# 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 T0354 numbered 1 through 130 Created new target T0354 from T0354.a2m # command:CPU_time= 6.277 sec, elapsed time= 6.320 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y2qA/T0354-1y2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y2qA expands to /projects/compbio/data/pdb/1y2q.pdb.gz 1y2qA:# T0354 read from 1y2qA/T0354-1y2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y2qA read from 1y2qA/T0354-1y2qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y2qA to template set # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSLF 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSEL # choosing archetypes in rotamer library T0354 42 :GD 1y2qA 89 :AK T0354 45 :NRQVKALANSVQVKLKEAGVDIVGS 1y2qA 91 :PSVAMDILNRVYQGLKERGFNVGKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 1y2qA/T0354-1y2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1y2qA/T0354-1y2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y2qA read from 1y2qA/T0354-1y2qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSLF 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSEL T0354 42 :GDSNRQV 1y2qA 89 :AKPSVAM T0354 50 :ALANSVQVKLKEAGVDIVGS 1y2qA 96 :DILNRVYQGLKERGFNVGKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 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 1y2qA/T0354-1y2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1y2qA/T0354-1y2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y2qA read from 1y2qA/T0354-1y2qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSL 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSE T0354 41 :TGDSNRQVK 1y2qA 88 :LAKPSVAMD T0354 51 :LANSVQVKLKEAGVDIVGSE 1y2qA 97 :ILNRVYQGLKERGFNVGKAP Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 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 1mp9A/T0354-1mp9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mp9A expands to /projects/compbio/data/pdb/1mp9.pdb.gz 1mp9A:# T0354 read from 1mp9A/T0354-1mp9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp9A read from 1mp9A/T0354-1mp9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mp9A to template set # found chain 1mp9A in template set T0354 23 :IELDTSKLTSLF 1mp9A 50 :LIFRLESPKITS T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVD 1mp9A 67 :GKMVVTGAKSTDELIKAVKRIIKTLKKYGMQ T0354 66 :IVGSEG 1mp9A 103 :KIQIQN T0354 72 :HESGEWVL 1mp9A 155 :FSSGKMVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 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 1mp9A/T0354-1mp9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1mp9A/T0354-1mp9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp9A read from 1mp9A/T0354-1mp9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mp9A in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVL 1mp9A 67 :GKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVA Number of specific fragments extracted= 1 number of extra gaps= 0 total=14 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 1mp9A/T0354-1mp9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1mp9A/T0354-1mp9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mp9A read from 1mp9A/T0354-1mp9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mp9A in template set T0354 20 :KDIIELDTSKL 1mp9A 47 :FPGLIFRLESP T0354 31 :TSLFQRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVL 1mp9A 63 :IFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 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 2gfgA/T0354-2gfgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gfgA expands to /projects/compbio/data/pdb/2gfg.pdb.gz 2gfgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 764, because occupancy 0.5 <= existing 0.500 in 2gfgA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 2gfgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 2gfgA/T0354-2gfgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfgA read from 2gfgA/T0354-2gfgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gfgA to template set # found chain 2gfgA in template set T0354 9 :LAIEALEDIKG 2gfgA 100 :EVMDALRDLSI T0354 26 :DTSK 2gfgA 111 :PISQ T0354 30 :LTSLFQRMIVATGDSNRQVKALANSVQV 2gfgA 142 :YLGIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGS 2gfgA 170 :TFSISQVPT Number of specific fragments extracted= 4 number of extra gaps= 0 total=20 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 2gfgA/T0354-2gfgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 2gfgA/T0354-2gfgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfgA read from 2gfgA/T0354-2gfgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfgA in template set T0354 10 :AIEALEDIKG 2gfgA 101 :VMDALRDLSI T0354 26 :DTSKL 2gfgA 111 :PISQL T0354 32 :SLFQRMIVATGDSNRQVKALANSVQV 2gfgA 144 :GIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGSE 2gfgA 170 :TFSISQVPTE Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 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 2gfgA/T0354-2gfgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 2gfgA/T0354-2gfgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfgA read from 2gfgA/T0354-2gfgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfgA in template set T0354 10 :AIEALEDI 2gfgA 101 :VMDALRDL T0354 18 :KGKDI 2gfgA 114 :QLKHI T0354 23 :IELDTSKL 2gfgA 126 :AEISYEQG T0354 31 :TSLFQRMIVATGDSNRQVKALANSVQV 2gfgA 143 :LGIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGSEG 2gfgA 170 :TFSISQVPTEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 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 1v6tA/T0354-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v6tA expands to /projects/compbio/data/pdb/1v6t.pdb.gz 1v6tA:# T0354 read from 1v6tA/T0354-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0354-1v6tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v6tA to template set # found chain 1v6tA in template set T0354 1 :MEIQEISKLAIEALED 1v6tA 187 :EDKEEIAERVISMVKD T0354 26 :DTSK 1v6tA 206 :RAIN T0354 30 :LTSLFQRMIVATGDSNRQVK 1v6tA 212 :WVDLKVDTICVHGDNPKAVE T0354 51 :LANSVQVKLKEAGVDIVG 1v6tA 232 :ITSYIRKVLEEEGVKIVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 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 1v6tA/T0354-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1v6tA/T0354-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0354-1v6tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6tA in template set T0354 2 :EIQEISKLAIEALED 1v6tA 188 :DKEEIAERVISMVKD T0354 17 :IKG 1v6tA 208 :ING T0354 29 :KLTSLFQRMIVATGDSNRQVK 1v6tA 211 :EWVDLKVDTICVHGDNPKAVE T0354 51 :LANSVQVKLKEAGVDIVG 1v6tA 232 :ITSYIRKVLEEEGVKIVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 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 1v6tA/T0354-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1v6tA/T0354-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6tA read from 1v6tA/T0354-1v6tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6tA in template set T0354 1 :MEIQEISKLAIEALEDI 1v6tA 187 :EDKEEIAERVISMVKDG T0354 18 :KGKDIIELDT 1v6tA 206 :RAINGEWVDL T0354 34 :FQRMIVATGDSNRQVKA 1v6tA 216 :KVDTICVHGDNPKAVEI T0354 52 :ANSVQVKLKEAGVDIVGSE 1v6tA 233 :TSYIRKVLEEEGVKIVPMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=41 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 1g7uA/T0354-1g7uA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g7uA expands to /projects/compbio/data/pdb/1g7u.pdb.gz 1g7uA:# T0354 read from 1g7uA/T0354-1g7uA-t06-local-adpstyle5.a2m # 1g7uA read from 1g7uA/T0354-1g7uA-t06-local-adpstyle5.a2m # adding 1g7uA to template set # found chain 1g7uA in template set T0354 12 :EALEDIKGKDIIELDTSKLTSLFQRMIVATGDSNRQVKALAN 1g7uA 185 :SIMKKVSGNSPVIFDVTHALQCRDPFVAASGGRRAQVAELAR Number of specific fragments extracted= 1 number of extra gaps= 0 total=42 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 1ufkA/T0354-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ufkA expands to /projects/compbio/data/pdb/1ufk.pdb.gz 1ufkA:# T0354 read from 1ufkA/T0354-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0354-1ufkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ufkA to template set # found chain 1ufkA in template set T0354 7 :SKLAIEALEDIKGK 1ufkA 155 :LPQAEANAKRNGVR T0354 21 :DIIELDTSKLTSLFQ 1ufkA 170 :RFLEGSLEAALPFGP T0354 36 :RMIVATGDSNRQ 1ufkA 186 :DLLVANLYAELH T0354 50 :ALAN 1ufkA 203 :RYRE T0354 54 :SVQVKLKEAGVDIVGSEGHES 1ufkA 226 :LVREAMAGAGFRPLEEAAEGE T0354 77 :WVLVDAG 1ufkA 247 :WVLLAYG Number of specific fragments extracted= 6 number of extra gaps= 0 total=48 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 1ufkA/T0354-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1ufkA/T0354-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0354-1ufkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufkA in template set T0354 9 :LAIEALEDIKGK 1ufkA 157 :QAEANAKRNGVR T0354 21 :DIIELDTSKLTSLFQ 1ufkA 170 :RFLEGSLEAALPFGP T0354 36 :RMIVATGDSNRQ 1ufkA 186 :DLLVANLYAELH T0354 50 :ALAN 1ufkA 203 :RYRE T0354 54 :SVQVKLKEAGVDIVGSEGHES 1ufkA 226 :LVREAMAGAGFRPLEEAAEGE T0354 77 :WVLVDAG 1ufkA 247 :WVLLAYG Number of specific fragments extracted= 6 number of extra gaps= 0 total=54 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 1ufkA/T0354-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1ufkA/T0354-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufkA read from 1ufkA/T0354-1ufkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufkA in template set T0354 4 :QEISKLAIEAL 1ufkA 198 :AALAPRYREAL T0354 32 :SLFQRMIVATGDSNR 1ufkA 209 :VPGGRALLTGILKDR T0354 52 :ANSVQVKLKEAGVDIVGSE 1ufkA 224 :APLVREAMAGAGFRPLEEA T0354 73 :ESGEWVLVDAG 1ufkA 243 :AEGEWVLLAYG Number of specific fragments extracted= 4 number of extra gaps= 0 total=58 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 1vgjA/T0354-1vgjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vgjA expands to /projects/compbio/data/pdb/1vgj.pdb.gz 1vgjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1vgjA/T0354-1vgjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vgjA read from 1vgjA/T0354-1vgjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vgjA to template set # found chain 1vgjA in template set T0354 3 :IQEISKLAIEALEDI 1vgjA 50 :TEEQAEEIKNILKKI T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vgjA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=61 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 1vgjA/T0354-1vgjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vgjA/T0354-1vgjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vgjA read from 1vgjA/T0354-1vgjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vgjA in template set T0354 4 :QEISKLAIEALEDI 1vgjA 51 :EEQAEEIKNILKKI T0354 18 :KGK 1vgjA 67 :KYK T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vgjA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=65 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 1vgjA/T0354-1vgjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vgjA/T0354-1vgjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vgjA read from 1vgjA/T0354-1vgjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vgjA in template set T0354 2 :EIQEISKLAIEALEDIKGKD 1vgjA 53 :QAEEIKNILKKIAEKYKKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIVGSEG 1vgjA 100 :IREMAREIEDELAKLGFKKEGNFV T0354 78 :VLVDAGDV 1vgjA 124 :AHITLGRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=69 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 1vljA/T0354-1vljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vljA expands to /projects/compbio/data/pdb/1vlj.pdb.gz 1vljA:Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 1vljA Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 1vljA # T0354 read from 1vljA/T0354-1vljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vljA read from 1vljA/T0354-1vljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vljA to template set # found chain 1vljA in template set T0354 10 :AIEALEDIKGKDIIELDTSKL 1vljA 22 :IGEEIKNAGIRKVLFLYGGGS T0354 48 :VKA 1vljA 43 :IKK T0354 51 :LANSVQVKLKEAGVDIVGSEG 1vljA 48 :VYDQVVDSLKKHGIEWVEVSG Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 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 1vljA/T0354-1vljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vljA/T0354-1vljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vljA read from 1vljA/T0354-1vljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vljA in template set T0354 10 :AIEALEDIKGKDI 1vljA 22 :IGEEIKNAGIRKV T0354 37 :MIVATGDS 1vljA 35 :LFLYGGGS T0354 48 :VKA 1vljA 43 :IKK T0354 51 :LANSVQVKLKEAGVDIVGSEGH 1vljA 48 :VYDQVVDSLKKHGIEWVEVSGV T0354 73 :ESGEWVLVDA 1vljA 157 :KTKEKYGVSS Number of specific fragments extracted= 5 number of extra gaps= 0 total=77 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 1vljA/T0354-1vljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vljA/T0354-1vljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vljA read from 1vljA/T0354-1vljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vljA in template set T0354 10 :AIEALEDIKGKDI 1vljA 22 :IGEEIKNAGIRKV T0354 37 :MIVATGD 1vljA 35 :LFLYGGG T0354 47 :QVKA 1vljA 42 :SIKK T0354 51 :LANSVQVKLKEAGVDIVGSEGHESG 1vljA 48 :VYDQVVDSLKKHGIEWVEVSGVKPN Number of specific fragments extracted= 4 number of extra gaps= 0 total=81 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 1jdqA/T0354-1jdqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jdqA expands to /projects/compbio/data/pdb/1jdq.pdb.gz 1jdqA:# T0354 read from 1jdqA/T0354-1jdqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdqA read from 1jdqA/T0354-1jdqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jdqA to template set # found chain 1jdqA in template set T0354 5 :EISKLAIEALEDIKGKDIIELDTSKLT 1jdqA 38 :VPDVETKRALQNMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 3 number of extra gaps= 0 total=84 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 1jdqA/T0354-1jdqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1jdqA/T0354-1jdqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdqA read from 1jdqA/T0354-1jdqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jdqA in template set T0354 6 :ISKLAIE 1jdqA 42 :ETKRALQ T0354 16 :DIKGKDIIELDTSKLT 1jdqA 49 :NMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=88 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 1jdqA/T0354-1jdqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1jdqA/T0354-1jdqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdqA read from 1jdqA/T0354-1jdqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jdqA in template set T0354 4 :QEISKL 1jdqA 40 :DVETKR T0354 13 :ALEDIKGKDIIELDTSKLT 1jdqA 46 :ALQNMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 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 1aisA/T0354-1aisA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aisA expands to /projects/compbio/data/pdb/1ais.pdb.gz 1aisA:# T0354 read from 1aisA/T0354-1aisA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisA read from 1aisA/T0354-1aisA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aisA to template set # found chain 1aisA in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDI 1aisA 63 :GKLVVTGAKSVQDIERAVAKLAQKLKSIGVKF T0354 67 :VGSEG 1aisA 98 :PQIDV T0354 72 :HESGEWVL 1aisA 151 :FSSGKIVC Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 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 1aisA/T0354-1aisA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1aisA/T0354-1aisA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisA read from 1aisA/T0354-1aisA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aisA in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGH 1aisA 63 :GKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQI T0354 73 :ESGEWVL 1aisA 152 :SSGKIVC Number of specific fragments extracted= 2 number of extra gaps= 0 total=97 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 1aisA/T0354-1aisA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1aisA/T0354-1aisA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aisA read from 1aisA/T0354-1aisA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aisA in template set Warning: unaligning (T0354)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1aisA)P53 Warning: unaligning (T0354)L30 because of BadResidue code BAD_PEPTIDE at template residue (1aisA)P53 T0354 21 :DIIELDTS 1aisA 44 :PGIICHLD T0354 31 :TSLFQR 1aisA 54 :KVALLI T0354 37 :MIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEW 1aisA 65 :LVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNM Number of specific fragments extracted= 3 number of extra gaps= 1 total=100 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 1wqaA/T0354-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0354 read from 1wqaA/T0354-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0354-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0354 48 :VKALANSVQVKLKEAGVDIVGSEG 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDG T0354 72 :HESGEWVLVDAGD 1wqaA 410 :IFEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=103 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 1wqaA/T0354-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1wqaA/T0354-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0354-1wqaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0354 48 :VKALANSVQVKLKEAGVDIVGSEGH 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDGA T0354 73 :ESGEWVLVDAGD 1wqaA 411 :FEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=106 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/T0354-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1wqaA/T0354-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wqaA read from 1wqaA/T0354-1wqaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wqaA in template set T0354 12 :EALEDIKGK 1wqaA 362 :ELIDELPKY T0354 23 :IELDTSKL 1wqaA 371 :YQIKTKRH T0354 42 :GDSN 1wqaA 379 :VEGD T0354 48 :VKALANSVQVKLKEAGVDIVGSEGH 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDGA T0354 73 :ESGEWVLVDAGD 1wqaA 411 :FEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dlyA/T0354-1dlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dlyA expands to /projects/compbio/data/pdb/1dly.pdb.gz 1dlyA:# T0354 read from 1dlyA/T0354-1dlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dlyA read from 1dlyA/T0354-1dlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dlyA to template set # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALEDIKG 1dlyA 37 :DMKVQRSKQFAFLAYALG T0354 27 :TSK 1dlyA 59 :WKG T0354 30 :LTSLFQ 1dlyA 64 :MRTAHK T0354 44 :SNRQVKALANSVQVKLKEAGVD 1dlyA 76 :SDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=116 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dlyA/T0354-1dlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1dlyA/T0354-1dlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dlyA read from 1dlyA/T0354-1dlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALEDIKG 1dlyA 37 :DMKVQRSKQFAFLAYALG T0354 28 :SKLTSLF 1dlyA 69 :KDLVPHL T0354 44 :SNRQVKALANSVQVKLKEAGVD 1dlyA 76 :SDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dlyA/T0354-1dlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1dlyA/T0354-1dlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dlyA read from 1dlyA/T0354-1dlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALE 1dlyA 37 :DMKVQRSKQFAFLA T0354 16 :DIKGKD 1dlyA 58 :EWKGKD T0354 28 :SKLTSL 1dlyA 69 :KDLVPH T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1dlyA 75 :LSDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=123 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s69A/T0354-1s69A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s69A expands to /projects/compbio/data/pdb/1s69.pdb.gz 1s69A:# T0354 read from 1s69A/T0354-1s69A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s69A read from 1s69A/T0354-1s69A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s69A to template set # found chain 1s69A in template set T0354 1 :MEIQEISKLAIEALEDIKG 1s69A 38 :VDMAKQRAHQKAFLTYAFG T0354 20 :KD 1s69A 58 :TD T0354 26 :DTSK 1s69A 60 :KYDG T0354 42 :GDSNRQVKALANSVQVKLKEAGVD 1s69A 78 :GLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=127 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s69A/T0354-1s69A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1s69A/T0354-1s69A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s69A read from 1s69A/T0354-1s69A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s69A in template set T0354 1 :MEIQEISKLAIEALEDIKG 1s69A 38 :VDMAKQRAHQKAFLTYAFG T0354 20 :KD 1s69A 58 :TD T0354 26 :DTSKL 1s69A 60 :KYDGR T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1s69A 79 :LNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=131 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s69A/T0354-1s69A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1s69A/T0354-1s69A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s69A read from 1s69A/T0354-1s69A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s69A in template set T0354 1 :MEIQEISKLAIEALED 1s69A 38 :VDMAKQRAHQKAFLTY T0354 17 :IKGKD 1s69A 55 :FGGTD T0354 26 :DTSKLTS 1s69A 60 :KYDGRYM T0354 42 :GDSNRQVKALANSVQVKLKEAGVD 1s69A 78 :GLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=135 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0354-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wy7A expands to /projects/compbio/data/pdb/1wy7.pdb.gz 1wy7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1wy7A/T0354-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0354-1wy7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wy7A to template set # found chain 1wy7A in template set T0354 3 :IQEISKLAIEALEDIKGK 1wy7A 81 :DKEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDSN 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFGS T0354 46 :RQVKALA 1wy7A 132 :PFLLKAF T0354 53 :NSVQVKLKEAGVDIVGSEG 1wy7A 156 :RFIEKFSWEHGFVVTHRLT T0354 72 :HESGEWVLVDA 1wy7A 190 :LERITVDIYRF Number of specific fragments extracted= 5 number of extra gaps= 0 total=140 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0354-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1wy7A/T0354-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0354-1wy7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wy7A in template set T0354 4 :QEISKLAIEALEDIKGK 1wy7A 82 :KEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDS 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFG T0354 45 :NRQVKALA 1wy7A 131 :RPFLLKAF T0354 53 :NSVQVKLKEAGVDIVGSEGH 1wy7A 156 :RFIEKFSWEHGFVVTHRLTT T0354 73 :ESGEWVLVDA 1wy7A 191 :ERITVDIYRF Number of specific fragments extracted= 5 number of extra gaps= 0 total=145 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/T0354-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1wy7A/T0354-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wy7A read from 1wy7A/T0354-1wy7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wy7A in template set T0354 4 :QEISKLAIEALEDIKGK 1wy7A 82 :KEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDSN 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFGS T0354 53 :NSVQVKLKEA 1wy7A 131 :RPFLLKAFEI T0354 76 :E 1wy7A 142 :D T0354 78 :VL 1wy7A 143 :VV T0354 85 :VVVHVMLPAVRDYYD 1wy7A 145 :YSIHLAKPEVRRFIE T0354 102 :A 1wy7A 160 :K Number of specific fragments extracted= 7 number of extra gaps= 0 total=152 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0354-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1usgA expands to /projects/compbio/data/pdb/1usg.pdb.gz 1usgA:# T0354 read from 1usgA/T0354-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0354-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1usgA to template set # found chain 1usgA in template set T0354 6 :ISKLAIEAL 1usgA 124 :QGPTAAKYI T0354 15 :EDIKGKDIIELDTSK 1usgA 134 :ETVKPQRIAIIHDKQ T0354 46 :RQVKALANSVQVKLKEAGVDIVGSEGHESG 1usgA 149 :QYGEGLARSVQDGLKAANANVVFFDGITAG Number of specific fragments extracted= 3 number of extra gaps= 0 total=155 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0354-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1usgA/T0354-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0354-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set T0354 6 :ISKLAIEALEDI 1usgA 124 :QGPTAAKYILET T0354 18 :KGKDIIELDTSK 1usgA 137 :KPQRIAIIHDKQ T0354 46 :RQVKALANSVQVKLKEAGVDIVGSEGHESGE 1usgA 149 :QYGEGLARSVQDGLKAANANVVFFDGITAGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=158 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/T0354-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1usgA/T0354-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0354-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set T0354 6 :ISKLAIEAL 1usgA 124 :QGPTAAKYI T0354 15 :EDIKGKDI 1usgA 134 :ETVKPQRI T0354 38 :IVATGDSNRQ 1usgA 142 :AIIHDKQQYG T0354 49 :KALANSVQVKLKEAGVDIVGSEGHESGE 1usgA 152 :EGLARSVQDGLKAANANVVFFDGITAGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=162 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdxA/T0354-1vdxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vdxA expands to /projects/compbio/data/pdb/1vdx.pdb.gz 1vdxA:# T0354 read from 1vdxA/T0354-1vdxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdxA read from 1vdxA/T0354-1vdxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vdxA to template set # found chain 1vdxA in template set T0354 4 :QEISKLAIEALEDI 1vdxA 51 :EEQAEEIKNILKKI T0354 18 :KGKD 1vdxA 69 :KKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vdxA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=166 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdxA/T0354-1vdxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vdxA/T0354-1vdxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdxA read from 1vdxA/T0354-1vdxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdxA in template set T0354 4 :QEISKLAIEALEDI 1vdxA 51 :EEQAEEIKNILKKI T0354 18 :KGK 1vdxA 67 :KYK T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vdxA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=170 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdxA/T0354-1vdxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1vdxA/T0354-1vdxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdxA read from 1vdxA/T0354-1vdxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdxA in template set T0354 2 :EIQEISKLAIEALEDIKGKD 1vdxA 53 :QAEEIKNILKKIAEKYKKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIVGS 1vdxA 100 :IREMAREIEDELAKLGFKKEGN Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qysA/T0354-1qysA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qysA expands to /projects/compbio/data/pdb/1qys.pdb.gz 1qysA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1qysA/T0354-1qysA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qysA read from 1qysA/T0354-1qysA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qysA to template set # found chain 1qysA in template set T0354 3 :IQEISKLAIEALEDIKGKD 1qysA 29 :LQKVLNELMDYIKKQGAKR T0354 36 :RMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSE 1qysA 48 :VRISITARTKKEAEKFAAILIKVFAELGYNDINVT T0354 72 :HESGEWVL 1qysA 83 :FDGDTVTV Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qysA/T0354-1qysA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1qysA/T0354-1qysA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qysA read from 1qysA/T0354-1qysA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qysA in template set T0354 3 :IQEISKLAIEALEDIKGK 1qysA 29 :LQKVLNELMDYIKKQGAK T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSE 1qysA 47 :RVRISITARTKKEAEKFAAILIKVFAELGYNDINVT T0354 72 :HESGEWVL 1qysA 83 :FDGDTVTV Number of specific fragments extracted= 3 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qysA/T0354-1qysA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1qysA/T0354-1qysA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qysA read from 1qysA/T0354-1qysA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qysA in template set T0354 2 :EIQEISKLAIEALEDIKGKDII 1qysA 28 :ELQKVLNELMDYIKKQGAKRVR T0354 38 :IVATGDSNRQVKALANSVQVKLKEAGVDIVGSEG 1qysA 50 :ISITARTKKEAEKFAAILIKVFAELGYNDINVTF T0354 73 :ESGE 1qysA 84 :DGDT Number of specific fragments extracted= 3 number of extra gaps= 0 total=182 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtxA/T0354-1rtxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rtxA expands to /projects/compbio/data/pdb/1rtx.pdb.gz 1rtxA:# T0354 read from 1rtxA/T0354-1rtxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtxA read from 1rtxA/T0354-1rtxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rtxA to template set # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALED 1rtxA 62 :DGRYMREAHKELVEN T0354 41 :TGDSNRQVKALANSVQVKLKEAGVD 1rtxA 77 :HGLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=184 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtxA/T0354-1rtxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1rtxA/T0354-1rtxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtxA read from 1rtxA/T0354-1rtxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALED 1rtxA 62 :DGRYMREAHKELVEN T0354 41 :TGDSNRQVKALANSVQVKLKEAGVD 1rtxA 77 :HGLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=186 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtxA/T0354-1rtxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1rtxA/T0354-1rtxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rtxA read from 1rtxA/T0354-1rtxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALEDIK 1rtxA 62 :DGRYMREAHKELVENHG T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1rtxA 79 :LNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=188 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1dA/T0354-1e1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e1dA expands to /projects/compbio/data/pdb/1e1d.pdb.gz 1e1dA:# T0354 read from 1e1dA/T0354-1e1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1dA read from 1e1dA/T0354-1e1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e1dA to template set # found chain 1e1dA in template set T0354 1 :MEIQEISKLA 1e1dA 349 :KDFSALIAQA T0354 17 :IKGKDIIELDTSK 1e1dA 359 :KKCPPPVEIETGS T0354 39 :VATGDSNRQVKALANSVQVKLKEAGVD 1e1dA 372 :IVGGFAHHQVLALADKVVEAVKSGAIK T0354 84 :DVVVHVM 1e1dA 399 :RFVVMAG T0354 91 :LPAVRDYYD 1e1dA 409 :RQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=193 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1dA/T0354-1e1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1e1dA/T0354-1e1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1dA read from 1e1dA/T0354-1e1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e1dA in template set T0354 2 :EIQEISKLA 1e1dA 350 :DFSALIAQA T0354 17 :IKGKDIIELDTSK 1e1dA 359 :KKCPPPVEIETGS T0354 39 :VATGDSNRQVKALANSVQVKLKEAGV 1e1dA 372 :IVGGFAHHQVLALADKVVEAVKSGAI T0354 83 :GDVVVHVM 1e1dA 398 :KRFVVMAG T0354 91 :LPAVRDYYD 1e1dA 409 :RQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=198 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1dA/T0354-1e1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1e1dA/T0354-1e1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e1dA read from 1e1dA/T0354-1e1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e1dA in template set T0354 2 :EIQEISKLA 1e1dA 350 :DFSALIAQA T0354 17 :IKGKDIIELDTSKL 1e1dA 359 :KKCPPPVEIETGSI T0354 40 :ATGDSNRQVKALANSVQVKLKEAGVD 1e1dA 373 :VGGFAHHQVLALADKVVEAVKSGAIK T0354 84 :DVVVHV 1e1dA 399 :RFVVMA T0354 90 :MLPAVRDYYD 1e1dA 408 :GRQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=203 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rz3A/T0354-1rz3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rz3A expands to /projects/compbio/data/pdb/1rz3.pdb.gz 1rz3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1rz3A/T0354-1rz3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rz3A read from 1rz3A/T0354-1rz3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rz3A to template set # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 37 :MIVATGDSN 1rz3A 26 :GIDGLSRSG T0354 48 :VKALANSVQVKLKEAGVDIVGS 1rz3A 35 :KTTLANQLSQTLREQGISVCVF Number of specific fragments extracted= 3 number of extra gaps= 0 total=206 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rz3A/T0354-1rz3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1rz3A/T0354-1rz3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rz3A read from 1rz3A/T0354-1rz3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 37 :MIVATGDSN 1rz3A 26 :GIDGLSRSG T0354 48 :VKALANSVQVKLKEAGVDIVGS 1rz3A 35 :KTTLANQLSQTLREQGISVCVF Number of specific fragments extracted= 3 number of extra gaps= 0 total=209 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rz3A/T0354-1rz3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0354 read from 1rz3A/T0354-1rz3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rz3A read from 1rz3A/T0354-1rz3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 39 :VATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHE 1rz3A 26 :GIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDD T0354 88 :HVMLPAVR 1rz3A 61 :HIVERAKR Number of specific fragments extracted= 3 number of extra gaps= 0 total=212 Will force an alignment to be made, even if fragment is small Number of alignments=58 # command:CPU_time= 13.062 sec, elapsed time= 27.065 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 58 Adding 8385 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.092 sec, elapsed time= 27.097 sec. # command:Reading probabilities from T0354.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 12.657 Optimizing... Probability sum: -249.283, CN propb: -249.283 weights: 0.115 constraints: 326 # command:CPU_time= 19.333 sec, elapsed time= 33.376 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 326 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 326 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 371 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 371 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 6684 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 6684 # command:CPU_time= 19.465 sec, elapsed time= 33.626 sec. # command: