# 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/T0287/ # command:# Making conformation for sequence T0287 numbered 1 through 199 Created new target T0287 from T0287.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0287/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0287//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0287/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0287//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0287/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0287/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0287/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sas/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2sas expands to /projects/compbio/data/pdb/2sas.pdb.gz 2sas:Warning: there is no chain 2sas will retry with 2sasA # T0287 read from 2sas/merged-good-all-a2m # 2sas read from 2sas/merged-good-all-a2m # adding 2sas to template set # found chain 2sas in template set T0287 35 :DEK 2sas 4 :DFQ # choosing archetypes in rotamer library T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLLESETMELLHAIAENPNFLFS 2sas 45 :SLSDADYKSMQASLEDEWRDLKGRADINKDDVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2sas read from 2sas/merged-good-all-a2m # found chain 2sas in template set T0287 35 :DEK 2sas 4 :DFQ T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLLESETMELLHAIAENPNFLFS 2sas 45 :SLSDADYKSMQASLEDEWRDLKGRADINKDDVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 2sas read from 2sas/merged-good-all-a2m # found chain 2sas in template set T0287 35 :DEK 2sas 4 :DFQ T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLLESETMELLHAIAENPNFLFS 2sas 45 :SLSDADYKSMQASLEDEWRDLKGRADINKDDVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1tmxA/merged-good-all-a2m # 1tmxA read from 1tmxA/merged-good-all-a2m # found chain 1tmxA in training set T0287 13 :ADSKDKKEKLIESLQE 1tmxA 7 :AEQQAREQDLVERVLR T0287 29 :NELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDK 1tmxA 25 :DATADPRLKQVMQALTRHLHAFLREVRLTEAEWET T0287 65 :LRNYMKDYRAV 1tmxA 60 :GIGFLTDAGHV T0287 80 :GVDKFKKVYRLLESETMELLHAIAENPN 1tmxA 73 :ERRQEFILLSDVLGASMQTIAMNNEAHG T0287 108 :FLFSKFDRSILGIFL 1tmxA 111 :FFVEGSPRIESGGDI T0287 123 :PFFSKPIMFKMSIREMD 1tmxA 128 :GAAGEPCWVEGTVTDTD T0287 146 :GTNLPLLKLFVMTDEE 1tmxA 145 :GNPVPDARIEVWEADD Number of specific fragments extracted= 7 number of extra gaps= 0 total=16 Number of alignments=4 # 1tmxA read from 1tmxA/merged-good-all-a2m # found chain 1tmxA in training set T0287 13 :ADSKDKKEKLIESLQE 1tmxA 7 :AEQQAREQDLVERVLR T0287 29 :NELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDK 1tmxA 25 :DATADPRLKQVMQALTRHLHAFLREVRLTEAEWET T0287 65 :LRNYMKDYRAV 1tmxA 60 :GIGFLTDAGHV T0287 80 :GVDKFKKVYRLLESETMELLHAIAENPN 1tmxA 73 :ERRQEFILLSDVLGASMQTIAMNNEAHG T0287 108 :FLFSKFDRSILGIFL 1tmxA 111 :FFVEGSPRIESGGDI T0287 123 :PFFSKPIMFKMSIREMD 1tmxA 128 :GAAGEPCWVEGTVTDTD T0287 146 :GTNLPLLKLFVMTDEE 1tmxA 145 :GNPVPDARIEVWEADD Number of specific fragments extracted= 7 number of extra gaps= 0 total=23 Number of alignments=5 # 1tmxA read from 1tmxA/merged-good-all-a2m # found chain 1tmxA in training set T0287 13 :ADSKDKKEKLIESLQE 1tmxA 7 :AEQQAREQDLVERVLR T0287 29 :NELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDK 1tmxA 25 :DATADPRLKQVMQALTRHLHAFLREVRLTEAEWET T0287 65 :LRNYMKDYRAV 1tmxA 60 :GIGFLTDAGHV T0287 80 :GVDKFKKVYRLLESETMELLHAIAENPN 1tmxA 73 :ERRQEFILLSDVLGASMQTIAMNNEAHG T0287 108 :FLFSKFDRSILGIFL 1tmxA 111 :FFVEGSPRIESGGDI T0287 123 :PFFSKPIMFKMSIREMD 1tmxA 128 :GAAGEPCWVEGTVTDTD T0287 146 :GTNLPLLKLFVMTDEE 1tmxA 145 :GNPVPDARIEVWEADD Number of specific fragments extracted= 7 number of extra gaps= 0 total=30 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1josA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1josA/merged-good-all-a2m # 1josA read from 1josA/merged-good-all-a2m # found chain 1josA in training set Warning: unaligning (T0287)K83 because first residue in template chain is (1josA)R7 T0287 84 :FKKVYRLLESETMELLHAIAENPNFL 1josA 8 :SDRVAQEIQKEIAVILQREVKDPRIG T0287 127 :K 1josA 34 :M T0287 133 :MSI 1josA 35 :VTV T0287 140 :SQIEL 1josA 38 :SDVEV T0287 146 :GTNLPLLKLFVM 1josA 43 :SSDLSYAKIFVT T0287 158 :TDEEVNFYANLKTIEQYNDYVRDLLMK 1josA 58 :DHDEMAIEQGMKGLEKASPYIRSLLGK Number of specific fragments extracted= 6 number of extra gaps= 0 total=36 Number of alignments=7 # 1josA read from 1josA/merged-good-all-a2m # found chain 1josA in training set Warning: unaligning (T0287)K83 because first residue in template chain is (1josA)R7 T0287 84 :FKKVYRLLESETMELLHAIAENPNFL 1josA 8 :SDRVAQEIQKEIAVILQREVKDPRIG T0287 127 :K 1josA 34 :M T0287 133 :MSI 1josA 35 :VTV T0287 140 :SQIEL 1josA 38 :SDVEV T0287 146 :GTNLPLLKLFVM 1josA 43 :SSDLSYAKIFVT T0287 158 :TDEEVNFYANLKTIEQYNDYVRDLLMK 1josA 58 :DHDEMAIEQGMKGLEKASPYIRSLLGK Number of specific fragments extracted= 6 number of extra gaps= 0 total=42 Number of alignments=8 # 1josA read from 1josA/merged-good-all-a2m # found chain 1josA in training set Warning: unaligning (T0287)K83 because first residue in template chain is (1josA)R7 T0287 84 :FKKVYRLLESETMELLHAIAENPNFL 1josA 8 :SDRVAQEIQKEIAVILQREVKDPRIG T0287 127 :K 1josA 34 :M T0287 133 :MSI 1josA 35 :VTV T0287 140 :SQIEL 1josA 38 :SDVEV T0287 146 :GTNLPLLKLFVM 1josA 43 :SSDLSYAKIFVT T0287 158 :TDEEVNFYANLKTIEQYNDYVRDLLMK 1josA 58 :DHDEMAIEQGMKGLEKASPYIRSLLGK Number of specific fragments extracted= 6 number of extra gaps= 0 total=48 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sz9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sz9A expands to /projects/compbio/data/pdb/1sz9.pdb.gz 1sz9A:# T0287 read from 1sz9A/merged-good-all-a2m # 1sz9A read from 1sz9A/merged-good-all-a2m # adding 1sz9A to template set # found chain 1sz9A in template set T0287 5 :MRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDF 1sz9A 9 :VKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEK T0287 51 :FKQMHTNKGALDKVLRNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAE 1sz9A 57 :PKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFK T0287 105 :NPN 1sz9A 114 :NPN T0287 146 :GTNLPLL 1sz9A 117 :DTGLPLF T0287 167 :NLKTIEQYNDYVRD 1sz9A 124 :EGSALEKIEQFLIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=53 Number of alignments=10 # 1sz9A read from 1sz9A/merged-good-all-a2m # found chain 1sz9A in template set T0287 5 :MRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDF 1sz9A 9 :VKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEK T0287 51 :FKQMHTNKGALDKVLRNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAE 1sz9A 57 :PKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFK T0287 105 :NPN 1sz9A 114 :NPN T0287 146 :GTNLPLL 1sz9A 117 :DTGLPLF T0287 167 :NLKTIEQYNDYVRD 1sz9A 124 :EGSALEKIEQFLIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=58 Number of alignments=11 # 1sz9A read from 1sz9A/merged-good-all-a2m # found chain 1sz9A in template set T0287 5 :MRKLFSMIADSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDF 1sz9A 9 :VKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEK T0287 51 :FKQMHTNKGALDKVLRNYMKDYRAVIKSIGVDKFKKVYRLLESETMELLHAIAE 1sz9A 57 :PKQKLYAFYALDSICKNVGSPYTIYFSRNLFNLYKRTYLLVDNTTRTKLINMFK T0287 105 :NPN 1sz9A 114 :NPN T0287 146 :GTNLPLL 1sz9A 117 :DTGLPLF T0287 167 :NLKTIEQYNDYVRD 1sz9A 124 :EGSALEKIEQFLIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=63 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dk0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1dk0A/merged-good-all-a2m # 1dk0A read from 1dk0A/merged-good-all-a2m # found chain 1dk0A in training set Warning: unaligning (T0287)E92 because last residue in template chain is (1dk0A)A174 T0287 50 :FFKQMHTNKGALDKVLRNYMKDY 1dk0A 136 :VYGLMSGDTGALETALNGILDDY T0287 78 :SIGVD 1dk0A 159 :GLSVN T0287 83 :KFKKVYRLL 1dk0A 165 :TFDQVAAAT Number of specific fragments extracted= 3 number of extra gaps= 0 total=66 Number of alignments=13 # 1dk0A read from 1dk0A/merged-good-all-a2m # found chain 1dk0A in training set Warning: unaligning (T0287)E92 because last residue in template chain is (1dk0A)A174 T0287 50 :FFKQMHTNKGALDKVLRNYMKDY 1dk0A 136 :VYGLMSGDTGALETALNGILDDY T0287 78 :SIGVD 1dk0A 159 :GLSVN T0287 83 :KFKKVYRLL 1dk0A 165 :TFDQVAAAT Number of specific fragments extracted= 3 number of extra gaps= 0 total=69 Number of alignments=14 # 1dk0A read from 1dk0A/merged-good-all-a2m # found chain 1dk0A in training set Warning: unaligning (T0287)E92 because last residue in template chain is (1dk0A)A174 T0287 50 :FFKQMHTNKGALDKVLRNYMKDY 1dk0A 136 :VYGLMSGDTGALETALNGILDDY T0287 78 :SIGVD 1dk0A 159 :GLSVN T0287 83 :KFKKVYRLL 1dk0A 165 :TFDQVAAAT Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dh3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dh3A expands to /projects/compbio/data/pdb/1dh3.pdb.gz 1dh3A:# T0287 read from 1dh3A/merged-good-all-a2m # 1dh3A read from 1dh3A/merged-good-all-a2m # adding 1dh3A to template set # found chain 1dh3A in template set Warning: unaligning (T0287)E30 because of BadResidue code BAD_PEPTIDE in next template residue (1dh3A)A316 Warning: unaligning (T0287)L31 because of BadResidue code BAD_PEPTIDE at template residue (1dh3A)A316 T0287 7 :KLFSMIADSKDKKEKLIESLQEN 1dh3A 292 :KNREAARESRRKKKEYVKSLENR T0287 32 :LNTDEKKKIIDQIKTMH 1dh3A 317 :VLENQNKTLIEELKALK Number of specific fragments extracted= 2 number of extra gaps= 1 total=74 Number of alignments=16 # 1dh3A read from 1dh3A/merged-good-all-a2m # found chain 1dh3A in template set Warning: unaligning (T0287)E30 because of BadResidue code BAD_PEPTIDE in next template residue (1dh3A)A316 Warning: unaligning (T0287)L31 because of BadResidue code BAD_PEPTIDE at template residue (1dh3A)A316 T0287 7 :KLFSMIADSKDKKEKLIESLQEN 1dh3A 292 :KNREAARESRRKKKEYVKSLENR T0287 32 :LNTDEKKKIIDQIKTMH 1dh3A 317 :VLENQNKTLIEELKALK Number of specific fragments extracted= 2 number of extra gaps= 1 total=76 Number of alignments=17 # 1dh3A read from 1dh3A/merged-good-all-a2m # found chain 1dh3A in template set Warning: unaligning (T0287)E30 because of BadResidue code BAD_PEPTIDE in next template residue (1dh3A)A316 Warning: unaligning (T0287)L31 because of BadResidue code BAD_PEPTIDE at template residue (1dh3A)A316 T0287 7 :KLFSMIADSKDKKEKLIESLQEN 1dh3A 292 :KNREAARESRRKKKEYVKSLENR T0287 32 :LNTDEKKKIIDQIKTMH 1dh3A 317 :VLENQNKTLIEELKALK Number of specific fragments extracted= 2 number of extra gaps= 1 total=78 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g24A expands to /projects/compbio/data/pdb/1g24.pdb.gz 1g24A:# T0287 read from 1g24A/merged-good-all-a2m # 1g24A read from 1g24A/merged-good-all-a2m # adding 1g24A to template set # found chain 1g24A in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGA 1g24A 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGV T0287 81 :VDKF 1g24A 97 :INGF T0287 92 :ESETMELLHAIAENPNFL 1g24A 101 :PSNLIKQVELLDKSFNKM T0287 124 :FFSKPIMF 1g24A 119 :KTPENIML T0287 132 :KMSIREMDSQIE 1g24A 129 :GDDPAYLGTEFQ T0287 144 :LYGTNLPL 1g24A 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 1g24A 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=85 Number of alignments=19 # 1g24A read from 1g24A/merged-good-all-a2m # found chain 1g24A in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGA 1g24A 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGV T0287 81 :VDKF 1g24A 97 :INGF T0287 92 :ESETMELLHAIAENPNFL 1g24A 101 :PSNLIKQVELLDKSFNKM T0287 124 :FFSKPIMF 1g24A 119 :KTPENIML T0287 132 :KMSIREMDSQIE 1g24A 129 :GDDPAYLGTEFQ T0287 144 :LYGTNLPL 1g24A 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 1g24A 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 Number of alignments=20 # 1g24A read from 1g24A/merged-good-all-a2m # found chain 1g24A in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGA 1g24A 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGV T0287 81 :VDKF 1g24A 97 :INGF T0287 92 :ESETMELLHAIAENPNFL 1g24A 101 :PSNLIKQVELLDKSFNKM T0287 124 :FFSKPIMF 1g24A 119 :KTPENIML T0287 132 :KMSIREMDSQIE 1g24A 129 :GDDPAYLGTEFQ T0287 144 :LYGTNLPL 1g24A 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 1g24A 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=99 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1alvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1alvA expands to /projects/compbio/data/pdb/1alv.pdb.gz 1alvA:# T0287 read from 1alvA/merged-good-all-a2m # 1alvA read from 1alvA/merged-good-all-a2m # adding 1alvA to template set # found chain 1alvA in template set T0287 15 :SKDKKEKLIESLQENE 1alvA 138 :GIDTCRSMVAVMDSDT T0287 31 :LLNTDEKKKIIDQIKTMHDFFKQMHTNK 1alvA 156 :KLGFEEFKYLWNNIKKWQAIYKQFDVDR T0287 69 :MKDYRAVIKSIGVDKFKKVYRL 1alvA 189 :SSELPGAFEAAGFHLNEHLYSM T0287 98 :LLHAIAENPN 1alvA 211 :IIRRYSDEGG Number of specific fragments extracted= 4 number of extra gaps= 0 total=103 Number of alignments=22 # 1alvA read from 1alvA/merged-good-all-a2m # found chain 1alvA in template set T0287 15 :SKDKKEKLIESLQENE 1alvA 138 :GIDTCRSMVAVMDSDT T0287 31 :LLNTDEKKKIIDQIKTMHDFFKQMHTNK 1alvA 156 :KLGFEEFKYLWNNIKKWQAIYKQFDVDR T0287 69 :MKDYRAVIKSIGVDKFKKVYRL 1alvA 189 :SSELPGAFEAAGFHLNEHLYSM T0287 98 :LLHAIAENPN 1alvA 211 :IIRRYSDEGG Number of specific fragments extracted= 4 number of extra gaps= 0 total=107 Number of alignments=23 # 1alvA read from 1alvA/merged-good-all-a2m # found chain 1alvA in template set T0287 15 :SKDKKEKLIESLQENE 1alvA 138 :GIDTCRSMVAVMDSDT T0287 31 :LLNTDEKKKIIDQIKTMHDFFKQMHTNK 1alvA 156 :KLGFEEFKYLWNNIKKWQAIYKQFDVDR T0287 69 :MKDYRAVIKSIGVDKFKKVYRL 1alvA 189 :SSELPGAFEAAGFHLNEHLYSM T0287 98 :LLHAIAENPN 1alvA 211 :IIRRYSDEGG Number of specific fragments extracted= 4 number of extra gaps= 0 total=111 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cunA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cunA expands to /projects/compbio/data/pdb/2cun.pdb.gz 2cunA:# T0287 read from 2cunA/merged-good-all-a2m # 2cunA read from 2cunA/merged-good-all-a2m # adding 2cunA to template set # found chain 2cunA in template set T0287 20 :EKLIESLQENELLNT 2cunA 175 :EKEIEALMRAYYSKD T0287 37 :KKKI 2cunA 190 :SPKI T0287 44 :IKTMHDFFKQMHTNK 2cunA 201 :VEDSLKVVENVLRRE T0287 59 :GALDK 2cunA 224 :GLVAN T0287 64 :VLRNY 2cunA 232 :LAKGF T0287 69 :MKDYRAVIKSIG 2cunA 239 :GRKNVEFMKKKG T0287 81 :VDKFKKVYRLLES 2cunA 252 :LDYVKHAEEILDE T0287 121 :FLPFFSKPIMFKMSI 2cunA 265 :FYPYIRTPVDFAVDY T0287 139 :DSQ 2cunA 280 :KGE T0287 152 :LKLFVMTDEEVNFYANLK 2cunA 283 :RVEIDLLSENRGLLHQYQ T0287 172 :EQYNDYVRDLLMKF 2cunA 306 :KRTAEKYREILMKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=122 Number of alignments=25 # 2cunA read from 2cunA/merged-good-all-a2m # found chain 2cunA in template set T0287 20 :EKLIESLQENELLNT 2cunA 175 :EKEIEALMRAYYSKD T0287 37 :KKKI 2cunA 190 :SPKI T0287 44 :IKTMHDFFKQMHTNK 2cunA 201 :VEDSLKVVENVLRRE T0287 59 :GALDK 2cunA 224 :GLVAN T0287 64 :VLRNY 2cunA 232 :LAKGF T0287 69 :MKDYRAVIKSIG 2cunA 239 :GRKNVEFMKKKG T0287 81 :VDKFKKVYRLLES 2cunA 252 :LDYVKHAEEILDE T0287 121 :FLPFFSKPIMFKMSI 2cunA 265 :FYPYIRTPVDFAVDY T0287 139 :DSQ 2cunA 280 :KGE T0287 152 :LKLFVMTDEEVNFYANLK 2cunA 283 :RVEIDLLSENRGLLHQYQ T0287 172 :EQYNDYVRDLLMKF 2cunA 306 :KRTAEKYREILMKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=133 Number of alignments=26 # 2cunA read from 2cunA/merged-good-all-a2m # found chain 2cunA in template set T0287 20 :EKLIESLQENELLNT 2cunA 175 :EKEIEALMRAYYSKD T0287 37 :KKKI 2cunA 190 :SPKI T0287 44 :IKTMHDFFKQMHTNK 2cunA 201 :VEDSLKVVENVLRRE T0287 59 :GALDK 2cunA 224 :GLVAN T0287 64 :VLRNY 2cunA 232 :LAKGF T0287 69 :MKDYRAVIKSIG 2cunA 239 :GRKNVEFMKKKG T0287 81 :VDKFKKVYRLLES 2cunA 252 :LDYVKHAEEILDE T0287 121 :FLPFFSKPIMFKMSI 2cunA 265 :FYPYIRTPVDFAVDY T0287 139 :DSQ 2cunA 280 :KGE T0287 152 :LKLFVMTDEEVNFYANLK 2cunA 283 :RVEIDLLSENRGLLHQYQ T0287 172 :EQYNDYVRDLLMKF 2cunA 306 :KRTAEKYREILMKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=144 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9kB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a9kB expands to /projects/compbio/data/pdb/2a9k.pdb.gz 2a9kB:# T0287 read from 2a9kB/merged-good-all-a2m # 2a9kB read from 2a9kB/merged-good-all-a2m # adding 2a9kB to template set # found chain 2a9kB in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKG 2a9kB 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKG T0287 80 :GVDKF 2a9kB 96 :VINGF T0287 92 :ESETMELLHAIAENPNFLF 2a9kB 101 :PSNLIKQVELLDKSFNKMK T0287 125 :FSKPIMFKMS 2a9kB 120 :TPENIMLFRG T0287 135 :IREMDSQIE 2a9kB 132 :PAYLGTEFQ T0287 144 :LYGTNLPL 2a9kB 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 2a9kB 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=151 Number of alignments=28 # 2a9kB read from 2a9kB/merged-good-all-a2m # found chain 2a9kB in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKG 2a9kB 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKG T0287 80 :GVDKF 2a9kB 96 :VINGF T0287 92 :ESETMELLHAIAENPNFLF 2a9kB 101 :PSNLIKQVELLDKSFNKMK T0287 125 :FSKPIMFKMS 2a9kB 120 :TPENIMLFRG T0287 135 :IREMDSQIE 2a9kB 132 :PAYLGTEFQ T0287 144 :LYGTNLPL 2a9kB 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 2a9kB 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=158 Number of alignments=29 # 2a9kB read from 2a9kB/merged-good-all-a2m # found chain 2a9kB in template set T0287 14 :DSKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKG 2a9kB 50 :TNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKG T0287 80 :GVDKF 2a9kB 96 :VINGF T0287 92 :ESETMELLHAIAENPNFLF 2a9kB 101 :PSNLIKQVELLDKSFNKMK T0287 125 :FSKPIMFKMS 2a9kB 120 :TPENIMLFRG T0287 135 :IREMDSQIE 2a9kB 132 :PAYLGTEFQ T0287 144 :LYGTNLPL 2a9kB 143 :LLNSNGTI T0287 167 :NLKTIEQYNDYV 2a9kB 151 :NKTAFEKAKAKF Number of specific fragments extracted= 7 number of extra gaps= 0 total=165 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1e9gA/merged-good-all-a2m # 1e9gA read from 1e9gA/merged-good-all-a2m # found chain 1e9gA in training set T0287 37 :KKKIIDQIKTMHDFFKQMHTNK 1e9gA 212 :KKYALDIIKETHDSWKQLIAGK Number of specific fragments extracted= 1 number of extra gaps= 0 total=166 Number of alignments=31 # 1e9gA read from 1e9gA/merged-good-all-a2m # found chain 1e9gA in training set T0287 37 :KKKIIDQIKTMHDFFKQMHTNK 1e9gA 212 :KKYALDIIKETHDSWKQLIAGK Number of specific fragments extracted= 1 number of extra gaps= 0 total=167 Number of alignments=32 # 1e9gA read from 1e9gA/merged-good-all-a2m # found chain 1e9gA in training set T0287 37 :KKKIIDQIKTMHDFFKQMHTNK 1e9gA 212 :KKYALDIIKETHDSWKQLIAGK Number of specific fragments extracted= 1 number of extra gaps= 0 total=168 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dc1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1dc1A/merged-good-all-a2m # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0287)E104 because of BadResidue code BAD_PEPTIDE in next template residue (1dc1A)D164 Warning: unaligning (T0287)N105 because of BadResidue code BAD_PEPTIDE at template residue (1dc1A)D164 Warning: unaligning (T0287)L149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0287 15 :SKDKKEKLIESLQENELLNTDEK 1dc1A 87 :TEDDKKESINNLIENFLEPAGEE T0287 40 :IIDQIKTMHDFFKQ 1dc1A 110 :FIDELIFRYLLFQG T0287 59 :GALDKVLRNYMKDYRA 1dc1A 124 :DSLGGTMRNIAGALAQ T0287 85 :KKVYRL 1dc1A 140 :QKLTRA T0287 95 :TMELLHAI 1dc1A 146 :IISALDIA T0287 103 :A 1dc1A 162 :S T0287 106 :PNFL 1dc1A 165 :KKYT T0287 110 :FSKFDRSILGIFLPFFSKP 1dc1A 177 :DYELETFAKGISWTINGKH T0287 129 :IMFKMSIREMDSQIE 1dc1A 198 :LMYNITVSLVKKNVD T0287 144 :LYGTN 1dc1A 215 :LFNCE T0287 150 :PLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMK 1dc1A 233 :EKYLLLGELKGGIDPAGADEHWKTANTALTRIRNK T0287 191 :MKEKGVQ 1dc1A 268 :FSEKGLS Number of specific fragments extracted= 12 number of extra gaps= 1 total=180 Number of alignments=34 # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0287)E104 because of BadResidue code BAD_PEPTIDE in next template residue (1dc1A)D164 Warning: unaligning (T0287)N105 because of BadResidue code BAD_PEPTIDE at template residue (1dc1A)D164 Warning: unaligning (T0287)L149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0287 15 :SKDKKEKLIESLQENELLNTDEK 1dc1A 87 :TEDDKKESINNLIENFLEPAGEE T0287 40 :IIDQIKTMHDFFKQ 1dc1A 110 :FIDELIFRYLLFQG T0287 59 :GALDKVLRNYMKDYRA 1dc1A 124 :DSLGGTMRNIAGALAQ T0287 85 :KKVYRL 1dc1A 140 :QKLTRA T0287 95 :TMELLHAI 1dc1A 146 :IISALDIA T0287 103 :A 1dc1A 162 :S T0287 106 :PNFL 1dc1A 165 :KKYT T0287 110 :FSKFDRSILGIFLPFFSKP 1dc1A 177 :DYELETFAKGISWTINGKH T0287 129 :IMFKMSIREMDSQIE 1dc1A 198 :LMYNITVSLVKKNVD T0287 144 :LYGTN 1dc1A 215 :LFNCE T0287 150 :PLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMK 1dc1A 233 :EKYLLLGELKGGIDPAGADEHWKTANTALTRIRNK T0287 191 :MKEKGVQ 1dc1A 268 :FSEKGLS Number of specific fragments extracted= 12 number of extra gaps= 1 total=192 Number of alignments=35 # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0287)E104 because of BadResidue code BAD_PEPTIDE in next template residue (1dc1A)D164 Warning: unaligning (T0287)N105 because of BadResidue code BAD_PEPTIDE at template residue (1dc1A)D164 Warning: unaligning (T0287)L149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0287 15 :SKDKKEKLIESLQENELLNTDEK 1dc1A 87 :TEDDKKESINNLIENFLEPAGEE T0287 40 :IIDQIKTMHDFFKQ 1dc1A 110 :FIDELIFRYLLFQG T0287 59 :GALDKVLRNYMKDYRA 1dc1A 124 :DSLGGTMRNIAGALAQ T0287 85 :KKVYRL 1dc1A 140 :QKLTRA T0287 95 :TMELLHAI 1dc1A 146 :IISALDIA T0287 103 :A 1dc1A 162 :S T0287 106 :PNFL 1dc1A 165 :KKYT T0287 110 :FSKFDRSILGIFLPFFSKP 1dc1A 177 :DYELETFAKGISWTINGKH T0287 129 :IMFKMSIREMDSQIE 1dc1A 198 :LMYNITVSLVKKNVD T0287 144 :LYGTN 1dc1A 215 :LFNCE T0287 150 :PLLKLFVMTDEEVNFYANLKTIEQYNDYVRDLLMK 1dc1A 233 :EKYLLLGELKGGIDPAGADEHWKTANTALTRIRNK T0287 191 :MKEKGVQ 1dc1A 268 :FSEKGLS Number of specific fragments extracted= 12 number of extra gaps= 1 total=204 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0b/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1b0b/merged-good-all-a2m # 1b0b read from 1b0b/merged-good-all-a2m # found chain 1b0b in training set T0287 5 :MRKLFSMIADS 1b0b 25 :GPEFFMALFDA T0287 19 :KEKLIESLQ 1b0b 36 :HDDVFAKFS T0287 28 :ENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRA 1b0b 52 :KGTVKNTPEMAAQAQSFKGLVSNWVDNLDNAGALEGQCKTFAANHKA T0287 77 :KSIGVDKFKKVYRLLESE 1b0b 99 :RGISAGQLEAAFKVLAGF T0287 95 :TMELLHAIAE 1b0b 123 :DEGAWTAVAG Number of specific fragments extracted= 5 number of extra gaps= 0 total=209 Number of alignments=37 # 1b0b read from 1b0b/merged-good-all-a2m # found chain 1b0b in training set T0287 5 :MRKLFSMIADS 1b0b 25 :GPEFFMALFDA T0287 19 :KEKLIESLQ 1b0b 36 :HDDVFAKFS T0287 28 :ENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRA 1b0b 52 :KGTVKNTPEMAAQAQSFKGLVSNWVDNLDNAGALEGQCKTFAANHKA T0287 77 :KSIGVDKFKKVYRLLESE 1b0b 99 :RGISAGQLEAAFKVLAGF T0287 95 :TMELLHAIAE 1b0b 123 :DEGAWTAVAG Number of specific fragments extracted= 5 number of extra gaps= 0 total=214 Number of alignments=38 # 1b0b read from 1b0b/merged-good-all-a2m # found chain 1b0b in training set T0287 5 :MRKLFSMIADS 1b0b 25 :GPEFFMALFDA T0287 19 :KEKLIESLQ 1b0b 36 :HDDVFAKFS T0287 28 :ENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRA 1b0b 52 :KGTVKNTPEMAAQAQSFKGLVSNWVDNLDNAGALEGQCKTFAANHKA T0287 77 :KSIGVDKFKKVYRLLESE 1b0b 99 :RGISAGQLEAAFKVLAGF T0287 95 :TMELLHAIAE 1b0b 123 :DEGAWTAVAG Number of specific fragments extracted= 5 number of extra gaps= 0 total=219 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c02A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c02A expands to /projects/compbio/data/pdb/1c02.pdb.gz 1c02A:# T0287 read from 1c02A/merged-good-all-a2m # 1c02A read from 1c02A/merged-good-all-a2m # adding 1c02A to template set # found chain 1c02A in template set T0287 4 :NMRKLFSMIADSKDKKEKLIE 1c02A 13 :ILNEIISMDDDDSDFSKGLII T0287 39 :KIIDQIKTMHDFFKQMHTNKGALDK 1c02A 34 :QFIDQAQTTFAQMQRQLDGEKNLTE T0287 65 :LRNYMKDYRAVIKSIGVDKFKKVYRL 1c02A 59 :LDNLGHFLKGSSAALGLQRIAWVCER T0287 99 :LHAIAENPNFLFSKF 1c02A 85 :IQNLGRKMQHFFPNK T0287 114 :DRSILG 1c02A 108 :DKSIIN T0287 132 :KMSIREMDSQIELYGTNL 1c02A 114 :GINIDEDDEEIKIQVDDK T0287 159 :DEEVNFYANL 1c02A 132 :DENSIYLILI T0287 169 :KTIEQYN 1c02A 143 :KALNQSR T0287 178 :VRDLLMKFDLEKYM 1c02A 150 :LEFKLARIELSKYY Number of specific fragments extracted= 9 number of extra gaps= 0 total=228 Number of alignments=40 # 1c02A read from 1c02A/merged-good-all-a2m # found chain 1c02A in template set T0287 4 :NMRKLFSMIADSKDKKEKLIE 1c02A 13 :ILNEIISMDDDDSDFSKGLII T0287 39 :KIIDQIKTMHDFFKQMHTNKGALDK 1c02A 34 :QFIDQAQTTFAQMQRQLDGEKNLTE T0287 65 :LRNYMKDYRAVIKSIGVDKFKKVYRL 1c02A 59 :LDNLGHFLKGSSAALGLQRIAWVCER T0287 99 :LHAIAENPNFLFSKF 1c02A 85 :IQNLGRKMQHFFPNK T0287 114 :DRSILG 1c02A 108 :DKSIIN T0287 132 :KMSIREMDSQIELYGTNL 1c02A 114 :GINIDEDDEEIKIQVDDK T0287 159 :DEEVNFYANL 1c02A 132 :DENSIYLILI T0287 169 :KTIEQYN 1c02A 143 :KALNQSR T0287 178 :VRDLLMKFDLEKYM 1c02A 150 :LEFKLARIELSKYY Number of specific fragments extracted= 9 number of extra gaps= 0 total=237 Number of alignments=41 # 1c02A read from 1c02A/merged-good-all-a2m # found chain 1c02A in template set T0287 4 :NMRKLFSMIADSKDKKEKLIE 1c02A 13 :ILNEIISMDDDDSDFSKGLII T0287 39 :KIIDQIKTMHDFFKQMHTNKGALDK 1c02A 34 :QFIDQAQTTFAQMQRQLDGEKNLTE T0287 65 :LRNYMKDYRAVIKSIGVDKFKKVYRL 1c02A 59 :LDNLGHFLKGSSAALGLQRIAWVCER T0287 99 :LHAIAENPNFLFSKF 1c02A 85 :IQNLGRKMQHFFPNK T0287 114 :DRSILG 1c02A 108 :DKSIIN T0287 132 :KMSIREMDSQIELYGTNL 1c02A 114 :GINIDEDDEEIKIQVDDK T0287 159 :DEEVNFYANL 1c02A 132 :DENSIYLILI T0287 169 :KTIEQYN 1c02A 143 :KALNQSR T0287 178 :VRDLLMKFDLEKYM 1c02A 150 :LEFKLARIELSKYY Number of specific fragments extracted= 9 number of extra gaps= 0 total=246 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2trcP/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2trcP expands to /projects/compbio/data/pdb/2trc.pdb.gz 2trcP:# T0287 read from 2trcP/merged-good-all-a2m # 2trcP read from 2trcP/merged-good-all-a2m # adding 2trcP to template set # found chain 2trcP in template set Warning: unaligning (T0287)Y68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)Q99 Warning: unaligning (T0287)K70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)Q99 Warning: unaligning (T0287)D71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)H102 Warning: unaligning (T0287)P106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)V165 Warning: unaligning (T0287)F108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)V165 T0287 47 :MHDFFKQMHTNKGALDKVLRN 2trcP 76 :EYELIHQDKEDEGCLRKYRRQ T0287 72 :YRAVIKS 2trcP 123 :FLETIEK T0287 80 :GVDKFKKVYRLLES 2trcP 144 :GVRGCDALNSSLEC T0287 101 :AIAEN 2trcP 158 :LAAEY T0287 109 :LF 2trcP 166 :KF T0287 111 :SKFDRSILGIFL 2trcP 179 :DRFSSDVLPTLL T0287 130 :MFK 2trcP 191 :VYK T0287 133 :MSIREMDSQIELYGTNLP 2trcP 196 :ELISNFISVAEQFAEDFF T0287 184 :KFDLEKYMKEKGV 2trcP 214 :AADVESFLNEYGL Number of specific fragments extracted= 9 number of extra gaps= 0 total=255 Number of alignments=43 # 2trcP read from 2trcP/merged-good-all-a2m # found chain 2trcP in template set Warning: unaligning (T0287)Y68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)Q99 Warning: unaligning (T0287)K70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)Q99 Warning: unaligning (T0287)D71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)H102 Warning: unaligning (T0287)P106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)V165 Warning: unaligning (T0287)F108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)V165 T0287 47 :MHDFFKQMHTNKGALDKVLRN 2trcP 76 :EYELIHQDKEDEGCLRKYRRQ T0287 72 :YRAVIKS 2trcP 123 :FLETIEK T0287 80 :GVDKFKKVYRLLES 2trcP 144 :GVRGCDALNSSLEC T0287 101 :AIAEN 2trcP 158 :LAAEY T0287 109 :LF 2trcP 166 :KF T0287 111 :SKFDRSILGIFL 2trcP 179 :DRFSSDVLPTLL T0287 130 :MFK 2trcP 191 :VYK T0287 133 :MSIREMDSQIELYGTNLP 2trcP 196 :ELISNFISVAEQFAEDFF T0287 184 :KFDLEKYMKEKGV 2trcP 214 :AADVESFLNEYGL Number of specific fragments extracted= 9 number of extra gaps= 0 total=264 Number of alignments=44 # 2trcP read from 2trcP/merged-good-all-a2m # found chain 2trcP in template set Warning: unaligning (T0287)Y68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)Q99 Warning: unaligning (T0287)K70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)Q99 Warning: unaligning (T0287)D71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)H102 Warning: unaligning (T0287)P106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2trcP)V165 Warning: unaligning (T0287)F108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2trcP)V165 T0287 47 :MHDFFKQMHTNKGALDKVLRN 2trcP 76 :EYELIHQDKEDEGCLRKYRRQ T0287 72 :YRAVIKS 2trcP 123 :FLETIEK T0287 80 :GVDKFKKVYRLLES 2trcP 144 :GVRGCDALNSSLEC T0287 101 :AIAEN 2trcP 158 :LAAEY T0287 109 :LF 2trcP 166 :KF T0287 111 :SKFDRSILGIFL 2trcP 179 :DRFSSDVLPTLL T0287 130 :MFK 2trcP 191 :VYK T0287 133 :MSIREMDSQIELYGTNLP 2trcP 196 :ELISNFISVAEQFAEDFF T0287 184 :KFDLEKYMKEKGV 2trcP 214 :AADVESFLNEYGL Number of specific fragments extracted= 9 number of extra gaps= 0 total=273 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kobA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kobA expands to /projects/compbio/data/pdb/1kob.pdb.gz 1kobA:# T0287 read from 1kobA/merged-good-all-a2m # 1kobA read from 1kobA/merged-good-all-a2m # adding 1kobA to template set # found chain 1kobA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=273 # 1kobA read from 1kobA/merged-good-all-a2m # found chain 1kobA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=273 # 1kobA read from 1kobA/merged-good-all-a2m # found chain 1kobA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=273 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hzgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hzgA expands to /projects/compbio/data/pdb/1hzg.pdb.gz 1hzgA:# T0287 read from 1hzgA/merged-good-all-a2m # 1hzgA read from 1hzgA/merged-good-all-a2m # adding 1hzgA to template set # found chain 1hzgA in template set T0287 92 :ESETMELLHAIAE 1hzgA 722 :ESTSKSNFQKLSR T0287 105 :NPNFLFSKF 1hzgA 736 :NIDVLKGRG T0287 114 :DRSILGIFLPF 1hzgA 748 :STRQRAIYPYF T0287 125 :FSKPIMFKMSIREMDSQ 1hzgA 765 :EQQPLFFYIKKDRFDNH T0287 143 :ELYGTNLPLLKLFV 1hzgA 791 :TVGPNGIPTLNTYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=278 Number of alignments=46 # 1hzgA read from 1hzgA/merged-good-all-a2m # found chain 1hzgA in template set T0287 92 :ESETMELLHAIAE 1hzgA 722 :ESTSKSNFQKLSR T0287 105 :NPNFLFSKF 1hzgA 736 :NIDVLKGRG T0287 114 :DRSILGIFLPF 1hzgA 748 :STRQRAIYPYF T0287 125 :FSKPIMFKMSIREMDSQ 1hzgA 765 :EQQPLFFYIKKDRFDNH T0287 143 :ELYGTNLPLLKLFV 1hzgA 791 :TVGPNGIPTLNTYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=283 Number of alignments=47 # 1hzgA read from 1hzgA/merged-good-all-a2m # found chain 1hzgA in template set T0287 92 :ESETMELLHAIAE 1hzgA 722 :ESTSKSNFQKLSR T0287 105 :NPNFLFSKF 1hzgA 736 :NIDVLKGRG T0287 114 :DRSILGIFLPF 1hzgA 748 :STRQRAIYPYF T0287 125 :FSKPIMFKMSIREMDSQ 1hzgA 765 :EQQPLFFYIKKDRFDNH T0287 143 :ELYGTNLPLLKLFV 1hzgA 791 :TVGPNGIPTLNTYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=288 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hh8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1hh8A/merged-good-all-a2m # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set T0287 24 :ESLQEN 1hh8A 8 :SLWNEG T0287 30 :ELLNTDEKKKIIDQIKT 1hh8A 15 :LAADKKDWKGALDAFSA T0287 47 :MHDFFKQMHTNKGALDKVLRNYMKD 1hh8A 42 :NIGCMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVIK 1hh8A 76 :QRGMLY T0287 79 :IGVDKFKKVYRLLES 1hh8A 82 :YQTEKYDLAIKDLKE T0287 98 :L 1hh8A 97 :A T0287 102 :IAENPNFLF 1hh8A 98 :LIQLRGNQL T0287 113 :FDRSILGIFLPFF 1hh8A 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1hh8A 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKE 1hh8A 159 :IDKAMEC Number of specific fragments extracted= 10 number of extra gaps= 0 total=298 Number of alignments=49 # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set T0287 24 :ESLQEN 1hh8A 8 :SLWNEG T0287 30 :ELLNTDEKKKIIDQIKT 1hh8A 15 :LAADKKDWKGALDAFSA T0287 47 :MHDFFKQMHTNKGALDKVLRNYMKD 1hh8A 42 :NIGCMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVIK 1hh8A 76 :QRGMLY T0287 79 :IGVDKFKKVYRLLES 1hh8A 82 :YQTEKYDLAIKDLKE T0287 98 :L 1hh8A 97 :A T0287 102 :IAENPNFLF 1hh8A 98 :LIQLRGNQL T0287 113 :FDRSILGIFLPFF 1hh8A 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1hh8A 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKE 1hh8A 159 :IDKAMEC Number of specific fragments extracted= 10 number of extra gaps= 0 total=308 Number of alignments=50 # 1hh8A read from 1hh8A/merged-good-all-a2m # found chain 1hh8A in training set T0287 24 :ESLQEN 1hh8A 8 :SLWNEG T0287 30 :ELLNTDEKKKIIDQIKT 1hh8A 15 :LAADKKDWKGALDAFSA T0287 47 :MHDFFKQMHTNKGALDKVLRNYMKD 1hh8A 42 :NIGCMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVIK 1hh8A 76 :QRGMLY T0287 79 :IGVDKFKKVYRLLES 1hh8A 82 :YQTEKYDLAIKDLKE T0287 98 :L 1hh8A 97 :A T0287 102 :IAENPNFLF 1hh8A 98 :LIQLRGNQL T0287 113 :FDRSILGIFLPFF 1hh8A 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1hh8A 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKE 1hh8A 159 :IDKAMEC Number of specific fragments extracted= 10 number of extra gaps= 0 total=318 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b7eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b7eA expands to /projects/compbio/data/pdb/2b7e.pdb.gz 2b7eA:# T0287 read from 2b7eA/merged-good-all-a2m # 2b7eA read from 2b7eA/merged-good-all-a2m # adding 2b7eA to template set # found chain 2b7eA in template set Warning: unaligning (T0287)D14 because first residue in template chain is (2b7eA)G1 T0287 15 :SKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKD 2b7eA 2 :AMEAEKEFITMLKENQVDSTWSFSRIISELGTRDPRYWMVDDDPLWKKEMFEKYLSN Number of specific fragments extracted= 1 number of extra gaps= 0 total=319 Number of alignments=52 # 2b7eA read from 2b7eA/merged-good-all-a2m # found chain 2b7eA in template set Warning: unaligning (T0287)D14 because first residue in template chain is (2b7eA)G1 T0287 15 :SKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKD 2b7eA 2 :AMEAEKEFITMLKENQVDSTWSFSRIISELGTRDPRYWMVDDDPLWKKEMFEKYLSN Number of specific fragments extracted= 1 number of extra gaps= 0 total=320 Number of alignments=53 # 2b7eA read from 2b7eA/merged-good-all-a2m # found chain 2b7eA in template set Warning: unaligning (T0287)D14 because first residue in template chain is (2b7eA)G1 T0287 15 :SKDKKEKLIESLQENELLNTDEKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKD 2b7eA 2 :AMEAEKEFITMLKENQVDSTWSFSRIISELGTRDPRYWMVDDDPLWKKEMFEKYLSN Number of specific fragments extracted= 1 number of extra gaps= 0 total=321 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1knqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1knqA expands to /projects/compbio/data/pdb/1knq.pdb.gz 1knqA:Skipped atom 277, because occupancy 0.5 <= existing 0.500 in 1knqA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1knqA Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 1knqA Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 1knqA # T0287 read from 1knqA/merged-good-all-a2m # 1knqA read from 1knqA/merged-good-all-a2m # adding 1knqA to template set # found chain 1knqA in template set Warning: unaligning (T0287)K184 because last residue in template chain is (1knqA)K173 T0287 19 :KEKLIESLQENELLNTDEKKKIIDQIK 1knqA 44 :PRRNIEKMASGEPLNDDDRKPWLQALN T0287 49 :DFFKQMHT 1knqA 71 :DAAFAMQR T0287 57 :NK 1knqA 80 :NK T0287 68 :YMKDYRAVIKSI 1knqA 90 :LKKHYRDLLREG T0287 80 :GVDKF 1knqA 113 :DFDVI T0287 99 :LHAIAENPNFLFSK 1knqA 118 :ESRLKARKGHFFKT T0287 116 :SIL 1knqA 132 :QML T0287 136 :REMDSQIELYGTNLPLLKLFVMTD 1knqA 135 :VTQFETLQEPGADETDVLVVDIDQ T0287 170 :TIEQYNDYVRDLLM 1knqA 159 :PLEGVVASTIEVIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=330 Number of alignments=55 # 1knqA read from 1knqA/merged-good-all-a2m # found chain 1knqA in template set Warning: unaligning (T0287)K184 because last residue in template chain is (1knqA)K173 T0287 19 :KEKLIESLQENELLNTDEKKKIIDQIK 1knqA 44 :PRRNIEKMASGEPLNDDDRKPWLQALN T0287 49 :DFFKQMHT 1knqA 71 :DAAFAMQR T0287 57 :NK 1knqA 80 :NK T0287 68 :YMKDYRAVIKSI 1knqA 90 :LKKHYRDLLREG T0287 80 :GVDKF 1knqA 113 :DFDVI T0287 99 :LHAIAENPNFLFSK 1knqA 118 :ESRLKARKGHFFKT T0287 116 :SIL 1knqA 132 :QML T0287 136 :REMDSQIELYGTNLPLLKLFVMTD 1knqA 135 :VTQFETLQEPGADETDVLVVDIDQ T0287 170 :TIEQYNDYVRDLLM 1knqA 159 :PLEGVVASTIEVIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=339 Number of alignments=56 # 1knqA read from 1knqA/merged-good-all-a2m # found chain 1knqA in template set Warning: unaligning (T0287)K184 because last residue in template chain is (1knqA)K173 T0287 19 :KEKLIESLQENELLNTDEKKKIIDQIK 1knqA 44 :PRRNIEKMASGEPLNDDDRKPWLQALN T0287 49 :DFFKQMHT 1knqA 71 :DAAFAMQR T0287 57 :NK 1knqA 80 :NK T0287 68 :YMKDYRAVIKSI 1knqA 90 :LKKHYRDLLREG T0287 80 :GVDKF 1knqA 113 :DFDVI T0287 99 :LHAIAENPNFLFSK 1knqA 118 :ESRLKARKGHFFKT T0287 116 :SIL 1knqA 132 :QML T0287 136 :REMDSQIELYGTNLPLLKLFVMTD 1knqA 135 :VTQFETLQEPGADETDVLVVDIDQ T0287 170 :TIEQYNDYVRDLLM 1knqA 159 :PLEGVVASTIEVIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=348 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f7lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1f7lA/merged-good-all-a2m # 1f7lA read from 1f7lA/merged-good-all-a2m # found chain 1f7lA in training set Warning: unaligning (T0287)D159 because last residue in template chain is (1f7lA)R118 T0287 5 :MRKLFSMIADSKDKKEKLI 1f7lA 12 :LKRIASMAGRQKRFAERIL T0287 37 :KKKIIDQIKTM 1f7lA 31 :TRSELDQYYEL T0287 57 :NKGALDKVLRNYMKDYRAVIKSIGVD 1f7lA 42 :SEKRKNEFLAGRFAAKEAFSKAFGTG T0287 109 :LFSKFDRSILGIFLPFFSKPIM 1f7lA 68 :IGRQLSFQDIEIRKDQNGKPYI T0287 134 :SIREMDS 1f7lA 90 :ICTKLSP T0287 141 :QIELYGTNLPLLKLFVMT 1f7lA 100 :HVSITHTKEYAAAQVVIE Number of specific fragments extracted= 6 number of extra gaps= 0 total=354 Number of alignments=58 # 1f7lA read from 1f7lA/merged-good-all-a2m # found chain 1f7lA in training set Warning: unaligning (T0287)D159 because last residue in template chain is (1f7lA)R118 T0287 5 :MRKLFSMIADSKDKKEKLI 1f7lA 12 :LKRIASMAGRQKRFAERIL T0287 37 :KKKIIDQIKTM 1f7lA 31 :TRSELDQYYEL T0287 57 :NKGALDKVLRNYMKDYRAVIKSIGVD 1f7lA 42 :SEKRKNEFLAGRFAAKEAFSKAFGTG T0287 109 :LFSKFDRSILGIFLPFFSKPIM 1f7lA 68 :IGRQLSFQDIEIRKDQNGKPYI T0287 134 :SIREMDS 1f7lA 90 :ICTKLSP T0287 141 :QIELYGTNLPLLKLFVMT 1f7lA 100 :HVSITHTKEYAAAQVVIE Number of specific fragments extracted= 6 number of extra gaps= 0 total=360 Number of alignments=59 # 1f7lA read from 1f7lA/merged-good-all-a2m # found chain 1f7lA in training set Warning: unaligning (T0287)D159 because last residue in template chain is (1f7lA)R118 T0287 5 :MRKLFSMIADSKDKKEKLI 1f7lA 12 :LKRIASMAGRQKRFAERIL T0287 37 :KKKIIDQIKTM 1f7lA 31 :TRSELDQYYEL T0287 57 :NKGALDKVLRNYMKDYRAVIKSIGVD 1f7lA 42 :SEKRKNEFLAGRFAAKEAFSKAFGTG T0287 109 :LFSKFDRSILGIFLPFFSKPIM 1f7lA 68 :IGRQLSFQDIEIRKDQNGKPYI T0287 134 :SIREMDS 1f7lA 90 :ICTKLSP T0287 141 :QIELYGTNLPLLKLFVMT 1f7lA 100 :HVSITHTKEYAAAQVVIE Number of specific fragments extracted= 6 number of extra gaps= 0 total=366 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e96B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e96B expands to /projects/compbio/data/pdb/1e96.pdb.gz 1e96B:# T0287 read from 1e96B/merged-good-all-a2m # 1e96B read from 1e96B/merged-good-all-a2m # adding 1e96B to template set # found chain 1e96B in template set T0287 18 :KKEKLIESLQE 1e96B 5 :EAISLWNEGVL T0287 31 :LLNTDEKKKIIDQIKTMHD 1e96B 16 :AADKKDWKGALDAFSAVQD T0287 50 :FFKQMHTNKGALDKVLRNYMKD 1e96B 45 :CMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVI 1e96B 76 :QRGML T0287 78 :SIGVDKFKKVYRLLES 1e96B 81 :YYQTEKYDLAIKDLKE T0287 101 :AIAENPNFLF 1e96B 97 :ALIQLRGNQL T0287 113 :FDRSILGIFLPFF 1e96B 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1e96B 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKEKGVQN 1e96B 159 :IDKAMECVWKQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=375 Number of alignments=61 # 1e96B read from 1e96B/merged-good-all-a2m # found chain 1e96B in template set T0287 18 :KKEKLIESLQE 1e96B 5 :EAISLWNEGVL T0287 31 :LLNTDEKKKIIDQIKTMHD 1e96B 16 :AADKKDWKGALDAFSAVQD T0287 50 :FFKQMHTNKGALDKVLRNYMKD 1e96B 45 :CMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVI 1e96B 76 :QRGML T0287 78 :SIGVDKFKKVYRLLES 1e96B 81 :YYQTEKYDLAIKDLKE T0287 101 :AIAENPNFLF 1e96B 97 :ALIQLRGNQL T0287 113 :FDRSILGIFLPFF 1e96B 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1e96B 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKEKGVQN 1e96B 159 :IDKAMECVWKQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=384 Number of alignments=62 # 1e96B read from 1e96B/merged-good-all-a2m # found chain 1e96B in template set T0287 18 :KKEKLIESLQE 1e96B 5 :EAISLWNEGVL T0287 31 :LLNTDEKKKIIDQIKTMHD 1e96B 16 :AADKKDWKGALDAFSAVQD T0287 50 :FFKQMHTNKGALDKVLRNYMKD 1e96B 45 :CMYTILKNMTEAEKAFTRSINR T0287 72 :YRAVI 1e96B 76 :QRGML T0287 78 :SIGVDKFKKVYRLLES 1e96B 81 :YYQTEKYDLAIKDLKE T0287 101 :AIAENPNFLF 1e96B 97 :ALIQLRGNQL T0287 113 :FDRSILGIFLPFF 1e96B 107 :IDYKILGLQFKLF T0287 162 :VNFYANLKTIEQYNDYVRDLLMKFD 1e96B 128 :AFMYAKKEEWKKAEEQLALATSMKS T0287 187 :LEKYMKEKGVQN 1e96B 159 :IDKAMECVWKQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=393 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a8y/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a8y expands to /projects/compbio/data/pdb/1a8y.pdb.gz 1a8y:Warning: there is no chain 1a8y will retry with 1a8yA # T0287 read from 1a8y/merged-good-all-a2m # 1a8y read from 1a8y/merged-good-all-a2m # adding 1a8y to template set # found chain 1a8y in template set Warning: unaligning (T0287)G146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a8y)P334 Warning: unaligning (T0287)K169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a8y)P334 Warning: unaligning (T0287)L182 because last residue in template chain is (1a8y)L347 T0287 79 :IGVDKFKKVYRLLES 1a8y 257 :EADPDGYEFLEILKS T0287 98 :LLHAIAENPNFL 1a8y 272 :VAQDNTDNPDLS T0287 110 :FSKFDRSI 1a8y 289 :PDDFPLLV T0287 121 :FLPFFSKPIMFKMSIREMD 1a8y 303 :FDIDLSAPQIGVVNVTDAD T0287 142 :IELY 1a8y 322 :SVWM T0287 170 :TIEQYNDYVRDL 1a8y 335 :SAEELEDWLEDV Number of specific fragments extracted= 6 number of extra gaps= 0 total=399 Number of alignments=64 # 1a8y read from 1a8y/merged-good-all-a2m # found chain 1a8y in template set Warning: unaligning (T0287)G146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a8y)P334 Warning: unaligning (T0287)K169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a8y)P334 Warning: unaligning (T0287)L182 because last residue in template chain is (1a8y)L347 T0287 79 :IGVDKFKKVYRLLES 1a8y 257 :EADPDGYEFLEILKS T0287 98 :LLHAIAENPNFL 1a8y 272 :VAQDNTDNPDLS T0287 110 :FSKFDRSI 1a8y 289 :PDDFPLLV T0287 121 :FLPFFSKPIMFKMSIREMD 1a8y 303 :FDIDLSAPQIGVVNVTDAD T0287 142 :IELY 1a8y 322 :SVWM T0287 170 :TIEQYNDYVRDL 1a8y 335 :SAEELEDWLEDV Number of specific fragments extracted= 6 number of extra gaps= 0 total=405 Number of alignments=65 # 1a8y read from 1a8y/merged-good-all-a2m # found chain 1a8y in template set Warning: unaligning (T0287)G146 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1a8y)P334 Warning: unaligning (T0287)K169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a8y)P334 Warning: unaligning (T0287)L182 because last residue in template chain is (1a8y)L347 T0287 79 :IGVDKFKKVYRLLES 1a8y 257 :EADPDGYEFLEILKS T0287 98 :LLHAIAENPNFL 1a8y 272 :VAQDNTDNPDLS T0287 110 :FSKFDRSI 1a8y 289 :PDDFPLLV T0287 121 :FLPFFSKPIMFKMSIREMD 1a8y 303 :FDIDLSAPQIGVVNVTDAD T0287 142 :IELY 1a8y 322 :SVWM T0287 170 :TIEQYNDYVRDL 1a8y 335 :SAEELEDWLEDV Number of specific fragments extracted= 6 number of extra gaps= 0 total=411 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g5aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0287 read from 1g5aA/merged-good-all-a2m # 1g5aA read from 1g5aA/merged-good-all-a2m # found chain 1g5aA in training set Warning: unaligning (T0287)S2 because first residue in template chain is (1g5aA)S1 T0287 3 :NNMRKLFSMIAD 1g5aA 2 :PNSQYLKTRILD T0287 15 :SKDKK 1g5aA 16 :TPEQR T0287 24 :ESLQENELLNT 1g5aA 21 :AGIEKSEDWRQ T0287 36 :EKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYR 1g5aA 32 :FSRRMDTHFPKLMNELDSVYGNNEALLPMLEMLLAQAW T0287 86 :KVYRLLESETMELLHAIAENPNFLFSK 1g5aA 70 :QSYSQRNSSLKDIDIARENNPDWILSN T0287 115 :RSILGIFL 1g5aA 97 :KQVGGVCY T0287 162 :VN 1g5aA 105 :VD T0287 164 :FYANLKTIEQYNDYVRDL 1g5aA 108 :FAGDLKGLKDKIPYFQEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=419 Number of alignments=67 # 1g5aA read from 1g5aA/merged-good-all-a2m # found chain 1g5aA in training set Warning: unaligning (T0287)S2 because first residue in template chain is (1g5aA)S1 T0287 3 :NNMRKLFSMIAD 1g5aA 2 :PNSQYLKTRILD T0287 15 :SKDKK 1g5aA 16 :TPEQR T0287 24 :ESLQENELLNT 1g5aA 21 :AGIEKSEDWRQ T0287 36 :EKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYR 1g5aA 32 :FSRRMDTHFPKLMNELDSVYGNNEALLPMLEMLLAQAW T0287 86 :KVYRLLESETMELLHAIAENPNFLFSK 1g5aA 70 :QSYSQRNSSLKDIDIARENNPDWILSN T0287 115 :RSILGIFL 1g5aA 97 :KQVGGVCY T0287 162 :VN 1g5aA 105 :VD T0287 164 :FYANLKTIEQYNDYVRDL 1g5aA 108 :FAGDLKGLKDKIPYFQEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=427 Number of alignments=68 # 1g5aA read from 1g5aA/merged-good-all-a2m # found chain 1g5aA in training set Warning: unaligning (T0287)S2 because first residue in template chain is (1g5aA)S1 T0287 3 :NNMRKLFSMIAD 1g5aA 2 :PNSQYLKTRILD T0287 15 :SKDKK 1g5aA 16 :TPEQR T0287 24 :ESLQENELLNT 1g5aA 21 :AGIEKSEDWRQ T0287 36 :EKKKIIDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYR 1g5aA 32 :FSRRMDTHFPKLMNELDSVYGNNEALLPMLEMLLAQAW T0287 86 :KVYRLLESETMELLHAIAENPNFLFSK 1g5aA 70 :QSYSQRNSSLKDIDIARENNPDWILSN T0287 115 :RSILGIFL 1g5aA 97 :KQVGGVCY T0287 162 :VN 1g5aA 105 :VD T0287 164 :FYANLKTIEQYNDYVRDL 1g5aA 108 :FAGDLKGLKDKIPYFQEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=435 Number of alignments=69 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 69 Adding 1465 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: -337.4072, CN propb: -337.4072 weights: 0.3619 constraints: 244 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 244 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 244 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1221 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1221 # 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 1465 # command: