGVIIGSAM T0355 263 :ELAR 1rd5A 242 :SPKQ T0355 267 :VRSFVAAARPGLEAL 1rd5A 247 :LRRLEEYARGMKNAL Number of specific fragments extracted= 16 number of extra gaps= 3 total=1918 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x1zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x1zA expands to /projects/compbio/data/pdb/1x1z.pdb.gz 1x1zA:Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1x1zA Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1x1zA # T0355 read from 1x1zA/merged-good-all-a2m # 1x1zA read from 1x1zA/merged-good-all-a2m # adding 1x1zA to template set # found chain 1x1zA in template set Warning: unaligning (T0355)G277 because last residue in template chain is (1x1zA)L225 T0355 32 :PGAPRYRNAS 1x1zA 14 :RLILAMDLMN T0355 46 :YDACMRDAERL 1x1zA 24 :RDDALRVTGEV T0355 61 :MHGLIVE 1x1zA 38 :IDTVKIG T0355 82 :PETSA 1x1zA 45 :YPLVL T0355 93 :DRI 1x1zA 50 :SEG T0355 102 :PVGINVLANA 1x1zA 53 :MDIIAEFRKR T0355 112 :PIPAFAIAKAGG 1x1zA 64 :GCRIIADFKVAD T0355 128 :RVNQWAN 1x1zA 79 :TNEKICR T0355 136 :YVANEGFMEGRAAEAM 1x1zA 86 :ATFKAGADAIIVHGFP T0355 152 :RYRSLLRAEHIKVFADSHV 1x1zA 108 :ACLNVAEEMGREVFLLTEM T0355 172 :HGAHAIT 1x1zA 127 :SHPGAEM T0355 182 :SIDELTR 1x1zA 134 :FIQGAAD T0355 189 :DLAF 1x1zA 150 :GVKN T0355 194 :DADGV 1x1zA 154 :YVGPS T0355 202 :G 1x1zA 159 :T T0355 210 :SLEEIEEIGAATH 1x1zA 160 :RPERLSRLREIIG T0355 223 :LPLLVGS 1x1zA 175 :SFLISPG T0355 230 :GVN 1x1zA 186 :GGD T0355 236 :IVEILKRTSGVIVASSLKEGGV 1x1zA 189 :PGETLRFADAIIVGRSIYLADN T0355 263 :ELARVRSFVAAARP 1x1zA 211 :PAAAAAGIIESIKD Number of specific fragments extracted= 20 number of extra gaps= 0 total=1938 Number of alignments=118 # 1x1zA read from 1x1zA/merged-good-all-a2m # found chain 1x1zA in template set Warning: unaligning (T0355)R18 because first residue in template chain is (1x1zA)V11 Warning: unaligning (T0355)G277 because last residue in template chain is (1x1zA)L225 T0355 19 :SKALIGMIHCPA 1x1zA 12 :MNRLILAMDLMN T0355 46 :YDACMRDAERLIE 1x1zA 24 :RDDALRVTGEVRE T0355 61 :MHGLIVE 1x1zA 38 :IDTVKIG T0355 88 :MSVVTDRI 1x1zA 45 :YPLVLSEG T0355 103 :VGINVLANAPIPAFAIAKAGGAKFIRVNQWANA 1x1zA 54 :DIIAEFRKRFGCRIIADFKVADIPETNEKICRA T0355 137 :VANEGFMEGRAAEAM 1x1zA 87 :TFKAGADAIIVHGFP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1x1zA 104 :DSVRACLNVAEEMGREVFLLTEM T0355 177 :ITAD 1x1zA 127 :SHPG T0355 181 :RSIDELTRDLAFFDA 1x1zA 137 :GAADEIARMGVDLGV T0355 197 :GVIAT 1x1zA 153 :NYVGP T0355 208 :SASLEEIEEIGAAT 1x1zA 158 :STRPERLSRLREII T0355 222 :HLPLLVGS 1x1zA 174 :DSFLISPG T0355 230 :GVNE 1x1zA 186 :GGDP T0355 237 :VEILKRTSGVIVASSLKEG 1x1zA 190 :GETLRFADAIIVGRSIYLA T0355 261 :PVELARVRSFVAAARP 1x1zA 209 :DNPAAAAAGIIESIKD Number of specific fragments extracted= 15 number of extra gaps= 0 total=1953 Number of alignments=119 # 1x1zA read from 1x1zA/merged-good-all-a2m # found chain 1x1zA in template set Warning: unaligning (T0355)G277 because last residue in template chain is (1x1zA)L225 T0355 21 :ALIGM 1x1zA 15 :LILAM T0355 27 :HC 1x1zA 20 :DL T0355 40 :ASMDAI 1x1zA 22 :MNRDDA T0355 50 :MRDAERLIEG 1x1zA 28 :LRVTGEVREY T0355 61 :MHGLIVE 1x1zA 38 :IDTVKIG T0355 83 :ETSA 1x1zA 46 :PLVL T0355 91 :VTDRIVRTAGVPVGINVLANA 1x1zA 55 :IIAEFRKRFGCRIIADFKVAD T0355 112 :PIPAFAIAKAGGAKFIRVNQW 1x1zA 80 :NEKICRATFKAGADAIIVHGF T0355 142 :FMEGRAAEAMRYRSLLRA 1x1zA 101 :PGADSVRACLNVAEEMGR T0355 163 :KVFADSHV 1x1zA 119 :EVFLLTEM T0355 173 :GAHAITADR 1x1zA 127 :SHPGAEMFI T0355 182 :SIDELTRDLAFFDADGVI 1x1zA 138 :AADEIARMGVDLGVKNYV T0355 206 :GNSASLEEIEEIGA 1x1zA 156 :GPSTRPERLSRLRE T0355 220 :ATHLP 1x1zA 172 :GQDSF T0355 226 :LVGSGV 1x1zA 177 :LISPGV T0355 236 :IVEILKRTSGVIVASSLKEGGV 1x1zA 189 :PGETLRFADAIIVGRSIYLADN T0355 264 :LARVRSFVAAARP 1x1zA 212 :AAAAAGIIESIKD Number of specific fragments extracted= 17 number of extra gaps= 0 total=1970 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gox/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gox expands to /projects/compbio/data/pdb/1gox.pdb.gz 1gox:Warning: there is no chain 1gox will retry with 1goxA # T0355 read from 1gox/merged-good-all-a2m # 1gox read from 1gox/merged-good-all-a2m # adding 1gox to template set # found chain 1gox in template set Warning: unaligning (T0355)A99 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)W108 Warning: unaligning (T0355)G100 because of BadResidue code BAD_PEPTIDE at template residue (1gox)W108 Warning: unaligning (T0355)A119 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)Y129 Warning: unaligning (T0355)K120 because of BadResidue code BAD_PEPTIDE at template residue (1gox)Y129 Warning: unaligning (T0355)R242 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)G245 Warning: unaligning (T0355)L252 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)A256 Warning: unaligning (T0355)K253 because of BadResidue code BAD_PEPTIDE at template residue (1gox)A256 T0355 64 :LIVE 1gox 73 :IMIA T0355 73 :PFSKPDDIGPE 1gox 77 :PTAMQKMAHPE T0355 84 :TSAFMSVVTDRIVR 1gox 89 :EYATARAASAAGTI T0355 98 :T 1gox 106 :S T0355 101 :VPVGINVLAN 1gox 109 :ATSSVEEVAS T0355 111 :APIPAFAI 1gox 120 :GPGIRFFQ T0355 121 :AGG 1gox 130 :VYK T0355 129 :VNQWAN 1gox 137 :VAQLVR T0355 136 :YVANEGFMEGRA 1gox 143 :RAERAGFKAIAL T0355 148 :AEAMRY 1gox 156 :VDTPRL T0355 206 :GNSASLEEIEEIGAATHLPLLVGSGVNEGNIVEILK 1gox 208 :DRSLSWKDVAWLQTITSLPILVKGVITAEDARLAVQ T0355 243 :TSGVIVASS 1gox 246 :AAGIIVSNH T0355 254 :EGGVWWN 1gox 257 :RQLDYVP T0355 262 :V 1gox 265 :T T0355 264 :LARVRSFVAAA 1gox 266 :IMALEEVVKAA Number of specific fragments extracted= 15 number of extra gaps= 4 total=1985 Number of alignments=121 # 1gox read from 1gox/merged-good-all-a2m # found chain 1gox in template set Warning: unaligning (T0355)M25 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)Y129 Warning: unaligning (T0355)I26 because of BadResidue code BAD_PEPTIDE at template residue (1gox)Y129 Warning: unaligning (T0355)P114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gox)G198 Warning: unaligning (T0355)K120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gox)G198 Warning: unaligning (T0355)F193 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)G245 Warning: unaligning (T0355)D194 because of BadResidue code BAD_PEPTIDE at template residue (1gox)G245 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)A256 Warning: unaligning (T0355)Q203 because of BadResidue code BAD_PEPTIDE at template residue (1gox)A256 T0355 12 :IQEIFGRSKA 1gox 113 :VEEVASTGPG T0355 22 :LIG 1gox 125 :FFQ T0355 27 :HCPA 1gox 130 :VYKD T0355 46 :YDACMRDAERLIEGGMHGLIVE 1gox 134 :RNVVAQLVRRAERAGFKAIALT T0355 70 :GDVP 1gox 156 :VDTP T0355 79 :DIGP 1gox 160 :RLGR T0355 88 :MSVVTDRIVRT 1gox 164 :READIKNRFVL T0355 99 :AGVPV 1gox 176 :PFLTL T0355 107 :VLANAPI 1gox 181 :KNFEGID T0355 129 :VNQWANA 1gox 199 :LSSYVAG T0355 137 :VANEGFM 1gox 206 :QIDRSLS T0355 152 :RYRSLL 1gox 214 :KDVAWL T0355 162 :IKV 1gox 220 :QTI T0355 166 :ADSHVKHGA 1gox 223 :TSLPILVKG T0355 177 :ITADRSIDELTR 1gox 232 :VITAEDARLAVQ T0355 195 :ADGVIAT 1gox 246 :AAGIIVS T0355 204 :RTGNSAS 1gox 257 :RQLDYVP T0355 211 :L 1gox 265 :T T0355 212 :EEIEEIGAAT 1gox 267 :MALEEVVKAA T0355 223 :LPLLVGSGV 1gox 280 :IPVFLDGGV T0355 232 :NEGNIVEILKR 1gox 290 :RGTDVFKALAL T0355 243 :TSGVIVASSLKEGGV 1gox 302 :AAGVFIGRPVVFSLA T0355 261 :PVELARVRSFVAAARPGLEAL 1gox 317 :AEGEAGVKKVLQMMRDEFELT Number of specific fragments extracted= 23 number of extra gaps= 4 total=2008 Number of alignments=122 # 1gox read from 1gox/merged-good-all-a2m # found chain 1gox in template set Warning: unaligning (T0355)H27 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)Y129 Warning: unaligning (T0355)C28 because of BadResidue code BAD_PEPTIDE at template residue (1gox)Y129 Warning: unaligning (T0355)V103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gox)G198 Warning: unaligning (T0355)G104 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gox)G198 Warning: unaligning (T0355)F193 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)G245 Warning: unaligning (T0355)D194 because of BadResidue code BAD_PEPTIDE at template residue (1gox)G245 Warning: unaligning (T0355)R204 because of BadResidue code BAD_PEPTIDE in next template residue (1gox)A256 Warning: unaligning (T0355)T205 because of BadResidue code BAD_PEPTIDE at template residue (1gox)A256 T0355 12 :IQEIFGRSKALIGMI 1gox 113 :VEEVASTGPGIRFFQ T0355 29 :P 1gox 130 :V T0355 37 :YRN 1gox 131 :YKD T0355 46 :YDACMRDAERLIEGGMHGLIVENHGDVP 1gox 134 :RNVVAQLVRRAERAGFKAIALTVDTPRL T0355 74 :FSKPDDIGPE 1gox 172 :FVLPPFLTLK T0355 97 :RTAGVP 1gox 182 :NFEGID T0355 134 :NAYVANEGFMEGRAAEAMRYR 1gox 203 :VAGQIDRSLSWKDVAWLQTIT T0355 161 :HIKVFADSHVK 1gox 224 :SLPILVKGVIT T0355 184 :DELTRDLAF 1gox 235 :AEDARLAVQ T0355 195 :ADGVIATGQ 1gox 246 :AAGIIVSNH T0355 206 :GNS 1gox 257 :RQL T0355 209 :ASLEEIEEIGA 1gox 264 :ATIMALEEVVK T0355 220 :ATHLPLLVGSGV 1gox 277 :QGRIPVFLDGGV T0355 232 :NEGNIVEIL 1gox 290 :RGTDVFKAL T0355 242 :RTSGVIVA 1gox 301 :GAAGVFIG T0355 263 :ELARVRSFVAAARPGLEAL 1gox 319 :GEAGVKKVLQMMRDEFELT Number of specific fragments extracted= 16 number of extra gaps= 4 total=2024 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1yA expands to /projects/compbio/data/pdb/1h1y.pdb.gz 1h1yA:# T0355 read from 1h1yA/merged-good-all-a2m # 1h1yA read from 1h1yA/merged-good-all-a2m # adding 1h1yA to template set # found chain 1h1yA in template set Warning: unaligning (T0355)G277 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1yA)Q224 Warning: unaligning (T0355)L278 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h1yA)Q224 T0355 33 :GAPRYRNASMD 1h1yA 8 :IAPSMLSSDFA T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 1h1yA 19 :NLAAEADRMVRLGADWLHMDIMDGH T0355 74 :FSKPDDIG 1h1yA 44 :FVPNLTIG T0355 82 :PETS 1h1yA 53 :PVIQ T0355 107 :VLANAPIPAFAIAKAGG 1h1yA 57 :SLRKHTKAYLDCHLMVT T0355 128 :RVNQWAN 1h1yA 74 :NPSDYVE T0355 136 :YVANEGFMEGRAA 1h1yA 81 :PLAKAGASGFTFH T0355 155 :SLLRAEHIKVFADSHVKHGAHAIT 1h1yA 106 :QSIKAKGMRPGVSLRPGTPVEEVF T0355 182 :SIDELTRDLAFFDA 1h1yA 130 :PLVEAENPVELVLV T0355 200 :AT 1h1yA 144 :MT T0355 202 :GQRTGNSASLEEIEEIGAATH 1h1yA 151 :GGQKFMPEMMEKVRALRKKYP T0355 223 :LPLLVGSGVNEGNIVEILKR 1h1yA 173 :LDIEVDGGLGPSTIDVAASA T0355 243 :TSGVIVASSLKEGGV 1h1yA 194 :ANCIVAGSSIFGAAE T0355 263 :ELARVRSFVAAARP 1h1yA 209 :PGEVISALRKSVEG Number of specific fragments extracted= 14 number of extra gaps= 1 total=2038 Number of alignments=124 # 1h1yA read from 1h1yA/merged-good-all-a2m # found chain 1h1yA in template set Warning: unaligning (T0355)S19 because first residue in template chain is (1h1yA)A5 Warning: unaligning (T0355)G277 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1yA)Q224 Warning: unaligning (T0355)L278 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1h1yA)Q224 T0355 20 :KALIGM 1h1yA 6 :AKIAPS T0355 37 :YRNASMD 1h1yA 12 :MLSSDFA T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 1h1yA 19 :NLAAEADRMVRLGADWLHMDIMDGH T0355 74 :FSKPDDIGP 1h1yA 44 :FVPNLTIGA T0355 103 :VGINVLANAPIPAFAIAKAGG 1h1yA 53 :PVIQSLRKHTKAYLDCHLMVT T0355 128 :RVNQWANA 1h1yA 74 :NPSDYVEP T0355 137 :VANEGFMEGRA 1h1yA 82 :LAKAGASGFTF T0355 148 :AEAM 1h1yA 94 :IEVS T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1h1yA 99 :DNWQELIQSIKAKGMRPGVSLRP T0355 177 :ITADRSIDELTRD 1h1yA 122 :GTPVEEVFPLVEA T0355 190 :L 1h1yA 138 :V T0355 196 :DGVIAT 1h1yA 139 :ELVLVM T0355 202 :GQRTGNSASLEEIEEIGAAT 1h1yA 151 :GGQKFMPEMMEKVRALRKKY T0355 222 :HLPLLVGSGVNEGNIVEILKR 1h1yA 172 :SLDIEVDGGLGPSTIDVAASA T0355 243 :TSGVIVASSLKEG 1h1yA 194 :ANCIVAGSSIFGA T0355 261 :PVELARVRSFVAAARP 1h1yA 207 :AEPGEVISALRKSVEG Number of specific fragments extracted= 16 number of extra gaps= 1 total=2054 Number of alignments=125 # 1h1yA read from 1h1yA/merged-good-all-a2m # found chain 1h1yA in template set Warning: unaligning (T0355)G277 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1h1yA)Q224 T0355 21 :ALI 1h1yA 7 :KIA T0355 29 :PAFPGAPRYR 1h1yA 10 :PSMLSSDFAN T0355 49 :CMRDAERLIEGGMHGLIVENHGDVPFSKP 1h1yA 20 :LAAEADRMVRLGADWLHMDIMDGHFVPNL T0355 79 :DIGPETS 1h1yA 49 :TIGAPVI T0355 93 :DRIVRTAGVPVGINVLANAPIPAFAIAKAGGAKFIRVN 1h1yA 56 :QSLRKHTKAYLDCHLMVTNPSDYVEPLAKAGASGFTFH T0355 140 :EGFMEGRAAEAMRYRSLLR 1h1yA 94 :IEVSRDNWQELIQSIKAKG T0355 162 :IKVFADSH 1h1yA 113 :MRPGVSLR T0355 179 :ADRSIDELTRDLAF 1h1yA 121 :PGTPVEEVFPLVEA T0355 193 :FDADGVIATGQRTGNSAS 1h1yA 136 :NPVELVLVMTVEPGFGGQ T0355 211 :LEEIEEIGA 1h1yA 160 :MEKVRALRK T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1h1yA 170 :YPSLDIEVDGGLGPSTIDVAASA T0355 243 :TSGVIVASSLKEGGV 1h1yA 194 :ANCIVAGSSIFGAAE T0355 264 :LARVRSFVAAARP 1h1yA 210 :GEVISALRKSVEG Number of specific fragments extracted= 13 number of extra gaps= 1 total=2067 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1km4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1km4A/merged-good-all-a2m # 1km4A read from 1km4A/merged-good-all-a2m # found chain 1km4A in training set Warning: unaligning (T0355)A274 because last residue in template chain is (1km4A)I222 T0355 30 :AFPGAPRYRNAS 1km4A 12 :MNRLILAMDLMN T0355 46 :YDACMRDAERLIEG 1km4A 24 :RDDALRVTGEVREY T0355 61 :MHGLIVE 1km4A 38 :IDTVKIG T0355 82 :PETSA 1km4A 45 :YPLVL T0355 93 :DRI 1km4A 50 :SEG T0355 102 :PVGINVLANA 1km4A 53 :MDIIAEFRKR T0355 112 :PIPAFAIAKAGG 1km4A 64 :GCRIIADFAVAD T0355 128 :RVNQWAN 1km4A 79 :TNEKICR T0355 136 :YVANEGFMEGRAAEAM 1km4A 86 :ATFKAGADAIIVHGFP T0355 152 :RYRSLLRAEHIKVFADSHV 1km4A 108 :ACLNVAEEMGREVFLLTEM T0355 172 :HGAHAIT 1km4A 127 :SHPGAEM T0355 182 :SIDELTR 1km4A 134 :FIQGAAD T0355 189 :DLAF 1km4A 150 :GVKN T0355 194 :DADGV 1km4A 154 :YVGPS T0355 202 :G 1km4A 159 :T T0355 210 :SLEEIEEIGAATH 1km4A 160 :RPERLSRLREIIG T0355 223 :LPLLVGS 1km4A 175 :SFLISPG T0355 230 :GVN 1km4A 186 :GGD T0355 236 :IVEILKRTSGVIVASSLKEGGV 1km4A 189 :PGETLRFADAIIVGRSIYLADN T0355 263 :ELARVRSFVAA 1km4A 211 :PAAAAAGIIES Number of specific fragments extracted= 20 number of extra gaps= 0 total=2087 Number of alignments=127 # 1km4A read from 1km4A/merged-good-all-a2m # found chain 1km4A in training set Warning: unaligning (T0355)R18 because first residue in template chain is (1km4A)V11 Warning: unaligning (T0355)A274 because last residue in template chain is (1km4A)I222 T0355 19 :SKALIGMIHCPA 1km4A 12 :MNRLILAMDLMN T0355 46 :YDACMRDAERLIEG 1km4A 24 :RDDALRVTGEVREY T0355 61 :MHGLIVE 1km4A 38 :IDTVKIG T0355 88 :MSVVTDRI 1km4A 45 :YPLVLSEG T0355 103 :VGINVLANAPIPAFAIAKAGGAKFIRVNQWANA 1km4A 54 :DIIAEFRKRFGCRIIADFAVADIPETNEKICRA T0355 137 :VANEGFMEGRAAEAM 1km4A 87 :TFKAGADAIIVHGFP T0355 152 :RYRSLLRAEHIKVFADSHVKHGA 1km4A 104 :DSVRACLNVAEEMGREVFLLTEM T0355 177 :ITAD 1km4A 127 :SHPG T0355 181 :RSIDELTRDLAFFDA 1km4A 137 :GAADEIARMGVDLGV T0355 197 :GVIAT 1km4A 153 :NYVGP T0355 208 :SASLEEIEEIGAAT 1km4A 158 :STRPERLSRLREII T0355 222 :HLPLLVGS 1km4A 174 :DSFLISPG T0355 230 :GVNE 1km4A 186 :GGDP T0355 237 :VEILKRTSGVIVASSLKEG 1km4A 190 :GETLRFADAIIVGRSIYLA T0355 261 :PVELARVRSFVAA 1km4A 209 :DNPAAAAAGIIES Number of specific fragments extracted= 15 number of extra gaps= 0 total=2102 Number of alignments=128 # 1km4A read from 1km4A/merged-good-all-a2m # found chain 1km4A in training set Warning: unaligning (T0355)A274 because last residue in template chain is (1km4A)I222 T0355 20 :KALIGM 1km4A 14 :RLILAM T0355 38 :RNASMDA 1km4A 20 :DLMNRDD T0355 49 :CMRDAERLIEG 1km4A 27 :ALRVTGEVREY T0355 61 :MHGLIVE 1km4A 38 :IDTVKIG T0355 83 :ETSA 1km4A 46 :PLVL T0355 91 :VTDRIVRTAGVPVGINVLANA 1km4A 55 :IIAEFRKRFGCRIIADFAVAD T0355 112 :PIPAFAIAKAGGAKFIRVNQW 1km4A 80 :NEKICRATFKAGADAIIVHGF T0355 142 :FMEGRAAEAMRYRSLLRA 1km4A 101 :PGADSVRACLNVAEEMGR T0355 161 :HIKVFADSHVKH 1km4A 119 :EVFLLTEMSHPG T0355 177 :ITADR 1km4A 131 :AEMFI T0355 182 :SIDELTRDLAFFDADGVI 1km4A 138 :AADEIARMGVDLGVKNYV T0355 206 :GNSASLEEIEEIGA 1km4A 156 :GPSTRPERLSRLRE T0355 220 :ATHLPL 1km4A 172 :GQDSFL T0355 227 :VGSGV 1km4A 178 :ISPGV T0355 232 :N 1km4A 188 :D T0355 236 :IVEILKRTSGVIVASSLKEGGV 1km4A 189 :PGETLRFADAIIVGRSIYLADN T0355 264 :LARVRSFVAA 1km4A 212 :AAAAAGIIES Number of specific fragments extracted= 17 number of extra gaps= 0 total=2119 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gokA expands to /projects/compbio/data/pdb/2gok.pdb.gz 2gokA:# T0355 read from 2gokA/merged-good-all-a2m # 2gokA read from 2gokA/merged-good-all-a2m # adding 2gokA to template set # found chain 2gokA in template set T0355 39 :NASMDAIYDACMRDAERLIEGGMHGLIVENHGDV 2gokA 127 :ALSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGL T0355 80 :IGPETSAFMSV 2gokA 161 :DIETELKMLRV T0355 105 :INVLANAPIPAFAIAKAGGAKF 2gokA 172 :ARRLETLRPVRIVTSYLAAHAT T0355 127 :IRVNQWANAYVANE 2gokA 195 :ADYKGRNADYITDV T0355 150 :AMRYRSLLRAEHI 2gokA 209 :VLPGLEKAHAEGL T0355 163 :KVF 2gokA 223 :DAV T0355 166 :ADSHVKHGAHAIT 2gokA 228 :FCEGIAFSVKEID T0355 182 :SIDELTR 2gokA 241 :RVFAAAQ T0355 194 :DADGVIATGQRTGNS 2gokA 250 :GLPVKLHAEQLSNLG T0355 213 :EIEEIGAA 2gokA 265 :GAELAASY T0355 222 :H 2gokA 273 :N T0355 223 :LPLLVGSGVNEGNIVEILKR 2gokA 275 :LSADHLEYLDETGAKALAKA T0355 243 :TSGVIVASSLKEGGVWW 2gokA 296 :TVAVLLPGAFYALREKQ T0355 264 :LARVRSF 2gokA 316 :VQALRDA Number of specific fragments extracted= 14 number of extra gaps= 0 total=2133 Number of alignments=130 # 2gokA read from 2gokA/merged-good-all-a2m # found chain 2gokA in template set T0355 40 :ASMDAIYDACMRDAERLIEGGMHGLIVENHGDV 2gokA 128 :LSDEVLVAQALPRLDTLLSEGVSTIEIKSGYGL T0355 80 :IGPETSAFM 2gokA 161 :DIETELKML T0355 103 :VGINVLANAPIPAFAIAKAG 2gokA 170 :RVARRLETLRPVRIVTSYLA T0355 123 :GAKF 2gokA 194 :PADY T0355 127 :IRVNQWANAYVAN 2gokA 199 :GRNADYITDVVLP T0355 157 :LRAEHIKVFA 2gokA 212 :GLEKAHAEGL T0355 167 :DSH 2gokA 223 :DAV T0355 170 :VKHGA 2gokA 228 :FCEGI T0355 177 :ITADRSIDELTRDLAFFDADGVIATGQRTGN 2gokA 233 :AFSVKEIDRVFAAAQQRGLPVKLHAEQLSNL T0355 210 :SL 2gokA 264 :GG T0355 214 :IEEIGA 2gokA 266 :AELAAS T0355 221 :THLPLLVGSGV 2gokA 272 :YNALSADHLEY T0355 232 :NEGNIVEILKR 2gokA 284 :DETGAKALAKA T0355 243 :TSGVIVASSLKEGGVWWN 2gokA 296 :TVAVLLPGAFYALREKQL T0355 264 :LARVRSF 2gokA 316 :VQALRDA Number of specific fragments extracted= 15 number of extra gaps= 0 total=2148 Number of alignments=131 # 2gokA read from 2gokA/merged-good-all-a2m # found chain 2gokA in template set T0355 40 :ASMDAIYDACMRDAERLIEGGMHGLIVENHGD 2gokA 128 :LSDEVLVAQALPRLDTLLSEGVSTIEIKSGYG T0355 80 :IGPETSAFMSVVTDRIVRTAGVPVGINVLANA 2gokA 160 :LDIETELKMLRVARRLETLRPVRIVTSYLAAH T0355 112 :PIPAFAIAKAGGA 2gokA 209 :VLPGLEKAHAEGL T0355 130 :NQWANAYVANEGFMEGRAAEAMRYRSLLRA 2gokA 222 :ADAVDGFCEGIAFSVKEIDRVFAAAQQRGL T0355 161 :HIKVFADSHVK 2gokA 252 :PVKLHAEQLSN T0355 181 :RS 2gokA 263 :LG T0355 186 :LTRDLAFFDADGVIATGQ 2gokA 265 :GAELAASYNALSADHLEY T0355 209 :ASLEEIEEIGAATH 2gokA 283 :LDETGAKALAKAGT T0355 225 :LLVGS 2gokA 297 :VAVLL T0355 231 :VNEGNIVEI 2gokA 314 :PPVQALRDA T0355 242 :RTSGVIVASSLKEGGVWWN 2gokA 323 :GAEIALATDCNPGTSPLTS Number of specific fragments extracted= 11 number of extra gaps= 0 total=2159 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yadA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yadA expands to /projects/compbio/data/pdb/1yad.pdb.gz 1yadA:# T0355 read from 1yadA/merged-good-all-a2m # 1yadA read from 1yadA/merged-good-all-a2m # adding 1yadA to template set # found chain 1yadA in template set Warning: unaligning (T0355)P32 because first residue in template chain is (1yadA)M1 Warning: unaligning (T0355)I199 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yadA)R135 T0355 33 :GAPRYRNASMD 1yadA 2 :ELHAITDDSKP T0355 46 :YDACMRDAERLI 1yadA 13 :VEELARIIITIQ T0355 61 :MHGLIV 1yadA 27 :VDFIHI T0355 75 :SKPDDIGPETSAFMSVVTDRIVRTAGV 1yadA 33 :RERSKSAADILKLLDLIFEGGIDKRKL T0355 118 :IAKA 1yadA 60 :VMNG T0355 128 :RVN 1yadA 64 :RVD T0355 136 :YVANEGFMEGRAAEAMRYRSLLRA 1yadA 67 :IALFSTIHRVQLPSGSFSPKQIRA T0355 160 :EHIKVFADSH 1yadA 93 :PHLHIGRSVH T0355 173 :GAHAIT 1yadA 103 :SLEEAV T0355 182 :SIDE 1yadA 109 :QAEK T0355 188 :RDLAFFDADGV 1yadA 113 :EDADYVLFGHV T0355 210 :SLEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1yadA 136 :GVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQA T0355 243 :TSGVIVASSLKEGGV 1yadA 170 :ADGIAVMSGIFSSAE T0355 263 :ELARVRSFVAAARPG 1yadA 185 :PLEAARRYSRKLKEM Number of specific fragments extracted= 14 number of extra gaps= 0 total=2173 Number of alignments=133 # 1yadA read from 1yadA/merged-good-all-a2m # found chain 1yadA in template set Warning: unaligning (T0355)K20 because first residue in template chain is (1yadA)M1 Warning: unaligning (T0355)I199 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yadA)R135 T0355 21 :ALIGMIHCPAF 1yadA 2 :ELHAITDDSKP T0355 46 :YDACMRDAERLIEG 1yadA 13 :VEELARIIITIQNE T0355 61 :MHGLIVE 1yadA 27 :VDFIHIR T0355 76 :KPDDIGPETSAFMSVVTDRIVRTAGV 1yadA 34 :ERSKSAADILKLLDLIFEGGIDKRKL T0355 117 :AIAK 1yadA 60 :VMNG T0355 128 :RVNQ 1yadA 64 :RVDI T0355 137 :VANEGFMEGRAAEAM 1yadA 68 :ALFSTIHRVQLPSGS T0355 152 :R 1yadA 84 :S T0355 158 :RAEHIKVFADSHVKHGA 1yadA 85 :PKQIRARFPHLHIGRSV T0355 178 :TADRSIDELTRD 1yadA 102 :HSLEEAVQAEKE T0355 190 :LAFFDADGV 1yadA 115 :ADYVLFGHV T0355 210 :SLEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1yadA 136 :GVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQA T0355 243 :TSGVIVASSLKEG 1yadA 170 :ADGIAVMSGIFSS T0355 261 :PVELARVRSFVAAARPG 1yadA 183 :AEPLEAARRYSRKLKEM Number of specific fragments extracted= 14 number of extra gaps= 0 total=2187 Number of alignments=134 # 1yadA read from 1yadA/merged-good-all-a2m # found chain 1yadA in template set Warning: unaligning (T0355)K20 because first residue in template chain is (1yadA)M1 Warning: unaligning (T0355)S210 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yadA)R135 T0355 21 :ALIGMI 1yadA 2 :ELHAIT T0355 37 :YRNASMDAIYDACMR 1yadA 8 :DDSKPVEELARIIIT T0355 56 :LIE 1yadA 23 :IQN T0355 61 :MHGLIVENH 1yadA 27 :VDFIHIRER T0355 79 :DIGPETSA 1yadA 36 :SKSAADIL T0355 90 :VVTDRIVRTA 1yadA 44 :KLLDLIFEGG T0355 106 :NVLANAPI 1yadA 59 :LVMNGRVD T0355 118 :IAKAGGAKFIRV 1yadA 67 :IALFSTIHRVQL T0355 139 :NEGFMEGR 1yadA 79 :PSGSFSPK T0355 152 :RYRSL 1yadA 87 :QIRAR T0355 159 :AEHIKVFADSH 1yadA 92 :FPHLHIGRSVH T0355 182 :SIDELTR 1yadA 103 :SLEEAVQ T0355 190 :LAFFDADGVIAT 1yadA 110 :AEKEDADYVLFG T0355 211 :LEEIEEIGAATHLPLLVGSGVNEGNIVEILKR 1yadA 137 :VSLLSDIKQRISIPVIAIGGMTPDRLRDVKQA T0355 243 :TSGVIVASSLKEGGV 1yadA 170 :ADGIAVMSGIFSSAE T0355 264 :LARVRSFVAAARPG 1yadA 186 :LEAARRYSRKLKEM Number of specific fragments extracted= 16 number of extra gaps= 0 total=2203 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tqxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tqxA expands to /projects/compbio/data/pdb/1tqx.pdb.gz 1tqxA:# T0355 read from 1tqxA/merged-good-all-a2m # 1tqxA read from 1tqxA/merged-good-all-a2m # adding 1tqxA to template set # found chain 1tqxA in template set Warning: unaligning (T0355)L281 because last residue in template chain is (1tqxA)Y224 T0355 32 :PGAPRYRNASMD 1tqxA 7 :IIAPSVLASNIS T0355 48 :ACMRDAERLIEGGMHGLIVENHGDV 1tqxA 19 :KLAEETQRMESLGAEWIHLDVMDMH T0355 74 :FSKPDDIGPE 1tqxA 44 :FVPNLSFGPP T0355 104 :GINVLAN 1tqxA 54 :VINNLKK T0355 111 :APIPAFAIAKAGG 1tqxA 62 :TKSIFFDVHLMVE T0355 128 :RVNQWAN 1tqxA 75 :YPEKYVP T0355 136 :YVA 1tqxA 82 :LLK T0355 141 :GFMEGRAAEAMRYR 1tqxA 85 :TSNQLTFHFEALNE T0355 155 :SLLRAEHIKVFADSHVKHGAHAIT 1tqxA 108 :KEIRDNNLWCGISIKPKTDVQKLV T0355 182 :SIDEL 1tqxA 132 :PILDT T0355 188 :RDLAFFDA 1tqxA 137 :NLINTVLV T0355 200 :AT 1tqxA 145 :MT T0355 202 :GQRTGNSASLEEIEEIGAATH 1tqxA 152 :GGQSFMHDMMGKVSFLRKKYK T0355 223 :LPLLVGSGVNEGNIVEILKR 1tqxA 174 :LNIQVDGGLNIETTEISASH T0355 243 :TSGVIVASSLKEGGV 1tqxA 195 :ANIIVAGTSIFNAED T0355 267 :VRSFVAAARPGLEA 1tqxA 210 :PKYVIDTMRVSVQK Number of specific fragments extracted= 16 number of extra gaps= 0 total=2219 Number of alignments=136 # 1tqxA read from 1tqxA/merged-good-all-a2m # found chain 1tqxA in template set Warning: unaligning (T0355)S19 because first residue in template chain is (1tqxA)L4 Warning: unaligning (T0355)G277 because last residue in template chain is (1tqxA)Y224 T0355 20 :KALIGM 1tqxA 5 :KAIIAP T0355 36 :RYRNASMDA 1tqxA 11 :SVLASNISK T0355 49 :CMRDAERLIEGGMHGLIVENHGDV 1tqxA 20 :LAEETQRMESLGAEWIHLDVMDMH T0355 74 :FSKPDDIGP 1tqxA 44 :FVPNLSFGP T0355 103 :VGINVLANAP 1tqxA 53 :PVINNLKKYT T0355 113 :IPAFAIAKAGG 1tqxA 64 :SIFFDVHLMVE T0355 128 :RVNQWANA 1tqxA 75 :YPEKYVPL T0355 137 :VANE 1tqxA 83 :LKTS T0355 143 :MEGRAAEAM 1tqxA 87 :NQLTFHFEA T0355 152 :RYRS 1tqxA 98 :EDTE T0355 156 :LLRAEHIKVFADSHVKHGA 1tqxA 105 :QLAKEIRDNNLWCGISIKP T0355 177 :ITADRSIDELTRD 1tqxA 124 :KTDVQKLVPILDT T0355 193 :FDADGVIAT 1tqxA 137 :NLINTVLVM T0355 202 :GQRTGNSASLEEIEEIGAAT 1tqxA 152 :GGQSFMHDMMGKVSFLRKKY T0355 222 :HLPLLVGSGVNEGNIVEILKR 1tqxA 173 :NLNIQVDGGLNIETTEISASH T0355 243 :TSGVIVASSLKEG 1tqxA 195 :ANIIVAGTSIFNA T0355 261 :PVELARVRSFVAAARP 1tqxA 208 :EDPKYVIDTMRVSVQK Number of specific fragments extracted= 17 number of extra gaps= 0 total=2236 Number of alignments=137 # 1tqxA read from 1tqxA/merged-good-all-a2m # found chain 1tqxA in template set Warning: unaligning (T0355)S19 because first residue in template chain is (1tqxA)L4 T0355 20 :KALIGMIHCP 1tqxA 5 :KAIIAPSVLA T0355 34 :APRYR 1tqxA 15 :SNISK T0355 49 :CMRDAERLIEGGMHGLIVENH 1tqxA 20 :LAEETQRMESLGAEWIHLDVM T0355 71 :DVPFSKPDDIGPETSA 1tqxA 41 :DMHFVPNLSFGPPVIN T0355 94 :RIVRTA 1tqxA 57 :NLKKYT T0355 100 :GVPVGINVLANAPI 1tqxA 64 :SIFFDVHLMVEYPE T0355 125 :KFI 1tqxA 78 :KYV T0355 130 :NQWANAY 1tqxA 87 :NQLTFHF T0355 141 :GFMEGRAAEAMRYRSLLRAEHIKVFADSHV 1tqxA 94 :EALNEDTERCIQLAKEIRDNNLWCGISIKP T0355 180 :DRSIDELTRDLAFFDADGVIATG 1tqxA 124 :KTDVQKLVPILDTNLINTVLVMT T0355 203 :QRTGNSAS 1tqxA 150 :GFGGQSFM T0355 211 :LEEIEEIGA 1tqxA 161 :MGKVSFLRK T0355 220 :ATHLPLLVGSGVNEGNIVEILKR 1tqxA 171 :YKNLNIQVDGGLNIETTEISASH T0355 243 :TSGVIVASSLKEGGV 1tqxA 195 :ANIIVAGTSIFNAED T0355 264 :LARVRSFVAAARP 1tqxA 211 :KYVIDTMRVSVQK Number of specific fragments extracted= 15 number of extra gaps= 0 total=2251 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yxyA expands to /projects/compbio/data/pdb/1yxy.pdb.gz 1yxyA:# T0355 read from 1yxyA/merged-good-all-a2m # 1yxyA read from 1yxyA/merged-good-all-a2m # adding 1yxyA to template set # found chain 1yxyA in template set Warning: unaligning (T0355)D6 because first residue in template chain is (1yxyA)K4 T0355 7 :NAANAIQEIFG 1yxyA 5 :PTKEKLMEQLK T0355 19 :SKALIGMIHCPAFPGAP 1yxyA 16 :GGIIVSCQALPGEPLYS T0355 40 :AS 1yxyA 35 :GG T0355 48 :ACMRDAERLIEGGMHGLIVE 1yxyA 37 :IMPLMAKAAQEAGAVGIRAN T0355 101 :VPVGINVLANAPIPAFAIAKA 1yxyA 57 :SVRDIKEIQAITDLPIIGIIK T0355 122 :GGAKFIRVNQWAN 1yxyA 83 :QEPFITATMTEVD T0355 136 :YVANEGFM 1yxyA 96 :QLAALNIA T0355 145 :GRAAEAM 1yxyA 104 :VIAMDCT T0355 155 :SLLRA 1yxyA 125 :RQVKE T0355 160 :EHIKVFADSHV 1yxyA 132 :PNQLLMADIST T0355 174 :AHAIT 1yxyA 143 :FDEGL T0355 182 :SIDEL 1yxyA 148 :VAHQA T0355 189 :DLAFFDADGV 1yxyA 153 :GIDFVGTTLS T0355 202 :G 1yxyA 163 :G T0355 203 :QRTGNSASLEEIEEIGAA 1yxyA 168 :SRQEAGPDVALIEALCKA T0355 222 :HLPLLVGSGV 1yxyA 186 :GIAVIAEGKI T0355 232 :NEGNIVEILKR 1yxyA 197 :SPEEAKKINDL T0355 243 :TSGVIVASSLK 1yxyA 209 :VAGIVVGGAIT T0355 260 :NPVELA 1yxyA 220 :RPKEIA T0355 276 :PG 1yxyA 226 :ER Number of specific fragments extracted= 20 number of extra gaps= 0 total=2271 Number of alignments=139 # 1yxyA read from 1yxyA/merged-good-all-a2m # found chain 1yxyA in template set Warning: unaligning (T0355)D6 because first residue in template chain is (1yxyA)K4 T0355 7 :NAANAIQEIFGRSK 1yxyA 5 :PTKEKLMEQLKGGI T0355 25 :MIHCPAFPGAPRY 1yxyA 19 :IVSCQALPGEPLY T0355 41 :SMD 1yxyA 32 :SET T0355 46 :YDACMRDAERLIEGGMHGLIVE 1yxyA 35 :GGIMPLMAKAAQEAGAVGIRAN T0355 101 :VPVGINVLANAPIPAFAIAKA 1yxyA 57 :SVRDIKEIQAITDLPIIGIIK T0355 122 :GGAKFIRVNQWANA 1yxyA 83 :QEPFITATMTEVDQ T0355 137 :VANEGFMEGRA 1yxyA 97 :LAALNIAVIAM T0355 148 :AEAMRY 1yxyA 115 :HDGLDI T0355 155 :SLLRAEHIKVFADSHVKHG 1yxyA 121 :ASFIRQVKEKYPNQLLMAD T0355 177 :ITADRSIDELTR 1yxyA 140 :ISTFDEGLVAHQ T0355 193 :FDADGVIAT 1yxyA 152 :AGIDFVGTT T0355 202 :G 1yxyA 163 :G T0355 203 :QRTGNSASLEEIEEIGAA 1yxyA 168 :SRQEAGPDVALIEALCKA T0355 222 :HLPLLVGSGV 1yxyA 186 :GIAVIAEGKI T0355 232 :NEGNIVEILKR 1yxyA 197 :SPEEAKKINDL T0355 243 :TSGVIVASSLKE 1yxyA 209 :VAGIVVGGAITR T0355 261 :PVELAR 1yxyA 221 :PKEIAE Number of specific fragments extracted= 17 number of extra gaps= 0 total=2288 Number of alignments=140 # 1yxyA read from 1yxyA/merged-good-all-a2m # found chain 1yxyA in template set T0355 7 :NAANAIQEIFGRSK 1yxyA 5 :PTKEKLMEQLKGGI T0355 25 :MIHCPAFPGAPRYRNAS 1yxyA 19 :IVSCQALPGEPLYSETG T0355 49 :CMRDAERLIEGGMHGLIVEN 1yxyA 38 :MPLMAKAAQEAGAVGIRANS T0355 89 :SVVTDRIVRTAGVPV 1yxyA 58 :VRDIKEIQAITDLPI T0355 105 :INVL 1yxyA 73 :IGII T0355 109 :ANAPIPAFAIAKAGGAKFIRVNQ 1yxyA 87 :ITATMTEVDQLAALNIAVIAMDC T0355 134 :NAYVANEGFM 1yxyA 110 :TKRDRHDGLD T0355 147 :AAEAMRYRSL 1yxyA 120 :IASFIRQVKE T0355 158 :RAEHIKVFADSHV 1yxyA 130 :KYPNQLLMADIST T0355 184 :DELTRDLAFFDADGVIAT 1yxyA 143 :FDEGLVAHQAGIDFVGTT T0355 202 :GQ 1yxyA 163 :GY T0355 204 :RTGNSASLEEIEEIGAA 1yxyA 169 :RQEAGPDVALIEALCKA T0355 222 :HLPLLVGSGV 1yxyA 186 :GIAVIAEGKI T0355 232 :NEGNIVEILKR 1yxyA 197 :SPEEAKKINDL T0355 243 :TSGVIVASSL 1yxyA 209 :VAGIVVGGAI T0355 272 :AAARPGLEALE 1yxyA 222 :KEIAERFIEAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2304 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vzwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vzwA expands to /projects/compbio/data/pdb/1vzw.pdb.gz 1vzwA:Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 1vzwA Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 1vzwA # T0355 read from 1vzwA/merged-good-all-a2m # 1vzwA read from 1vzwA/merged-good-all-a2m # adding 1vzwA to template set # found chain 1vzwA in template set Warning: unaligning (T0355)I162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vzwA)K124 Warning: unaligning (T0355)K163 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vzwA)K124 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE in next template residue (1vzwA)I168 Warning: unaligning (T0355)Q203 because of BadResidue code BAD_PEPTIDE at template residue (1vzwA)I168 Warning: unaligning (T0355)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzwA)G176 T0355 49 :CMRDAERLIEGGMHGLIVE 1vzwA 34 :PLEAALAWQRSGAEWLHLV T0355 88 :MSVVTDR 1vzwA 53 :DLDAAFG T0355 96 :VR 1vzwA 60 :TG T0355 100 :GVPVGINVLANAPIPAFAIAKAG 1vzwA 62 :DNRALIAEVAQAMDIKVELSGGI T0355 128 :RVNQWAN 1vzwA 85 :RDDDTLA T0355 136 :YVANEGFMEGRAAEAMRYR 1vzwA 92 :AALATGCTRVNLGTAALET T0355 155 :SLLRAEH 1vzwA 116 :KVIAEHG T0355 164 :VFADSH 1vzwA 125 :IAVGLD T0355 177 :ITADRSIDELTRDLAFFDADGVIAT 1vzwA 142 :TRDGGDLYETLDRLNKEGCARYVVT T0355 209 :ASLEEIEEIGAATHLPLLVGSGV 1vzwA 177 :PNLELLKNVCAATDRPVVASGGV T0355 232 :NEGNIVEILKR 1vzwA 201 :SLDDLRAIAGL T0355 243 :TSGVIVASSLKE 1vzwA 216 :VEGAIVGKALYA T0355 257 :VWWN 1vzwA 228 :KAFT T0355 267 :VRSFVAAA 1vzwA 232 :LEEALEAT Number of specific fragments extracted= 14 number of extra gaps= 2 total=2318 Number of alignments=142 # 1vzwA read from 1vzwA/merged-good-all-a2m # found chain 1vzwA in template set Warning: unaligning (T0355)R18 because first residue in template chain is (1vzwA)S2 Warning: unaligning (T0355)P35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vzwA)E28 Warning: unaligning (T0355)A166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vzwA)K124 Warning: unaligning (T0355)D167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vzwA)K124 Warning: unaligning (T0355)G206 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzwA)G176 T0355 19 :SKALIGMIHCPAFPGA 1vzwA 3 :KLELLPAVDVRDGQAV T0355 46 :YDACMRDAERLIEGGMHGLI 1vzwA 31 :YGSPLEAALAWQRSGAEWLH T0355 66 :VE 1vzwA 52 :VD T0355 92 :TDRIVRTAGVPVGINVLANAPIPAFAIAKAGGA 1vzwA 54 :LDAAFGTGDNRALIAEVAQAMDIKVELSGGIRD T0355 130 :NQWANA 1vzwA 87 :DDTLAA T0355 137 :VANEGFMEGRAAEAM 1vzwA 93 :ALATGCTRVNLGTAA T0355 152 :RYRSLLRAEHIKVF 1vzwA 109 :ETPEWVAKVIAEHG T0355 168 :SHVKH 1vzwA 125 :IAVGL T0355 173 :GAHAITADRSIDELTRDLAFFDADGVIAT 1vzwA 138 :GRGWTRDGGDLYETLDRLNKEGCARYVVT T0355 209 :ASLEEIEEIGAATHLPLLVGSGV 1vzwA 177 :PNLELLKNVCAATDRPVVASGGV T0355 232 :NEGNIVEILKR 1vzwA 201 :SLDDLRAIAGL T0355 243 :TSGVIVASSLKEGGV 1vzwA 216 :VEGAIVGKALYAKAF T0355 259 :W 1vzwA 231 :T T0355 267 :VRSFVAAA 1vzwA 232 :LEEALEAT Number of specific fragments extracted= 14 number of extra gaps= 1 total=2332 Number of alignments=143 # 1vzwA read from 1vzwA/merged-good-all-a2m # found chain 1vzwA in template set Warning: unaligning (T0355)R18 because first residue in template chain is (1vzwA)S2 Warning: unaligning (T0355)A34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzwA)E28 Warning: unaligning (T0355)E160 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vzwA)K124 Warning: unaligning (T0355)H161 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vzwA)K124 Warning: unaligning (T0355)G202 because of BadResidue code BAD_PEPTIDE in next template residue (1vzwA)I168 Warning: unaligning (T0355)Q203 because of BadResidue code BAD_PEPTIDE at template residue (1vzwA)I168 Warning: unaligning (T0355)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vzwA)G176 T0355 19 :SKALIGMIHC 1vzwA 3 :KLELLPAVDV T0355 35 :PRYRN 1vzwA 29 :TSYGS T0355 49 :CMRDAERLIEGGMHGLIVEN 1vzwA 34 :PLEAALAWQRSGAEWLHLVD T0355 76 :KPDDIGPETSA 1vzwA 58 :FGTGDNRALIA T0355 94 :RIVRTAGVPVGINVLANA 1vzwA 69 :EVAQAMDIKVELSGGIRD T0355 113 :IPAFAIAKAGGAKF 1vzwA 87 :DDTLAAALATGCTR T0355 129 :VNQWANAYV 1vzwA 101 :VNLGTAALE T0355 146 :RAAEAMRYRSLLR 1vzwA 110 :TPEWVAKVIAEHG T0355 162 :IKVFADSHVK 1vzwA 125 :IAVGLDVRGT T0355 172 :HGAHAITADRSIDELTRDLAFFDADGVIAT 1vzwA 137 :RGRGWTRDGGDLYETLDRLNKEGCARYVVT T0355 209 :ASLEEIEEIGAATHLPLLVGSGV 1vzwA 177 :PNLELLKNVCAATDRPVVASGGV T0355 232 :NEGNIVEILKR 1vzwA 201 :SLDDLRAIAGL T0355 243 :TSGVIVASSLKEGGVW 1vzwA 216 :VEGAIVGKALYAKAFT T0355 267 :VRSFVAAA 1vzwA 232 :LEEALEAT Number of specific fragments extracted= 14 number of extra gaps= 2 total=2346 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vh7A expands to /projects/compbio/data/pdb/1vh7.pdb.gz 1vh7A:Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1vh7A Skipped atom 688, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 690, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 692, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 694, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 890, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 892, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 894, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 896, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 925, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1031, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1033, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1035, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1037, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1039, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1370, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1372, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1374, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1376, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1835, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1837, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1839, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1841, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1843, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1923, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1925, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1927, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1929, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1931, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1933, because occupancy 0.350 <= existing 0.650 in 1vh7A Skipped atom 1935, because occupancy 0.350 <= existing 0.650 in 1vh7A # T0355 read from 1vh7A/merged-good-all-a2m # 1vh7A read from 1vh7A/merged-good-all-a2m # adding 1vh7A to template set # found chain 1vh7A in template set T0355 41 :S 1vh7A 31 :D T0355 49 :CMRDAERLIEGGMH 1vh7A 32 :PVELGKFYSEIGID T0355 63 :GLIVE 1vh7A 47 :LVFLD T0355 74 :FSKPDDIGPETSAF 1vh7A 52 :ITASVEKRKTMLEL T0355 105 :INVLANAPIPAFAIAKAGG 1vh7A 66 :VEKVAEQIDIPFTVGGGIH T0355 128 :RVNQWA 1vh7A 85 :DFETAS T0355 136 :YVANEGFMEGRAAEAM 1vh7A 91 :ELILRGADKVSINTAA T0355 153 :YR 1vh7A 107 :VE T0355 155 :SLLRAEHIK 1vh7A 115 :QIAQTFGSQ T0355 164 :VFADS 1vh7A 125 :VVVAI T0355 174 :AHAIT 1vh7A 154 :RDWVV T0355 182 :SIDEL 1vh7A 159 :EVEKR T0355 189 :DLAFFDADGVI 1vh7A 164 :GAGEILLTSID T0355 202 :GQRTGNSASLEEIEEIGAATHLPLLVGSGV 1vh7A 175 :RDGTKSGYDTEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1vh7A 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLK 1vh7A 218 :ADAALAASVFH T0355 254 :EGGV 1vh7A 230 :REID T0355 267 :VRSFVAAARP 1vh7A 234 :VRELKEYLKK Number of specific fragments extracted= 18 number of extra gaps= 0 total=2364 Number of alignments=145 # 1vh7A read from 1vh7A/merged-good-all-a2m # found chain 1vh7A in template set Warning: unaligning (T0355)R18 because first residue in template chain is (1vh7A)L2 T0355 19 :SKALIGMIHCPAFPGAPRYRNASMDA 1vh7A 3 :AKRIIACLDVKDGRVVKGTNFENLRD T0355 46 :YDACMRDAERLIEGGMHGLIV 1vh7A 29 :SGDPVELGKFYSEIGIDELVF T0355 70 :GDVP 1vh7A 50 :LDIT T0355 80 :IGPETSAFM 1vh7A 54 :ASVEKRKTM T0355 102 :PVGINVLANAPIPAFAIAKAGGAKF 1vh7A 63 :LELVEKVAEQIDIPFTVGGGIHDFE T0355 128 :RVNQWANA 1vh7A 88 :TASELILR T0355 141 :GFMEGRAAEAM 1vh7A 96 :GADKVSINTAA T0355 152 :RYRSLLRAEHIKVFADS 1vh7A 108 :ENPSLITQIAQTFGSQA T0355 183 :IDELTRDLAFFDADGVIAT 1vh7A 153 :LRDWVVEVEKRGAGEILLT T0355 202 :GQRTGN 1vh7A 177 :GTKSGY T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1vh7A 183 :DTEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1vh7A 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLKEGGVW 1vh7A 218 :ADAALAASVFHFREID T0355 267 :VRSFVAAARP 1vh7A 234 :VRELKEYLKK Number of specific fragments extracted= 14 number of extra gaps= 0 total=2378 Number of alignments=146 # 1vh7A read from 1vh7A/merged-good-all-a2m # found chain 1vh7A in template set T0355 19 :SKALIGMIHCP 1vh7A 3 :AKRIIACLDVK T0355 31 :FPGAPRYRN 1vh7A 23 :FENLRDSGD T0355 49 :CMRDAERLIEGGMHGLIVENHG 1vh7A 32 :PVELGKFYSEIGIDELVFLDIT T0355 80 :IGPETSAFMSVVTDRIVRTAGVPVGINVLANAPIPAFAIAKA 1vh7A 54 :ASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILR T0355 123 :GAKFIRVNQWAN 1vh7A 96 :GADKVSINTAAV T0355 145 :GRAAEAMRYRSLLRAEHIKVFADSHVKHGAHAI 1vh7A 108 :ENPSLITQIAQTFGSQAVVVAIDAKRVDGEFMV T0355 178 :TADRSIDELTRDLAFFDADGVIATGQRT 1vh7A 148 :NTGILLRDWVVEVEKRGAGEILLTSIDR T0355 206 :G 1vh7A 177 :G T0355 207 :NSASLEEIEEIGAATHLPLLVGSGV 1vh7A 180 :SGYDTEMIRFVRPLTTLPIIASGGA T0355 232 :NEGNIVEILKR 1vh7A 206 :KMEHFLEAFLA T0355 243 :TSGVIVASSLKEGG 1vh7A 218 :ADAALAASVFHFRE T0355 262 :VE 1vh7A 232 :ID T0355 267 :VRSFVAAARP 1vh7A 234 :VRELKEYLKK Number of specific fragments extracted= 13 number of extra gaps= 0 total=2391 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1vhnA/merged-good-all-a2m # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set T0355 16 :FGRSKALIGMIHCPAFPGAPRYRNAS 1vhnA 43 :LMNSQKTEELLPQPHERNVAVQIFGS T0355 43 :D 1vhnA 69 :E T0355 46 :YDACMRDAERLIEG 1vhnA 70 :PNELSEAARILSEK T0355 61 :MHGLIVE 1vhnA 84 :YKWIDLN T0355 70 :GDVPF 1vhnA 91 :AGCPV T0355 82 :PET 1vhnA 96 :RKV T0355 92 :TDRI 1vhnA 99 :VKEG T0355 96 :VRTAGVPVGINVLANAPIPAFAIAKAGGAKFIRVNQWAN 1vhnA 109 :KDLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYR T0355 136 :YVANEGFMEGRAAEAMRYR 1vhnA 148 :ILVEEGVDEVFIHTRTVVQ T0355 159 :AE 1vhnA 167 :SF T0355 174 :AHAIT 1vhnA 169 :TGRAE T0355 184 :DELTRDLAF 1vhnA 174 :WKALSVLEK T0355 222 :HLPLLVGSGV 1vhnA 183 :RIPTFVSGDI T0355 232 :NEGNIVEILKR 1vhnA 194 :TPEDAKRALEE T0355 243 :TSGVIVA 1vhnA 207 :CDGLLVA T0355 250 :SSLKEGGVWW 1vhnA 224 :KQIKDFLRSG T0355 261 :PVELARVRSFVAAARPGLEAL 1vhnA 241 :EEILRTFERHLELLIKTKGER Number of specific fragments extracted= 17 number of extra gaps= 0 total=2408 Number of alignments=148 # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set T0355 9 :ANAIQEIF 1vhnA 46 :SQKTEELL T0355 17 :GRSKALIGMIHCPA 1vhnA 56 :PHERNVAVQIFGSE T0355 46 :YDACMRDAERLIEG 1vhnA 70 :PNELSEAARILSEK T0355 61 :MHGLIVE 1vhnA 84 :YKWIDLN T0355 70 :GDVPF 1vhnA 91 :AGCPV T0355 81 :GP 1vhnA 96 :RK T0355 91 :VTDRI 1vhnA 98 :VVKEG T0355 96 :VRTAGVPVGINVLANAPIPAFAIAKAGGAKFIRVNQWANA 1vhnA 109 :KDLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYRI T0355 137 :VANEGFMEGRAAE 1vhnA 149 :LVEEGVDEVFIHT T0355 202 :GQRTG 1vhnA 166 :QSFTG T0355 208 :SASLEEI 1vhnA 171 :RAEWKAL T0355 219 :AAT 1vhnA 178 :SVL T0355 222 :HLPLLVGSGV 1vhnA 183 :RIPTFVSGDI T0355 232 :NEGNIVEILKR 1vhnA 194 :TPEDAKRALEE T0355 243 :TSGVIVASSLKEGG 1vhnA 207 :CDGLLVARGAIGRP T0355 257 :VWW 1vhnA 236 :SEP T0355 261 :PVELARVRSFVAAARPGLEA 1vhnA 241 :EEILRTFERHLELLIKTKGE Number of specific fragments extracted= 17 number of extra gaps= 0 total=2425 Number of alignments=149 # 1vhnA read from 1vhnA/merged-good-all-a2m # found chain 1vhnA in training set T0355 17 :GRSKALIGMI 1vhnA 57 :HERNVAVQIF T0355 39 :NASMDAIYD 1vhnA 67 :GSEPNELSE T0355 52 :DAERLIE 1vhnA 76 :AARILSE T0355 60 :GMHGLIVENHGDV 1vhnA 83 :KYKWIDLNAGCPV T0355 73 :PFSKP 1vhnA 106 :ALLKD T0355 85 :SAFMSVVTDRIVRTAGVPVGINVLA 1vhnA 111 :LRHFRYIVRELRKSVSGKFSVKTRL T0355 141 :GFMEGRAAEAMRYRSLLRAEH 1vhnA 136 :GWEKNEVEEIYRILVEEGVDE T0355 164 :VFADSHVK 1vhnA 157 :VFIHTRTV T0355 174 :AHAITADRSID 1vhnA 165 :VQSFTGRAEWK T0355 214 :IE 1vhnA 177 :LS T0355 219 :A 1vhnA 179 :V T0355 220 :ATHLPLLVGSGV 1vhnA 181 :EKRIPTFVSGDI T0355 232 :NEGNIVEILKR 1vhnA 194 :TPEDAKRALEE T0355 243 :TSGVIVASSLKEGG 1vhnA 207 :CDGLLVARGAIGRP T0355 257 :VWWNPVELARVRSFVAAARPGLEALEH 1vhnA 233 :GKYSEPSREEILRTFERHLELLIKTKG Number of specific fragments extracted= 15 number of extra gaps= 0 total=2440 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xm3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0355 read from 1xm3A/merged-good-all-a2m # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set T0355 30 :AFPGAPRYRNASMD 1xm3A 64 :SKYTLLPNTAGAST T0355 46 :YDACMRDAERLIEGG 1xm3A 78 :AEEAVRIARLAKASG T0355 61 :MHGLIVENHGD 1xm3A 94 :CDMIKVEVIGC T0355 75 :SKPDDIGP 1xm3A 105 :SRSLLPDP T0355 83 :ETSAFMS 1xm3A 114 :ETLKASE T0355 136 :YVANEGFMEGRAAEAMRYR 1xm3A 121 :QLLEEGFIVLPYTSDDVVL T0355 155 :SLLRAEHI 1xm3A 141 :RKLEELGV T0355 189 :DLAFFDADGV 1xm3A 149 :HAIMPGASPI T0355 202 :GQRTGN 1xm3A 159 :GSGQGI T0355 209 :ASLEEIEEIGAATHLPLLVGSGV 1xm3A 165 :LNPLNLSFIIEQAKVPVIVDAGI T0355 232 :NEGNIVEILKR 1xm3A 189 :SPKDAAYAMEL T0355 243 :TSGVIVASSLKEGGV 1xm3A 201 :ADGVLLNTAVSGADD T0355 263 :ELARVRSFVAAARPGLEALEHHHHHH 1xm3A 216 :PVKMARAMKLAVEAGRLSYEAGRIPL Number of specific fragments extracted= 13 number of extra gaps= 0 total=2453 Number of alignments=151 # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set T0355 19 :SKALIGM 1xm3A 65 :KYTLLPN T0355 28 :CPAFPG 1xm3A 72 :TAGAST T0355 46 :YDACMRDAERLIEGG 1xm3A 78 :AEEAVRIARLAKASG T0355 61 :MHGLIVE 1xm3A 94 :CDMIKVE T0355 148 :AEAM 1xm3A 107 :SLLP T0355 152 :RYRSLLRAEHIKVFADSHVKH 1xm3A 113 :VETLKASEQLLEEGFIVLPYT T0355 177 :ITADRSIDELTR 1xm3A 134 :SDDVVLARKLEE T0355 193 :FDADGVIATGQRTGNSA 1xm3A 146 :LGVHAIMPGASPIGSGQ T0355 210 :SLEEIEEIGAATHLPLLVGSGV 1xm3A 166 :NPLNLSFIIEQAKVPVIVDAGI T0355 232 :NEGNIVEILKR 1xm3A 189 :SPKDAAYAMEL T0355 243 :TSGVIVASSLKEG 1xm3A 201 :ADGVLLNTAVSGA T0355 261 :PVELARVRSFVAAARPGLEALEHHHHHH 1xm3A 214 :DDPVKMARAMKLAVEAGRLSYEAGRIPL Number of specific fragments extracted= 12 number of extra gaps= 0 total=2465 Number of alignments=152 # 1xm3A read from 1xm3A/merged-good-all-a2m # found chain 1xm3A in training set T0355 20 :KALIGM 1xm3A 66 :YTLLPN T0355 34 :APRYR 1xm3A 72 :TAGAS T0355 41 :SMDA 1xm3A 77 :TAEE T0355 49 :CMRDAERLIEGG 1xm3A 81 :AVRIARLAKASG T0355 61 :MHGLIVENHGD 1xm3A 94 :CDMIKVEVIGC T0355 75 :SKPDDIGPETSA 1xm3A 105 :SRSLLPDPVETL T0355 90 :VVTDRIVR 1xm3A 117 :KASEQLLE T0355 160 :EHIKVFADSHVK 1xm3A 125 :EGFIVLPYTSDD T0355 184 :DELTRDLAFFDADGVIATGQRTGNS 1xm3A 137 :VVLARKLEELGVHAIMPGASPIGSG T0355 209 :ASLEEIEEIGAATHLPLLVGSGV 1xm3A 165 :LNPLNLSFIIEQAKVPVIVDAGI T0355 232 :NEGNIVEILKR 1xm3A 189 :SPKDAAYAMEL T0355 243 :TSGVIVASSLKEGGV 1xm3A 201 :ADGVLLNTAVSGADD T0355 264 :LARVRSFVAAARPGLEALEHHHHHH 1xm3A 217 :VKMARAMKLAVEAGRLSYEAGRIPL Number of specific fragments extracted= 13 number of extra gaps= 0 total=2478 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ep3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ep3A expands to /projects/compbio/data/pdb/1ep3.pdb.gz 1ep3A:# T0355 read from 1ep3A/merged-good-all-a2m # 1ep3A read from 1ep3A/merged-good-all-a2m # adding 1ep3A to template set # found chain 1ep3A in template set Warning: unaligning (T0355)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0355)A148 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0355 9 :ANAIQEIFG 1ep3A 89 :LPWLNENFP T0355 19 :SKALIGMIHCPA 1ep3A 98 :ELPIIANVAGSE T0355 46 :YDACMRDAERLIE 1ep3A 110 :EADYVAVCAKIGD T0355 59 :GGMHGLIVE 1ep3A 124 :ANVKAIELN T0355 70 :GDVPFSKPD 1ep3A 133 :ISCPNVKHG T0355 79 :DIGPETSAF 1ep3A 147 :TDPEVAAAL T0355 105 :INVLANAPIPAFAIAKAGGAK 1ep3A 156 :VKACKAVSKVPLYVKLSPNVT T0355 128 :RVNQWAN 1ep3A 177 :DIVPIAK T0355 136 :YVANEGFMEGR 1ep3A 184 :AVEAAGADGLT T0355 149 :EAM 1ep3A 197 :NTL T0355 164 :VFADSHVKHGAHAIT 1ep3A 200 :MGVRFDLKTRQPILA T0355 180 :DRS 1ep3A 215 :NIT T0355 198 :VIATGQR 1ep3A 218 :GGLSGPA T0355 206 :GNSASLEEIEEIGAATHLPLLVGSGV 1ep3A 225 :IKPVALKLIHQVAQDVDIPIIGMGGV T0355 232 :NEGNIVEILKR 1ep3A 252 :NAQDVLEMYMA T0355 243 :TSGVIVASSLKEGGVW 1ep3A 264 :ASAVAVGTANFADPFV T0355 260 :NPVELARVRSFVAA 1ep3A 280 :CPKIIDKLPELMDQ T0355 274 :ARPGLEALEHH 1ep3A 299 :LESLIQEVKEG Number of specific fragments extracted= 18 number of extra gaps= 1 total=2496 Number of alignments=154 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0355)A147 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0355)A148 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0355 3 :TISDNAANAIQEIFG 1ep3A 83 :VIMTEKLPWLNENFP T0355 19 :SKALIGMIHCPA 1ep3A 98 :ELPIIANVAGSE T0355 46 :YDACMRDAERLIE 1ep3A 110 :EADYVAVCAKIGD T0355 59 :GGMHGLIVE 1ep3A 124 :ANVKAIELN T0355 70 :GDVPFSKPD 1ep3A 133 :ISCPNVKHG T0355 79 :DIGPETSA 1ep3A 147 :TDPEVAAA T0355 104 :GINVLANAPIPAFAIAKAGGAK 1ep3A 155 :LVKACKAVSKVPLYVKLSPNVT T0355 128 :RVNQWANA 1ep3A 177 :DIVPIAKA T0355 137 :VANEGFMEGR 1ep3A 185 :VEAAGADGLT T0355 149 :E 1ep3A 197 :N T0355 170 :VKHGA 1ep3A 198 :TLMGV T0355 177 :ITADRS 1ep3A 203 :RFDLKT T0355 191 :AFFDA 1ep3A 210 :QPILA T0355 196 :DGVIATGQRTG 1ep3A 216 :ITGGLSGPAIK T0355 208 :SASLEEIEEIGAATHLPLLVGSGV 1ep3A 227 :PVALKLIHQVAQDVDIPIIGMGGV T0355 232 :NEGNIVEILKR 1ep3A 252 :NAQDVLEMYMA T0355 243 :TSGVIVASSLKEGGVWW 1ep3A 264 :ASAVAVGTANFADPFVC T0355 261 :PVELARVRSFVAA 1ep3A 281 :PKIIDKLPELMDQ T0355 274 :ARPGLEALEHHH 1ep3A 299 :LESLIQEVKEGK Number of specific fragments extracted= 19 number of extra gaps= 1 total=2515 Number of alignments=155 # 1ep3A read from 1ep3A/merged-good-all-a2m # found chain 1ep3A in template set Warning: unaligning (T0355)A200 because of BadResidue code BAD_PEPTIDE in next template residue (1ep3A)I196 Warning: unaligning (T0355)T201 because of BadResidue code BAD_PEPTIDE at template residue (1ep3A)I196 T0355 4 :ISDNAANAIQEIFG 1ep3A 84 :IMTEKLPWLNENFP T0355 19 :SKALIGMIH 1ep3A 98 :ELPIIANVA T0355 39 :NASMDAI 1ep3A 107 :GSEEADY T0355 50 :MRDAERLIEG 1ep3A 114 :VAVCAKIGDA T0355 60 :GMHGLIVENH 1ep3A 125 :NVKAIELNIS T0355 72 :VPFSKPDD 1ep3A 135 :CPNVKHGG T0355 80 :IGPETSA 1ep3A 147 :TDPEVAA T0355 90 :VVTDRIVRTAGVPVGINVLANA 1ep3A 154 :ALVKACKAVSKVPLYVKLSPNV T0355 181 :RSIDELTRDLAFFDADGVI 1ep3A 176 :TDIVPIAKAVEAAGADGLT T0355 202 :G 1ep3A 197 :N T0355 203 :QRTGNSA 1ep3A 206 :LKTRQPI T0355 211 :LEEIEEIGAATHLPLLVGSGV 1ep3A 230 :LKLIHQVAQDVDIPIIGMGGV T0355 232 :NEGNIVEILKR 1ep3A 252 :NAQDVLEMYMA T0355 243 :TSGVIVASSLKE 1ep3A 264 :ASAVAVGTANFA T0355 263 :E 1ep3A 276 :D T0355 266 :RVRSFVAAARPGLEALE 1ep3A 279 :VCPKIIDKLPELMDQYR Number of specific fragments extracted= 16 number of extra gaps= 1 total=2531 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xc4A/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/T0355/1xc4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0355/1xc4A/merged-good-all-a2m.gz for input Trying 1xc4A/merged-good-all-a2m Error: Couldn't open file 1xc4A/merged-good-all-a2m or 1xc4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vlwA expands to /projects/compbio/data/pdb/1vlw.pdb.gz 1vlwA:# T0355 read from 1vlwA/merged-good-all-a2m # 1vlwA read from 1vlwA/merged-good-all-a2m # adding 1vlwA to template set # found chain 1vlwA in template set Warning: unaligning (T0355)A8 because first residue in template chain is (1vlwA)H-1 Warning: unaligning (T0355)S19 because of BadResidue code BAD_PEPTIDE in next template residue (1vlwA)K11 Warning: unaligning (T0355)K20 because of BadResidue code BAD_PEPTIDE at template residue (1vlwA)K11 Warning: unaligning (T0355)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T44 Warning: unaligning (T0355)D71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T44 Warning: unaligning (T0355)V227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T156 Warning: unaligning (T0355)G228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T156 T0355 9 :ANAIQEIFGR 1vlwA 0 :HMKMEELFKK T0355 22 :LIGMIHCPA 1vlwA 12 :IVAVLRANS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1vlwA 21 :VEEAKEKALAVFEGGVHLIEIT T0355 72 :V 1vlwA 45 :V T0355 79 :DIGPETSA 1vlwA 46 :PDADTVIK T0355 104 :GINVLANAPIPAFAI 1vlwA 54 :ELSFLKEKGAIIGAG T0355 128 :RVN 1vlwA 69 :TVT T0355 131 :QWAN 1vlwA 74 :EQCR T0355 136 :YVANEGFMEGRAAEAMRYR 1vlwA 78 :KAVESGAEFIVSPHLDEEI T0355 155 :SLLRAEHIKVFADSHV 1vlwA 98 :QFCKEKGVFYMPGVMT T0355 174 :AHAIT 1vlwA 114 :PTELV T0355 182 :SIDEL 1vlwA 119 :KAMKL T0355 189 :DLAF 1vlwA 124 :GHTI T0355 198 :VIAT 1vlwA 128 :LKLF T0355 202 :G 1vlwA 133 :G T0355 207 :NSASLEEIEEIGAATH 1vlwA 134 :EVVGPQFVKAMKGPFP T0355 223 :LPLL 1vlwA 151 :VKFV T0355 229 :SGVNEGNIVEILKR 1vlwA 157 :GGVNLDNVCEWFKA T0355 243 :TSGVIVASSLKEG 1vlwA 172 :VLAVGVGSALVKG T0355 259 :WNPVELARVRSFVAAARP 1vlwA 185 :TPDEVREKAKAFVEKIRG Number of specific fragments extracted= 20 number of extra gaps= 3 total=2551 Number of alignments=157 # 1vlwA read from 1vlwA/merged-good-all-a2m # found chain 1vlwA in template set Warning: unaligning (T0355)A8 because first residue in template chain is (1vlwA)H-1 Warning: unaligning (T0355)K20 because of BadResidue code BAD_PEPTIDE in next template residue (1vlwA)K11 Warning: unaligning (T0355)A21 because of BadResidue code BAD_PEPTIDE at template residue (1vlwA)K11 Warning: unaligning (T0355)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T44 Warning: unaligning (T0355)D71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T44 Warning: unaligning (T0355)V227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T156 Warning: unaligning (T0355)G228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T156 T0355 9 :ANAIQEIFG 1vlwA 0 :HMKMEELFK T0355 19 :S 1vlwA 9 :K T0355 22 :LIGMIHCPA 1vlwA 12 :IVAVLRANS T0355 46 :YDACMRDAERLIEGGMHGLIVE 1vlwA 21 :VEEAKEKALAVFEGGVHLIEIT T0355 72 :VP 1vlwA 45 :VP T0355 100 :GVPVGINV 1vlwA 47 :DADTVIKE T0355 108 :LANAPIP 1vlwA 58 :LKEKGAI T0355 116 :FAI 1vlwA 65 :IGA T0355 120 :KAGGA 1vlwA 68 :GTVTS T0355 130 :NQWANA 1vlwA 73 :VEQCRK T0355 137 :VANEGFMEGRAAEA 1vlwA 79 :AVESGAEFIVSPHL T0355 154 :RSLLRAEHIKVFADSHVK 1vlwA 93 :DEEISQFCKEKGVFYMPG T0355 177 :ITADRSIDELTR 1vlwA 111 :VMTPTELVKAMK T0355 193 :FDADGVIAT 1vlwA 123 :LGHTILKLF T0355 206 :GNSASLEEIEEIGAAT 1vlwA 133 :GEVVGPQFVKAMKGPF T0355 222 :HLPLL 1vlwA 150 :NVKFV T0355 229 :SGVNEGNIVEILKR 1vlwA 157 :GGVNLDNVCEWFKA T0355 243 :TSGVIVASSLKEG 1vlwA 172 :VLAVGVGSALVKG T0355 259 :WNPVELARVRSFVAAARP 1vlwA 185 :TPDEVREKAKAFVEKIRG Number of specific fragments extracted= 19 number of extra gaps= 3 total=2570 Number of alignments=158 # 1vlwA read from 1vlwA/merged-good-all-a2m # found chain 1vlwA in template set Warning: unaligning (T0355)I15 because of BadResidue code BAD_PEPTIDE in next template residue (1vlwA)K11 Warning: unaligning (T0355)A21 because of BadResidue code BAD_PEPTIDE at template residue (1vlwA)K11 Warning: unaligning (T0355)N68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T44 Warning: unaligning (T0355)H69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T44 Warning: unaligning (T0355)V227 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vlwA)T156 Warning: unaligning (T0355)G228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vlwA)T156 T0355 6 :DNAANAIQE 1vlwA 1 :MKMEELFKK T0355 22 :LIGMIHC 1vlwA 12 :IVAVLRA T0355 40 :ASMDAI 1vlwA 19 :NSVEEA T0355 50 :MRDAERLIEGGMHGLIVE 1vlwA 25 :KEKALAVFEGGVHLIEIT T0355 80 :IGPE 1vlwA 45 :VPDA T0355 89 :SVVTDRIVRTA 1vlwA 49 :DTVIKELSFLK T0355 100 :GVPVGIN 1vlwA 62 :GAIIGAG T0355 109 :ANAPIPAFAIAKAGGAKFIR 1vlwA 69 :TVTSVEQCRKAVESGAEFIV T0355 139 :NEG 1vlwA 89 :SPH T0355 143 :MEG 1vlwA 92 :LDE T0355 149 :EAMRYRSLLR 1vlwA 95 :EISQFCKEKG T0355 162 :IKVFADSHV 1vlwA 105 :VFYMPGVMT T0355 184 :DELTRDLAFFDADGVIA 1vlwA 114 :PTELVKAMKLGHTILKL T0355 205 :TGNSASLEEIEEIGA 1vlwA 132 :PGEVVGPQFVKAMKG T0355 220 :ATHLPLL 1vlwA 148 :FPNVKFV T0355 229 :SGVNEGNIVEILKR 1vlwA 157 :GGVNLDNVCEWFKA T0355 243 :TSGVIVASSLKEG 1vlwA 172 :VLAVGVGSALVKG T0355 263 :E 1vlwA 185 :T T0355 264 :LARVRSFVAAARP 1vlwA 190 :REKAKAFVEKIRG Number of specific fragments extracted= 19 number of extra gaps= 3 total=2589 Number of alignments=159 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 159 Adding 7686 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: -527.8049, CN propb: -527.8049 weights: 0.2088 constraints: 1019 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1019 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1019 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 6667 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 6667 # 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 7686 # command: