# 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 T0327 numbered 1 through 102 Created new target T0327 from T0327.a2m # command:CPU_time= 6.313 sec, elapsed time= 6.363 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbxA/T0327-1tbxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tbxA expands to /projects/compbio/data/pdb/1tbx.pdb.gz 1tbxA: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 # T0327 read from 1tbxA/T0327-1tbxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbxA read from 1tbxA/T0327-1tbxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tbxA to template set # found chain 1tbxA in template set T0327 9 :AILKEIFEGN 1tbxA 12 :IVLAYLYDNE # choosing archetypes in rotamer library T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIG 1tbxA 33 :NAEFPMSTATFYDAKKFLIQEGFVKE T0327 50 :HYSDDRPHLY 1tbxA 59 :RQERGEKRLY T0327 65 :LTEKGENYLKENGTWSKAYKTIKEI 1tbxA 69 :LTEKGKLFAISLKTAIETYKQIKKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 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 1tbxA/T0327-1tbxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1tbxA/T0327-1tbxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbxA read from 1tbxA/T0327-1tbxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tbxA in template set T0327 7 :RYAILKEIFEGN 1tbxA 10 :EAIVLAYLYDNE T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIG 1tbxA 34 :AEFPMSTATFYDAKKFLIQEGFVKE T0327 50 :HYSDDRPHLY 1tbxA 59 :RQERGEKRLY T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1tbxA 69 :LTEKGKLFAISLKTAIETYKQIKKRH Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 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 1tbxA/T0327-1tbxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1tbxA/T0327-1tbxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbxA read from 1tbxA/T0327-1tbxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tbxA in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 1tbxA 34 :AEFPMSTATFYDAKKFLIQEGFVKERQE T0327 53 :DDRPHL 1tbxA 62 :RGEKRL T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEI 1tbxA 68 :YLTEKGKLFAISLKTAIETYKQIKKR Number of specific fragments extracted= 3 number of extra gaps= 0 total=11 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 1ub9A/T0327-1ub9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0327 read from 1ub9A/T0327-1ub9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub9A read from 1ub9A/T0327-1ub9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0327 3 :KDKLRYAILKEIFEGN 1ub9A 14 :GNPVRLGIMIFLLPRR T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 39 :VLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 64 :ELTEKGENYLKENGTWSKAYKT 1ub9A 75 :EITDFGMEEAKRFLSSLKAVID Number of specific fragments extracted= 3 number of extra gaps= 0 total=14 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 1ub9A/T0327-1ub9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1ub9A/T0327-1ub9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub9A read from 1ub9A/T0327-1ub9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ub9A in template set T0327 3 :KDKLRYAILKEIF 1ub9A 14 :GNPVRLGIMIFLL T0327 17 :GN 1ub9A 28 :RR T0327 19 :TP 1ub9A 31 :AP T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 40 :LDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 64 :ELTEKGENYLKENGTWSKAYKT 1ub9A 75 :EITDFGMEEAKRFLSSLKAVID Number of specific fragments extracted= 5 number of extra gaps= 0 total=19 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 1ub9A/T0327-1ub9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1ub9A/T0327-1ub9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ub9A read from 1ub9A/T0327-1ub9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ub9A in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1ub9A 40 :LDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTV T0327 63 :PELTEKGENYLKENGTWSKAYK 1ub9A 74 :VEITDFGMEEAKRFLSSLKAVI Number of specific fragments extracted= 2 number of extra gaps= 0 total=21 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 2a61A/T0327-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.5 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0327 read from 2a61A/T0327-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0327-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a61A to template set # found chain 2a61A in template set T0327 4 :DKLRYAILKEIFEGNTP 2a61A 33 :TPAQFDILQKIYFEGPK T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 58 :LGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 64 :ELTEKGENYLKENGTWSKAY 2a61A 93 :VITRKGEEVIEKVIERRENF T0327 86 :IKEIKD 2a61A 113 :IEKITS Number of specific fragments extracted= 4 number of extra gaps= 0 total=25 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 2a61A/T0327-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2a61A/T0327-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0327-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a61A in template set T0327 4 :DKLRYAILKEIF 2a61A 33 :TPAQFDILQKIY T0327 16 :EGNTP 2a61A 46 :EGPKR T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 58 :LGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 64 :ELTEKGENYLKENGTWSKAY 2a61A 93 :VITRKGEEVIEKVIERRENF T0327 86 :IKEIKD 2a61A 113 :IEKITS Number of specific fragments extracted= 5 number of extra gaps= 0 total=30 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 2a61A/T0327-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2a61A/T0327-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0327-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a61A in template set T0327 2 :NKDKLRYAI 2a61A 50 :RPGELSVLL T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2a61A 59 :GVAKSTVTGLVKRLEADGYLTRTPDPADRRAYF T0327 63 :PELTEKGENYLKENGTWSKAYK 2a61A 92 :LVITRKGEEVIEKVIERRENFI T0327 87 :KEIK 2a61A 114 :EKIT Number of specific fragments extracted= 4 number of extra gaps= 0 total=34 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 2fbiA/T0327-2fbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0327 read from 2fbiA/T0327-2fbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbiA read from 2fbiA/T0327-2fbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 5 :KLRYAILKEIFEGN 2fbiA 34 :EQQWRVIRILRQQG T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 56 :NQACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 60 :K 2fbiA 93 :N T0327 65 :LTEKGENYLKENGT 2fbiA 94 :LTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 6 number of extra gaps= 1 total=40 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 2fbiA/T0327-2fbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fbiA/T0327-2fbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbiA read from 2fbiA/T0327-2fbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 5 :KLRYAILKEIF 2fbiA 34 :EQQWRVIRILR T0327 16 :EGN 2fbiA 46 :QGE T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 57 :QACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 60 :K 2fbiA 93 :N T0327 65 :LTEKGENYLKENGT 2fbiA 94 :LTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 7 number of extra gaps= 1 total=47 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 2fbiA/T0327-2fbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fbiA/T0327-2fbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbiA read from 2fbiA/T0327-2fbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbiA in template set Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0327)D54 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYS 2fbiA 58 :ACILRPSMTGVLARLERDGIVRRWKAP T0327 55 :RPHLY 2fbiA 87 :QRRVY T0327 63 :PELTEKGENYLKENGT 2fbiA 92 :VNLTEKGQQCFVSMSG T0327 79 :WSKAYKTIKEI 2fbiA 109 :MEKNYQRIQER Number of specific fragments extracted= 4 number of extra gaps= 1 total=51 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 2f2eA/T0327-2f2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f2eA expands to /projects/compbio/data/pdb/2f2e.pdb.gz 2f2eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2f2eA # T0327 read from 2f2eA/T0327-2f2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2eA read from 2f2eA/T0327-2f2eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f2eA to template set # found chain 2f2eA in template set T0327 4 :DKLRYAILKEIFEGNTP 2f2eA 23 :DGWSMLIVRDAFEGLTR T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 2f2eA 44 :QKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRL T0327 66 :TEKG 2f2eA 83 :TDKG T0327 74 :KENGTWSKAYKTIKE 2f2eA 87 :RALFPLLVAIRQWGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 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 2f2eA/T0327-2f2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2f2eA/T0327-2f2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2eA read from 2f2eA/T0327-2f2eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f2eA in template set T0327 5 :KLRYAILKEIFEGNTP 2f2eA 24 :GWSMLIVRDAFEGLTR T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 2f2eA 46 :SLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRL T0327 66 :TEKG 2f2eA 83 :TDKG T0327 74 :KENGTWSKAYKTIKE 2f2eA 87 :RALFPLLVAIRQWGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 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 2f2eA/T0327-2f2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2f2eA/T0327-2f2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f2eA read from 2f2eA/T0327-2f2eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f2eA in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPH 2f2eA 47 :LGLAKNILAARLRNLVEHGVMVAVPAESGSHQ T0327 62 :GPELTEKGENY 2f2eA 79 :EYRLTDKGRAL T0327 77 :GTWSKAYKTIKE 2f2eA 90 :FPLLVAIRQWGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 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 2g7uA/T0327-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA: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 # T0327 read from 2g7uA/T0327-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0327-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g7uA to template set # found chain 2g7uA in template set T0327 6 :LRYAIL 2g7uA 14 :RGFAVL T0327 13 :EIFEGNTP 2g7uA 20 :LAFDAQRP T0327 21 :LSEND 2g7uA 29 :PTLAE T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAG T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKDWIK 2g7uA 65 :WSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=67 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 2g7uA/T0327-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2g7uA/T0327-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0327-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g7uA in template set T0327 5 :KLRYAIL 2g7uA 13 :ERGFAVL T0327 13 :EIFEGNTP 2g7uA 20 :LAFDAQRP T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAG T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKDWIK 2g7uA 65 :WSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 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 2g7uA/T0327-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2g7uA/T0327-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0327-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g7uA in template set T0327 3 :KDKLRYA 2g7uA 31 :LAELATE T0327 26 :IGVTEDQFDDAVNFLKREGYIIGV 2g7uA 38 :AGLSRPAVRRILLTLQKLGYVAGS T0327 53 :DDRPHL 2g7uA 62 :GGRWSL T0327 62 :GPELTEKGENYLKENGTWSKAYKTIKEIKDW 2g7uA 68 :TPRVLSIGQHYSESHALIEAAMPRLLEVAEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=75 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 1z7uA/T0327-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z7uA expands to /projects/compbio/data/pdb/1z7u.pdb.gz 1z7uA: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 60, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1z7uA 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 259, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 299, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 313, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1z7uA # T0327 read from 1z7uA/T0327-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0327-1z7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z7uA to template set # found chain 1z7uA in template set T0327 4 :DKLRYAILKEIFEGNTP 1z7uA 18 :GKWKLSLMDELFQGTKR T0327 21 :LS 1z7uA 42 :LD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 78 :TLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=79 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 1z7uA/T0327-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1z7uA/T0327-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0327-1z7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7uA in template set T0327 3 :KDKLRYAILKEIFEGNTP 1z7uA 17 :NGKWKLSLMDELFQGTKR T0327 21 :LS 1z7uA 42 :LD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 78 :TLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=83 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 1z7uA/T0327-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1z7uA/T0327-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z7uA read from 1z7uA/T0327-1z7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z7uA in template set T0327 3 :KDKLRYAIL 1z7uA 35 :NGELMRALD T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVE T0327 63 :PELTEKGENYLKENGTWSKAYKTIKEIKD 1z7uA 77 :YTLTPEGYALYDALSSLCHWGETFAQKKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=86 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 2fswA/T0327-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA 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 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA 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 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0327 read from 2fswA/T0327-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0327-2fswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fswA to template set # found chain 2fswA in template set T0327 6 :LRYAI 2fswA 27 :IIFQI T0327 11 :LKEIF 2fswA 41 :LKRAI T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fswA 46 :PGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVE T0327 60 :KLGP 2fswA 81 :SLTP T0327 66 :TEKGENYLKENGTWS 2fswA 86 :GEKVLPIIDEIAKFG Number of specific fragments extracted= 5 number of extra gaps= 0 total=91 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 2fswA/T0327-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fswA/T0327-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0327-2fswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fswA in template set T0327 5 :KLRYAI 2fswA 26 :LIIFQI T0327 11 :LKEIFEG 2fswA 41 :LKRAIPG T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fswA 48 :ISEKMLIDELKFLCGKGLIKKKQYPEVPPRVE T0327 60 :KLGP 2fswA 81 :SLTP T0327 66 :TEKGENYLKENGTWS 2fswA 86 :GEKVLPIIDEIAKFG Number of specific fragments extracted= 5 number of extra gaps= 0 total=96 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 2fswA/T0327-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fswA/T0327-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fswA read from 2fswA/T0327-2fswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fswA in template set T0327 5 :KLRYAI 2fswA 40 :ELKRAI T0327 16 :E 2fswA 46 :P T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYK 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEY T0327 64 :ELTEKGENYLKE 2fswA 81 :SLTPLGEKVLPI T0327 79 :WSKAYKT 2fswA 93 :IDEIAKF Number of specific fragments extracted= 5 number of extra gaps= 0 total=101 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 1r7jA/T0327-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r7jA expands to /projects/compbio/data/pdb/1r7j.pdb.gz 1r7jA:# T0327 read from 1r7jA/T0327-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0327-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r7jA to template set # found chain 1r7jA in template set T0327 2 :NKDKLRYAILKEIF 1r7jA 5 :SKLEIIQAILEACK T0327 17 :GNTP 1r7jA 19 :SGSP T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIG 1r7jA 28 :YGANLSYALTGRYIKMLMDLEIIRQ T0327 52 :SDD 1r7jA 53 :EGK T0327 57 :HL 1r7jA 56 :QY T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=107 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 1r7jA/T0327-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1r7jA/T0327-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0327-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r7jA in template set T0327 2 :NKDKLRYAILKEIFEGN 1r7jA 5 :SKLEIIQAILEACKSGS T0327 20 :P 1r7jA 22 :P T0327 26 :IGVTEDQFDDAVNFLKREGYII 1r7jA 30 :ANLSYALTGRYIKMLMDLEIIR T0327 51 :YSDD 1r7jA 52 :QEGK T0327 57 :HL 1r7jA 56 :QY T0327 64 :ELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 58 :MLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=113 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 1r7jA/T0327-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1r7jA/T0327-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0327-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r7jA in template set T0327 3 :KDKLRYA 1r7jA 23 :KTRIMYG T0327 26 :IGVTEDQFDDAVNFLKREGYIIGV 1r7jA 30 :ANLSYALTGRYIKMLMDLEIIRQE T0327 53 :DDR 1r7jA 54 :GKQ T0327 63 :PELTEKGENYLKENGTWSKAYKTIKEIKD 1r7jA 57 :YMLTKKGEELLEDIRKFNEMRKNMDQLKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=117 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 1xmaA/T0327-1xmaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xmaA expands to /projects/compbio/data/pdb/1xma.pdb.gz 1xmaA:Skipped atom 237, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 239, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 241, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 243, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 245, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 440, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 722, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 724, because occupancy 0.350 <= existing 0.650 in 1xmaA # T0327 read from 1xmaA/T0327-1xmaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmaA read from 1xmaA/T0327-1xmaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xmaA to template set # found chain 1xmaA in template set Warning: unaligning (T0327)D53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)P56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 4 :DKLRYAILKEIFEGN 1xmaA 9 :GYVDTIILSLLIEGD T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 52 :S 1xmaA 68 :E T0327 57 :HLYKL 1xmaA 73 :RRTYY T0327 64 :ELTEKGENYLKENGT 1xmaA 78 :RITPEGIKYYKQKCE T0327 82 :AYKTIKEIKD 1xmaA 93 :EWELTKKVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=123 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 1xmaA/T0327-1xmaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1xmaA/T0327-1xmaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmaA read from 1xmaA/T0327-1xmaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xmaA in template set Warning: unaligning (T0327)D53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)P56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 5 :KLRYAILKEIFEGN 1xmaA 10 :YVDTIILSLLIEGD T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 52 :S 1xmaA 68 :E T0327 57 :HLYKL 1xmaA 73 :RRTYY T0327 64 :ELTEKGENYLKENGT 1xmaA 78 :RITPEGIKYYKQKCE T0327 82 :AYKTIKEIKD 1xmaA 93 :EWELTKKVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=129 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 1xmaA/T0327-1xmaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1xmaA/T0327-1xmaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xmaA read from 1xmaA/T0327-1xmaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xmaA in template set Warning: unaligning (T0327)S52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0327)R55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 T0327 5 :KLRYAILKEI 1xmaA 28 :EISKNIRIKT T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 1xmaA 38 :DELYVIKETTLYSAFARLEKNGYIKSYYG T0327 56 :PHLY 1xmaA 73 :RRTY T0327 63 :PELTEKGENYLKENGT 1xmaA 77 :YRITPEGIKYYKQKCE T0327 82 :AYKTIKEIK 1xmaA 93 :EWELTKKVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=134 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 1jgsA/T0327-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0327 read from 1jgsA/T0327-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0327-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0327 5 :KLRYAILKEIFEGN 1jgsA 40 :AAQFKVLCSIRCAA T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSD 1jgsA 62 :KVLSVDLGALTRMLDRLVCKGWVERLPNPN T0327 54 :DRPHLYK 1jgsA 93 :KRGVLVK T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1jgsA 100 :LTTGGAAICEQCHQLVGQDLHQELTK Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 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 1jgsA/T0327-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1jgsA/T0327-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0327-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgsA in template set T0327 4 :DKLRYAILKEIF 1jgsA 39 :TAAQFKVLCSIR T0327 18 :N 1jgsA 53 :A T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSD 1jgsA 64 :LSVDLGALTRMLDRLVCKGWVERLPNPN T0327 54 :DRPHLYK 1jgsA 93 :KRGVLVK T0327 65 :LTEKGENYLKENGTWSKAYKTIKEIK 1jgsA 100 :LTTGGAAICEQCHQLVGQDLHQELTK Number of specific fragments extracted= 5 number of extra gaps= 0 total=143 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 1jgsA/T0327-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1jgsA/T0327-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0327-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgsA in template set T0327 4 :DKLRYAI 1jgsA 58 :VELKKVL T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1jgsA 65 :SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVL T0327 63 :PELTEKGENYLKENGTWSKA 1jgsA 98 :VKLTTGGAAICEQCHQLVGQ T0327 84 :KTIKEIK 1jgsA 118 :DLHQELT Number of specific fragments extracted= 4 number of extra gaps= 0 total=147 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 1yyvA/T0327-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yyvA expands to /projects/compbio/data/pdb/1yyv.pdb.gz 1yyvA:Skipped atom 310, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 312, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 314, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 316, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 318, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 320, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 322, because occupancy 0.490 <= existing 0.510 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms 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: CH1 for alphabet: pdb_atoms 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 637, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 639, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 641, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 643, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 645, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 647, because occupancy 0.460 <= existing 0.540 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms # T0327 read from 1yyvA/T0327-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0327-1yyvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yyvA to template set # found chain 1yyvA in template set Warning: unaligning (T0327)D25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 4 :DKLRYAILKEIFEGN 1yyvA 31 :SRWGVLILVALRDGT T0327 26 :IGVT 1yyvA 56 :GGVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 64 :ELTEKGENYL 1yyvA 91 :SLTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 6 number of extra gaps= 1 total=153 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 1yyvA/T0327-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1yyvA/T0327-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0327-1yyvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yyvA in template set Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 4 :DKLRYAILKEIFEGNTP 1yyvA 31 :SRWGVLILVALRDGTHR T0327 27 :GVT 1yyvA 57 :GVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 60 :K 1yyvA 91 :S T0327 65 :LTEKGENYL 1yyvA 92 :LTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 7 number of extra gaps= 1 total=160 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 1yyvA/T0327-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1yyvA/T0327-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yyvA read from 1yyvA/T0327-1yyvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yyvA in template set Warning: unaligning (T0327)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0327)Q32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0327)K74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0327)N76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0327 27 :GVT 1yyvA 57 :GVS T0327 33 :FDDAVNFLKREGY 1yyvA 63 :LAQSLQALEQDGF T0327 48 :GVHYSDDRPHLY 1yyvA 78 :RVSYPVVPPHVE T0327 63 :PELTEKGENYL 1yyvA 90 :YSLTPLGEQVS T0327 77 :GTWSKAYKTI 1yyvA 104 :AALADWIELN Number of specific fragments extracted= 5 number of extra gaps= 1 total=165 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 1hw1A/T0327-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hw1A expands to /projects/compbio/data/pdb/1hw1.pdb.gz 1hw1A:# T0327 read from 1hw1A/T0327-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0327-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hw1A to template set # found chain 1hw1A in template set T0327 4 :DKLRYAILKEIFEGNTP 1hw1A 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEND 1hw1A 31 :LPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1hw1A 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDDRP 1hw1A 64 :QHGKP T0327 59 :YKLG 1hw1A 69 :TKVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 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 1hw1A/T0327-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1hw1A/T0327-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0327-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set T0327 4 :DKLRYAILKEIFEGNTP 1hw1A 10 :GFAEEYIIESIWNNRFP T0327 21 :LSEN 1hw1A 31 :LPAE T0327 26 :IGVTEDQFDDAVNFLKREGYII 1hw1A 41 :IGVTRTTLREVLQRLARDGWLT T0327 51 :YSDDRPH 1hw1A 63 :IQHGKPT T0327 60 :KLG 1hw1A 70 :KVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 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 1hw1A/T0327-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1hw1A/T0327-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0327-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set T0327 3 :KDKLRYAILKEIFEGNTPLSEND 1hw1A 13 :EEYIIESIWNNRFPPGTILPAER T0327 26 :IGVTEDQFDDAVNFLKREGYIIG 1hw1A 41 :IGVTRTTLREVLQRLARDGWLTI T0327 52 :SDDRPH 1hw1A 64 :QHGKPT Number of specific fragments extracted= 3 number of extra gaps= 0 total=178 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 1mkmA/T0327-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0327 read from 1mkmA/T0327-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0327-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mkmA to template set # found chain 1mkmA in template set T0327 1 :MNKDKLRYAILKEIFEGNTPLSEN 1mkmA 1 :MNTLKKAFEILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYI 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFV T0327 50 :HYSDDRPHLY 1mkmA 51 :LRKKDKRYVP T0327 62 :GPELTEKGENYLKENGTWSKAYKTIKEIKD 1mkmA 61 :GYKLIEYGSFVLRRFNIRDIAHDHLVDIMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=182 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 1mkmA/T0327-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1mkmA/T0327-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0327-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkmA in template set T0327 1 :MNKDKLRYAILKEIFEGNTPLSEN 1mkmA 1 :MNTLKKAFEILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYI 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFV T0327 50 :HYSDDRPHL 1mkmA 51 :LRKKDKRYV T0327 61 :LGPELTEKGENYLKENGTWSKAYKTIKEIKDW 1mkmA 60 :PGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=186 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 1mkmA/T0327-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1mkmA/T0327-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0327-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkmA in template set T0327 10 :ILKEIFEGNTPLSEN 1mkmA 10 :ILDFIVKNPGDVSVS T0327 25 :DIGVTEDQFDDAVNFLKREGYIIG 1mkmA 29 :KFNMSVSNAYKYMVVLEEKGFVLR T0327 52 :SDDRP 1mkmA 53 :KKDKR T0327 59 :YKLGPELTEKGENYLKENGTWSKAYKTIKEIKD 1mkmA 58 :YVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=190 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 2fbhA/T0327-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0327 read from 2fbhA/T0327-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0327-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0327)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0327)R7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 4 :DK 2fbhA 34 :SQ T0327 8 :YAILKEIFEGNTPLSEND 2fbhA 38 :WLVLLHLARHRDSPTQRE T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDR 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDR T0327 56 :PHLY 2fbhA 92 :KHIV T0327 65 :LTEKGENYLKENGTWSKAYKT 2fbhA 96 :LTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 5 number of extra gaps= 2 total=195 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 2fbhA/T0327-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fbhA/T0327-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0327-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbhA in template set Warning: unaligning (T0327)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0327)R7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 5 :K 2fbhA 35 :Q T0327 8 :YAILKEIFEGNTPLSEND 2fbhA 38 :WLVLLHLARHRDSPTQRE T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDD 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAED T0327 55 :RPHLY 2fbhA 91 :AKHIV T0327 65 :LTEKGENYLKENGTWSKAYKT 2fbhA 96 :LTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 5 number of extra gaps= 2 total=200 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 2fbhA/T0327-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2fbhA/T0327-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0327-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbhA in template set Warning: unaligning (T0327)I26 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0327)G27 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0327 28 :VTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKH T0327 63 :PELTEKGENYLKENGTWSKAYKT 2fbhA 94 :IVLTPKADVLIADIEAIAASVRN Number of specific fragments extracted= 2 number of extra gaps= 1 total=202 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 1p4xA/T0327-1p4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p4xA expands to /projects/compbio/data/pdb/1p4x.pdb.gz 1p4xA:# T0327 read from 1p4xA/T0327-1p4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4xA read from 1p4xA/T0327-1p4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p4xA to template set # found chain 1p4xA in template set T0327 5 :KLRYAILKEIFEGNTP 1p4xA 158 :FVEFTILAIITSQNKN T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSD 1p4xA 182 :ETIHHKYPQTVRALNNLKKQGYLIKERSTE T0327 54 :DRPHLYKLGP 1p4xA 213 :ERKILIHMDD T0327 77 :GTWSKAYKTIKEIKDWIKLEHHHH 1p4xA 223 :AQQDHAEQLLAQVNQLLADKDHLH Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 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 1p4xA/T0327-1p4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1p4xA/T0327-1p4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4xA read from 1p4xA/T0327-1p4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p4xA in template set T0327 5 :KLRYAILKEIFEGN 1p4xA 158 :FVEFTILAIITSQN T0327 19 :TP 1p4xA 173 :NI T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 1p4xA 184 :IHHKYPQTVRALNNLKKQGYLIKERSTEDERKIL T0327 60 :KLGP 1p4xA 219 :HMDD T0327 77 :GTWSKAYKTIKEIKDWIKLEHHHH 1p4xA 223 :AQQDHAEQLLAQVNQLLADKDHLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=211 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 1p4xA/T0327-1p4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 1p4xA/T0327-1p4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p4xA read from 1p4xA/T0327-1p4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p4xA in template set T0327 26 :IGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKL 1p4xA 184 :IHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIH T0327 65 :LTEKGEN 1p4xA 220 :MDDAQQD T0327 81 :KAYKTIKEIKDW 1p4xA 227 :HAEQLLAQVNQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=214 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 3rubS/T0327-3rubS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3rubS expands to /projects/compbio/data/pdb/3rub.pdb.gz 3rubS:# T0327 read from 3rubS/T0327-3rubS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rubS read from 3rubS/T0327-3rubS-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3rubS to template set # found chain 3rubS in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHY 3rubS 16 :SYLPDLSQEQLLSEVEYLLKNGWVPCLEF T0327 52 :SD 3rubS 58 :SP T0327 54 :DRPHLYKLGPEL 3rubS 63 :DGRYWTMWKLPM T0327 75 :ENGTWSKAYKTIKEIKDW 3rubS 76 :GCTDATQVLAEVEEAKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 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 3rubS/T0327-3rubS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 3rubS/T0327-3rubS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rubS read from 3rubS/T0327-3rubS-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3rubS in template set T0327 20 :PLSENDI 3rubS 6 :PINKKKY T0327 27 :GVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 3rubS 20 :DLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVY T0327 60 :KLGPELTEK 3rubS 56 :NKSPGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDW 3rubS 74 :MFGCTDATQVLAEVEEAKKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=222 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 3rubS/T0327-3rubS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 3rubS/T0327-3rubS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3rubS read from 3rubS/T0327-3rubS-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3rubS in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 3rubS 17 :YLPDLSQEQLLSEVEYLLKNGWVPCLEFETEHGFVYREN T0327 66 :TEKGENYLKENGTWSKA 3rubS 77 :CTDATQVLAEVEEAKKA Number of specific fragments extracted= 2 number of extra gaps= 0 total=224 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 8rucI/T0327-8rucI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 8rucI expands to /projects/compbio/data/pdb/8ruc.pdb.gz 8rucI:# T0327 read from 8rucI/T0327-8rucI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8rucI read from 8rucI/T0327-8rucI-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 8rucI to template set # found chain 8rucI in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 8rucI 16 :SYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREH T0327 63 :PELTEK 8rucI 59 :PGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDW 8rucI 74 :MFGCTDPAQVLNELEECKKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=227 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 8rucI/T0327-8rucI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 8rucI/T0327-8rucI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8rucI read from 8rucI/T0327-8rucI-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 8rucI in template set T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLY 8rucI 17 :YLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVY T0327 60 :KLGPELTEK 8rucI 56 :HNSPGYYDG T0327 73 :LKENGTWSKAYKTIKEIKDWI 8rucI 74 :MFGCTDPAQVLNELEECKKEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=230 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 8rucI/T0327-8rucI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 8rucI/T0327-8rucI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 8rucI read from 8rucI/T0327-8rucI-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 8rucI in template set T0327 23 :ENDIGVTEDQFDDAVNFLKREGYIIGVHYSDDRPHLYKLG 8rucI 16 :SYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREH T0327 63 :PELTEKGENYLKENG 8rucI 77 :CTDPAQVLNELEECK Number of specific fragments extracted= 2 number of extra gaps= 0 total=232 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 2cg4A/T0327-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cg4A expands to /projects/compbio/data/pdb/2cg4.pdb.gz 2cg4A:# T0327 read from 2cg4A/T0327-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0327-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cg4A to template set # found chain 2cg4A in template set Warning: unaligning (T0327)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 T0327 4 :DKLRYAILKEIFEGNTP 2cg4A 7 :DNLDRGILEALMGNART T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 30 :KQFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SD 2cg4A 60 :SP T0327 54 :DRPHLY 2cg4A 65 :GYDVGC T0327 60 :KL 2cg4A 75 :IL T0327 62 :GPELTEKGENYLKENG 2cg4A 78 :SAKDYPSALAKLESLD Number of specific fragments extracted= 6 number of extra gaps= 1 total=238 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 2cg4A/T0327-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2cg4A/T0327-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0327-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cg4A in template set Warning: unaligning (T0327)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cg4A)I6 T0327 4 :DKLRYAILKEIF 2cg4A 7 :DNLDRGILEALM T0327 16 :EGNTP 2cg4A 20 :NARTA T0327 25 :DIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 31 :QFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SD 2cg4A 60 :SP T0327 54 :DRPHLY 2cg4A 65 :GYDVGC T0327 60 :KLG 2cg4A 75 :ILK T0327 63 :PELTEKGENYLKENG 2cg4A 79 :AKDYPSALAKLESLD Number of specific fragments extracted= 7 number of extra gaps= 1 total=245 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 2cg4A/T0327-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2cg4A/T0327-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0327-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cg4A in template set T0327 4 :DKLRYAILKEIFEGNTP 2cg4A 8 :NLDRGILEALMGNARTA T0327 24 :NDIGVTEDQFDDAVNFLKREGYIIGVHY 2cg4A 30 :KQFGVSPETIHVRVEKMKQAGIITGARI T0327 52 :SDDRPH 2cg4A 63 :QLGYDV T0327 58 :LYKLGPELTEKGENYLKE 2cg4A 74 :IILKSAKDYPSALAKLES Number of specific fragments extracted= 4 number of extra gaps= 0 total=249 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 2b0lA/T0327-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0327 read from 2b0lA/T0327-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0327-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0327)E16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0327)G17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 6 :LRYAILKEIF 2b0lA 182 :SELEAIEHIF T0327 18 :NTP 2b0lA 194 :LDG T0327 24 :NDIGVTEDQFD 2b0lA 208 :DRVGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DRPHLYKL 2b0lA 238 :KGTYIKVL T0327 66 :TE 2b0lA 246 :NN T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 8 number of extra gaps= 4 total=257 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/T0327-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2b0lA/T0327-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0327-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0lA in template set Warning: unaligning (T0327)E16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0327)G17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 5 :KLRYAILKEIF 2b0lA 181 :YSELEAIEHIF T0327 18 :NTP 2b0lA 194 :LDG T0327 26 :IGVTEDQFD 2b0lA 210 :VGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DR 2b0lA 238 :KG T0327 57 :HLYKLG 2b0lA 240 :TYIKVL T0327 66 :TE 2b0lA 246 :NN T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 9 number of extra gaps= 4 total=266 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/T0327-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0327 read from 2b0lA/T0327-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0327-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0lA in template set Warning: unaligning (T0327)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0327)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0327)I46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0327)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0327)V49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0327)H50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0327)Y51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0327)S52 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0327)D53 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 T0327 26 :IGVTEDQFD 2b0lA 210 :VGITRSVIV T0327 37 :VNFLKREGY 2b0lA 221 :LRKLESAGV T0327 48 :G 2b0lA 232 :S T0327 54 :DRPHLYKLG 2b0lA 238 :KGTYIKVLN T0327 67 :E 2b0lA 247 :N T0327 84 :KTIKEIK 2b0lA 248 :KFLIELE Number of specific fragments extracted= 6 number of extra gaps= 3 total=272 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 14.301 sec, elapsed time= 15.722 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 5151 constraints to all_contacts Done adding distance constraints # command:CPU_time= 14.324 sec, elapsed time= 15.747 sec. # command:Reading probabilities from T0327.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 23.210 Optimizing... Probability sum: -174.358, CN propb: -174.358 weights: 0.253 constraints: 146 # command:CPU_time= 15.816 sec, elapsed time= 17.292 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 146 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 146 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 338 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 338 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 3887 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 3887 # command:CPU_time= 15.894 sec, elapsed time= 17.470 sec. # command: