# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0287 numbered 1 through 199 Created new target T0287 from T0287.a2m # command:CPU_time= 6.466 sec, elapsed time= 6.828 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0b/T0287-1b0b-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b0b expands to /projects/compbio/data/pdb/1b0b.pdb.gz 1b0b:Warning: there is no chain 1b0b will retry with 1b0bA Bad short name: C1A for alphabet: pdb_atoms Bad short name: C2A for alphabet: pdb_atoms Bad short name: OAC for alphabet: pdb_atoms Skipped atom 80, because occupancy 0.5 <= existing 0.500 in 1b0b Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1b0b Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1b0b # T0287 read from 1b0b/T0287-1b0b-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0b read from 1b0b/T0287-1b0b-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b0b to template set # found chain 1b0b in template set T0287 5 :MRKLFSMIADS 1b0b 25 :GPEFFMALFDA # choosing archetypes in rotamer library 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=5 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0b/T0287-1b0b-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1b0b/T0287-1b0b-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0b read from 1b0b/T0287-1b0b-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b0b in template 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=10 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0b/T0287-1b0b-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1b0b/T0287-1b0b-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0b read from 1b0b/T0287-1b0b-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b0b in template 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=15 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1josA/T0287-1josA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1josA expands to /projects/compbio/data/pdb/1jos.pdb.gz 1josA:Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 1josA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1josA # T0287 read from 1josA/T0287-1josA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1josA read from 1josA/T0287-1josA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1josA to template set # found chain 1josA in template 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=21 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1josA/T0287-1josA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1josA/T0287-1josA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1josA read from 1josA/T0287-1josA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1josA in template 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=27 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1josA/T0287-1josA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1josA/T0287-1josA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1josA read from 1josA/T0287-1josA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1josA in template 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=33 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmxA/T0287-1tmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tmxA expands to /projects/compbio/data/pdb/1tmx.pdb.gz 1tmxA:Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1688, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1690, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1865, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 2183, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 1tmxA Skipped atom 2187, because occupancy 0.500 <= existing 0.500 in 1tmxA # T0287 read from 1tmxA/T0287-1tmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tmxA read from 1tmxA/T0287-1tmxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tmxA to template set # found chain 1tmxA in template 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=40 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmxA/T0287-1tmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1tmxA/T0287-1tmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tmxA read from 1tmxA/T0287-1tmxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tmxA in template 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=47 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmxA/T0287-1tmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1tmxA/T0287-1tmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tmxA read from 1tmxA/T0287-1tmxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tmxA in template 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=54 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dc1A/T0287-1dc1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dc1A expands to /projects/compbio/data/pdb/1dc1.pdb.gz 1dc1A:Skipped atom 153, because occupancy 0.430 <= existing 0.570 in 1dc1A Skipped atom 155, because occupancy 0.430 <= existing 0.570 in 1dc1A Skipped atom 157, because occupancy 0.430 <= existing 0.570 in 1dc1A Skipped atom 159, because occupancy 0.430 <= existing 0.570 in 1dc1A Skipped atom 2070, because occupancy 0.350 <= existing 0.650 in 1dc1A Skipped atom 2297, because occupancy 0.450 <= existing 0.550 in 1dc1A Skipped atom 2308, because occupancy 0.490 <= existing 0.510 in 1dc1A # T0287 read from 1dc1A/T0287-1dc1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dc1A read from 1dc1A/T0287-1dc1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dc1A to template set # found chain 1dc1A in template 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=66 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dc1A/T0287-1dc1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1dc1A/T0287-1dc1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dc1A read from 1dc1A/T0287-1dc1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dc1A in template 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=78 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dc1A/T0287-1dc1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1dc1A/T0287-1dc1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dc1A read from 1dc1A/T0287-1dc1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dc1A in template 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=90 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9kB/T0287-2a9kB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a9kB expands to /projects/compbio/data/pdb/2a9k.pdb.gz 2a9kB:# T0287 read from 2a9kB/T0287-2a9kB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9kB read from 2a9kB/T0287-2a9kB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=97 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9kB/T0287-2a9kB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 2a9kB/T0287-2a9kB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9kB read from 2a9kB/T0287-2a9kB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=104 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9kB/T0287-2a9kB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 2a9kB/T0287-2a9kB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9kB read from 2a9kB/T0287-2a9kB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=111 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g24A/T0287-1g24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g24A expands to /projects/compbio/data/pdb/1g24.pdb.gz 1g24A:# T0287 read from 1g24A/T0287-1g24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g24A read from 1g24A/T0287-1g24A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=118 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g24A/T0287-1g24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1g24A/T0287-1g24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g24A read from 1g24A/T0287-1g24A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=125 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g24A/T0287-1g24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1g24A/T0287-1g24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g24A read from 1g24A/T0287-1g24A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=132 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sas/T0287-2sas-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0287-2sas-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2sas read from 2sas/T0287-2sas-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2sas to template set # found chain 2sas in template set Warning: unaligning (T0287)E92 because of BadResidue code BAD_PEPTIDE in next template residue (2sas)D60 Warning: unaligning (T0287)S93 because of BadResidue code BAD_PEPTIDE at template residue (2sas)D60 T0287 35 :DEK 2sas 4 :DFQ T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLL 2sas 45 :SLSDADYKSMQASL T0287 94 :ETMELLHAIAENPNFLFS 2sas 61 :EWRDLKGRADINKDDVVS Number of specific fragments extracted= 4 number of extra gaps= 1 total=136 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sas/T0287-2sas-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 2sas/T0287-2sas-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2sas read from 2sas/T0287-2sas-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2sas in template set Warning: unaligning (T0287)E92 because of BadResidue code BAD_PEPTIDE in next template residue (2sas)D60 Warning: unaligning (T0287)S93 because of BadResidue code BAD_PEPTIDE at template residue (2sas)D60 T0287 35 :DEK 2sas 4 :DFQ T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLL 2sas 45 :SLSDADYKSMQASL T0287 94 :ETMELLHAIAENPNFLFS 2sas 61 :EWRDLKGRADINKDDVVS Number of specific fragments extracted= 4 number of extra gaps= 1 total=140 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sas/T0287-2sas-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 2sas/T0287-2sas-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2sas read from 2sas/T0287-2sas-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2sas in template set Warning: unaligning (T0287)E92 because of BadResidue code BAD_PEPTIDE in next template residue (2sas)D60 Warning: unaligning (T0287)S93 because of BadResidue code BAD_PEPTIDE at template residue (2sas)D60 T0287 35 :DEK 2sas 4 :DFQ T0287 41 :IDQIKTMHDFFKQMHTNKGALDKVLRNYMKDYRAVIK 2sas 7 :KQKIKFTFDFFLDMNHDGSIQDNDFEDMMTRYKEVNK T0287 78 :SIGVDKFKKVYRLL 2sas 45 :SLSDADYKSMQASL T0287 94 :ETMELLHAIAENPNFLFS 2sas 61 :EWRDLKGRADINKDDVVS Number of specific fragments extracted= 4 number of extra gaps= 1 total=144 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1knqA/T0287-1knqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1knqA expands to /projects/compbio/data/pdb/1knq.pdb.gz 1knqA:Skipped atom 277, because occupancy 0.500 <= 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/T0287-1knqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knqA read from 1knqA/T0287-1knqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=153 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1knqA/T0287-1knqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1knqA/T0287-1knqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knqA read from 1knqA/T0287-1knqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=162 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1knqA/T0287-1knqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1knqA/T0287-1knqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knqA read from 1knqA/T0287-1knqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=171 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sz9A/T0287-1sz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sz9A expands to /projects/compbio/data/pdb/1sz9.pdb.gz 1sz9A:# T0287 read from 1sz9A/T0287-1sz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz9A read from 1sz9A/T0287-1sz9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=176 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sz9A/T0287-1sz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1sz9A/T0287-1sz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz9A read from 1sz9A/T0287-1sz9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=181 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sz9A/T0287-1sz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1sz9A/T0287-1sz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sz9A read from 1sz9A/T0287-1sz9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=186 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9gA/T0287-1e9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1e9gA/T0287-1e9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9gA read from 1e9gA/T0287-1e9gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=187 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9gA/T0287-1e9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1e9gA/T0287-1e9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9gA read from 1e9gA/T0287-1e9gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=188 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9gA/T0287-1e9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0287 read from 1e9gA/T0287-1e9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e9gA read from 1e9gA/T0287-1e9gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=189 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 12.861 sec, elapsed time= 15.442 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 19701 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.912 sec, elapsed time= 15.496 sec. # command:Reading probabilities from T0287.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.174 Optimizing... Probability sum: -346.597, CN propb: -346.597 weights: 0.371 constraints: 196 # command:CPU_time= 14.838 sec, elapsed time= 17.431 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 196 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 196 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 492 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 492 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 17457 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 17457 # command:CPU_time= 15.168 sec, elapsed time= 18.038 sec. # command: