# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0287//projects/compbio/experiments/protein-predict/casp7/T0287/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0287//projects/compbio/experiments/protein-predict/casp7/T0287/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0287/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0287/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0287)L31.CB, (T0287)I40.CB) [> 2.8951 = 4.8252 < 6.2727] w=1.0000 to align # Constraint # added constraint: constraint((T0287)L26.CB, (T0287)I44.CB) [> 3.3167 = 5.5279 < 7.1863] w=1.0000 to align # Constraint # added constraint: constraint((T0287)L26.CB, (T0287)I40.CB) [> 3.6408 = 6.0679 < 7.8883] w=0.9561 to align # Constraint # added constraint: constraint((T0287)Y72.CB, (T0287)F84.CB) [> 3.5315 = 5.8858 < 7.6516] w=0.9183 to align # Constraint # added constraint: constraint((T0287)E92.CB, (T0287)A103.CB) [> 3.8365 = 6.3941 < 8.3123] w=0.9052 to align # Constraint # added constraint: constraint((T0287)F110.CB, (T0287)F125.CB) [> 3.0589 = 5.0982 < 6.6276] w=0.7352 to align # Constraint # added constraint: constraint((T0287)I23.CB, (T0287)I44.CB) [> 4.0302 = 6.7170 < 8.7320] w=0.7156 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)L99.CB) [> 3.9399 = 6.5665 < 8.5364] w=0.7052 to align # Constraint # added constraint: constraint((T0287)L31.CB, (T0287)Q43.CB) [> 3.5004 = 5.8340 < 7.5842] w=0.6749 to align # Constraint # added constraint: constraint((T0287)A74.CB, (T0287)V87.CB) [> 2.9503 = 4.9172 < 6.3923] w=0.6749 to align # Constraint # added constraint: constraint((T0287)A74.CB, (T0287)Y88.CB) [> 4.2471 = 7.0785 < 9.2021] w=0.6749 to align # Constraint # added constraint: constraint((T0287)L182.CB, (T0287)M191.CB) [> 3.9876 = 6.6460 < 8.6398] w=0.6749 to align # Constraint # added constraint: constraint((T0287)K58.CB, (T0287)G80.CA) [> 4.3503 = 7.2505 < 9.4257] w=0.6672 to align # Constraint # added constraint: constraint((T0287)L90.CB, (T0287)A101.CB) [> 3.7581 = 6.2635 < 8.1425] w=0.6478 to align # Constraint # added constraint: constraint((T0287)I135.CB, (T0287)L154.CB) [> 3.9621 = 6.6035 < 8.5846] w=0.6268 to align # Constraint # added constraint: constraint((T0287)L144.CB, (T0287)K153.CB) [> 3.9036 = 6.5061 < 8.4579] w=0.6237 to align # Constraint # added constraint: constraint((T0287)I142.CB, (T0287)F155.CB) [> 3.6545 = 6.0908 < 7.9180] w=0.6237 to align # Constraint # added constraint: constraint((T0287)M5.CB, (T0287)I40.CB) [> 4.3405 = 7.2341 < 9.4044] w=0.6163 to align # Constraint # added constraint: constraint((T0287)I117.CB, (T0287)M138.CB) [> 3.8758 = 6.4596 < 8.3975] w=0.5903 to align # Constraint # added constraint: constraint((T0287)L65.CB, (T0287)I76.CB) [> 3.8328 = 6.3880 < 8.3044] w=0.5848 to align # Constraint # added constraint: constraint((T0287)L61.CB, (T0287)I76.CB) [> 3.4244 = 5.7073 < 7.4194] w=0.5848 to align # Constraint # added constraint: constraint((T0287)V81.CB, (T0287)L99.CB) [> 3.3396 = 5.5659 < 7.2357] w=0.5669 to align # Constraint # added constraint: constraint((T0287)L151.CB, (T0287)I171.CB) [> 3.6580 = 6.0966 < 7.9256] w=0.5626 to align # Constraint # added constraint: constraint((T0287)Y165.CB, (T0287)Y174.CB) [> 2.5286 = 4.2143 < 5.4786] w=0.5600 to align # Constraint # added constraint: constraint((T0287)Y72.CB, (T0287)Y88.CB) [> 3.6606 = 6.1010 < 7.9313] w=0.5488 to align # Constraint # added constraint: constraint((T0287)I120.CB, (T0287)M138.CB) [> 4.6503 = 7.7504 < 10.0756] w=0.5419 to align # Constraint # added constraint: constraint((T0287)M54.CB, (T0287)V64.CB) [> 3.7852 = 6.3088 < 8.2014] w=0.5417 to align # Constraint # added constraint: constraint((T0287)L91.CB, (T0287)I102.CB) [> 3.9001 = 6.5002 < 8.4502] w=0.5407 to align # Constraint # added constraint: constraint((T0287)F51.CB, (T0287)L61.CB) [> 3.7690 = 6.2817 < 8.1662] w=0.5270 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)V178.CB) [> 4.1265 = 6.8775 < 8.9407] w=0.5246 to align # Constraint # added constraint: constraint((T0287)I135.CB, (T0287)L152.CB) [> 3.4285 = 5.7142 < 7.4285] w=0.5046 to align # Constraint # added constraint: constraint((T0287)S78.CB, (T0287)L90.CB) [> 3.7213 = 6.2022 < 8.0628] w=0.4966 to align # Constraint # added constraint: constraint((T0287)D62.CB, (T0287)V81.CB) [> 4.4085 = 7.3474 < 9.5516] w=0.4966 to align # Constraint # added constraint: constraint((T0287)A103.CB, (T0287)Y174.CB) [> 4.1599 = 6.9332 < 9.0131] w=0.4888 to align # Constraint # added constraint: constraint((T0287)A103.CB, (T0287)I171.CB) [> 4.4851 = 7.4752 < 9.7178] w=0.4888 to align # Constraint # added constraint: constraint((T0287)A13.CB, (T0287)L26.CB) [> 4.4638 = 7.4396 < 9.6715] w=0.4781 to align # Constraint # added constraint: constraint((T0287)F9.CB, (T0287)I40.CB) [> 3.8716 = 6.4527 < 8.3885] w=0.4781 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)I44.CB) [> 4.6560 = 7.7601 < 10.0881] w=0.4781 to align # Constraint # added constraint: constraint((T0287)R6.CB, (T0287)I41.CB) [> 3.6906 = 6.1511 < 7.9964] w=0.4781 to align # Constraint # added constraint: constraint((T0287)M5.CB, (T0287)K45.CB) [> 3.8623 = 6.4371 < 8.3683] w=0.4781 to align # Constraint # added constraint: constraint((T0287)M5.CB, (T0287)I44.CB) [> 3.5792 = 5.9654 < 7.7550] w=0.4781 to align # Constraint # added constraint: constraint((T0287)M47.CB, (T0287)Y68.CB) [> 3.6647 = 6.1079 < 7.9403] w=0.4649 to align # Constraint # added constraint: constraint((T0287)R73.CB, (T0287)F84.CB) [> 4.2703 = 7.1172 < 9.2523] w=0.4534 to align # Constraint # added constraint: constraint((T0287)L26.CB, (T0287)K39.CB) [> 4.5726 = 7.6210 < 9.9074] w=0.4533 to align # Constraint # added constraint: constraint((T0287)F108.CB, (T0287)N167.CB) [> 2.8964 = 4.8273 < 6.2754] w=0.4509 to align # Constraint # added constraint: constraint((T0287)F108.CB, (T0287)F164.CB) [> 4.1191 = 6.8651 < 8.9246] w=0.4509 to align # Constraint # added constraint: constraint((T0287)N107.CB, (T0287)N167.CB) [> 4.4132 = 7.3554 < 9.5620] w=0.4509 to align # Constraint # added constraint: constraint((T0287)L118.CB, (T0287)Q141.CB) [> 4.7459 = 7.9099 < 10.2829] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I117.CB, (T0287)F155.CB) [> 3.5665 = 5.9442 < 7.7275] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I117.CB, (T0287)L154.CB) [> 3.6110 = 6.0183 < 7.8238] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I117.CB, (T0287)K153.CB) [> 2.6871 = 4.4785 < 5.8220] w=0.4477 to align # Constraint # added constraint: constraint((T0287)R115.CB, (T0287)K153.CB) [> 4.1277 = 6.8795 < 8.9433] w=0.4477 to align # Constraint # added constraint: constraint((T0287)D114.CB, (T0287)F155.CB) [> 3.7039 = 6.1732 < 8.0251] w=0.4477 to align # Constraint # added constraint: constraint((T0287)L98.CB, (T0287)F108.CB) [> 3.1500 = 5.2500 < 6.8251] w=0.4477 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)L154.CB) [> 2.8674 = 4.7790 < 6.2126] w=0.4477 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)K153.CB) [> 4.0451 = 6.7419 < 8.7645] w=0.4477 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)L152.CB) [> 4.7322 = 7.8870 < 10.2530] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I120.CB, (T0287)V156.CB) [> 4.2918 = 7.1530 < 9.2989] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I120.CB, (T0287)F155.CB) [> 4.4698 = 7.4496 < 9.6846] w=0.4477 to align # Constraint # added constraint: constraint((T0287)I120.CB, (T0287)L154.CB) [> 2.8084 = 4.6806 < 6.0848] w=0.4477 to align # Constraint # added constraint: constraint((T0287)L118.CB, (T0287)V156.CB) [> 3.1165 = 5.1943 < 6.7525] w=0.4477 to align # Constraint # added constraint: constraint((T0287)L118.CB, (T0287)L154.CB) [> 3.7125 = 6.1874 < 8.0437] w=0.4477 to align # Constraint # added constraint: constraint((T0287)V75.CB, (T0287)V87.CB) [> 4.1451 = 6.9085 < 8.9811] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V75.CB, (T0287)L91.CB) [> 4.7689 = 7.9481 < 10.3326] w=0.4465 to align # Constraint # added constraint: constraint((T0287)I76.CB, (T0287)V87.CB) [> 4.7715 = 7.9524 < 10.3382] w=0.4465 to align # Constraint # added constraint: constraint((T0287)I79.CB, (T0287)F164.CB) [> 3.9784 = 6.6307 < 8.6199] w=0.4465 to align # Constraint # added constraint: constraint((T0287)I79.CB, (T0287)N167.CB) [> 4.7541 = 7.9235 < 10.3006] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)F164.CB) [> 2.9632 = 4.9387 < 6.4202] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)N167.CB) [> 3.1785 = 5.2975 < 6.8868] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)L168.CB) [> 3.0491 = 5.0818 < 6.6064] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V87.CB, (T0287)F164.CB) [> 3.1460 = 5.2433 < 6.8163] w=0.4465 to align # Constraint # added constraint: constraint((T0287)K58.CB, (T0287)I76.CB) [> 3.9999 = 6.6665 < 8.6664] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F50.CB, (T0287)Y72.CB) [> 4.1360 = 6.8933 < 8.9613] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F50.CB, (T0287)L61.CB) [> 4.5953 = 7.6589 < 9.9565] w=0.4465 to align # Constraint # added constraint: constraint((T0287)I41.CB, (T0287)H55.CB) [> 3.8047 = 6.3411 < 8.2435] w=0.4465 to align # Constraint # added constraint: constraint((T0287)L32.CB, (T0287)F51.CB) [> 4.3869 = 7.3115 < 9.5049] w=0.4465 to align # Constraint # added constraint: constraint((T0287)L181.CB, (T0287)Y190.CB) [> 4.7059 = 7.8431 < 10.1960] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V178.CB, (T0287)Y190.CB) [> 3.5888 = 5.9813 < 7.7757] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V178.CB, (T0287)L187.CB) [> 3.9355 = 6.5592 < 8.5270] w=0.4465 to align # Constraint # added constraint: constraint((T0287)Y165.CB, (T0287)Y177.CB) [> 3.7066 = 6.1777 < 8.0310] w=0.4465 to align # Constraint # added constraint: constraint((T0287)N163.CB, (T0287)Y190.CB) [> 4.5575 = 7.5958 < 9.8746] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V162.CB, (T0287)Y190.CB) [> 4.1535 = 6.9225 < 8.9992] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V162.CB, (T0287)L181.CB) [> 3.8481 = 6.4134 < 8.3375] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V162.CB, (T0287)N175.CB) [> 4.5261 = 7.5435 < 9.8066] w=0.4465 to align # Constraint # added constraint: constraint((T0287)V162.CB, (T0287)Y174.CB) [> 2.6714 = 4.4524 < 5.7881] w=0.4465 to align # Constraint # added constraint: constraint((T0287)Y88.CB, (T0287)F164.CB) [> 2.7863 = 4.6439 < 6.0371] w=0.4465 to align # Constraint # added constraint: constraint((T0287)Y88.CB, (T0287)Y165.CB) [> 4.2499 = 7.0832 < 9.2082] w=0.4465 to align # Constraint # added constraint: constraint((T0287)N105.CB, (T0287)F124.CB) [> 4.4500 = 7.4167 < 9.6417] w=0.4465 to align # Constraint # added constraint: constraint((T0287)L109.CB, (T0287)F125.CB) [> 3.9760 = 6.6267 < 8.6147] w=0.4465 to align # Constraint # added constraint: constraint((T0287)L109.CB, (T0287)K184.CB) [> 3.9904 = 6.6506 < 8.6458] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F110.CB, (T0287)P123.CB) [> 3.3989 = 5.6649 < 7.3643] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F110.CB, (T0287)F124.CB) [> 3.9543 = 6.5905 < 8.5676] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F110.CB, (T0287)D186.CB) [> 3.9653 = 6.6089 < 8.5915] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F113.CB, (T0287)P123.CB) [> 4.5257 = 7.5429 < 9.8058] w=0.4465 to align # Constraint # added constraint: constraint((T0287)F113.CB, (T0287)F124.CB) [> 3.1279 = 5.2132 < 6.7771] w=0.4465 to align # Constraint # added constraint: constraint((T0287)I40.CB, (T0287)I102.CB) [> 4.0208 = 6.7014 < 8.7118] w=0.4243 to align # Constraint # added constraint: constraint((T0287)Q43.CB, (T0287)L98.CB) [> 4.3889 = 7.3149 < 9.5093] w=0.4243 to align # Constraint # added constraint: constraint((T0287)F50.CB, (T0287)L98.CB) [> 4.4726 = 7.4543 < 9.6906] w=0.4243 to align # Constraint # added constraint: constraint((T0287)L32.CB, (T0287)F108.CB) [> 3.7127 = 6.1878 < 8.0441] w=0.4243 to align # Constraint # added constraint: constraint((T0287)L151.CB, (T0287)L168.CB) [> 4.4406 = 7.4011 < 9.6214] w=0.4243 to align # Constraint # added constraint: constraint((T0287)L151.CB, (T0287)N167.CB) [> 3.4270 = 5.7116 < 7.4251] w=0.4243 to align # Constraint # added constraint: constraint((T0287)Y145.CB, (T0287)N167.CB) [> 4.0003 = 6.6672 < 8.6674] w=0.4243 to align # Constraint # added constraint: constraint((T0287)L144.CB, (T0287)T170.CB) [> 2.9915 = 4.9858 < 6.4815] w=0.4243 to align # Constraint # added constraint: constraint((T0287)L144.CB, (T0287)N167.CB) [> 3.8646 = 6.4410 < 8.3733] w=0.4243 to align # Constraint # added constraint: constraint((T0287)I142.CB, (T0287)Y174.CB) [> 4.0134 = 6.6890 < 8.6957] w=0.4243 to align # Constraint # added constraint: constraint((T0287)I142.CB, (T0287)T170.CB) [> 3.8417 = 6.4028 < 8.3236] w=0.4243 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)Y177.CB) [> 4.2482 = 7.0803 < 9.2043] w=0.4243 to align # Constraint # added constraint: constraint((T0287)M54.CB, (T0287)V81.CB) [> 4.4798 = 7.4663 < 9.7062] w=0.4243 to align # Constraint # added constraint: constraint((T0287)M54.CB, (T0287)L99.CB) [> 4.7595 = 7.9325 < 10.3123] w=0.4243 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)M96.CB) [> 2.6557 = 4.4262 < 5.7541] w=0.4243 to align # Constraint # added constraint: constraint((T0287)I135.CB, (T0287)L144.CB) [> 2.3624 = 3.9373 < 5.1185] w=0.4243 to align # Constraint # added constraint: constraint((T0287)M47.CB, (T0287)V64.CB) [> 3.9861 = 6.6435 < 8.6365] w=0.4093 to align # Constraint # added constraint: constraint((T0287)I142.CB, (T0287)K153.CB) [> 3.9147 = 6.5246 < 8.4819] w=0.3953 to align # Constraint # added constraint: constraint((T0287)L22.CB, (T0287)M47.CB) [> 2.9862 = 4.9771 < 6.4702] w=0.3946 to align # Constraint # added constraint: constraint((T0287)I23.CB, (T0287)M47.CB) [> 3.8000 = 6.3333 < 8.2333] w=0.3946 to align # Constraint # added constraint: constraint((T0287)Q53.CB, (T0287)Y72.CB) [> 4.6083 = 7.6805 < 9.9847] w=0.3946 to align # Constraint # added constraint: constraint((T0287)I171.CB, (T0287)K194.CB) [> 3.9086 = 6.5143 < 8.4685] w=0.3946 to align # Constraint # added constraint: constraint((T0287)A166.CB, (T0287)K194.CB) [> 3.8117 = 6.3528 < 8.2586] w=0.3946 to align # Constraint # added constraint: constraint((T0287)A101.CB, (T0287)F124.CB) [> 4.4884 = 7.4807 < 9.7249] w=0.3946 to align # Constraint # added constraint: constraint((T0287)S78.CB, (T0287)V87.CB) [> 2.3148 = 3.8579 < 5.0153] w=0.3946 to align # Constraint # added constraint: constraint((T0287)F9.CB, (T0287)L32.CB) [> 4.6877 = 7.8127 < 10.1566] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F9.CB, (T0287)I41.CB) [> 3.9020 = 6.5034 < 8.4544] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F9.CB, (T0287)I44.CB) [> 4.5978 = 7.6630 < 9.9618] w=0.3645 to align # Constraint # added constraint: constraint((T0287)S10.CB, (T0287)L31.CB) [> 4.6205 = 7.7008 < 10.0111] w=0.3645 to align # Constraint # added constraint: constraint((T0287)M11.CB, (T0287)L90.CB) [> 3.3996 = 5.6660 < 7.3658] w=0.3645 to align # Constraint # added constraint: constraint((T0287)M11.CB, (T0287)E94.CB) [> 3.6216 = 6.0361 < 7.8469] w=0.3645 to align # Constraint # added constraint: constraint((T0287)I12.CB, (T0287)L22.CB) [> 3.4720 = 5.7866 < 7.5226] w=0.3645 to align # Constraint # added constraint: constraint((T0287)I12.CB, (T0287)I23.CB) [> 4.6417 = 7.7362 < 10.0571] w=0.3645 to align # Constraint # added constraint: constraint((T0287)I12.CB, (T0287)K86.CB) [> 4.4970 = 7.4950 < 9.7435] w=0.3645 to align # Constraint # added constraint: constraint((T0287)I12.CB, (T0287)V87.CB) [> 3.4225 = 5.7042 < 7.4154] w=0.3645 to align # Constraint # added constraint: constraint((T0287)I12.CB, (T0287)L90.CB) [> 2.8359 = 4.7264 < 6.1443] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F9.CB, (T0287)L31.CB) [> 4.7339 = 7.8898 < 10.2568] w=0.3645 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)L90.CB) [> 4.3036 = 7.1727 < 9.3246] w=0.3645 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)I41.CB) [> 4.5208 = 7.5347 < 9.7951] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F51.CB, (T0287)I102.CB) [> 4.3374 = 7.2290 < 9.3977] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F51.CB, (T0287)V64.CB) [> 3.7594 = 6.2657 < 8.1454] w=0.3645 to align # Constraint # added constraint: constraint((T0287)F50.CB, (T0287)V64.CB) [> 3.2915 = 5.4859 < 7.1316] w=0.3645 to align # Constraint # added constraint: constraint((T0287)S25.CB, (T0287)I79.CB) [> 3.4981 = 5.8301 < 7.5791] w=0.3645 to align # Constraint # added constraint: constraint((T0287)A13.CB, (T0287)L22.CB) [> 3.8269 = 6.3782 < 8.2916] w=0.3645 to align # Constraint # added constraint: constraint((T0287)A13.CB, (T0287)I23.CB) [> 2.3356 = 3.8927 < 5.0605] w=0.3645 to align # Constraint # added constraint: constraint((T0287)T95.CB, (T0287)L154.CB) [> 3.5651 = 5.9418 < 7.7243] w=0.3506 to align # Constraint # added constraint: constraint((T0287)M96.CB, (T0287)S134.CB) [> 4.4484 = 7.4140 < 9.6382] w=0.3506 to align # Constraint # added constraint: constraint((T0287)L98.CB, (T0287)L181.CB) [> 2.9416 = 4.9026 < 6.3734] w=0.3506 to align # Constraint # added constraint: constraint((T0287)L98.CB, (T0287)L182.CB) [> 4.3287 = 7.2145 < 9.3789] w=0.3506 to align # Constraint # added constraint: constraint((T0287)L99.CB, (T0287)S134.CB) [> 4.6037 = 7.6728 < 9.9747] w=0.3506 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)L144.CB) [> 2.3471 = 3.9118 < 5.0853] w=0.3506 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)L149.CB) [> 3.5102 = 5.8504 < 7.6055] w=0.3506 to align # Constraint # added constraint: constraint((T0287)L91.CB, (T0287)L154.CB) [> 4.4366 = 7.3943 < 9.6126] w=0.3506 to align # Constraint # added constraint: constraint((T0287)M133.CB, (T0287)M157.CB) [> 4.5529 = 7.5882 < 9.8646] w=0.3506 to align # Constraint # added constraint: constraint((T0287)M133.CB, (T0287)N167.CB) [> 4.4369 = 7.3948 < 9.6132] w=0.3506 to align # Constraint # added constraint: constraint((T0287)M133.CB, (T0287)I171.CB) [> 4.5386 = 7.5644 < 9.8337] w=0.3506 to align # Constraint # added constraint: constraint((T0287)S134.CB, (T0287)V156.CB) [> 3.9430 = 6.5716 < 8.5431] w=0.3506 to align # Constraint # added constraint: constraint((T0287)I135.CB, (T0287)V156.CB) [> 3.3780 = 5.6299 < 7.3189] w=0.3506 to align # Constraint # added constraint: constraint((T0287)E143.CB, (T0287)L152.CB) [> 4.1083 = 6.8471 < 8.9012] w=0.3506 to align # Constraint # added constraint: constraint((T0287)V156.CB, (T0287)I171.CB) [> 4.3836 = 7.3061 < 9.4979] w=0.3506 to align # Constraint # added constraint: constraint((T0287)L99.CB, (T0287)V156.CB) [> 4.3605 = 7.2675 < 9.4477] w=0.3506 to align # Constraint # added constraint: constraint((T0287)H100.CB, (T0287)M133.CB) [> 4.2343 = 7.0572 < 9.1744] w=0.3506 to align # Constraint # added constraint: constraint((T0287)I102.CB, (T0287)Y177.CB) [> 4.6263 = 7.7105 < 10.0237] w=0.3506 to align # Constraint # added constraint: constraint((T0287)I102.CB, (T0287)V178.CB) [> 4.2034 = 7.0057 < 9.1074] w=0.3506 to align # Constraint # added constraint: constraint((T0287)N105.CB, (T0287)A166.CB) [> 4.6665 = 7.7775 < 10.1107] w=0.3506 to align # Constraint # added constraint: constraint((T0287)M138.CB, (T0287)L181.CB) [> 3.3714 = 5.6190 < 7.3047] w=0.3287 to align # Constraint # added constraint: constraint((T0287)L99.CB, (T0287)F110.CB) [> 3.7400 = 6.2333 < 8.1033] w=0.3198 to align # Constraint # added constraint: constraint((T0287)I129.CB, (T0287)Y145.CB) [> 4.5117 = 7.5194 < 9.7753] w=0.2964 to align # Constraint # added constraint: constraint((T0287)M130.CB, (T0287)Y145.CB) [> 3.8518 = 6.4196 < 8.3455] w=0.2964 to align # Constraint # added constraint: constraint((T0287)I41.CB, (T0287)V75.CB) [> 2.7808 = 4.6347 < 6.0251] w=0.2809 to align # Constraint # added constraint: constraint((T0287)M54.CB, (T0287)Y68.CB) [> 3.9419 = 6.5698 < 8.5407] w=0.2776 to align # Constraint # added constraint: constraint((T0287)F113.CB, (T0287)M157.CB) [> 4.4234 = 7.3724 < 9.5841] w=0.2762 to align # Constraint # added constraint: constraint((T0287)F113.CB, (T0287)F155.CB) [> 3.5737 = 5.9561 < 7.7429] w=0.2762 to align # Constraint # added constraint: constraint((T0287)L109.CB, (T0287)M157.CB) [> 3.7836 = 6.3059 < 8.1977] w=0.2762 to align # Constraint # added constraint: constraint((T0287)F108.CB, (T0287)M157.CB) [> 3.8236 = 6.3726 < 8.2844] w=0.2762 to align # Constraint # added constraint: constraint((T0287)P106.CB, (T0287)M138.CB) [> 4.4067 = 7.3444 < 9.5478] w=0.2762 to align # Constraint # added constraint: constraint((T0287)V75.CB, (T0287)F84.CB) [> 3.0573 = 5.0956 < 6.6243] w=0.2762 to align # Constraint # added constraint: constraint((T0287)R136.CB, (T0287)L149.CB) [> 3.7838 = 6.3063 < 8.1981] w=0.2762 to align # Constraint # added constraint: constraint((T0287)F131.CB, (T0287)V156.CB) [> 4.6824 = 7.8039 < 10.1451] w=0.2762 to align # Constraint # added constraint: constraint((T0287)L118.CB, (T0287)K132.CB) [> 4.6650 = 7.7750 < 10.1075] w=0.2762 to align # Constraint # added constraint: constraint((T0287)L122.CB, (T0287)V156.CB) [> 3.5608 = 5.9347 < 7.7151] w=0.2762 to align # Constraint # added constraint: constraint((T0287)L122.CB, (T0287)T158.CB) [> 4.5359 = 7.5599 < 9.8279] w=0.2762 to align # Constraint # added constraint: constraint((T0287)F125.CB, (T0287)E161.CB) [> 2.6028 = 4.3380 < 5.6394] w=0.2762 to align # Constraint # added constraint: constraint((T0287)I120.CB, (T0287)I129.CB) [> 3.1495 = 5.2492 < 6.8239] w=0.2731 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)L118.CB) [> 3.9509 = 6.5849 < 8.5604] w=0.2368 to align # Constraint # added constraint: constraint((T0287)T95.CB, (T0287)I129.CB) [> 4.0348 = 6.7246 < 8.7420] w=0.2284 to align # Constraint # added constraint: constraint((T0287)M96.CB, (T0287)F113.CB) [> 3.6169 = 6.0282 < 7.8367] w=0.2284 to align # Constraint # added constraint: constraint((T0287)M96.CB, (T0287)I120.CB) [> 3.8352 = 6.3920 < 8.3096] w=0.2284 to align # Constraint # added constraint: constraint((T0287)L99.CB, (T0287)L122.CB) [> 3.4866 = 5.8110 < 7.5543] w=0.2284 to align # Constraint # added constraint: constraint((T0287)M69.CB, (T0287)V162.CB) [> 4.4517 = 7.4196 < 9.6454] w=0.2284 to align # Constraint # added constraint: constraint((T0287)L152.CB, (T0287)M191.CB) [> 4.4410 = 7.4017 < 9.6222] w=0.2284 to align # Constraint # added constraint: constraint((T0287)L152.CB, (T0287)V196.CB) [> 4.3948 = 7.3246 < 9.5220] w=0.2284 to align # Constraint # added constraint: constraint((T0287)M183.CB, (T0287)E193.CB) [> 4.0427 = 6.7378 < 8.7591] w=0.2284 to align # Constraint # added constraint: constraint((T0287)F121.CB, (T0287)N148.CB) [> 3.8793 = 6.4655 < 8.4051] w=0.2284 to align # Constraint # added constraint: constraint((T0287)H48.CB, (T0287)L61.CB) [> 4.4888 = 7.4814 < 9.7258] w=0.2117 to align # Constraint # added constraint: constraint((T0287)V64.CB, (T0287)I76.CB) [> 4.5851 = 7.6418 < 9.9343] w=0.2117 to align # Constraint # added constraint: constraint((T0287)M69.CB, (T0287)L151.CB) [> 4.6383 = 7.7305 < 10.0497] w=0.1831 to align # Constraint # added constraint: constraint((T0287)A60.CB, (T0287)L98.CB) [> 4.1002 = 6.8337 < 8.8839] w=0.1772 to align # Constraint # added constraint: constraint((T0287)L98.CB, (T0287)F110.CB) [> 3.7637 = 6.2728 < 8.1546] w=0.1772 to align # Constraint # added constraint: constraint((T0287)L61.CB, (T0287)L109.CB) [> 3.3547 = 5.5912 < 7.2685] w=0.1772 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)M69.CB) [> 3.5286 = 5.8810 < 7.6452] w=0.1583 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)L65.CB) [> 4.2039 = 7.0064 < 9.1084] w=0.1583 to align # Constraint # added constraint: constraint((T0287)Y68.CB, (T0287)M138.CB) [> 4.2801 = 7.1334 < 9.2735] w=0.1426 to align # Constraint # added constraint: constraint((T0287)R73.CB, (T0287)L149.CB) [> 4.2859 = 7.1432 < 9.2862] w=0.1426 to align # Constraint # added constraint: constraint((T0287)K77.CB, (T0287)L151.CB) [> 4.4491 = 7.4152 < 9.6398] w=0.1426 to align # Constraint # added constraint: constraint((T0287)L154.CB, (T0287)L181.CB) [> 4.6013 = 7.6687 < 9.9694] w=0.1426 to align # Constraint # added constraint: constraint((T0287)K153.CB, (T0287)L182.CB) [> 4.6639 = 7.7732 < 10.1052] w=0.1426 to align # Constraint # added constraint: constraint((T0287)L118.CB, (T0287)M138.CB) [> 3.2203 = 5.3672 < 6.9773] w=0.1426 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)H100.CB) [> 4.4710 = 7.4517 < 9.6873] w=0.1426 to align # Constraint # added constraint: constraint((T0287)F121.CB, (T0287)M130.CB) [> 4.2533 = 7.0888 < 9.2154] w=0.1389 to align # Constraint # added constraint: constraint((T0287)M11.CB, (T0287)L22.CB) [> 3.5418 = 5.9029 < 7.6738] w=0.1383 to align # Constraint # added constraint: constraint((T0287)M11.CB, (T0287)N29.CB) [> 4.6038 = 7.6729 < 9.9748] w=0.1383 to align # Constraint # added constraint: constraint((T0287)P150.CB, (T0287)L168.CB) [> 3.5972 = 5.9954 < 7.7940] w=0.1383 to align # Constraint # added constraint: constraint((T0287)L152.CB, (T0287)L168.CB) [> 4.7243 = 7.8738 < 10.2360] w=0.1383 to align # Constraint # added constraint: constraint((T0287)L65.CB, (T0287)L152.CB) [> 4.4115 = 7.3525 < 9.5582] w=0.1383 to align # Constraint # added constraint: constraint((T0287)L65.CB, (T0287)P106.CB) [> 4.6034 = 7.6724 < 9.9741] w=0.1383 to align # Constraint # added constraint: constraint((T0287)M130.CB, (T0287)F155.CB) [> 3.9909 = 6.6515 < 8.6469] w=0.1182 to align # Constraint # added constraint: constraint((T0287)F121.CB, (T0287)Y165.CB) [> 4.5612 = 7.6020 < 9.8826] w=0.1135 to align # Constraint # added constraint: constraint((T0287)M69.CB, (T0287)I79.CB) [> 2.3897 = 3.9829 < 5.1777] w=0.1020 to align # Constraint # added constraint: constraint((T0287)L65.CB, (T0287)L168.CB) [> 3.5160 = 5.8600 < 7.6180] w=0.1004 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)L22.CB) [> 4.0138 = 6.6897 < 8.6966] w=0.1004 to align # Constraint # added constraint: constraint((T0287)M133.CB, (T0287)F185.CB) [> 4.6836 = 7.8060 < 10.1478] w=0.1004 to align # Constraint # added constraint: constraint((T0287)I117.CB, (T0287)F185.CB) [> 3.9200 = 6.5333 < 8.4933] w=0.1004 to align # Constraint # added constraint: constraint((T0287)I142.CB, (T0287)A166.CB) [> 3.7714 = 6.2857 < 8.1714] w=0.1004 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)M183.CB) [> 3.6667 = 6.1112 < 7.9446] w=0.1004 to align # Constraint # added constraint: constraint((T0287)F84.CB, (T0287)R179.CB) [> 2.8468 = 4.7447 < 6.1681] w=0.1004 to align # Constraint # added constraint: constraint((T0287)K83.CB, (T0287)M183.CB) [> 4.3962 = 7.3271 < 9.5252] w=0.1004 to align # Constraint # added constraint: constraint((T0287)K83.CB, (T0287)L182.CB) [> 4.3424 = 7.2374 < 9.4086] w=0.1004 to align # Constraint # added constraint: constraint((T0287)L91.CB, (T0287)L187.CB) [> 4.2772 = 7.1287 < 9.2673] w=0.0942 to align # Constraint # added constraint: constraint((T0287)V75.CB, (T0287)L109.CB) [> 4.3791 = 7.2986 < 9.4881] w=0.0942 to align # Constraint # added constraint: constraint((T0287)I76.CB, (T0287)F131.CB) [> 2.6637 = 4.4394 < 5.7713] w=0.0942 to align # Constraint # added constraint: constraint((T0287)L122.CB, (T0287)M138.CB) [> 4.7118 = 7.8529 < 10.2088] w=0.0942 to align # Constraint # added constraint: constraint((T0287)M130.CB, (T0287)V196.CB) [> 3.4025 = 5.6709 < 7.3722] w=0.0942 to align # Constraint # added constraint: constraint((T0287)I135.CB, (T0287)V196.CB) [> 4.2819 = 7.1366 < 9.2776] w=0.0942 to align # Constraint # added constraint: constraint((T0287)Y145.CB, (T0287)L187.CB) [> 4.3195 = 7.1991 < 9.3589] w=0.0942 to align # Constraint # added constraint: constraint((T0287)L149.CB, (T0287)L187.CB) [> 4.0652 = 6.7754 < 8.8080] w=0.0942 to align # Constraint # added constraint: constraint((T0287)A101.CB, (T0287)L187.CB) [> 3.7598 = 6.2663 < 8.1462] w=0.0942 to align # Constraint # added constraint: constraint((T0287)L122.CB, (T0287)F131.CB) [> 4.0147 = 6.6912 < 8.6985] w=0.0942 to align # Constraint # added constraint: constraint((T0287)F121.CB, (T0287)M138.CB) [> 2.9982 = 4.9970 < 6.4961] w=0.0942 to align # Constraint # added constraint: constraint((T0287)V75.CB, (T0287)K169.CB) [> 3.8481 = 6.4136 < 8.3376] w=0.0734 to align # Constraint # added constraint: constraint((T0287)H55.CB, (T0287)F121.CB) [> 2.8261 = 4.7101 < 6.1231] w=0.0734 to align # Constraint # added constraint: constraint((T0287)A60.CB, (T0287)I79.CB) [> 4.4042 = 7.3403 < 9.5424] w=0.0734 to align # Constraint # added constraint: constraint((T0287)K132.CB, (T0287)L154.CB) [> 2.8906 = 4.8176 < 6.2629] w=0.0734 to align # Constraint # added constraint: constraint((T0287)F131.CB, (T0287)M157.CB) [> 4.2291 = 7.0485 < 9.1630] w=0.0734 to align # Constraint # added constraint: constraint((T0287)I129.CB, (T0287)T158.CB) [> 4.6159 = 7.6932 < 10.0012] w=0.0734 to align # Constraint # added constraint: constraint((T0287)F121.CB, (T0287)F131.CB) [> 4.1031 = 6.8385 < 8.8900] w=0.0680 to align # Constraint # added constraint: constraint((T0287)Y68.CB, (T0287)I120.CB) [> 3.3628 = 5.6046 < 7.2860] w=0.0448 to align # Constraint # added constraint: constraint((T0287)M5.CB, (T0287)P150.CB) [> 3.9151 = 6.5251 < 8.4826] w=0.0448 to align # Constraint # added constraint: constraint((T0287)L8.CB, (T0287)L151.CB) [> 4.6391 = 7.7319 < 10.0515] w=0.0448 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0287/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0287/decoys/ # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file short.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 188 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 188 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 193 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/MIG_FROST_FLEX_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_FLEX_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_FLEX_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 186 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # Found a chain break before 32 # copying to AlignedFragments data structure # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 193 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0287)P106.CA and (T0287)F110.CA only 0.000 apart, marking (T0287)F110.CA as missing WARNING: atoms too close: (T0287)I120.CA and (T0287)P123.CA only 0.000 apart, marking (T0287)P123.CA as missing WARNING: atoms too close: (T0287)F121.CA and (T0287)K132.CA only 0.000 apart, marking (T0287)K132.CA as missing WARNING: atoms too close: (T0287)L122.CA and (T0287)M133.CA only 0.000 apart, marking (T0287)M133.CA as missing WARNING: atoms too close: (T0287)T147.CA and (T0287)E160.CA only 0.000 apart, marking (T0287)E160.CA as missing WARNING: atoms too close: (T0287)N148.CA and (T0287)E161.CA only 0.000 apart, marking (T0287)E161.CA as missing WARNING: atoms too close: (T0287)M157.CA and (T0287)V162.CA only 0.000 apart, marking (T0287)V162.CA as missing WARNING: atoms too close: (T0287)T158.CA and (T0287)N163.CA only 0.000 apart, marking (T0287)N163.CA as missing WARNING: atoms too close: (T0287)D159.CA and (T0287)A166.CA only 0.000 apart, marking (T0287)A166.CA as missing WARNING: atoms too close: (T0287)F164.CA and (T0287)I171.CA only 0.000 apart, marking (T0287)I171.CA as missing WARNING: atoms too close: (T0287)Y165.CA and (T0287)E172.CA only 0.000 apart, marking (T0287)E172.CA as missing # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0287)L32.CA and (T0287)N33.CA only 0.000 apart, marking (T0287)N33.CA as missing WARNING: atoms too close: (T0287)M138.CA and (T0287)L154.CA only 0.000 apart, marking (T0287)L154.CA as missing WARNING: atoms too close: (T0287)D139.CA and (T0287)D159.CA only 0.000 apart, marking (T0287)D159.CA as missing WARNING: atoms too close: (T0287)F164.CA and (T0287)N167.CA only 0.000 apart, marking (T0287)N167.CA as missing WARNING: atoms too close: (T0287)Y165.CA and (T0287)L168.CA only 0.000 apart, marking (T0287)L168.CA as missing # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0287)D71.CA and (T0287)Y72.CA only 0.000 apart, marking (T0287)Y72.CA as missing WARNING: atoms too close: (T0287)L90.CA and (T0287)E97.CA only 0.000 apart, marking (T0287)E97.CA as missing WARNING: atoms too close: (T0287)L91.CA and (T0287)L98.CA only 0.000 apart, marking (T0287)L98.CA as missing WARNING: atoms too close: (T0287)E92.CA and (T0287)L99.CA only 0.000 apart, marking (T0287)L99.CA as missing WARNING: atoms too close: (T0287)S93.CA and (T0287)H100.CA only 0.000 apart, marking (T0287)H100.CA as missing WARNING: atoms too close: (T0287)F185.CA and (T0287)D186.CA only 0.000 apart, marking (T0287)D186.CA as missing # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0287)P106.CA and (T0287)F110.CA only 0.000 apart, marking (T0287)F110.CA as missing WARNING: atoms too close: (T0287)I120.CA and (T0287)P123.CA only 0.000 apart, marking (T0287)P123.CA as missing WARNING: atoms too close: (T0287)F121.CA and (T0287)K132.CA only 0.000 apart, marking (T0287)K132.CA as missing WARNING: atoms too close: (T0287)L122.CA and (T0287)M133.CA only 0.000 apart, marking (T0287)M133.CA as missing WARNING: atoms too close: (T0287)T147.CA and (T0287)E160.CA only 0.000 apart, marking (T0287)E160.CA as missing WARNING: atoms too close: (T0287)N148.N and (T0287)E161.N only 0.000 apart, marking (T0287)E161.N as missing WARNING: atoms too close: (T0287)N148.CA and (T0287)E161.CA only 0.000 apart, marking (T0287)E161.CA as missing WARNING: atoms too close: (T0287)N148.CB and (T0287)E161.CB only 0.000 apart, marking (T0287)E161.CB as missing WARNING: atoms too close: (T0287)N148.C and (T0287)E161.C only 0.000 apart, marking (T0287)E161.C as missing WARNING: atoms too close: (T0287)M157.CA and (T0287)V162.CA only 0.000 apart, marking (T0287)V162.CA as missing WARNING: atoms too close: (T0287)T158.CA and (T0287)N163.CA only 0.000 apart, marking (T0287)N163.CA as missing WARNING: atoms too close: (T0287)D159.CA and (T0287)A166.CA only 0.000 apart, marking (T0287)D159.CA as missing WARNING: atoms too close: (T0287)F164.CA and (T0287)I171.CA only 0.000 apart, marking (T0287)I171.CA as missing WARNING: atoms too close: (T0287)Y165.CA and (T0287)E172.CA only 0.000 apart, marking (T0287)E172.CA as missing # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 186 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0287)K38.O and (T0287)K39.N only 0.000 apart, marking (T0287)K39.N as missing WARNING: atoms too close: (T0287)M130.O and (T0287)F131.N only 0.000 apart, marking (T0287)F131.N as missing # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 186 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 WARNING: atom 674 has residue number 1 < previous residue 195 in servers/mGen-3D_TS1.pdb.gz # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0287 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.9023 model score 1.9673 model score 2.0201 model score 1.8030 model score 1.9669 model score 1.6649 model score 2.0627 model score 2.2003 model score 2.3962 model score 2.1820 model score 2.1919 model score 2.0191 model score 2.1773 model score 2.5636 model score 2.1494 model score 2.4311 model score 2.0191 model score 2.1773 model score 2.5636 model score 2.1494 model score 2.4311 model score 1.9401 model score 2.0839 model score 2.1052 model score 1.7092 model score 1.6103 model score 1.4843 model score 1.3751 model score 1.5426 model score 1.4782 model score 1.6899 model score 2.1041 model score 1.8814 model score 1.6894 model score 1.8156 model score 1.5715 model score 1.5262 model score 2.2613 model score 2.2491 model score 2.1518 model score 2.1903 model score 2.1441 model score 1.9598 model score 2.1709 model score 1.5603 model score 1.5969 model score 1.8751 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.2491 model score 2.1903 model score 2.1441 model score 2.2597 model score 2.2806 model score 1.8570 model score 2.1405 model score 2.2783 model score 2.0719 model score 2.0333 model score 1.7086 model score 1.7653 model score 1.9804 model score 2.0518 model score 1.7876 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.2024 model score 2.0354 model score 1.2963 model score 1.4351 model score 1.9634 model score 1.8895 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0268 model score 1.7838 model score 2.2830 model score 2.1716 model score 2.2543 model score 2.2209 model score 2.6785 model score 2.6785 model score 2.2196 model score 2.2196 model score 2.2196 model score 1.5237 model score 1.5634 model score 1.3815 model score 1.6847 model score 1.4555 model score 1.9178 model score 1.9757 model score 1.7813 model score 1.9674 model score 2.0336 model score 2.1221 model score 2.1824 model score 1.9748 model score 2.0278 model score 2.7563 model score 1.8497 model score 1.5262 model score 1.7296 model score 1.6452 model score 1.6584 model score 1.9178 model score 1.9617 model score 2.0718 model score 1.9205 model score 2.0376 model score 1.9813 model score 2.0045 model score 2.0848 model score 1.9806 model score 1.9029 model score 2.1374 model score 2.1227 model score 2.1225 model score 2.0277 model score 1.8310 model score 1.8700 model score 1.4928 model score 1.8164 model score 1.5973 model score 1.6161 model score 1.9752 model score 1.7326 model score 2.0909 model score 2.1309 model score 2.0998 model score 2.1447 model score 2.0741 model score 1.7671 model score 1.9752 model score 1.6487 model score 2.0667 model score 1.8994 model score 1.9152 model score 1.7992 model score 1.9636 model score 2.0728 model score 2.0751 model score 1.7175 model score 1.8766 model score 1.9360 model score 1.7876 model score 1.7068 model score 1.8154 model score 1.9390 model score 1.8008 model score 1.8110 model score 1.6581 model score 1.9023 model score 1.9673 model score 2.0201 model score 1.8030 model score 1.9669 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.9747 model score 1.0509 model score 1.0002 model score 1.4652 model score 1.2417 model score 1.9926 model score 1.8117 model score 2.1789 model score 1.9636 model score 1.8338 model score 2.0195 model score 2.2689 model score 2.0881 model score 1.8046 model 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USE_META, weight: 0.5337 cost: 1.9102 min: 1.0002 max: 2.7563 USE_META, weight: 0.4850 cost: 2.0051 min: 1.0002 max: 2.7563 USE_META, weight: 0.4143 cost: 2.1430 min: 1.0002 max: 2.7563 USE_META, weight: 0.4344 cost: 2.1038 min: 1.0002 max: 2.7563 USE_META, weight: 0.4343 cost: 2.1040 min: 1.0002 max: 2.7563 USE_META, weight: 0.4450 cost: 2.0831 min: 1.0002 max: 2.7563 USE_META, weight: 0.6617 cost: 1.6603 min: 1.0002 max: 2.7563 USE_META, weight: 0.5812 cost: 1.8174 min: 1.0002 max: 2.7563 USE_META, weight: 0.7672 cost: 1.4544 min: 1.0002 max: 2.7563 USE_META, weight: 0.5919 cost: 1.7965 min: 1.0002 max: 2.7563 USE_META, weight: 0.8952 cost: 1.2046 min: 1.0002 max: 2.7563 USE_META, weight: 0.6375 cost: 1.7076 min: 1.0002 max: 2.7563 USE_META, weight: 0.6417 cost: 1.6994 min: 1.0002 max: 2.7563 USE_EVALUE, weight: 0.3958 eval: 37.9480 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3958 eval: 37.9480 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3958 eval: 37.9480 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6169 eval: 24.1980 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6169 eval: 24.1980 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6169 eval: 24.1980 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.7830 eval: 13.8690 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.7830 eval: 13.8690 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.7830 eval: 13.8690 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3089 eval: 43.3550 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3089 eval: 43.3550 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3089 eval: 43.3550 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2278 eval: 48.3990 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2278 eval: 48.3990 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2278 eval: 48.3990 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6555 eval: 21.8000 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6555 eval: 21.8000 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.6555 eval: 21.8000 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4547 eval: 34.2860 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4547 eval: 34.2860 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4547 eval: 34.2860 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1310 eval: 54.4160 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1310 eval: 54.4160 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1310 eval: 54.4160 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1639 eval: 52.3680 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1639 eval: 52.3680 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1639 eval: 52.3680 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4930 eval: 31.9060 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4930 eval: 31.9060 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.4930 eval: 31.9060 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2910 eval: 44.4670 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2910 eval: 44.4670 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2910 eval: 44.4670 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.5101 eval: 30.8420 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.5101 eval: 30.8420 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.5101 eval: 30.8420 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8142 eval: 11.9300 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8142 eval: 11.9300 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8142 eval: 11.9300 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2242 eval: 48.6220 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2242 eval: 48.6220 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2242 eval: 48.6220 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2103 eval: 49.4820 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2103 eval: 49.4820 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2103 eval: 49.4820 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 1.0000 eval: 0.3740 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 1.0000 eval: 0.3740 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 1.0000 eval: 0.3740 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1159 eval: 55.3580 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1159 eval: 55.3580 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1159 eval: 55.3580 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1093 eval: 55.7640 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1093 eval: 55.7640 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1093 eval: 55.7640 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3185 eval: 42.7540 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3185 eval: 42.7540 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.3185 eval: 42.7540 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1000 eval: 56.3440 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1000 eval: 56.3440 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1000 eval: 56.3440 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8814 eval: 7.7500 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8814 eval: 7.7500 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.8814 eval: 7.7500 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1520 eval: 53.1130 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1520 eval: 53.1130 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.1520 eval: 53.1130 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2536 eval: 46.7920 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2536 eval: 46.7920 min: 0.3740 max: 56.3440 USE_EVALUE, weight: 0.2536 eval: 46.7920 min: 0.3740 max: 56.3440 Number of contacts in models: 239 Number of contacts in alignments: 69 NUMB_ALIGNS: 69 Adding 13946 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -352.1064, CN propb: -352.1064 weights: 0.2333 constraints: 319 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 319 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 319 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 13627 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 13627 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 13946 # command: