parameters: 0.6 1.3 0.5 200 50 # 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/T0323/ # command:# Making conformation for sequence T0323 numbered 1 through 221 Created new target T0323 from T0323.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0323/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0323//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0323/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0323//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0323/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0323/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0323/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fn7A/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/T0323/1fn7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1fn7A/merged-good-all-a2m.gz for input Trying 1fn7A/merged-good-all-a2m Error: Couldn't open file 1fn7A/merged-good-all-a2m or 1fn7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2abk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2abk expands to /projects/compbio/data/pdb/2abk.pdb.gz 2abk:Warning: there is no chain 2abk will retry with 2abkA Skipped atom 1276, because occupancy 0.5 <= existing 0.500 in 2abk Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 2abk Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 2abk # T0323 read from 2abk/merged-good-all-a2m # 2abk read from 2abk/merged-good-all-a2m # adding 2abk to template set # found chain 2abk in template set T0323 15 :VAQDSRLFQFIEIAGEVQLPTKP 2abk 4 :AKRLEILTRLRENNPHPTTELNF # choosing archetypes in rotamer library T0323 38 :NPFQSLVSSIVEQQLSIKAASAIYGRV 2abk 28 :SPFELLIAVLLSAQATDVSVNKATAKL T0323 68 :VGGAL 2abk 55 :YPVAN T0323 74 :KPEQLYRVSDEAL 2abk 60 :TPAAMLELGVEGV T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLD 2abk 77 :KTIGLYNSKAENIIKTCRILLEQHNG T0323 118 :GAEAT 2abk 103 :EVPED T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 2abk 108 :RAALEALPGVGRKTANVVLNTAFGWP T0323 152 :VLSV 2abk 134 :TIAV T0323 157 :DVGLQRGAKWL 2abk 138 :DTHIFRVCNRT T0323 169 :GNGEGDGKKLLIYHGKAWAPYETVACLYLW 2abk 149 :QFAPGKNVEQVEEKLLKVVPAEFKVDCHHW T0323 199 :KAAGTFA 2abk 186 :TCIARKP T0323 210 :SLEELLHHGNQ 2abk 193 :RCGSCIIEDLC Number of specific fragments extracted= 12 number of extra gaps= 0 total=12 Number of alignments=1 # 2abk read from 2abk/merged-good-all-a2m # found chain 2abk in template set T0323 14 :IVAQDSRLFQFIEIAGEVQLPT 2abk 3 :KAKRLEILTRLRENNPHPTTEL T0323 36 :KPNPFQSLVSSIVEQQLSIKAASAIYGRV 2abk 26 :FSSPFELLIAVLLSAQATDVSVNKATAKL T0323 68 :VGGAL 2abk 55 :YPVAN T0323 74 :KPEQLYRVSDEAL 2abk 60 :TPAAMLELGVEGV T0323 87 :RQAGVSKRKIEYIRHVCEHVES 2abk 77 :KTIGLYNSKAENIIKTCRILLE T0323 114 :TELEGAEAT 2abk 99 :QHNGEVPED T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 2abk 108 :RAALEALPGVGRKTANVVLNTAFGWP T0323 152 :VLSV 2abk 134 :TIAV T0323 157 :DVGLQRGAKWLYGNGEG 2abk 138 :DTHIFRVCNRTQFAPGK T0323 175 :GKKLLIYHGKAWAP 2abk 155 :NVEQVEEKLLKVVP T0323 189 :YETVACLYLW 2abk 172 :KVDCHHWLIL T0323 199 :K 2abk 187 :C T0323 200 :AAGTFAEEYRSLEELLHHGN 2abk 189 :ARKPRCGSCIIEDLCEYKEK Number of specific fragments extracted= 13 number of extra gaps= 0 total=25 Number of alignments=2 # 2abk read from 2abk/merged-good-all-a2m # found chain 2abk in template set T0323 16 :AQDSRLFQFIEIAGEVQLP 2abk 5 :KRLEILTRLRENNPHPTTE T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRV 2abk 25 :NFSSPFELLIAVLLSAQATDVSVNKATAKL T0323 68 :VGG 2abk 55 :YPV T0323 72 :LEKPEQLYRVSDE 2abk 58 :ANTPAAMLELGVE T0323 85 :ALRQAGVSKRKIEYIRHVCEHVESG 2abk 75 :YIKTIGLYNSKAENIIKTCRILLEQ T0323 117 :EGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRL 2abk 100 :HNGEVPEDRAALEALPGVGRKTANVVLNTAFGWP T0323 153 :LSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 2abk 134 :TIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPA T0323 194 :CLYLWKAAGTFAEE 2abk 175 :CHHWLILHGRYTCI T0323 211 :LEELLHHGNQ 2abk 189 :ARKPRCGSCI Number of specific fragments extracted= 9 number of extra gaps= 0 total=34 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1muyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1muyA expands to /projects/compbio/data/pdb/1muy.pdb.gz 1muyA:# T0323 read from 1muyA/merged-good-all-a2m # 1muyA read from 1muyA/merged-good-all-a2m # adding 1muyA to template set # found chain 1muyA in template set Warning: unaligning (T0323)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1muyA)Q41 Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE at template residue (1muyA)Q41 T0323 15 :VAQDSRLFQFIEIAG 1muyA 5 :QFSAQVLDWYDKYGR T0323 30 :EVQLPTKPNPFQSLVSSIV 1muyA 21 :TLPWQIDKTPYKVWLSEVM T0323 51 :QLSIKAASAIYGRVEQL 1muyA 42 :QTQVATVIPYFERFMAR T0323 72 :LEKPEQLYRVSDEAL 1muyA 59 :FPTVTDLANAPLDEV T0323 87 :RQAGV 1muyA 76 :LWTGL T0323 92 :SKRKIEYIRHVCEHVESGRLD 1muyA 82 :YYARARNLHKAAQQVATLHGG T0323 118 :GAEAT 1muyA 103 :KFPET T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1muyA 108 :FEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNGEGDG 1muyA 134 :FPILDGNVKRVLARCYAVSGWPG T0323 176 :KKLLIYHGKAWAPYETVACLYLW 1muyA 161 :ENKLWSLSEQVTPAVGVERFNQA T0323 199 :KAAGT 1muyA 191 :ICTRS T0323 208 :YRSLEELLHHGN 1muyA 196 :KPKCSLCPLQNG Number of specific fragments extracted= 12 number of extra gaps= 1 total=46 Number of alignments=4 # 1muyA read from 1muyA/merged-good-all-a2m # found chain 1muyA in template set Warning: unaligning (T0323)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1muyA)Q41 Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE at template residue (1muyA)Q41 T0323 14 :IVAQDSRLFQFIEIAG 1muyA 4 :SQFSAQVLDWYDKYGR T0323 30 :EVQLPTKPNPFQSLVSSIV 1muyA 21 :TLPWQIDKTPYKVWLSEVM T0323 51 :QLSIKAASAIYGRVEQLV 1muyA 42 :QTQVATVIPYFERFMARF T0323 73 :EKPEQLYRVSDEAL 1muyA 60 :PTVTDLANAPLDEV T0323 87 :RQAGV 1muyA 76 :LWTGL T0323 92 :SKRKIEYIRHVCEHVES 1muyA 82 :YYARARNLHKAAQQVAT T0323 114 :TELEGAEAT 1muyA 99 :LHGGKFPET T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1muyA 108 :FEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 1muyA 134 :FPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSE T0323 189 :YETVACLYLW 1muyA 177 :VERFNQAMMD T0323 199 :K 1muyA 192 :C T0323 200 :AAGTFAEEYRSLEELLH 1muyA 194 :RSKPKCSLCPLQNGCIA Number of specific fragments extracted= 12 number of extra gaps= 1 total=58 Number of alignments=5 # 1muyA read from 1muyA/merged-good-all-a2m # found chain 1muyA in template set Warning: unaligning (T0323)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1muyA)Q41 Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE at template residue (1muyA)Q41 T0323 16 :AQDSRLFQFIEIAGEVQLP 1muyA 5 :QFSAQVLDWYDKYGRKTLP T0323 35 :TKPNPFQSLVSSIV 1muyA 26 :IDKTPYKVWLSEVM T0323 51 :QLSIKAASAIYGRVEQLV 1muyA 42 :QTQVATVIPYFERFMARF T0323 73 :EKPEQLYRVSDE 1muyA 60 :PTVTDLANAPLD T0323 85 :ALRQAGV 1muyA 76 :LWTGLGY T0323 93 :KRKIEYIRHVCEHVES 1muyA 83 :YARARNLHKAAQQVAT T0323 109 :GRL 1muyA 102 :GKF T0323 122 :TTVIEKLTAIKGIGQWTAEMFMMFSLGRL 1muyA 105 :PETFEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNG 1muyA 134 :FPILDGNVKRVLARCYAVS T0323 172 :EGDGKKLLIYHGKAWAP 1muyA 157 :KKEVENKLWSLSEQVTP T0323 189 :YETVACLYLWKAAG 1muyA 176 :GVERFNQAMMDLGA T0323 207 :EYRSLEELLHHGN 1muyA 190 :MICTRSKPKCSLC Number of specific fragments extracted= 12 number of extra gaps= 1 total=70 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ebmA expands to /projects/compbio/data/pdb/1ebm.pdb.gz 1ebmA:# T0323 read from 1ebmA/merged-good-all-a2m # 1ebmA read from 1ebmA/merged-good-all-a2m # adding 1ebmA to template set # found chain 1ebmA in template set T0323 4 :FSTD 1ebmA 102 :LDVT T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1ebmA 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1ebmA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFG T0323 70 :GALEKPEQLYR 1ebmA 179 :HGFPSLQALAG T0323 83 :DEALRQAGVSK 1ebmA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLDFTEL 1ebmA 204 :RARYVSASARAILEEQGGLAWL T0323 117 :EGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ebmA 229 :RESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ebmA 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGK 1ebmA 289 :KGPSP T0323 177 :KLLIYHGKA 1ebmA 297 :KELGNFFRS T0323 186 :WAPYETVACLYLW 1ebmA 307 :WGPYAGWAQAVLF Number of specific fragments extracted= 11 number of extra gaps= 0 total=81 Number of alignments=7 # 1ebmA read from 1ebmA/merged-good-all-a2m # found chain 1ebmA in template set T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1ebmA 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGG 1ebmA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFGP T0323 71 :ALEKPEQLYR 1ebmA 180 :GFPSLQALAG T0323 83 :DEALRQAGVSK 1ebmA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRL 1ebmA 204 :RARYVSASARAILEEQG T0323 112 :DFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ebmA 224 :WLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ebmA 268 :DVHMWHIAQRDYSWH T0323 172 :EGDG 1ebmA 289 :KGPS T0323 176 :KKLLIYHGKAWAP 1ebmA 296 :NKELGNFFRSLWG T0323 189 :YETVACLYLW 1ebmA 310 :YAGWAQAVLF Number of specific fragments extracted= 10 number of extra gaps= 0 total=91 Number of alignments=8 # 1ebmA read from 1ebmA/merged-good-all-a2m # found chain 1ebmA in template set T0323 2 :RYFSTDSPE 1ebmA 100 :FQLDVTLAQ T0323 11 :VKTIVAQDSRLFQFIEIAGEVQLP 1ebmA 110 :YHHWGSVDSHFQEVAQKFQGVRLL T0323 36 :KPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1ebmA 134 :RQDPIECLFSFICSSNNNIARITGMVERLCQAFGPR T0323 72 :LEKPEQLYR 1ebmA 181 :FPSLQALAG T0323 81 :VSDEALRQAGV 1ebmA 191 :EVEAHLRKLGL T0323 93 :KRKIEYIRHVCEHVESGRL 1ebmA 202 :GYRARYVSASARAILEEQG T0323 112 :DFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ebmA 224 :WLQQLRESSYEEAHKALCILPGVGTQVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ebmA 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYH 1ebmA 289 :KGPSPQTNKEL T0323 183 :GKAWAPYETVACLYLWKAA 1ebmA 304 :RSLWGPYAGWAQAVLFSAD Number of specific fragments extracted= 10 number of extra gaps= 0 total=101 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqrA/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/T0323/1yqrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1yqrA/merged-good-all-a2m.gz for input Trying 1yqrA/merged-good-all-a2m Error: Couldn't open file 1yqrA/merged-good-all-a2m or 1yqrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pu6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0323 read from 1pu6A/merged-good-all-a2m # 1pu6A read from 1pu6A/merged-good-all-a2m # found chain 1pu6A in training set T0323 18 :DSRLFQFIEI 1pu6A 5 :FEILKALKSL T0323 28 :AGEVQ 1pu6A 17 :LKNAP T0323 33 :LP 1pu6A 25 :WP T0323 38 :NPFQSLVSSIVEQQLSIKAASAIYGRVEQL 1pu6A 29 :LKFEALLGAVLTQNTKFEAVLKSLENLKNA T0323 69 :GGALEK 1pu6A 59 :FILEND T0323 75 :PEQLYRVSDEAL 1pu6A 69 :LKKIAYIEFSKL T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLDFT 1pu6A 85 :RPSGFYNQKAKRLIDLSGNILKDFQSFE T0323 115 :ELEGAEAT 1pu6A 114 :FKQEVTRE T0323 127 :KLTAIKGIGQWTAEMFMMFSLGR 1pu6A 122 :WLLDQKGIGKESADAILCYACAK T0323 151 :DVLSV 1pu6A 145 :EVMVV T0323 157 :DVGLQRGAKWL 1pu6A 150 :DKYSYLFLKKL T0323 169 :GNGEG 1pu6A 161 :GIEIE T0323 175 :GKKLLIYHGKAWAPYE 1pu6A 166 :DYDELQHFFEKGVQEN Number of specific fragments extracted= 13 number of extra gaps= 0 total=114 Number of alignments=10 # 1pu6A read from 1pu6A/merged-good-all-a2m # found chain 1pu6A in training set Warning: unaligning (T0323)W198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pu6A)I206 T0323 17 :QDSRLFQFIEI 1pu6A 4 :SFEILKALKSL T0323 28 :AGEVQLPTKPNP 1pu6A 17 :LKNAPAWWWPNA T0323 40 :FQSLVSSIVEQQLSIKAASAIYGRVEQL 1pu6A 31 :FEALLGAVLTQNTKFEAVLKSLENLKNA T0323 69 :GGALEK 1pu6A 59 :FILEND T0323 75 :PEQLYRVSDEAL 1pu6A 69 :LKKIAYIEFSKL T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLDFT 1pu6A 85 :RPSGFYNQKAKRLIDLSGNILKDFQSFE T0323 115 :ELEGAEAT 1pu6A 114 :FKQEVTRE T0323 127 :KLTAIKGIGQWTAEMFMMFSLGR 1pu6A 122 :WLLDQKGIGKESADAILCYACAK T0323 151 :DVLSV 1pu6A 145 :EVMVV T0323 157 :DVGLQRGAKWLYG 1pu6A 150 :DKYSYLFLKKLGI T0323 171 :GEG 1pu6A 163 :EIE T0323 175 :GKKLLIYHGKAWAP 1pu6A 166 :DYDELQHFFEKGVQ T0323 189 :YETVACLYL 1pu6A 195 :LAQLYARFH Number of specific fragments extracted= 13 number of extra gaps= 0 total=127 Number of alignments=11 # 1pu6A read from 1pu6A/merged-good-all-a2m # found chain 1pu6A in training set Warning: unaligning (T0323)K199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pu6A)I206 Warning: unaligning (T0323)A201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pu6A)I206 T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1pu6A 26 :PNALKFEALLGAVLTQNTKFEAVLKSLENLKNAFILE T0323 73 :EKPEQLYRV 1pu6A 63 :NDDEINLKK T0323 82 :SDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEG 1pu6A 80 :LAECVRPSGFYNQKAKRLIDLSGNILKDFQSFENFKQ T0323 119 :AE 1pu6A 118 :VT T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1pu6A 120 :REWLLDQKGIGKESADAILCYACAKE T0323 153 :LSVGDVGLQRGAKWL 1pu6A 146 :VMVVDKYSYLFLKKL T0323 169 :GNGEGDGKKLLIYHGKAWAPY 1pu6A 161 :GIEIEDYDELQHFFEKGVQEN T0323 190 :ETVACLYLW 1pu6A 195 :LAQLYARFH T0323 202 :GTFAEEYRSLE 1pu6A 207 :VEFSKQKLELK Number of specific fragments extracted= 9 number of extra gaps= 0 total=136 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ornA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0323 read from 1ornA/merged-good-all-a2m # 1ornA read from 1ornA/merged-good-all-a2m # found chain 1ornA in training set T0323 15 :VAQDSRLFQFIEIAGEVQLPTKP 1ornA 5 :QQIRYCLDEMAKMFPDAHCELVH T0323 38 :NPFQSLVSSIVEQQLSIKAASAIYGRVEQL 1ornA 29 :NPFELLIAVVLSAQCTDALVNKVTKRLFEK T0323 72 :LEKPEQLYRVSDEAL 1ornA 59 :YRTPHDYIAVPLEEL T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLD 1ornA 78 :RSIGLYRNKARNIQKLCAMLIDKYNG T0323 118 :GAEAT 1ornA 104 :EVPRD T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1ornA 109 :RDELMKLPGVGRKTANVVVSVAFGVP T0323 152 :VLSV 1ornA 135 :AIAV T0323 157 :DVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLW 1ornA 139 :DTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHR T0323 199 :KAAGTFA 1ornA 188 :HCKAQSP T0323 210 :SLEELLHHGN 1ornA 195 :QCPSCPLLHL Number of specific fragments extracted= 10 number of extra gaps= 0 total=146 Number of alignments=13 # 1ornA read from 1ornA/merged-good-all-a2m # found chain 1ornA in training set T0323 14 :IVAQDSRLFQFIEIAGEVQLPT 1ornA 4 :KQQIRYCLDEMAKMFPDAHCEL T0323 36 :KPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1ornA 27 :HRNPFELLIAVVLSAQCTDALVNKVTKRLFEKY T0323 73 :EKPEQLYRVSDEAL 1ornA 60 :RTPHDYIAVPLEEL T0323 87 :RQAGVSKRKIEYIRHVCEHVES 1ornA 78 :RSIGLYRNKARNIQKLCAMLID T0323 114 :TELEGAEAT 1ornA 100 :KYNGEVPRD T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1ornA 109 :RDELMKLPGVGRKTANVVVSVAFGVP T0323 152 :VLSV 1ornA 135 :AIAV T0323 157 :DVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 1ornA 139 :DTHVERVSKRLGFCRWDDSVLEVEKTLMKIIP T0323 189 :YETVACLYLW 1ornA 174 :WSITHHRMIF T0323 199 :K 1ornA 189 :C T0323 200 :AAGTFAEEYRSLEELLH 1ornA 191 :AQSPQCPSCPLLHLCRE Number of specific fragments extracted= 11 number of extra gaps= 0 total=157 Number of alignments=14 # 1ornA read from 1ornA/merged-good-all-a2m # found chain 1ornA in training set T0323 7 :DSPEVKTI 1ornA 3 :TKQQIRYC T0323 21 :LFQFIEIAGEVQLP 1ornA 11 :LDEMAKMFPDAHCE T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1ornA 26 :VHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKY T0323 73 :EKPEQLYRVSDEAL 1ornA 60 :RTPHDYIAVPLEEL T0323 87 :RQAGVSKRKIEYIRHVCEHVES 1ornA 78 :RSIGLYRNKARNIQKLCAMLID T0323 109 :GRL 1ornA 103 :GEV T0323 112 :DFT 1ornA 108 :DRD T0323 127 :KLTAIKGIGQWTAEMFMMFSLGRL 1ornA 111 :ELMKLPGVGRKTANVVVSVAFGVP T0323 153 :LSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 1ornA 135 :AIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIP T0323 189 :YETVACLYLWKAA 1ornA 173 :EWSITHHRMIFFG T0323 206 :EEYRSLEELLHHGNQ 1ornA 186 :RYHCKAQSPQCPSCP Number of specific fragments extracted= 11 number of extra gaps= 0 total=168 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lwyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lwyA expands to /projects/compbio/data/pdb/1lwy.pdb.gz 1lwyA:# T0323 read from 1lwyA/merged-good-all-a2m # 1lwyA read from 1lwyA/merged-good-all-a2m # adding 1lwyA to template set # found chain 1lwyA in template set T0323 4 :FSTD 1lwyA 102 :LDVT T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1lwyA 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1lwyA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFG T0323 70 :GALEKPEQLYR 1lwyA 179 :HGFPSLQALAG T0323 83 :DEALRQAGVSK 1lwyA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1lwyA 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1lwyA 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1lwyA 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGK 1lwyA 289 :KGPSP T0323 177 :KLLIYHGKA 1lwyA 297 :KELGNFFRS T0323 186 :WAPYETVACLYLW 1lwyA 307 :WGPYAGWAQAVLF Number of specific fragments extracted= 11 number of extra gaps= 0 total=179 Number of alignments=16 # 1lwyA read from 1lwyA/merged-good-all-a2m # found chain 1lwyA in template set T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1lwyA 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGG 1lwyA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFGP T0323 71 :ALEKPEQLYR 1lwyA 180 :GFPSLQALAG T0323 83 :DEALRQAGVSK 1lwyA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1lwyA 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1lwyA 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1lwyA 268 :DVHMWHIAQRDYSWH T0323 173 :GDG 1lwyA 290 :GPS T0323 176 :KKLLIYHGKAWAP 1lwyA 296 :NKELGNFFRSLWG T0323 189 :YETVACLYLW 1lwyA 310 :YAGWAQAVLF Number of specific fragments extracted= 10 number of extra gaps= 0 total=189 Number of alignments=17 # 1lwyA read from 1lwyA/merged-good-all-a2m # found chain 1lwyA in template set T0323 2 :RYFSTDSPE 1lwyA 100 :FQLDVTLAQ T0323 11 :VKTIVAQDSRLFQFIEIAGEVQLP 1lwyA 110 :YHHWGSVDSHFQEVAQKFQGVRLL T0323 36 :KPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1lwyA 134 :RQDPIECLFSFICSSNNNIARITGMVERLCQAFGPR T0323 72 :LEKPEQLYR 1lwyA 181 :FPSLQALAG T0323 81 :VSDEALRQAGV 1lwyA 191 :EVEAHLRKLGL T0323 93 :KRKIEYIRHVCEHVESGRL 1lwyA 202 :GYRARYVSASARAILEEQG T0323 112 :DFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1lwyA 224 :WLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1lwyA 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYH 1lwyA 289 :KGPSPQTNKEL T0323 183 :GKAWAPYETVACLYLWKAAG 1lwyA 304 :RSLWGPYAGWAQAVLFSADL Number of specific fragments extracted= 10 number of extra gaps= 0 total=199 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2csbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2csbA expands to /projects/compbio/data/pdb/2csb.pdb.gz 2csbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2044, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2046, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2048, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2050, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2052, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2054, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 2056, because occupancy 0.400 <= existing 0.600 in 2csbA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2751, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2753, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2755, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2757, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2759, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2761, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2763, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 2csbA Skipped atom 2810, because occupancy 0.500 <= existing 0.500 in 2csbA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3905, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3907, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3909, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 3911, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4115, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4117, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4119, because occupancy 0.400 <= existing 0.600 in 2csbA Skipped atom 4121, because occupancy 0.400 <= existing 0.600 in 2csbA # T0323 read from 2csbA/merged-good-all-a2m # 2csbA read from 2csbA/merged-good-all-a2m # adding 2csbA to template set # found chain 2csbA in template set Warning: unaligning (T0323)A16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 Warning: unaligning (T0323)Q17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2csbA)R250 T0323 4 :FSTDSPEVKTIV 2csbA 236 :IEYDERTAKRHV T0323 18 :DSRLFQFIEIAG 2csbA 251 :DRLLEELYEHLE T0323 30 :EVQLPTKP 2csbA 266 :ERYLRHPL T0323 38 :NPFQSLVSSIVEQQ 2csbA 276 :RWIVEHKRDIMRRY T0323 53 :SIKAASAIYGRVEQLVG 2csbA 290 :LEQRIVECALKLQDRYG T0323 74 :KPEQLYRVSDEAL 2csbA 376 :SIAGILATDLEEI T0323 87 :RQAGVSKRKIEYIRHVC 2csbA 393 :EEGRLSEEAYRAAVEIQ T0323 125 :IEKLTAIKGIGQWTAEMFM 2csbA 410 :LAELTKKEGVGRKTAERLL T0323 145 :FSLGR 2csbA 429 :RAFGN T0323 157 :DVGLQRGAKW 2csbA 434 :PERVKQLARE T0323 167 :LYGNG 2csbA 449 :LASVE T0323 172 :EGDGKKLLIYHGKAWAPYETV 2csbA 474 :RGIDRERAERLLKKYGGYSKV Number of specific fragments extracted= 12 number of extra gaps= 1 total=211 Number of alignments=19 # 2csbA read from 2csbA/merged-good-all-a2m # found chain 2csbA in template set Warning: unaligning (T0323)Q17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 T0323 4 :FSTDSPEVKTIVA 2csbA 236 :IEYDERTAKRHVK T0323 18 :DSRLFQFIEIAG 2csbA 251 :DRLLEELYEHLE T0323 30 :EVQLPTKPNPFQSLVSSIVEQQL 2csbA 268 :YLRHPLTRRWIVEHKRDIMRRYL T0323 54 :IKAASAIYGRVEQLVGG 2csbA 291 :EQRIVECALKLQDRYGI T0323 71 :A 2csbA 375 :E T0323 74 :KPEQLYRVSDEAL 2csbA 376 :SIAGILATDLEEI T0323 87 :RQAGVSKRKIEYIRHVC 2csbA 393 :EEGRLSEEAYRAAVEIQ T0323 125 :IEKLTAIKGIGQWTAEMFM 2csbA 410 :LAELTKKEGVGRKTAERLL T0323 145 :FSLGR 2csbA 429 :RAFGN T0323 157 :DVGLQRGAKW 2csbA 434 :PERVKQLARE T0323 167 :LYGNG 2csbA 449 :LASVE T0323 172 :EGDGKKLLIYHGKAWAPYETV 2csbA 474 :RGIDRERAERLLKKYGGYSKV Number of specific fragments extracted= 12 number of extra gaps= 1 total=223 Number of alignments=20 # 2csbA read from 2csbA/merged-good-all-a2m # found chain 2csbA in template set Warning: unaligning (T0323)Q17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2csbA)R250 T0323 2 :RYFSTDSPEVKTIVA 2csbA 234 :VNIEYDERTAKRHVK T0323 18 :DSRLFQFIEIAG 2csbA 251 :DRLLEELYEHLE T0323 30 :EVQLPTKPNPFQSLVSSIVE 2csbA 268 :YLRHPLTRRWIVEHKRDIMR T0323 51 :QLSIKAASAIYGRVEQLVGGA 2csbA 288 :RYLEQRIVECALKLQDRYGIR T0323 74 :KPEQLYRVSDEALRQAGVSKRKIEYIRHV 2csbA 345 :EAKSVNRTLATLIDEHGLSPDAADELIEH T0323 104 :EHVES 2csbA 386 :EEIER T0323 109 :GRLDFTEL 2csbA 395 :GRLSEEAY T0323 118 :GAEATTVIEKLTAIKGIGQWTAEMFM 2csbA 403 :RAAVEIQLAELTKKEGVGRKTAERLL T0323 145 :FSLGRL 2csbA 429 :RAFGNP T0323 158 :VGLQRG 2csbA 435 :ERVKQL T0323 164 :AKWLYGNG 2csbA 446 :IEKLASVE T0323 172 :EGDGKKLLIYHGKAWAPYET 2csbA 474 :RGIDRERAERLLKKYGGYSK Number of specific fragments extracted= 12 number of extra gaps= 1 total=235 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ngnA expands to /projects/compbio/data/pdb/1ngn.pdb.gz 1ngnA:Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1ngnA # T0323 read from 1ngnA/merged-good-all-a2m # 1ngnA read from 1ngnA/merged-good-all-a2m # adding 1ngnA to template set # found chain 1ngnA in template set Warning: unaligning (T0323)E30 because first residue in template chain is (1ngnA)K411 T0323 31 :VQLP 1ngnA 412 :WTPP T0323 37 :PNPFQSLVSSIVEQQLSIKAASAIYGRVEQL 1ngnA 428 :HDPWKLLIATIFLNRTSGKMAIPVLWEFLEK T0323 72 :LEKPEQLYRVSDEAL 1ngnA 459 :YPSAEVARAADWRDV T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLDFTE 1ngnA 478 :KPLGLYDLRAKTIIKFSDEYLTKQWRYPI T0323 130 :AIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWL 1ngnA 507 :ELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWL T0323 184 :K 1ngnA 545 :W Number of specific fragments extracted= 6 number of extra gaps= 0 total=241 Number of alignments=22 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set Warning: unaligning (T0323)E30 because first residue in template chain is (1ngnA)K411 T0323 31 :VQLPTKP 1ngnA 412 :WTPPRSP T0323 38 :NPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1ngnA 429 :DPWKLLIATIFLNRTSGKMAIPVLWEFLEKY T0323 73 :EKPEQLYRVSDEAL 1ngnA 460 :PSAEVARAADWRDV T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLDFTEL 1ngnA 478 :KPLGLYDLRAKTIIKFSDEYLTKQWRYPIE T0323 131 :IKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLY 1ngnA 508 :LHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLW Number of specific fragments extracted= 5 number of extra gaps= 0 total=246 Number of alignments=23 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set Warning: unaligning (T0323)E30 because first residue in template chain is (1ngnA)K411 T0323 31 :VQLPTK 1ngnA 412 :WTPPRS T0323 37 :PNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1ngnA 428 :HDPWKLLIATIFLNRTSGKMAIPVLWEFLEKYP T0323 74 :KPEQLYRVSDE 1ngnA 461 :SAEVARAADWR T0323 85 :ALRQAGVSKRKIEYIRHVCEHVESGRLDFT 1ngnA 476 :LLKPLGLYDLRAKTIIKFSDEYLTKQWRYP T0323 129 :TAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLY 1ngnA 506 :IELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLW Number of specific fragments extracted= 5 number of extra gaps= 0 total=251 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n3aA/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/T0323/1n3aA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1n3aA/merged-good-all-a2m.gz for input Trying 1n3aA/merged-good-all-a2m Error: Couldn't open file 1n3aA/merged-good-all-a2m or 1n3aA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mpgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0323 read from 1mpgA/merged-good-all-a2m # 1mpgA read from 1mpgA/merged-good-all-a2m # found chain 1mpgA in training set T0323 7 :DSPEVKTIVAQDSRL 1mpgA 67 :LEPVAAECLAKMSRL T0323 22 :FQFIEIAGE 1mpgA 89 :QIVNGALGR T0323 31 :VQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1mpgA 105 :LRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYG T0323 70 :GALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDF 1mpgA 153 :ICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPM T0323 118 :GA 1mpgA 197 :TI T0323 120 :EATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQR 1mpgA 201 :DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQ T0323 166 :WL 1mpgA 244 :RF T0323 172 :EGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAE 1mpgA 246 :PGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPD Number of specific fragments extracted= 8 number of extra gaps= 0 total=259 Number of alignments=25 # 1mpgA read from 1mpgA/merged-good-all-a2m # found chain 1mpgA in training set T0323 14 :IVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGG 1mpgA 88 :PQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGE T0323 71 :ALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELE 1mpgA 154 :CFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPG T0323 120 :EATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRG 1mpgA 201 :DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQR T0323 170 :NGEG 1mpgA 245 :FPGM T0323 175 :GKKLLIYHGKAWAPYETVACLYLWKAAGTFAE 1mpgA 249 :TPAQIRRYAERWKPWRSYALLHIWYTEGWQPD Number of specific fragments extracted= 5 number of extra gaps= 0 total=264 Number of alignments=26 # 1mpgA read from 1mpgA/merged-good-all-a2m # found chain 1mpgA in training set T0323 2 :RYFSTDSPEVK 1mpgA 82 :FDLQCNPQIVN T0323 19 :SRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1mpgA 93 :GALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGER T0323 72 :LEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLD 1mpgA 155 :FPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLP T0323 117 :EG 1mpgA 196 :MT T0323 119 :AEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGA 1mpgA 200 :GDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRF T0323 172 :EGDGKKLLIYHGKAWAPYETVACLYLW 1mpgA 246 :PGMTPAQIRRYAERWKPWRSYALLHIW Number of specific fragments extracted= 6 number of extra gaps= 0 total=270 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1weiA/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/T0323/1weiA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1weiA/merged-good-all-a2m.gz for input Trying 1weiA/merged-good-all-a2m Error: Couldn't open file 1weiA/merged-good-all-a2m or 1weiA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n3cA/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/T0323/1n3cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1n3cA/merged-good-all-a2m.gz for input Trying 1n3cA/merged-good-all-a2m Error: Couldn't open file 1n3cA/merged-good-all-a2m or 1n3cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m3qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m3qA expands to /projects/compbio/data/pdb/1m3q.pdb.gz 1m3qA:# T0323 read from 1m3qA/merged-good-all-a2m # 1m3qA read from 1m3qA/merged-good-all-a2m # adding 1m3qA to template set # found chain 1m3qA in template set T0323 4 :FSTD 1m3qA 102 :LDVT T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1m3qA 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1m3qA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFG T0323 70 :GALEKPEQLYR 1m3qA 179 :HGFPSLQALAG T0323 83 :DEALRQAGVSK 1m3qA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1m3qA 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1m3qA 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1m3qA 268 :EVHMWHIAQRDYSWH T0323 172 :EGDGK 1m3qA 289 :KGPSP T0323 177 :KLLIYHGKA 1m3qA 297 :KELGNFFRS T0323 186 :WAPYETVACLYLW 1m3qA 307 :WGPYAGWAQAVLF Number of specific fragments extracted= 11 number of extra gaps= 0 total=281 Number of alignments=28 # 1m3qA read from 1m3qA/merged-good-all-a2m # found chain 1m3qA in template set T0323 9 :PEVKTIVAQDSRLFQFIEIAGEVQL 1m3qA 108 :QLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGG 1m3qA 133 :LRQDPIECLFSFICSSNNNIARITGMVERLCQAFGP T0323 71 :ALEKPEQLYR 1m3qA 180 :GFPSLQALAG T0323 83 :DEALRQAGVSK 1m3qA 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1m3qA 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1m3qA 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1m3qA 268 :EVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYHGKAWAP 1m3qA 292 :SPQTNKELGNFFRSLWG T0323 189 :YETVACLYLW 1m3qA 310 :YAGWAQAVLF Number of specific fragments extracted= 9 number of extra gaps= 0 total=290 Number of alignments=29 # 1m3qA read from 1m3qA/merged-good-all-a2m # found chain 1m3qA in template set T0323 2 :RYFSTDS 1m3qA 100 :FQLDVTL T0323 9 :PEVKTIVAQDSRLFQFIEIAGEVQLP 1m3qA 108 :QLYHHWGSVDSHFQEVAQKFQGVRLL T0323 36 :KPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1m3qA 134 :RQDPIECLFSFICSSNNNIARITGMVERLCQAFGPR T0323 72 :LEKPEQLYR 1m3qA 181 :FPSLQALAG T0323 81 :VSDEALRQAGV 1m3qA 191 :EVEAHLRKLGL T0323 93 :KRKIEYIRHVCEHVESGRL 1m3qA 202 :GYRARYVSASARAILEEQG T0323 112 :DFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1m3qA 224 :WLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1m3qA 268 :EVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYH 1m3qA 289 :KGPSPQTNKEL T0323 183 :GKAWAPYETVACLYLWKAA 1m3qA 304 :RSLWGPYAGWAQAVLFSAD Number of specific fragments extracted= 10 number of extra gaps= 0 total=300 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kg2A/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/T0323/1kg2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kg2A/merged-good-all-a2m.gz for input Trying 1kg2A/merged-good-all-a2m Error: Couldn't open file 1kg2A/merged-good-all-a2m or 1kg2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p59A/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/T0323/1p59A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1p59A/merged-good-all-a2m.gz for input Trying 1p59A/merged-good-all-a2m Error: Couldn't open file 1p59A/merged-good-all-a2m or 1p59A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lmzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lmzA expands to /projects/compbio/data/pdb/1lmz.pdb.gz 1lmzA:# T0323 read from 1lmzA/merged-good-all-a2m # 1lmzA read from 1lmzA/merged-good-all-a2m # adding 1lmzA to template set # found chain 1lmzA in template set T0323 2 :RYFSTDSP 1lmzA 2 :ERCGWVSQ T0323 18 :DSRLFQFIEIAGEVQL 1lmzA 10 :DPLYIAYHDNEWGVPE T0323 37 :PN 1lmzA 26 :TD T0323 39 :PFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1lmzA 31 :LFEMICLEGQQAGLSWITVLKKRENYRACFHQF T0323 74 :KPEQLYRVSDEAL 1lmzA 64 :DPVKVAAMQEEDV T0323 87 :RQAGV 1lmzA 81 :QDAGI T0323 92 :SKRKIEYIRHVCEHVES 1lmzA 88 :HRGKIQAIIGNARAYLQ T0323 118 :GAEA 1lmzA 134 :EIPT T0323 122 :TTVIEKLTA 1lmzA 143 :DALSKALKK T0323 131 :IKGIGQWTAEMFM 1lmzA 154 :FKFVGTTICYSFM T0323 145 :FSLGRLD 1lmzA 167 :QACGLVN Number of specific fragments extracted= 11 number of extra gaps= 0 total=311 Number of alignments=31 # 1lmzA read from 1lmzA/merged-good-all-a2m # found chain 1lmzA in template set T0323 2 :RYFSTDSP 1lmzA 2 :ERCGWVSQ T0323 18 :DSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1lmzA 10 :DPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQF T0323 74 :KPEQLYRVSDEAL 1lmzA 64 :DPVKVAAMQEEDV T0323 87 :RQAGV 1lmzA 81 :QDAGI T0323 92 :SKRKIEYIRHVCEHVES 1lmzA 88 :HRGKIQAIIGNARAYLQ T0323 109 :GRL 1lmzA 109 :GEP T0323 112 :DFTELEGAEA 1lmzA 128 :QATTLSEIPT T0323 122 :TTVIEKLTA 1lmzA 143 :DALSKALKK T0323 131 :IKGIGQWTAEMFM 1lmzA 154 :FKFVGTTICYSFM T0323 145 :FSLGRLDV 1lmzA 167 :QACGLVND Number of specific fragments extracted= 10 number of extra gaps= 0 total=321 Number of alignments=32 # 1lmzA read from 1lmzA/merged-good-all-a2m # found chain 1lmzA in template set T0323 18 :DSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGA 1lmzA 10 :DPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACFHQF T0323 74 :KPEQLYRVSDEALRQA 1lmzA 64 :DPVKVAAMQEEDVERL T0323 91 :VSKRKIEYIRHVCEHVES 1lmzA 87 :RHRGKIQAIIGNARAYLQ T0323 139 :AEMFMMFSLGRLDVLSV 1lmzA 113 :ADFVWSFVNHQPQMTQA T0323 169 :GNGEGDGKKLLIYHGKAWAPY 1lmzA 132 :LSEIPTSTPASDALSKALKKR T0323 190 :ETVACLYLWKAAG 1lmzA 158 :GTTICYSFMQACG Number of specific fragments extracted= 6 number of extra gaps= 0 total=327 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kqjA/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/T0323/1kqjA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kqjA/merged-good-all-a2m.gz for input Trying 1kqjA/merged-good-all-a2m Error: Couldn't open file 1kqjA/merged-good-all-a2m or 1kqjA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mun/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0323 read from 1mun/merged-good-all-a2m # 1mun read from 1mun/merged-good-all-a2m # found chain 1mun in training set T0323 15 :VAQDSRLFQFIEIAG 1mun 5 :QFSAQVLDWYDKYGR T0323 30 :EVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQL 1mun 21 :TLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMAR T0323 72 :LEKPEQLYRVSDEAL 1mun 59 :FPTVTDLANAPLDEV T0323 87 :RQAGV 1mun 76 :LWTGL T0323 92 :SKRKIEYIRHVCEHVESGRLD 1mun 82 :YYARARNLHKAAQQVATLHGG T0323 118 :GAEAT 1mun 103 :KFPET T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1mun 108 :FEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNGEGDG 1mun 134 :FPILNGNVKRVLARCYAVSGWPG T0323 176 :KKLLIYHGKAWAPYETVACLYLW 1mun 161 :ENKLWSLSEQVTPAVGVERFNQA T0323 199 :KAAGT 1mun 191 :ICTRS T0323 208 :YRSLEELLHHGN 1mun 196 :KPKCSLCPLQNG Number of specific fragments extracted= 11 number of extra gaps= 0 total=338 Number of alignments=34 # 1mun read from 1mun/merged-good-all-a2m # found chain 1mun in training set T0323 14 :IVAQDSRLFQFIEIAG 1mun 4 :SQFSAQVLDWYDKYGR T0323 30 :EVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1mun 21 :TLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARF T0323 73 :EKPEQLYRVSDEAL 1mun 60 :PTVTDLANAPLDEV T0323 87 :RQAGV 1mun 76 :LWTGL T0323 92 :SKRKIEYIRHVCEHVES 1mun 82 :YYARARNLHKAAQQVAT T0323 114 :TELEGAEAT 1mun 99 :LHGGKFPET T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1mun 108 :FEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAP 1mun 134 :FPILNGNVKRVLARCYAVSGWPGKKEVENKLWSLSE T0323 189 :YETVACLYLW 1mun 177 :VERFNQAMMD T0323 199 :K 1mun 192 :C T0323 200 :AAGTFAEEYRSLEELLH 1mun 194 :RSKPKCSLCPLQNGCIA Number of specific fragments extracted= 11 number of extra gaps= 0 total=349 Number of alignments=35 # 1mun read from 1mun/merged-good-all-a2m # found chain 1mun in training set T0323 16 :AQDSRLFQFIEIAGEVQLP 1mun 5 :QFSAQVLDWYDKYGRKTLP T0323 35 :TKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1mun 26 :IDKTPYKVWLSEVMLQQTQVATVIPYFERFMARF T0323 73 :EKPEQLYRVSDE 1mun 60 :PTVTDLANAPLD T0323 85 :ALRQAGV 1mun 76 :LWTGLGY T0323 93 :KRKIEYIRHVCEHVES 1mun 83 :YARARNLHKAAQQVAT T0323 109 :GRL 1mun 102 :GKF T0323 122 :TTVIEKLTAIKGIGQWTAEMFMMFSLGRL 1mun 105 :PETFEEVAALPGVGRSTAGAILSLSLGKH T0323 153 :LSVGDVGLQRGAKWLYGNG 1mun 134 :FPILNGNVKRVLARCYAVS T0323 172 :EGDGKKLLIYHGKAWAP 1mun 157 :KKEVENKLWSLSEQVTP T0323 189 :YETVACLYLWKAAG 1mun 176 :GVERFNQAMMDLGA T0323 207 :EYRSLEELLHHGNQ 1mun 190 :MICTRSKPKCSLCP Number of specific fragments extracted= 11 number of extra gaps= 0 total=360 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ko9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ko9A expands to /projects/compbio/data/pdb/1ko9.pdb.gz 1ko9A:# T0323 read from 1ko9A/merged-good-all-a2m # 1ko9A read from 1ko9A/merged-good-all-a2m # adding 1ko9A to template set # found chain 1ko9A in template set Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE in next template residue (1ko9A)N149 Warning: unaligning (T0323)Q51 because of BadResidue code BAD_PEPTIDE at template residue (1ko9A)N149 T0323 4 :FSTD 1ko9A 102 :LDVT T0323 8 :SPEVKTIVAQDSRLFQFIEIAGEVQL 1ko9A 107 :AQLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVE 1ko9A 133 :LRQDPIECLFSFICS T0323 52 :LSIKAASAIYGRVEQLVG 1ko9A 150 :NNIARITGMVERLCQAFG T0323 70 :GALEKPEQLYR 1ko9A 179 :HGFPSLQALAG T0323 83 :DEALRQAGVSK 1ko9A 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1ko9A 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ko9A 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ko9A 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGK 1ko9A 289 :KGPSP T0323 177 :KLLIYHGKA 1ko9A 297 :KELGNFFRS T0323 186 :WAPYETVACLYLW 1ko9A 307 :WGPYAGWAQAVLF Number of specific fragments extracted= 12 number of extra gaps= 1 total=372 Number of alignments=37 # 1ko9A read from 1ko9A/merged-good-all-a2m # found chain 1ko9A in template set Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE in next template residue (1ko9A)N149 Warning: unaligning (T0323)Q51 because of BadResidue code BAD_PEPTIDE at template residue (1ko9A)N149 T0323 9 :PEVKTIVAQDSRLFQFIEIAGEVQL 1ko9A 108 :QLYHHWGSVDSHFQEVAQKFQGVRL T0323 35 :TKPNPFQSLVSSIVE 1ko9A 133 :LRQDPIECLFSFICS T0323 52 :LSIKAASAIYGRVEQLVGG 1ko9A 150 :NNIARITGMVERLCQAFGP T0323 71 :ALEKPEQLYR 1ko9A 180 :GFPSLQALAG T0323 83 :DEALRQAGVSK 1ko9A 193 :EAHLRKLGLGY T0323 95 :KIEYIRHVCEHVESGRLD 1ko9A 204 :RARYVSASARAILEEQGG T0323 113 :FTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ko9A 225 :LQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ko9A 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYHGKAWAP 1ko9A 292 :SPQTNKELGNFFRSLWG T0323 189 :YETVACLYLW 1ko9A 310 :YAGWAQAVLF Number of specific fragments extracted= 10 number of extra gaps= 1 total=382 Number of alignments=38 # 1ko9A read from 1ko9A/merged-good-all-a2m # found chain 1ko9A in template set Warning: unaligning (T0323)Q50 because of BadResidue code BAD_PEPTIDE in next template residue (1ko9A)N149 Warning: unaligning (T0323)Q51 because of BadResidue code BAD_PEPTIDE at template residue (1ko9A)N149 Warning: unaligning (T0323)G202 because last residue in template chain is (1ko9A)L323 T0323 2 :RYFSTDS 1ko9A 100 :FQLDVTL T0323 9 :PEVKTIVAQDSRLFQFIEIAGEVQLP 1ko9A 108 :QLYHHWGSVDSHFQEVAQKFQGVRLL T0323 36 :KPNPFQSLVSSIVE 1ko9A 134 :RQDPIECLFSFICS T0323 52 :LSIKAASAIYGRVEQLVGGA 1ko9A 150 :NNIARITGMVERLCQAFGPR T0323 72 :LEKPEQLYR 1ko9A 181 :FPSLQALAG T0323 81 :VSDEALRQAGV 1ko9A 191 :EVEAHLRKLGL T0323 93 :KRKIEYIRHVCEHVESGRL 1ko9A 202 :GYRARYVSASARAILEEQG T0323 112 :DFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSV 1ko9A 224 :WLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV T0323 157 :DVGLQRGAKWLYGNG 1ko9A 268 :DVHMWHIAQRDYSWH T0323 172 :EGDGKKLLIYH 1ko9A 289 :KGPSPQTNKEL T0323 183 :GKAWAPYETVACLYLWKAA 1ko9A 304 :RSLWGPYAGWAQAVLFSAD Number of specific fragments extracted= 11 number of extra gaps= 1 total=393 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kg4A/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/T0323/1kg4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kg4A/merged-good-all-a2m.gz for input Trying 1kg4A/merged-good-all-a2m Error: Couldn't open file 1kg4A/merged-good-all-a2m or 1kg4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqkA/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/T0323/1yqkA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1yqkA/merged-good-all-a2m.gz for input Trying 1yqkA/merged-good-all-a2m Error: Couldn't open file 1yqkA/merged-good-all-a2m or 1yqkA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rrqA/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/T0323/1rrqA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1rrqA/merged-good-all-a2m.gz for input Trying 1rrqA/merged-good-all-a2m Error: Couldn't open file 1rrqA/merged-good-all-a2m or 1rrqA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kg5A/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/T0323/1kg5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kg5A/merged-good-all-a2m.gz for input Trying 1kg5A/merged-good-all-a2m Error: Couldn't open file 1kg5A/merged-good-all-a2m or 1kg5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kg6A/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/T0323/1kg6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kg6A/merged-good-all-a2m.gz for input Trying 1kg6A/merged-good-all-a2m Error: Couldn't open file 1kg6A/merged-good-all-a2m or 1kg6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rrsA/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/T0323/1rrsA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1rrsA/merged-good-all-a2m.gz for input Trying 1rrsA/merged-good-all-a2m Error: Couldn't open file 1rrsA/merged-good-all-a2m or 1rrsA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kg7A/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/T0323/1kg7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0323/1kg7A/merged-good-all-a2m.gz for input Trying 1kg7A/merged-good-all-a2m Error: Couldn't open file 1kg7A/merged-good-all-a2m or 1kg7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1keaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1keaA expands to /projects/compbio/data/pdb/1kea.pdb.gz 1keaA:Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 854, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1keaA Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1keaA # T0323 read from 1keaA/merged-good-all-a2m # 1keaA read from 1keaA/merged-good-all-a2m # adding 1keaA to template set # found chain 1keaA in template set Warning: unaligning (T0323)S8 because first residue in template chain is (1keaA)D3 T0323 9 :PEVKTIVAQDSRLFQFIEIAG 1keaA 4 :ATNKKRKVFVSTILTFWNTDR T0323 30 :EVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQL 1keaA 26 :DFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVK T0323 72 :LEKPEQLYRVSDEAL 1keaA 64 :YKCFEDILKTPKSEI T0323 87 :RQAGVSKRKIEYIRHVCEHVESGRLD 1keaA 83 :KEIGLSNQRAEQLKELARVVINDYGG T0323 118 :GAEAT 1keaA 109 :RVPRN T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1keaA 114 :RKAILDLPGVGKYTCAAVMCLAFGKK T0323 152 :VLSV 1keaA 140 :AAMV T0323 157 :DVGLQRGAKWLYGNG 1keaA 144 :DANFVRVINRYFGGS T0323 172 :EGDGKKLLIYHGKAWAPYETVACLYLW 1keaA 162 :LNYNHKALWELAETLVPGGKCRDFNLG T0323 199 :KAAGTF 1keaA 196 :ICAPRK T0323 209 :RSLEELLHHGN 1keaA 202 :PKCEKCGMSKL Number of specific fragments extracted= 11 number of extra gaps= 0 total=404 Number of alignments=40 # 1keaA read from 1keaA/merged-good-all-a2m # found chain 1keaA in template set Warning: unaligning (T0323)S8 because first residue in template chain is (1keaA)D3 Warning: unaligning (T0323)Q220 because last residue in template chain is (1keaA)C219 T0323 9 :PEVKTIVAQDSRLFQFIEIAG 1keaA 4 :ATNKKRKVFVSTILTFWNTDR T0323 30 :EVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLV 1keaA 26 :DFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKY T0323 73 :EKPEQLYRVSDEAL 1keaA 65 :KCFEDILKTPKSEI T0323 87 :RQAGVSKRKIEYIRHVCEHVES 1keaA 83 :KEIGLSNQRAEQLKELARVVIN T0323 114 :TELEGAEAT 1keaA 105 :DYGGRVPRN T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1keaA 114 :RKAILDLPGVGKYTCAAVMCLAFGKK T0323 152 :VLSV 1keaA 140 :AAMV T0323 157 :DVGLQRGAKWLYG 1keaA 144 :DANFVRVINRYFG T0323 170 :NGEGDGKKLLIYHGKAWAP 1keaA 160 :ENLNYNHKALWELAETLVP T0323 189 :YETVACLYLW 1keaA 182 :CRDFNLGLMD T0323 199 :K 1keaA 197 :C T0323 200 :AAGTFAEEYRSLEELLHHGN 1keaA 199 :PRKPKCEKCGMSKLCSYYEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=416 Number of alignments=41 # 1keaA read from 1keaA/merged-good-all-a2m # found chain 1keaA in template set Warning: unaligning (T0323)S8 because first residue in template chain is (1keaA)D3 T0323 9 :PEVKTIVAQDSRLFQFIEI 1keaA 4 :ATNKKRKVFVSTILTFWNT T0323 28 :AGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVG 1keaA 24 :RRDFPWRHTRDPYVILITEILLRRTTAGHVKKIYDKFFVKYK T0323 74 :KPEQLYRVSDE 1keaA 66 :CFEDILKTPKS T0323 85 :ALRQAGVSKRKIEYIRHVCEHVES 1keaA 81 :DIKEIGLSNQRAEQLKELARVVIN T0323 109 :GRLD 1keaA 108 :GRVP T0323 119 :AE 1keaA 112 :RN T0323 125 :IEKLTAIKGIGQWTAEMFMMFSLGRL 1keaA 114 :RKAILDLPGVGKYTCAAVMCLAFGKK T0323 153 :LSVGDVGLQRGAKWLYGNG 1keaA 140 :AAMVDANFVRVINRYFGGS T0323 172 :EGDGKKLLIYHGKAWAPYETVACLYLWKAAG 1keaA 163 :NYNHKALWELAETLVPGGKCRDFNLGLMDFS T0323 206 :EEYRSLEELLHHGNQ 1keaA 194 :AIICAPRKPKCEKCG Number of specific fragments extracted= 10 number of extra gaps= 0 total=426 Number of alignments=42 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 42 Done printing distance constraints # command: