# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0523 numbered 1 through 120 Created new target T0523 from T0523.a2m # command:CPU_time= 5.977 sec, elapsed time= 6.681 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lyxA/T0523-3lyxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lyxA expands to /projects/compbio/data/pdb/3lyx.pdb.gz 3lyxA:# T0523 read from 3lyxA/T0523-3lyxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lyxA read from 3lyxA/T0523-3lyxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lyxA to template set # found chain 3lyxA in template set Warning: unaligning (T0523)T116 because last residue in template chain is (3lyxA)R121 T0523 2 :AIDYKTAFHLAPIGLVLSR 3lyxA 6 :LKQRAKAFDYVFDAIVVTD # choosing archetypes in rotamer library T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3lyxA 26 :QGFIIDWNKGSETLYGYSKEQAIGQPVNML T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3lyxA 56 :HVPGDTEHITSEVISAVENQGKWTGEIRMLHKDGHIGWIESMCVPI T0523 98 :DRTAPLAAGVWTFEDLSA 3lyxA 103 :GENYQMVGALGINRDITK 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 3lyxA/T0523-3lyxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3lyxA/T0523-3lyxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lyxA read from 3lyxA/T0523-3lyxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lyxA in template set Warning: unaligning (T0523)T116 because last residue in template chain is (3lyxA)R121 T0523 1 :PAIDYKTAFHLAPIGLVLSR 3lyxA 5 :ILKQRAKAFDYVFDAIVVTD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 3lyxA 26 :QGFIIDWNKGSETLYGYSKEQAIGQPVNMLHVP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3lyxA 59 :GDTEHITSEVISAVENQGKWTGEIRMLHKDGHIGWIESMCVPI T0523 98 :DRTAPLAAGVWTFEDLSA 3lyxA 103 :GENYQMVGALGINRDITK 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 3lyxA/T0523-3lyxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3lyxA/T0523-3lyxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lyxA read from 3lyxA/T0523-3lyxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lyxA in template set Warning: unaligning (T0523)T116 because last residue in template chain is (3lyxA)R121 T0523 1 :PAIDYKTAFHLAPIGLVLSR 3lyxA 5 :ILKQRAKAFDYVFDAIVVTD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3lyxA 26 :QGFIIDWNKGSETLYGYSKEQAIGQPVNMLH T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3lyxA 57 :VPGDTEHITSEVISAVENQGKWTGEIRMLHKDGHIGWIESMCVPI T0523 98 :DRTAPLAAGVWTFEDLSA 3lyxA 103 :GENYQMVGALGINRDITK Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 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 2z6cA/T0523-2z6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2z6cA expands to /projects/compbio/data/pdb/2z6c.pdb.gz 2z6cA:# T0523 read from 2z6cA/T0523-2z6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z6cA read from 2z6cA/T0523-2z6cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2z6cA to template set # found chain 2z6cA in template set Warning: unaligning (T0523)A83 because of BadResidue code BAD_PEPTIDE in next template residue (2z6cA)D270 Warning: unaligning (T0523)G84 because of BadResidue code BAD_PEPTIDE at template residue (2z6cA)D270 Warning: unaligning (T0523)R117 because last residue in template chain is (2z6cA)T304 T0523 2 :AIDYKTAFHLAPIGLVLSR 2z6cA 185 :SEDLKDALSTFQQTFVVSD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2z6cA 208 :DYPIMYASAGFFNMTGYTSKEVVGRNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKR 2z6cA 238 :QGSGTDADELAKIRETLAAGNNYCGRILNYK T0523 85 :GELFWCHVTGRAL 2z6cA 271 :GTSFWNLLTIAPI T0523 98 :DRTAPLAAGVWTFEDLSAT 2z6cA 285 :DESGKVLKFIGMQVEVSKH Number of specific fragments extracted= 5 number of extra gaps= 1 total=17 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 2z6cA/T0523-2z6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2z6cA/T0523-2z6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z6cA read from 2z6cA/T0523-2z6cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2z6cA in template set Warning: unaligning (T0523)A83 because of BadResidue code BAD_PEPTIDE in next template residue (2z6cA)D270 Warning: unaligning (T0523)G84 because of BadResidue code BAD_PEPTIDE at template residue (2z6cA)D270 T0523 2 :AIDYKTAFHLAPIGLVLSR 2z6cA 185 :SEDLKDALSTFQQTFVVSD T0523 21 :DR 2z6cA 205 :TK T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVLYPS 2z6cA 210 :PIMYASAGFFNMTGYTSKEVVGRNCRFLQGS T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKR 2z6cA 241 :GTDADELAKIRETLAAGNNYCGRILNYK T0523 85 :GELFWCHVTGRAL 2z6cA 271 :GTSFWNLLTIAPI T0523 98 :DRTAPLAAGVWTFEDLSAT 2z6cA 285 :DESGKVLKFIGMQVEVSKH Number of specific fragments extracted= 6 number of extra gaps= 1 total=23 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 2z6cA/T0523-2z6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2z6cA/T0523-2z6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2z6cA read from 2z6cA/T0523-2z6cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2z6cA in template set Warning: unaligning (T0523)A83 because of BadResidue code BAD_PEPTIDE in next template residue (2z6cA)D270 Warning: unaligning (T0523)G84 because of BadResidue code BAD_PEPTIDE at template residue (2z6cA)D270 T0523 12 :APIGLVLSR 2z6cA 198 :TFVVSDATK T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYP 2z6cA 208 :DYPIMYASAGFFNMTGYTSKEVVGRNCRFLQG T0523 54 :SDEFERIGERISPVMIAHGSYADDRIMKR 2z6cA 240 :SGTDADELAKIRETLAAGNNYCGRILNYK T0523 85 :GELFWCHVTGRAL 2z6cA 271 :GTSFWNLLTIAPI T0523 98 :DRTAPLAAGVWTFEDLSAT 2z6cA 285 :DESGKVLKFIGMQVEVSKH Number of specific fragments extracted= 5 number of extra gaps= 1 total=28 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 2gj3A/T0523-2gj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2gj3A/T0523-2gj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gj3A read from 2gj3A/T0523-2gj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gj3A in training set Warning: unaligning (T0523)L103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2gj3A)I127 Warning: unaligning (T0523)A104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2gj3A)I127 Warning: unaligning (T0523)R117 because last residue in template chain is (2gj3A)H140 T0523 1 :PAIDYKTAFHLAPIGLVLSR 2gj3A 23 :LPEIFRQTVEHAPIAISITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2gj3A 44 :KANILYANRAFRTITGYGSEEVLGKNESIL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2gj3A 74 :SNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPV T0523 98 :DRTAP 2gj3A 121 :NEAGE T0523 105 :AGVWTFEDLSAT 2gj3A 128 :YYLGMHRDTSEL Number of specific fragments extracted= 5 number of extra gaps= 1 total=33 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 2gj3A/T0523-2gj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2gj3A/T0523-2gj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gj3A read from 2gj3A/T0523-2gj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gj3A in training set Warning: unaligning (T0523)L103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2gj3A)I127 Warning: unaligning (T0523)A104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2gj3A)I127 Warning: unaligning (T0523)R117 because last residue in template chain is (2gj3A)H140 T0523 1 :PAIDYKTAFHLAPIGLVLSR 2gj3A 23 :LPEIFRQTVEHAPIAISITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 2gj3A 44 :KANILYANRAFRTITGYGSEEVLGKNESILSNG T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2gj3A 77 :TTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPV T0523 98 :DRTAP 2gj3A 121 :NEAGE T0523 105 :AGVWTFEDLSAT 2gj3A 128 :YYLGMHRDTSEL Number of specific fragments extracted= 5 number of extra gaps= 1 total=38 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 2gj3A/T0523-2gj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2gj3A/T0523-2gj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gj3A read from 2gj3A/T0523-2gj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gj3A in training set Warning: unaligning (T0523)L103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2gj3A)I127 Warning: unaligning (T0523)A104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2gj3A)I127 T0523 1 :PAIDYKTAFHLAPIGLVLSR 2gj3A 23 :LPEIFRQTVEHAPIAISITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDE 2gj3A 44 :KANILYANRAFRTITGYGSEEVLGKNESILSNGTTP T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2gj3A 80 :RLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPV T0523 98 :DRTAP 2gj3A 121 :NEAGE T0523 105 :AGVWTFEDLSAT 2gj3A 128 :YYLGMHRDTSEL Number of specific fragments extracted= 5 number of extra gaps= 1 total=43 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 2v0uA/T0523-2v0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2v0uA expands to /projects/compbio/data/pdb/2v0u.pdb.gz 2v0uA:Skipped atom 181, because occupancy 0.5 <= existing 0.500 in 2v0uA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 196, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 197, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 198, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 199, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 200, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 201, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 202, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 427, because occupancy 0.100 <= existing 0.900 in 2v0uA Skipped atom 428, because occupancy 0.100 <= existing 0.900 in 2v0uA Skipped atom 429, because occupancy 0.100 <= existing 0.900 in 2v0uA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2v0uA Skipped atom 858, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 859, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 861, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 862, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1070, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1071, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1072, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1073, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1074, because occupancy 0.400 <= existing 0.600 in 2v0uA Skipped atom 1075, because occupancy 0.400 <= existing 0.600 in 2v0uA # T0523 read from 2v0uA/T0523-2v0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v0uA read from 2v0uA/T0523-2v0uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2v0uA to template set # found chain 2v0uA in template set Warning: unaligning (T0523)D21 because of BadResidue code BAD_PEPTIDE at template residue (2v0uA)D424 T0523 11 :LAPIGLVLSR 2v0uA 410 :RIEKNFVITD T0523 22 :RVIEDCNDELAAIFRCARADLIGRSFEVL 2v0uA 425 :NPIIFASDSFLQLTEYSREEILGRNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2v0uA 454 :QGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRR 2v0uA 501 :DQKGDVQYFIGVQLDGTEHVR Number of specific fragments extracted= 4 number of extra gaps= 1 total=47 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 2v0uA/T0523-2v0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2v0uA/T0523-2v0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v0uA read from 2v0uA/T0523-2v0uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v0uA in template set Warning: unaligning (T0523)R22 because of BadResidue code BAD_PEPTIDE in next template residue (2v0uA)P423 T0523 11 :LAPIGLVLSR 2v0uA 410 :RIEKNFVITD T0523 21 :D 2v0uA 421 :R T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVLYPS 2v0uA 426 :PIIFASDSFLQLTEYSREEILGRNCRFLQGP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2v0uA 457 :ETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRR 2v0uA 501 :DQKGDVQYFIGVQLDGTEHVR Number of specific fragments extracted= 5 number of extra gaps= 1 total=52 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 2v0uA/T0523-2v0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2v0uA/T0523-2v0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v0uA read from 2v0uA/T0523-2v0uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v0uA in template set Warning: unaligning (T0523)D21 because of BadResidue code BAD_PEPTIDE at template residue (2v0uA)D424 T0523 12 :APIGLVLSR 2v0uA 411 :IEKNFVITD T0523 22 :RVIEDCNDELAAIFRCARADLIGRSFEVLYP 2v0uA 425 :NPIIFASDSFLQLTEYSREEILGRNCRFLQG T0523 54 :SDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2v0uA 456 :PETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRVA 2v0uA 501 :DQKGDVQYFIGVQLDGTEHVRDA Number of specific fragments extracted= 4 number of extra gaps= 1 total=56 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 3f1pA/T0523-3f1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3f1pA expands to /projects/compbio/data/pdb/3f1p.pdb.gz 3f1pA:Skipped atom 687, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 689, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 691, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 693, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 695, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 697, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 699, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 701, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 703, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 909, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 910, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 912, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 913, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 915, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 916, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 918, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 919, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 921, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 922, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 924, because occupancy 0.200 <= existing 0.530 in 3f1pA Skipped atom 925, because occupancy 0.270 <= existing 0.530 in 3f1pA Skipped atom 1064, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1066, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1068, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1070, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1072, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1074, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1076, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1078, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1080, because occupancy 0.490 <= existing 0.510 in 3f1pA Skipped atom 1115, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1117, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1119, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1121, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1123, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1125, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1127, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1147, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1149, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1151, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1153, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1155, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1157, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1169, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1171, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1173, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1175, because occupancy 0.330 <= existing 0.670 in 3f1pA Skipped atom 1363, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1365, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1367, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1369, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1371, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1373, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1375, because occupancy 0.460 <= existing 0.540 in 3f1pA Skipped atom 1851, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1853, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1855, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1859, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1861, because occupancy 0.500 <= existing 0.500 in 3f1pA Skipped atom 1863, because occupancy 0.500 <= existing 0.500 in 3f1pA # T0523 read from 3f1pA/T0523-3f1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pA read from 3f1pA/T0523-3f1pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f1pA to template set # found chain 3f1pA in template set Warning: unaligning (T0523)C90 because of BadResidue code BAD_PEPTIDE in next template residue (3f1pA)E320 Warning: unaligning (T0523)H91 because of BadResidue code BAD_PEPTIDE at template residue (3f1pA)E320 Warning: unaligning (T0523)R118 because last residue in template chain is (3f1pA)K349 T0523 14 :IGLVLSR 3f1pA 243 :TFLSEHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3f1pA 251 :DMKFTYCDDRITELIGYHPEELLGRSAYEF T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFW 3f1pA 281 :YHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW T0523 92 :VTGRAL 3f1pA 321 :TQGTVI T0523 98 :DRTAPLAAGVWTFEDLSATR 3f1pA 329 :PRNLQPQCIMCVNYVLSEIE Number of specific fragments extracted= 5 number of extra gaps= 1 total=61 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 3f1pA/T0523-3f1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3f1pA/T0523-3f1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pA read from 3f1pA/T0523-3f1pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f1pA in template set Warning: unaligning (T0523)C90 because of BadResidue code BAD_PEPTIDE in next template residue (3f1pA)E320 Warning: unaligning (T0523)H91 because of BadResidue code BAD_PEPTIDE at template residue (3f1pA)E320 T0523 13 :PIGLVLSR 3f1pA 242 :KTFLSEHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 3f1pA 251 :DMKFTYCDDRITELIGYHPEELLGRSAYEFYHA T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFW 3f1pA 284 :LDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW T0523 92 :VTGRAL 3f1pA 321 :TQGTVI T0523 98 :DRTAPLAAGVWTFEDLSAT 3f1pA 329 :PRNLQPQCIMCVNYVLSEI Number of specific fragments extracted= 5 number of extra gaps= 1 total=66 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 3f1pA/T0523-3f1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3f1pA/T0523-3f1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pA read from 3f1pA/T0523-3f1pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f1pA in template set Warning: unaligning (T0523)C90 because of BadResidue code BAD_PEPTIDE in next template residue (3f1pA)E320 Warning: unaligning (T0523)H91 because of BadResidue code BAD_PEPTIDE at template residue (3f1pA)E320 T0523 13 :PIGLVLSR 3f1pA 242 :KTFLSEHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3f1pA 251 :DMKFTYCDDRITELIGYHPEELLGRSAYEFY T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFW 3f1pA 282 :HALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVW T0523 92 :VTGRAL 3f1pA 321 :TQGTVI T0523 98 :DRTAPLAAGVWTFEDLSATR 3f1pA 329 :PRNLQPQCIMCVNYVLSEIE Number of specific fragments extracted= 5 number of extra gaps= 1 total=71 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 3ewkA/T0523-3ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ewkA expands to /projects/compbio/data/pdb/3ewk.pdb.gz 3ewkA:# T0523 read from 3ewkA/T0523-3ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ewkA read from 3ewkA/T0523-3ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ewkA to template set # found chain 3ewkA in template set Warning: unaligning (T0523)D26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)A112 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A112 Warning: unaligning (T0523)D98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)D183 Warning: unaligning (T0523)R99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)N184 Warning: unaligning (T0523)F110 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)R196 Warning: unaligning (T0523)E111 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)R196 Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)T199 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)T199 Warning: unaligning (T0523)A115 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A200 T0523 17 :VLSR 3ewkA 101 :SITD T0523 21 :DRVIE 3ewkA 106 :QGRIL T0523 28 :NDELAAIFRCARADLIGRSFEVL 3ewkA 113 :NDNFCAVSRYGREELVGQDHRIV T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3ewkA 136 :NSGYHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDSTIVPL T0523 100 :TAPLAAGVWT 3ewkA 185 :AGKPRQYISI T0523 112 :D 3ewkA 197 :D T0523 116 :TRR 3ewkA 201 :QKE Number of specific fragments extracted= 7 number of extra gaps= 4 total=78 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 3ewkA/T0523-3ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3ewkA/T0523-3ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ewkA read from 3ewkA/T0523-3ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ewkA in template set Warning: unaligning (T0523)D26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)A112 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A112 Warning: unaligning (T0523)D98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)D183 Warning: unaligning (T0523)R99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)N184 Warning: unaligning (T0523)F110 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)R196 Warning: unaligning (T0523)E111 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)R196 Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)T199 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)T199 Warning: unaligning (T0523)A115 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A200 T0523 17 :VLSR 3ewkA 101 :SITD T0523 21 :DRVIE 3ewkA 106 :QGRIL T0523 28 :NDELAAIFRCARADLIGRSFEVLYPS 3ewkA 113 :NDNFCAVSRYGREELVGQDHRIVNSG T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3ewkA 139 :YHGKAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDSTIVPL T0523 100 :TAPLAAGVWT 3ewkA 185 :AGKPRQYISI T0523 112 :D 3ewkA 197 :D T0523 116 :TRRV 3ewkA 201 :QKEA Number of specific fragments extracted= 7 number of extra gaps= 4 total=85 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 3ewkA/T0523-3ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3ewkA/T0523-3ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ewkA read from 3ewkA/T0523-3ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ewkA in template set Warning: unaligning (T0523)D26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)A112 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A112 Warning: unaligning (T0523)D98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)D183 Warning: unaligning (T0523)R99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)N184 Warning: unaligning (T0523)F110 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)R196 Warning: unaligning (T0523)E111 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)R196 Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ewkA)T199 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)T199 Warning: unaligning (T0523)A115 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ewkA)A200 T0523 16 :LVLSR 3ewkA 100 :VSITD T0523 21 :DRVIE 3ewkA 106 :QGRIL T0523 28 :NDELAAIFRCARADLIGRSFEVLYPSSDE 3ewkA 113 :NDNFCAVSRYGREELVGQDHRIVNSGYHG T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3ewkA 142 :KAYIRDMWRTISRGNIWQGEFCNRRKDGTRYWVDSTIVPL T0523 100 :TAPLAAGVWT 3ewkA 185 :AGKPRQYISI T0523 112 :D 3ewkA 197 :D T0523 116 :TRRVA 3ewkA 201 :QKEAE Number of specific fragments extracted= 7 number of extra gaps= 4 total=92 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 1x0oA/T0523-1x0oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x0oA expands to /projects/compbio/data/pdb/1x0o.pdb.gz 1x0oA:# T0523 read from 1x0oA/T0523-1x0oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x0oA read from 1x0oA/T0523-1x0oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x0oA to template set # found chain 1x0oA in template set T0523 13 :PIGLVLSR 1x0oA 10 :TEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1x0oA 19 :EGIFTFVDHRCVATVGYQPQELLGKNIVEF T0523 52 :PSSDEFERIGERISPVMIAH 1x0oA 49 :CHPEDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 1x0oA 70 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAPLAAGVWTFEDL 1x0oA 98 :PYSDEIEYIICTNTNV Number of specific fragments extracted= 5 number of extra gaps= 0 total=97 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 1x0oA/T0523-1x0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1x0oA/T0523-1x0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x0oA read from 1x0oA/T0523-1x0oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x0oA in template set T0523 13 :PIGLVLSR 1x0oA 10 :TEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1x0oA 19 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFCHP T0523 55 :DEFERIGERISPVMIAH 1x0oA 52 :EDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 1x0oA 70 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAPLAAGVWTFEDL 1x0oA 98 :PYSDEIEYIICTNTNV Number of specific fragments extracted= 5 number of extra gaps= 0 total=102 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 1x0oA/T0523-1x0oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1x0oA/T0523-1x0oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x0oA read from 1x0oA/T0523-1x0oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x0oA in template set T0523 13 :PIGLVLSR 1x0oA 10 :TEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 1x0oA 19 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFC T0523 53 :SSDEFERIGERISPVMIAH 1x0oA 50 :HPEDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 1x0oA 70 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAPLAAGVWTFEDLSAT 1x0oA 98 :PYSDEIEYIICTNTNVKNS Number of specific fragments extracted= 5 number of extra gaps= 0 total=107 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 1n9lA/T0523-1n9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n9lA expands to /projects/compbio/data/pdb/1n9l.pdb.gz 1n9lA:Skipped atom 308, because occupancy 0.300 <= existing 0.700 in 1n9lA Skipped atom 512, because occupancy 0.400 <= existing 0.600 in 1n9lA # T0523 read from 1n9lA/T0523-1n9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n9lA read from 1n9lA/T0523-1n9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n9lA to template set # found chain 1n9lA in template set Warning: unaligning (T0523)A115 because last residue in template chain is (1n9lA)S125 T0523 13 :PIGLVLSR 1n9lA 19 :RHTFVVAD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1n9lA 31 :DCPLVYASEGFYAMTGYGPDEVLGHNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1n9lA 61 :QGEGTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPI T0523 98 :DRTAPLAAGVWTFEDLS 1n9lA 108 :TPDGRVSKFVGVQVDVT Number of specific fragments extracted= 4 number of extra gaps= 0 total=111 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 1n9lA/T0523-1n9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1n9lA/T0523-1n9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n9lA read from 1n9lA/T0523-1n9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n9lA in template set Warning: unaligning (T0523)A115 because last residue in template chain is (1n9lA)S125 T0523 15 :GLVLSR 1n9lA 21 :TFVVAD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1n9lA 31 :DCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGE T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1n9lA 64 :GTDPKEVQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPI T0523 98 :DRTAPLAAGVWTFEDLS 1n9lA 108 :TPDGRVSKFVGVQVDVT Number of specific fragments extracted= 4 number of extra gaps= 0 total=115 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 1n9lA/T0523-1n9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1n9lA/T0523-1n9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n9lA read from 1n9lA/T0523-1n9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n9lA in template set T0523 12 :APIGLVLSR 1n9lA 21 :TFVVADATL T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDE 1n9lA 31 :DCPLVYASEGFYAMTGYGPDEVLGHNCRFLQGEGTD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1n9lA 67 :PKEVQKIRDAIKKGEACSVRLLNYRKDGTPFWNLLTVTPI T0523 98 :DRTAPLAAGVWTFEDLS 1n9lA 108 :TPDGRVSKFVGVQVDVT Number of specific fragments extracted= 4 number of extra gaps= 0 total=119 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 1ew0A/T0523-1ew0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ew0A expands to /projects/compbio/data/pdb/1ew0.pdb.gz 1ew0A:# T0523 read from 1ew0A/T0523-1ew0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ew0A read from 1ew0A/T0523-1ew0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ew0A to template set # found chain 1ew0A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (1ew0A)T251 T0523 3 :IDYKTAFHLAPIGLVLSR 1ew0A 137 :AHLRSILDTVPDATVVSA T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1ew0A 156 :DGTIVSFNAAAVRQFGYAEEEVIGQNLRIL T0523 52 :PSSDEFERIGERISPVMIAHGSY 1ew0A 186 :MPEPYRHEHDGYLQRYMATGEKR T0523 75 :ADDRIMKRAGGELFWCHVTGRAL 1ew0A 213 :DRVVSGQRKDGSTFPMKLAVGEM T0523 98 :DRTAP 1ew0A 237 :SGGER T0523 105 :AGVWTFEDL 1ew0A 242 :FFTGFIRDL Number of specific fragments extracted= 6 number of extra gaps= 0 total=125 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 1ew0A/T0523-1ew0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1ew0A/T0523-1ew0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ew0A read from 1ew0A/T0523-1ew0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ew0A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (1ew0A)T251 T0523 2 :AIDYKTAFHLAPIGLVLSR 1ew0A 136 :DAHLRSILDTVPDATVVSA T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1ew0A 156 :DGTIVSFNAAAVRQFGYAEEEVIGQNLRILMPE T0523 55 :DEFERIGERISPVMIAHGS 1ew0A 189 :PYRHEHDGYLQRYMATGEK T0523 74 :YADDRIMKRAGGELFWCHVTGRAL 1ew0A 212 :IDRVVSGQRKDGSTFPMKLAVGEM T0523 98 :DRTAPL 1ew0A 237 :SGGERF T0523 106 :GVWTFEDL 1ew0A 243 :FTGFIRDL Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 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 1ew0A/T0523-1ew0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1ew0A/T0523-1ew0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ew0A read from 1ew0A/T0523-1ew0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ew0A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (1ew0A)T251 T0523 5 :YKTAFHLAPIGLVLSR 1ew0A 139 :LRSILDTVPDATVVSA T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 1ew0A 156 :DGTIVSFNAAAVRQFGYAEEEVIGQNLRILM T0523 53 :SSDEFERIGERISPVMIAHGSY 1ew0A 187 :PEPYRHEHDGYLQRYMATGEKR T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAP 1ew0A 213 :DRVVSGQRKDGSTFPMKLAVGEMRSGGE T0523 104 :AAGVWTFEDL 1ew0A 241 :RFFTGFIRDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=136 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 3luqA/T0523-3luqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3luqA expands to /projects/compbio/data/pdb/3luq.pdb.gz 3luqA: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 # T0523 read from 3luqA/T0523-3luqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luqA read from 3luqA/T0523-3luqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3luqA to template set # found chain 3luqA in template set Warning: unaligning (T0523)R82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3luqA)G170 Warning: unaligning (T0523)G85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3luqA)G170 Warning: unaligning (T0523)S114 because last residue in template chain is (3luqA)T200 T0523 2 :AIDYKTAFHLAPIGLVLSR 3luqA 88 :DERLRLFTEHAPAALAMFD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3luqA 108 :EMRYLAVSRRWREDYGLGDGDILGMSHYDI T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMK 3luqA 138 :FPEIGEEWKSVHRRGLAGEVIRVEEDCFV T0523 86 :ELFWCHVTGRAL 3luqA 171 :RTQWLRWEVRPW T0523 98 :DRTAPLAAGVWTFEDL 3luqA 184 :EGEGRVGGVVIFTEDI Number of specific fragments extracted= 5 number of extra gaps= 0 total=141 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 3luqA/T0523-3luqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3luqA/T0523-3luqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luqA read from 3luqA/T0523-3luqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3luqA in template set Warning: unaligning (T0523)R82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3luqA)G170 Warning: unaligning (T0523)G85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3luqA)G170 Warning: unaligning (T0523)S114 because last residue in template chain is (3luqA)T200 T0523 1 :PAIDYKTAFHLAPIGLVLSR 3luqA 87 :SDERLRLFTEHAPAALAMFD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3luqA 108 :EMRYLAVSRRWREDYGLGDGDILGMSHYDIF T0523 53 :S 3luqA 139 :P T0523 55 :DEFERIGERISPVMIAH 3luqA 140 :EIGEEWKSVHRRGLAGE T0523 73 :SYADD 3luqA 157 :VIRVE T0523 78 :RIMK 3luqA 163 :DCFV T0523 86 :ELFWCHVTGRAL 3luqA 171 :RTQWLRWEVRPW T0523 98 :DRTAPLAAGVWTFEDL 3luqA 184 :EGEGRVGGVVIFTEDI Number of specific fragments extracted= 8 number of extra gaps= 0 total=149 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 3luqA/T0523-3luqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3luqA/T0523-3luqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3luqA read from 3luqA/T0523-3luqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3luqA in template set Warning: unaligning (T0523)R82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3luqA)G170 Warning: unaligning (T0523)G85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3luqA)G170 Warning: unaligning (T0523)S114 because last residue in template chain is (3luqA)T200 T0523 1 :PAIDYKTAFHLAPIGLVLSR 3luqA 87 :SDERLRLFTEHAPAALAMFD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3luqA 108 :EMRYLAVSRRWREDYGLGDGDILGMSHYDIF T0523 54 :SDEFERIGERISPVMIAHGSYADDRIMK 3luqA 139 :PEIGEEWKSVHRRGLAGEVIRVEEDCFV T0523 86 :ELFWCHVTGRAL 3luqA 171 :RTQWLRWEVRPW T0523 98 :DRTAPLAAGVWTFEDL 3luqA 184 :EGEGRVGGVVIFTEDI Number of specific fragments extracted= 5 number of extra gaps= 0 total=154 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 3gdiA/T0523-3gdiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gdiA expands to /projects/compbio/data/pdb/3gdi.pdb.gz 3gdiA:# T0523 read from 3gdiA/T0523-3gdiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gdiA read from 3gdiA/T0523-3gdiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gdiA to template set # found chain 3gdiA in template set T0523 14 :IGLVLSR 3gdiA 330 :IFTTTHT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3gdiA 338 :NCLFQAVDERAVPLLGYLPQDLIETPVLVQ T0523 52 :PSSDEFERIGERISPVMIAH 3gdiA 368 :LHPSDRPLMLAIHKKILQAG T0523 72 :GSYAD 3gdiA 389 :QPFDY T0523 77 :DRIMKRAGGELFWCHVTGRAL 3gdiA 395 :PIRFRTRNGEYITLDTSWSSF T0523 98 :DR 3gdiA 417 :NP T0523 100 :TAPLAAGVWT 3gdiA 420 :SRKISFIIGR T0523 111 :EDLSATRR 3gdiA 430 :HKVRVGPL T0523 119 :VA 3gdiA 439 :ED Number of specific fragments extracted= 9 number of extra gaps= 0 total=163 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 3gdiA/T0523-3gdiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3gdiA/T0523-3gdiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gdiA read from 3gdiA/T0523-3gdiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gdiA in template set T0523 13 :PIGLVLSR 3gdiA 329 :RIFTTTHT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 3gdiA 338 :NCLFQAVDERAVPLLGYLPQDLIETPVLVQLHP T0523 55 :DEFERIGERISPVMI 3gdiA 371 :SDRPLMLAIHKKILQ T0523 70 :AHGSYAD 3gdiA 387 :GGQPFDY T0523 77 :DRIMKRAGGELFWCHVTGRAL 3gdiA 395 :PIRFRTRNGEYITLDTSWSSF T0523 98 :DRTAPLAAGVWTFEDLSA 3gdiA 418 :PWSRKISFIIGRHKVRVG Number of specific fragments extracted= 6 number of extra gaps= 0 total=169 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 3gdiA/T0523-3gdiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3gdiA/T0523-3gdiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gdiA read from 3gdiA/T0523-3gdiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gdiA in template set T0523 13 :PIGLVLSR 3gdiA 329 :RIFTTTHT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3gdiA 338 :NCLFQAVDERAVPLLGYLPQDLIETPVLVQL T0523 53 :SSDEFERIGERISPVMIAHGSY 3gdiA 369 :HPSDRPLMLAIHKKILQAGGQP T0523 75 :ADDRIMKRAGGELFWCHVTGRAL 3gdiA 393 :YSPIRFRTRNGEYITLDTSWSSF T0523 98 :DRTAPLAAGVWTFEDLS 3gdiA 418 :PWSRKISFIIGRHKVRV Number of specific fragments extracted= 5 number of extra gaps= 0 total=174 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 2b02A/T0523-2b02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b02A expands to /projects/compbio/data/pdb/2b02.pdb.gz 2b02A: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 181, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2b02A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 805, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 807, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 809, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 811, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 813, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 815, because occupancy 0.200 <= existing 0.800 in 2b02A Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 2b02A Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2b02A # T0523 read from 2b02A/T0523-2b02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b02A read from 2b02A/T0523-2b02A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b02A to template set # found chain 2b02A in template set Warning: unaligning (T0523)L113 because last residue in template chain is (2b02A)V464 T0523 13 :PIGLVLSR 2b02A 361 :TEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2b02A 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEF T0523 52 :PSSDEFERIGERISPVMIAH 2b02A 400 :CHPEDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 2b02A 421 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DR 2b02A 448 :NP T0523 100 :TAPLAAGVWTFED 2b02A 451 :SDEIEYIICTNTN Number of specific fragments extracted= 6 number of extra gaps= 0 total=180 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 2b02A/T0523-2b02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2b02A/T0523-2b02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b02A read from 2b02A/T0523-2b02A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b02A in template set Warning: unaligning (T0523)L113 because last residue in template chain is (2b02A)V464 T0523 12 :APIGLVLSR 2b02A 360 :PTEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 2b02A 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFCHP T0523 55 :DEFERIGERISPVMIAH 2b02A 403 :EDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 2b02A 421 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAPLAAGVWTFED 2b02A 449 :PYSDEIEYIICTNTN Number of specific fragments extracted= 5 number of extra gaps= 0 total=185 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 2b02A/T0523-2b02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2b02A/T0523-2b02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b02A read from 2b02A/T0523-2b02A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b02A in template set T0523 12 :APIGLVLSR 2b02A 360 :PTEFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 2b02A 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFC T0523 53 :SSDEFERIGERISPVMIAHGSY 2b02A 401 :HPEDQQLLRDSFQQVVKLKGQV T0523 75 :ADDRIMKRAGGELFWCHVTGRAL 2b02A 424 :SVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAPLAAGVWT 2b02A 448 :NPYSDEIEYIIC Number of specific fragments extracted= 5 number of extra gaps= 0 total=190 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 3bwlA/T0523-3bwlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bwlA expands to /projects/compbio/data/pdb/3bwl.pdb.gz 3bwlA:Skipped atom 9, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 13, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 15, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 17, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 19, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 115, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 119, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 121, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 123, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 125, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 127, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 156, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 158, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 180, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 184, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 186, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 188, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 190, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 192, because occupancy 0.400 <= existing 0.600 in 3bwlA 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 366, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 3bwlA Skipped atom 503, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 507, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 509, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 511, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 513, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 515, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 517, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 519, because occupancy 0.400 <= existing 0.600 in 3bwlA 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 642, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 646, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 648, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 650, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 652, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 654, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 681, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 685, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 687, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 810, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 814, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 816, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 818, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 820, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 822, because occupancy 0.400 <= existing 0.600 in 3bwlA 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 880, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 884, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 938, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 942, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 944, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 946, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 948, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 950, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 952, because occupancy 0.400 <= existing 0.600 in 3bwlA Skipped atom 954, because occupancy 0.400 <= existing 0.600 in 3bwlA # T0523 read from 3bwlA/T0523-3bwlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwlA read from 3bwlA/T0523-3bwlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bwlA to template set # found chain 3bwlA in template set Warning: unaligning (T0523)L113 because last residue in template chain is (3bwlA)I508 T0523 2 :AIDYKTAFHLAPIGLVLSR 3bwlA 399 :SSRLEALFENSPDMIDVLD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3bwlA 419 :DGTICEVNQRFCAELGYDESEVLGRSIWEF T0523 52 :PSSDEFERIGERISPVM 3bwlA 449 :DLMFDAEDVQTQLSGFS T0523 70 :AHGSYADDRIMKRAGGELFWCHVTGRALDRTAPLA 3bwlA 466 :VDERRKFEGLYERRDGSTMSVEVHLLRFNLEGEDR T0523 106 :GVWTFED 3bwlA 501 :FLAISRD Number of specific fragments extracted= 5 number of extra gaps= 0 total=195 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 3bwlA/T0523-3bwlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3bwlA/T0523-3bwlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwlA read from 3bwlA/T0523-3bwlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwlA in template set Warning: unaligning (T0523)L113 because last residue in template chain is (3bwlA)I508 T0523 2 :AIDYKTAFHLAPIGLVLSR 3bwlA 399 :SSRLEALFENSPDMIDVLD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 3bwlA 419 :DGTICEVNQRFCAELGYDESEVLGRSIWEFDLM T0523 55 :DEFERIGERISPVM 3bwlA 452 :FDAEDVQTQLSGFS T0523 70 :AHGSYADDRIMKRAGGELFWCHVTGRALDRTAPLA 3bwlA 466 :VDERRKFEGLYERRDGSTMSVEVHLLRFNLEGEDR T0523 106 :GVWTFED 3bwlA 501 :FLAISRD Number of specific fragments extracted= 5 number of extra gaps= 0 total=200 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 3bwlA/T0523-3bwlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3bwlA/T0523-3bwlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwlA read from 3bwlA/T0523-3bwlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwlA in template set T0523 1 :PAIDYKTAFHLAPIGLVLSR 3bwlA 398 :TSSRLEALFENSPDMIDVLD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDE 3bwlA 419 :DGTICEVNQRFCAELGYDESEVLGRSIWEFDLMFDA T0523 58 :ERIGERISP 3bwlA 455 :EDVQTQLSG T0523 68 :MIAHGSYADDRIMKRAGGELFWCHVTGRAL 3bwlA 464 :FSVDERRKFEGLYERRDGSTMSVEVHLLRF T0523 98 :DRTAPLAAGVW 3bwlA 495 :LEGEDRFLAIS T0523 111 :ED 3bwlA 506 :RD Number of specific fragments extracted= 6 number of extra gaps= 0 total=206 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 1bywA/T0523-1bywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bywA expands to /projects/compbio/data/pdb/1byw.pdb.gz 1bywA:# T0523 read from 1bywA/T0523-1bywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bywA read from 1bywA/T0523-1bywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bywA to template set # found chain 1bywA in template set T0523 15 :GLVLSR 1bywA 28 :KFIIAN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 1bywA 38 :NCAVIYCNDGFCELCGYSRAEVMQRP T0523 47 :FEVL 1bywA 66 :CDFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1bywA 70 :HGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPV T0523 98 :DRTAPLAAGVWTFE 1bywA 117 :NEDGAVIMFILNFE 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=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bywA/T0523-1bywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1bywA/T0523-1bywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bywA read from 1bywA/T0523-1bywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bywA in template set T0523 13 :PIGLVLSR 1bywA 28 :KFIIANAR T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 1bywA 38 :NCAVIYCNDGFCELCGYSRAEVMQRP T0523 47 :FEVLYPS 1bywA 66 :CDFLHGP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1bywA 73 :CTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPV T0523 98 :DRTAPLAAGVWTFEDLSA 1bywA 117 :NEDGAVIMFILNFEVVME Number of specific fragments extracted= 5 number of extra gaps= 0 total=216 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 1bywA/T0523-1bywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1bywA/T0523-1bywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bywA read from 1bywA/T0523-1bywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bywA in template set T0523 14 :IGLVLSR 1bywA 27 :RKFIIAN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 1bywA 38 :NCAVIYCNDGFCELCGYSRAEVMQRP T0523 47 :FEVLY 1bywA 66 :CDFLH T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1bywA 71 :GPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPV T0523 98 :DRTAPLAAGVWTFEDLSA 1bywA 117 :NEDGAVIMFILNFEVVME Number of specific fragments extracted= 5 number of extra gaps= 0 total=221 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 3h9wA/T0523-3h9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h9wA expands to /projects/compbio/data/pdb/3h9w.pdb.gz 3h9wA: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 # T0523 read from 3h9wA/T0523-3h9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h9wA read from 3h9wA/T0523-3h9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h9wA to template set # found chain 3h9wA in template set Warning: unaligning (T0523)R118 because last residue in template chain is (3h9wA)H131 T0523 14 :IGLVLSR 3h9wA 24 :AIPWKIN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 3h9wA 33 :TMAFEYIGPQIEALLGWPQGSWKSVE T0523 47 :FEVL 3h9wA 60 :WATR T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3h9wA 64 :MHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHYVWIRDVVHVV T0523 98 :DRTAPLAAGVWTFEDLSATR 3h9wA 111 :DDSGEVEALIGFMFDISLEH Number of specific fragments extracted= 5 number of extra gaps= 0 total=226 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 3h9wA/T0523-3h9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3h9wA/T0523-3h9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h9wA read from 3h9wA/T0523-3h9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h9wA in template set Warning: unaligning (T0523)R118 because last residue in template chain is (3h9wA)H131 T0523 15 :GLVLSR 3h9wA 25 :IPWKIN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 3h9wA 33 :TMAFEYIGPQIEALLGWPQGSWKSVE T0523 47 :FEVLYPS 3h9wA 60 :WATRMHP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3h9wA 67 :EDQEWVVNFCVKQSECGVDHEADYRALHRDGHYVWIRDVVHVV T0523 98 :DRTAPLAAGVWTFEDLSATR 3h9wA 111 :DDSGEVEALIGFMFDISLEH Number of specific fragments extracted= 5 number of extra gaps= 0 total=231 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 3h9wA/T0523-3h9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3h9wA/T0523-3h9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h9wA read from 3h9wA/T0523-3h9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h9wA in template set Warning: unaligning (T0523)A12 because first residue in template chain is (3h9wA)K23 Warning: unaligning (T0523)R118 because last residue in template chain is (3h9wA)H131 T0523 13 :PIGLVLSR 3h9wA 24 :AIPWKINW T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3h9wA 33 :TMAFEYIGPQIEALLGWPQGSWKSVEDWATRMHPEDQEWVVNFCVKQSECGVDHEADYRALHRDGHYVWIRDVVHVV T0523 98 :DRTAPLAAGVWTFEDLSATR 3h9wA 111 :DDSGEVEALIGFMFDISLEH Number of specific fragments extracted= 3 number of extra gaps= 0 total=234 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 3f1pB/T0523-3f1pB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3f1pB expands to /projects/compbio/data/pdb/3f1p.pdb.gz 3f1pB:Skipped atom 2659, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2661, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2663, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2665, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2667, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2669, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2671, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2673, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2675, because occupancy 0.490 <= existing 0.510 in 3f1pB Skipped atom 2778, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2780, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2782, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2784, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2786, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2788, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2790, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2792, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2794, because occupancy 0.450 <= existing 0.550 in 3f1pB Skipped atom 2892, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2894, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2896, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2898, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2900, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2902, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2904, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 2906, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3136, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3138, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3140, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3142, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3144, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3146, because occupancy 0.460 <= existing 0.540 in 3f1pB Skipped atom 3175, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3177, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3179, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3181, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3183, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3185, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3187, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3189, because occupancy 0.400 <= existing 0.600 in 3f1pB Skipped atom 3444, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3446, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3448, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3450, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3452, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3454, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3456, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3458, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3528, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3530, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3532, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3534, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3536, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3538, because occupancy 0.470 <= existing 0.530 in 3f1pB Skipped atom 3606, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3609, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3612, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3615, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3618, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3621, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3624, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3627, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3630, because occupancy 0.250 <= existing 0.410 in 3f1pB Skipped atom 3730, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3732, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3734, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3736, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3738, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3740, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3742, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3744, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3746, because occupancy 0.440 <= existing 0.560 in 3f1pB Skipped atom 3835, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3837, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3839, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3841, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3843, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3845, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3847, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3849, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3993, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3995, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3997, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 3999, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 4001, because occupancy 0.500 <= existing 0.500 in 3f1pB Skipped atom 4003, because occupancy 0.500 <= existing 0.500 in 3f1pB # T0523 read from 3f1pB/T0523-3f1pB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pB read from 3f1pB/T0523-3f1pB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f1pB to template set # found chain 3f1pB in template set T0523 13 :PIGLVLSR 3f1pB 361 :TRFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3f1pB 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEF T0523 52 :PSSDEFERIGERISPVMIAH 3f1pB 400 :CHPEDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 3f1pB 421 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRT 3f1pB 448 :NPY T0523 101 :APLAAGVWTFEDL 3f1pB 452 :DEIEYIICTNTNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=240 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 3f1pB/T0523-3f1pB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3f1pB/T0523-3f1pB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pB read from 3f1pB/T0523-3f1pB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f1pB in template set T0523 13 :PIGLVLSR 3f1pB 361 :TRFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 3f1pB 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFCHP T0523 55 :DEFERIGERISPVMIAH 3f1pB 403 :EDQQLLRDSFQQVVKLK T0523 72 :GSYADDRIMKRAGGELFWCHVTGRAL 3f1pB 421 :QVLSVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRT 3f1pB 448 :NPY T0523 101 :APLAAGVWTFEDL 3f1pB 452 :DEIEYIICTNTNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=246 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 3f1pB/T0523-3f1pB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3f1pB/T0523-3f1pB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f1pB read from 3f1pB/T0523-3f1pB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f1pB in template set Warning: unaligning (T0523)T116 because last residue in template chain is (3f1pB)S467 T0523 13 :PIGLVLSR 3f1pB 361 :TRFISRHN T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 3f1pB 370 :EGIFTFVDHRCVATVGYQPQELLGKNIVEFC T0523 53 :SSDEFERIGERISPVMIAHGSY 3f1pB 401 :HPEDQQLLRDSFQQVVKLKGQV T0523 75 :ADDRIMKRAGGELFWCHVTGRAL 3f1pB 424 :SVMFRFRSKNQEWLWMRTSSFTF T0523 98 :DRTAP 3f1pB 448 :NPYSD T0523 103 :LAAGVWTFEDLSA 3f1pB 454 :IEYIICTNTNVKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=252 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 2pr5A/T0523-2pr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pr5A expands to /projects/compbio/data/pdb/2pr5.pdb.gz 2pr5A:Skipped atom 11, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 15, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 17, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 19, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 21, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 23, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 25, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 268, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 272, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 274, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 276, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 2pr5A Skipped atom 340, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 344, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 346, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 648, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 652, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 654, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 656, because occupancy 0.200 <= existing 0.800 in 2pr5A Skipped atom 717, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 721, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 723, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 725, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 727, because occupancy 0.400 <= existing 0.600 in 2pr5A Skipped atom 1012, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1016, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1018, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1020, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1059, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1061, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1063, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1065, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1067, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1069, because occupancy 0.300 <= existing 0.700 in 2pr5A Skipped atom 1071, because occupancy 0.300 <= existing 0.700 in 2pr5A # T0523 read from 2pr5A/T0523-2pr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pr5A read from 2pr5A/T0523-2pr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pr5A to template set # found chain 2pr5A in template set T0523 13 :PIGLVLSR 2pr5A 24 :RVGVVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2pr5A 36 :DNPIVYVNQGFVQMTGYETEEILGKNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pr5A 66 :QGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPM T0523 98 :DRT 2pr5A 113 :IED T0523 103 :LAAGVWTFEDLSATRR 2pr5A 116 :KTYFVGIQNDITKQKE T0523 119 :V 2pr5A 134 :K Number of specific fragments extracted= 6 number of extra gaps= 0 total=258 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 2pr5A/T0523-2pr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pr5A/T0523-2pr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pr5A read from 2pr5A/T0523-2pr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pr5A in template set T0523 12 :APIGLVLSR 2pr5A 23 :VRVGVVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 2pr5A 36 :DNPIVYVNQGFVQMTGYETEEILGKNCRFLQGK T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pr5A 69 :HTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPM T0523 98 :DRT 2pr5A 113 :IED T0523 103 :LAAGVWTFEDLSATRRV 2pr5A 116 :KTYFVGIQNDITKQKEY Number of specific fragments extracted= 5 number of extra gaps= 0 total=263 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 2pr5A/T0523-2pr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pr5A/T0523-2pr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pr5A read from 2pr5A/T0523-2pr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pr5A in template set T0523 12 :APIGLVLSR 2pr5A 23 :VRVGVVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 2pr5A 36 :DNPIVYVNQGFVQMTGYETEEILGKNCRFLQ T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRALDRTAP 2pr5A 67 :GKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDK T0523 104 :AAGVWTFEDLSATRRVA 2pr5A 117 :TYFVGIQNDITKQKEYE Number of specific fragments extracted= 4 number of extra gaps= 0 total=267 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 1xj4A/T0523-1xj4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xj4A expands to /projects/compbio/data/pdb/1xj4.pdb.gz 1xj4A:# T0523 read from 1xj4A/T0523-1xj4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xj4A read from 1xj4A/T0523-1xj4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xj4A to template set # found chain 1xj4A in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1xj4A)D154 Warning: unaligning (T0523)T116 because last residue in template chain is (1xj4A)H259 T0523 15 :GLVLSR 1xj4A 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1xj4A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNIL T0523 52 :PSSDEFERIGERISPVMIAHGSY 1xj4A 192 :MPEPDRSRHDSYISRYRTTSDPH T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAPLA 1xj4A 219 :GRIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDLSA 1xj4A 249 :FTGFVRDLTE Number of specific fragments extracted= 5 number of extra gaps= 0 total=272 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 1xj4A/T0523-1xj4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1xj4A/T0523-1xj4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xj4A read from 1xj4A/T0523-1xj4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xj4A in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1xj4A)D154 Warning: unaligning (T0523)T116 because last residue in template chain is (1xj4A)H259 T0523 15 :GLVLSR 1xj4A 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1xj4A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILMPE T0523 55 :DEFERIGERISPVMIAHGSYA 1xj4A 195 :PDRSRHDSYISRYRTTSDPHI T0523 76 :DDRIMKRAGGELFWCHVTGRALDRTAPLA 1xj4A 220 :RIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDLSA 1xj4A 249 :FTGFVRDLTE Number of specific fragments extracted= 5 number of extra gaps= 0 total=277 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 1xj4A/T0523-1xj4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1xj4A/T0523-1xj4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xj4A read from 1xj4A/T0523-1xj4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xj4A in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1xj4A)D154 T0523 15 :GLVLSR 1xj4A 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 1xj4A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILM T0523 53 :SSDEFERIGERISPVMIAHG 1xj4A 193 :PEPDRSRHDSYISRYRTTSD T0523 73 :SYADDRIMKRAGGELFWCHVTGRALDRTAP 1xj4A 217 :GIGRIVTGKRRDGTTFPMHLSIGEMQSGGE T0523 104 :AAGVWTFEDLSA 1xj4A 247 :PYFTGFVRDLTE Number of specific fragments extracted= 5 number of extra gaps= 0 total=282 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 3eehA/T0523-3eehA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3eehA expands to /projects/compbio/data/pdb/3eeh.pdb.gz 3eehA:# T0523 read from 3eehA/T0523-3eehA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eehA read from 3eehA/T0523-3eehA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3eehA to template set # found chain 3eehA in template set Warning: unaligning (T0523)A2 because first residue in template chain is (3eehA)E10 Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE in next template residue (3eehA)T125 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE at template residue (3eehA)T125 T0523 3 :IDYKTAFHLAPIGLVLSR 3eehA 11 :RRVRELTEATNDILWEFT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 3eehA 31 :LSEVLVINSAYEDIWGRSVAKLRENP T0523 47 :FEVL 3eehA 59 :FLNG T0523 52 :PSSDEFERIGERISPVM 3eehA 63 :IHPEDRELMKDTMQSLM T0523 70 :AHGSYADDRIMKRAGGELFWCHVTGRAL 3eehA 80 :DGESADVECRVNATEEYQRWVWIQGEPI T0523 98 :DRTAPLAAGVWTFED 3eehA 109 :NDAGETVRVAGFARD Number of specific fragments extracted= 6 number of extra gaps= 1 total=288 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 3eehA/T0523-3eehA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3eehA/T0523-3eehA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eehA read from 3eehA/T0523-3eehA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eehA in template set Warning: unaligning (T0523)A2 because first residue in template chain is (3eehA)E10 Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE in next template residue (3eehA)T125 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE at template residue (3eehA)T125 T0523 3 :IDYKTAFHLAPIGLVLSR 3eehA 11 :RRVRELTEATNDILWEFT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRS 3eehA 31 :LSEVLVINSAYEDIWGRSVAKLRENP T0523 47 :FEVLYPS 3eehA 59 :FLNGIHP T0523 55 :DEFERIGERISPVM 3eehA 66 :EDRELMKDTMQSLM T0523 70 :AHGSYADDRIMKRAGGELFWCHVTGRAL 3eehA 80 :DGESADVECRVNATEEYQRWVWIQGEPI T0523 98 :DRTAPLAAGVWTFED 3eehA 109 :NDAGETVRVAGFARD Number of specific fragments extracted= 6 number of extra gaps= 1 total=294 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 3eehA/T0523-3eehA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3eehA/T0523-3eehA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eehA read from 3eehA/T0523-3eehA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eehA in template set Warning: unaligning (T0523)L113 because of BadResidue code BAD_PEPTIDE in next template residue (3eehA)T125 Warning: unaligning (T0523)S114 because of BadResidue code BAD_PEPTIDE at template residue (3eehA)T125 T0523 3 :IDYKTAFHLAPIGLVLSR 3eehA 11 :RRVRELTEATNDILWEFT T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 3eehA 31 :LSEVLVINSAYEDIWGRSVAKLRENPHDFL T0523 51 :YPSSDEFERIGE 3eehA 62 :GIHPEDRELMKD T0523 64 :ISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3eehA 74 :TMQSLMDGESADVECRVNATEEYQRWVWIQGEPI T0523 98 :DRTAPLAAGVWTFED 3eehA 109 :NDAGETVRVAGFARD Number of specific fragments extracted= 5 number of extra gaps= 1 total=299 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 3d72A/T0523-3d72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3d72A expands to /projects/compbio/data/pdb/3d72.pdb.gz 3d72A:# T0523 read from 3d72A/T0523-3d72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d72A read from 3d72A/T0523-3d72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3d72A to template set # found chain 3d72A in template set Warning: unaligning (T0523)D112 because last residue in template chain is (3d72A)E184 T0523 13 :PIGLVLSR 3d72A 70 :SVALILCD T0523 21 :DR 3d72A 79 :KQ T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVL 3d72A 84 :PIVYASEAFLYMTGYSNAEVLGRNCRFL T0523 52 :PSSDE 3d72A 112 :QSPDG T0523 57 :FERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3d72A 128 :DSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 3d72A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 6 number of extra gaps= 0 total=305 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 3d72A/T0523-3d72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3d72A/T0523-3d72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d72A read from 3d72A/T0523-3d72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d72A in template set T0523 14 :IGLVLSR 3d72A 71 :VALILCD T0523 21 :DRV 3d72A 79 :KQK T0523 24 :IEDCNDELAAIFRCARADLIGRSFEVLYPS 3d72A 85 :IVYASEAFLYMTGYSNAEVLGRNCRFLQSP T0523 56 :EFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3d72A 127 :VDSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 3d72A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 5 number of extra gaps= 0 total=310 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 3d72A/T0523-3d72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3d72A/T0523-3d72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3d72A read from 3d72A/T0523-3d72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3d72A in template set Warning: unaligning (T0523)D112 because last residue in template chain is (3d72A)E184 T0523 13 :PIGLVLSR 3d72A 70 :SVALILCD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSS 3d72A 82 :DTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 3d72A 129 :SNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 3d72A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 4 number of extra gaps= 0 total=314 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pdrA/T0523-2pdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pdrA expands to /projects/compbio/data/pdb/2pdr.pdb.gz 2pdrA:# T0523 read from 2pdrA/T0523-2pdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pdrA read from 2pdrA/T0523-2pdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pdrA to template set # found chain 2pdrA in template set T0523 13 :PIGLVLSR 2pdrA 70 :SCALILCD T0523 21 :DR 2pdrA 79 :KQ T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVL 2pdrA 84 :PIVYASEAFLYMTGYSNAEVLGRNCRFL T0523 52 :PSSDE 2pdrA 112 :QSPDG T0523 57 :FERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pdrA 128 :DSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pdrA 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 6 number of extra gaps= 0 total=320 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pdrA/T0523-2pdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pdrA/T0523-2pdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pdrA read from 2pdrA/T0523-2pdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pdrA in template set Warning: unaligning (T0523)D112 because last residue in template chain is (2pdrA)E184 T0523 13 :PIGLVLSR 2pdrA 70 :SCALILCD T0523 21 :DR 2pdrA 79 :KQ T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVLYPS 2pdrA 84 :PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP T0523 56 :EFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pdrA 127 :VDSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pdrA 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 5 number of extra gaps= 0 total=325 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pdrA/T0523-2pdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pdrA/T0523-2pdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pdrA read from 2pdrA/T0523-2pdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pdrA in template set Warning: unaligning (T0523)D112 because last residue in template chain is (2pdrA)E184 T0523 13 :PIGLVLSR 2pdrA 70 :SCALILCD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSS 2pdrA 82 :DTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pdrA 129 :SNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pdrA 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 4 number of extra gaps= 0 total=329 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vv6A/T0523-2vv6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2vv6A expands to /projects/compbio/data/pdb/2vv6.pdb.gz 2vv6A:Skipped atom 24, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 25, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 26, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 27, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 28, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 43, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 45, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2vv6A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2vv6A Skipped atom 445, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 447, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 459, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 460, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 461, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 462, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 463, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 464, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 465, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 466, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 467, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 468, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 469, because occupancy 0.370 <= existing 0.630 in 2vv6A Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 547, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 548, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 549, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 551, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 553, because occupancy 0.400 <= existing 0.600 in 2vv6A Skipped atom 751, because occupancy 0.100 <= existing 0.900 in 2vv6A Skipped atom 752, because occupancy 0.100 <= existing 0.900 in 2vv6A Skipped atom 753, because occupancy 0.100 <= existing 0.900 in 2vv6A Skipped atom 754, because occupancy 0.100 <= existing 0.900 in 2vv6A Skipped atom 755, because occupancy 0.100 <= existing 0.900 in 2vv6A # T0523 read from 2vv6A/T0523-2vv6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vv6A read from 2vv6A/T0523-2vv6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vv6A to template set # found chain 2vv6A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (2vv6A)T257 T0523 13 :PIGLVLSR 2vv6A 153 :PDAMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2vv6A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNIL T0523 52 :PSSDEFERIGERISPVMIAHGSY 2vv6A 192 :MPEPDRSRHDSYISRYRTTSDPH T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAPLA 2vv6A 219 :GRIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDL 2vv6A 249 :FTGFVRDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=334 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vv6A/T0523-2vv6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2vv6A/T0523-2vv6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vv6A read from 2vv6A/T0523-2vv6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vv6A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (2vv6A)T257 T0523 13 :PIGLVLSR 2vv6A 153 :PDAMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 2vv6A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILMPE T0523 55 :DEFERIGERISPVMIAHGS 2vv6A 195 :PDRSRHDSYISRYRTTSDP T0523 74 :YADDRIMKRAGGELFWCHVTGRALDRTAPLA 2vv6A 218 :IGRIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDL 2vv6A 249 :FTGFVRDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=339 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vv6A/T0523-2vv6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2vv6A/T0523-2vv6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vv6A read from 2vv6A/T0523-2vv6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vv6A in template set Warning: unaligning (T0523)S114 because last residue in template chain is (2vv6A)T257 T0523 13 :PIGLVLSR 2vv6A 153 :PDAMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 2vv6A 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILM T0523 53 :SSDEFERIGERISPVMIAHGSY 2vv6A 193 :PEPDRSRHDSYISRYRTTSDPH T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAP 2vv6A 219 :GRIVTGKRRDGTTFPMHLSIGEMQSGGE T0523 104 :AAGVWTFEDL 2vv6A 247 :PYFTGFVRDL Number of specific fragments extracted= 5 number of extra gaps= 0 total=344 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pd8A/T0523-2pd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pd8A expands to /projects/compbio/data/pdb/2pd8.pdb.gz 2pd8A:Skipped atom 551, because occupancy 0.100 <= existing 0.900 in 2pd8A Skipped atom 553, because occupancy 0.100 <= existing 0.900 in 2pd8A Skipped atom 555, because occupancy 0.100 <= existing 0.900 in 2pd8A Skipped atom 557, because occupancy 0.100 <= existing 0.900 in 2pd8A Skipped atom 559, because occupancy 0.100 <= existing 0.900 in 2pd8A Skipped atom 561, because occupancy 0.100 <= existing 0.900 in 2pd8A # T0523 read from 2pd8A/T0523-2pd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pd8A read from 2pd8A/T0523-2pd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pd8A to template set # found chain 2pd8A in template set Warning: unaligning (T0523)D112 because last residue in template chain is (2pd8A)E184 T0523 14 :IGLVLSR 2pd8A 71 :SALILCD T0523 21 :DR 2pd8A 79 :KQ T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVL 2pd8A 84 :PIVYASEAFLYMTGYSNAEVLGRNCRFL T0523 52 :PSSDE 2pd8A 112 :QSPDG T0523 57 :FERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pd8A 128 :DSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pd8A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 6 number of extra gaps= 0 total=350 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pd8A/T0523-2pd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pd8A/T0523-2pd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pd8A read from 2pd8A/T0523-2pd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pd8A in template set Warning: unaligning (T0523)D112 because last residue in template chain is (2pd8A)E184 T0523 15 :GLVLSR 2pd8A 72 :ALILCD T0523 21 :DR 2pd8A 79 :KQ T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVLYPS 2pd8A 84 :PIVYASEAFLYMTGYSNAEVLGRNCRFLQSP T0523 56 :EFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pd8A 127 :VDSNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pd8A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 5 number of extra gaps= 0 total=355 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pd8A/T0523-2pd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2pd8A/T0523-2pd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pd8A read from 2pd8A/T0523-2pd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pd8A in template set Warning: unaligning (T0523)D112 because last residue in template chain is (2pd8A)E184 T0523 13 :PIGLVLSR 2pd8A 70 :SSALILCD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSS 2pd8A 82 :DTPIVYASEAFLYMTGYSNAEVLGRNCRFLQSPD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2pd8A 129 :SNTINTMRKAIDRNAEVQVEVVNFKKNGQRFVNFLTMIPV T0523 98 :DRTAPLAAGVWTFE 2pd8A 170 :DETGEYRYSMGFQC Number of specific fragments extracted= 4 number of extra gaps= 0 total=359 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3icyA/T0523-3icyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3icyA expands to /projects/compbio/data/pdb/3icy.pdb.gz 3icyA: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 434, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 3icyA 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 523, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3icyA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 3icyA 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 # T0523 read from 3icyA/T0523-3icyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3icyA read from 3icyA/T0523-3icyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3icyA to template set # found chain 3icyA in template set Warning: unaligning (T0523)G72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3icyA)S73 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3icyA)S73 Warning: unaligning (T0523)S114 because last residue in template chain is (3icyA)T115 T0523 3 :IDYKTAFHLAPIGLVLSR 3icyA 1 :EELQALVDNIPAAIYHLD T0523 21 :DRVIED 3icyA 20 :SGQATI T0523 36 :RCARADL 3icyA 27 :FRPPAFL T0523 43 :IG 3icyA 41 :AG T0523 45 :RSFEVL 3icyA 46 :LNTLSM T0523 52 :PSSDEFERIGERISPVMIAH 3icyA 52 :IHHDDRHMLSNAYSKLREAK T0523 74 :YADDRIMKRAGGELFWCHVTGRAL 3icyA 74 :LTLVYRIVTPEGKLHWIEDHMRSS T0523 98 :DRTAPLAAGVWTFEDL 3icyA 99 :SDDGLFSGIDGILCEV Number of specific fragments extracted= 8 number of extra gaps= 1 total=367 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3icyA/T0523-3icyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3icyA/T0523-3icyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3icyA read from 3icyA/T0523-3icyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3icyA in template set Warning: unaligning (T0523)G72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3icyA)S73 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3icyA)S73 Warning: unaligning (T0523)S114 because last residue in template chain is (3icyA)T115 T0523 2 :AIDYKTAFHLAPIGLVLSR 3icyA 0 :AEELQALVDNIPAAIYHLD T0523 21 :DRVIED 3icyA 20 :SGQATI T0523 36 :RCARADLIGRS 3icyA 27 :FRPPAFLKTLV T0523 47 :FEVLYPS 3icyA 48 :TLSMIHH T0523 55 :DEFERIGERISPVMIAH 3icyA 55 :DDRHMLSNAYSKLREAK T0523 74 :YADDRIMKRAGGELFWCHVTGRAL 3icyA 74 :LTLVYRIVTPEGKLHWIEDHMRSS T0523 98 :DRTAPLAAGVWTFEDL 3icyA 99 :SDDGLFSGIDGILCEV Number of specific fragments extracted= 7 number of extra gaps= 1 total=374 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3icyA/T0523-3icyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3icyA/T0523-3icyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3icyA read from 3icyA/T0523-3icyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3icyA in template set Warning: unaligning (T0523)G72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3icyA)S73 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3icyA)S73 Warning: unaligning (T0523)S114 because last residue in template chain is (3icyA)T115 T0523 1 :PAIDYKTAFHLAPIGLVLSR 3icyA -1 :NAEELQALVDNIPAAIYHLD T0523 21 :DRVIED 3icyA 20 :SGQATI T0523 38 :ARADL 3icyA 31 :AFLKT T0523 43 :IGRSFEVLY 3icyA 44 :TRLNTLSMI T0523 53 :SSDEFERIGERISPVMIAH 3icyA 53 :HHDDRHMLSNAYSKLREAK T0523 74 :YADDRIMKRAGGELFWCHVTGRAL 3icyA 74 :LTLVYRIVTPEGKLHWIEDHMRSS T0523 98 :DRTAPLAAGVWTFEDL 3icyA 99 :SDDGLFSGIDGILCEV Number of specific fragments extracted= 7 number of extra gaps= 1 total=381 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fc7A/T0523-3fc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3fc7A expands to /projects/compbio/data/pdb/3fc7.pdb.gz 3fc7A: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 # T0523 read from 3fc7A/T0523-3fc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fc7A read from 3fc7A/T0523-3fc7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fc7A to template set # found chain 3fc7A in template set Warning: unaligning (T0523)A12 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fc7A)P145 Warning: unaligning (T0523)P13 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fc7A)P145 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)N161 Warning: unaligning (T0523)N28 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)N161 Warning: unaligning (T0523)G44 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)Q178 Warning: unaligning (T0523)R45 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)Q178 Warning: unaligning (T0523)V49 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)V183 Warning: unaligning (T0523)L50 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)V183 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)T206 Warning: unaligning (T0523)Y74 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)T206 Warning: unaligning (T0523)G85 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)R215 Warning: unaligning (T0523)F88 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)R215 Warning: unaligning (T0523)L103 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)D231 Warning: unaligning (T0523)A104 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)D231 Warning: unaligning (T0523)S114 because last residue in template chain is (3fc7A)T241 T0523 14 :IGLVLSR 3fc7A 146 :DGIVHLT T0523 21 :DRVIED 3fc7A 154 :NGTILS T0523 29 :DELAAIFRCARADLI 3fc7A 162 :PSMAGRLGADPDTLV T0523 46 :SFE 3fc7A 179 :QLS T0523 52 :PSSDEFERIGERISPVMIAHG 3fc7A 184 :MDSEAANQRLEAGKSAVENGT T0523 75 :ADDRI 3fc7A 207 :RSEDA T0523 83 :AG 3fc7A 212 :VG T0523 89 :WCHVTGRALDRTAP 3fc7A 216 :HYHNQYIPVDSHRK T0523 105 :AGVWTFEDL 3fc7A 232 :TFQLVSRDI Number of specific fragments extracted= 9 number of extra gaps= 7 total=390 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fc7A/T0523-3fc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3fc7A/T0523-3fc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fc7A read from 3fc7A/T0523-3fc7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fc7A in template set Warning: unaligning (T0523)A12 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fc7A)P145 Warning: unaligning (T0523)P13 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fc7A)P145 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)N161 Warning: unaligning (T0523)N28 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)N161 Warning: unaligning (T0523)G44 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)Q178 Warning: unaligning (T0523)R45 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)Q178 Warning: unaligning (T0523)V49 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)V183 Warning: unaligning (T0523)L50 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)V183 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)T206 Warning: unaligning (T0523)Y74 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)T206 Warning: unaligning (T0523)G84 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)R215 Warning: unaligning (T0523)F88 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)R215 Warning: unaligning (T0523)L103 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)D231 Warning: unaligning (T0523)A104 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)D231 Warning: unaligning (T0523)S114 because last residue in template chain is (3fc7A)T241 T0523 14 :IGLVLSR 3fc7A 146 :DGIVHLT T0523 21 :DRVIED 3fc7A 154 :NGTILS T0523 29 :DELAAIFRCARADLI 3fc7A 162 :PSMAGRLGADPDTLV T0523 46 :SFE 3fc7A 179 :QLS T0523 51 :YPS 3fc7A 184 :MDS T0523 55 :DEFERIGERISPVMIAHG 3fc7A 187 :EAANQRLEAGKSAVENGT T0523 75 :ADDRIM 3fc7A 207 :RSEDAV T0523 83 :A 3fc7A 213 :G T0523 89 :WCHVTGRALDRTAP 3fc7A 216 :HYHNQYIPVDSHRK T0523 105 :AGVWTFEDL 3fc7A 232 :TFQLVSRDI Number of specific fragments extracted= 10 number of extra gaps= 7 total=400 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fc7A/T0523-3fc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 3fc7A/T0523-3fc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fc7A read from 3fc7A/T0523-3fc7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fc7A in template set Warning: unaligning (T0523)H10 because first residue in template chain is (3fc7A)S142 Warning: unaligning (T0523)A12 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fc7A)P145 Warning: unaligning (T0523)P13 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fc7A)P145 Warning: unaligning (T0523)C27 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)N161 Warning: unaligning (T0523)N28 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)N161 Warning: unaligning (T0523)G44 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)Q178 Warning: unaligning (T0523)R45 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)Q178 Warning: unaligning (T0523)V49 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)V183 Warning: unaligning (T0523)L50 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)V183 Warning: unaligning (T0523)S73 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)T206 Warning: unaligning (T0523)I79 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)T206 Warning: unaligning (T0523)L87 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)R215 Warning: unaligning (T0523)F88 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)R215 Warning: unaligning (T0523)L103 because of BadResidue code BAD_PEPTIDE in next template residue (3fc7A)D231 Warning: unaligning (T0523)A104 because of BadResidue code BAD_PEPTIDE at template residue (3fc7A)D231 Warning: unaligning (T0523)S114 because last residue in template chain is (3fc7A)T241 T0523 11 :L 3fc7A 143 :D T0523 14 :IGLVLSR 3fc7A 146 :DGIVHLT T0523 21 :DRVIED 3fc7A 154 :NGTILS T0523 29 :DELAAIFRCARADLI 3fc7A 162 :PSMAGRLGADPDTLV T0523 46 :SFE 3fc7A 179 :QLS T0523 51 :Y 3fc7A 184 :M T0523 53 :SSDEFERIGERISPVMIAHG 3fc7A 185 :DSEAANQRLEAGKSAVENGT T0523 80 :MKRAGGE 3fc7A 207 :RSEDAVG T0523 89 :WCHVTGRALDRTAP 3fc7A 216 :HYHNQYIPVDSHRK T0523 105 :AGVWTFEDL 3fc7A 232 :TFQLVSRDI Number of specific fragments extracted= 10 number of extra gaps= 7 total=410 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p97A/T0523-1p97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p97A expands to /projects/compbio/data/pdb/1p97.pdb.gz 1p97A:# T0523 read from 1p97A/T0523-1p97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p97A read from 1p97A/T0523-1p97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p97A to template set # found chain 1p97A in template set T0523 17 :VLSR 1p97A 10 :SRHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1p97A 15 :DMKFTYCDDRITELIGYHPEELLGRSAYEF T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1p97A 45 :YHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVI T0523 98 :DRTA 1p97A 92 :NPRN T0523 102 :PLAAGVWTFEDLSAT 1p97A 97 :QPQCIMCVNYVLSEI Number of specific fragments extracted= 5 number of extra gaps= 0 total=415 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p97A/T0523-1p97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1p97A/T0523-1p97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p97A read from 1p97A/T0523-1p97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p97A in template set Warning: unaligning (T0523)V119 because last residue in template chain is (1p97A)N114 T0523 13 :PIGLVLSR 1p97A 6 :KTFLSRHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1p97A 15 :DMKFTYCDDRITELIGYHPEELLGRSAYEFYHA T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1p97A 48 :LDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVI T0523 98 :DRTAPLAAGVWTFEDLSATRR 1p97A 93 :PRNLQPQCIMCVNYVLSEIEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=419 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p97A/T0523-1p97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1p97A/T0523-1p97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p97A read from 1p97A/T0523-1p97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p97A in template set T0523 12 :APIGLVLSR 1p97A 5 :SKTFLSRHS T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSD 1p97A 15 :DMKFTYCDDRITELIGYHPEELLGRSAYEFYHALD T0523 57 :FERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1p97A 50 :SENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVI T0523 98 :DRTAPLAAGVWTFEDLSATR 1p97A 93 :PRNLQPQCIMCVNYVLSEIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=423 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkrA/T0523-2wkrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wkrA expands to /projects/compbio/data/pdb/2wkr.pdb.gz 2wkrA:# T0523 read from 2wkrA/T0523-2wkrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkrA read from 2wkrA/T0523-2wkrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wkrA to template set # found chain 2wkrA in template set T0523 9 :FHLAPIGLVLSR 2wkrA 408 :LERIEKNFVITD T0523 21 :DR 2wkrA 421 :RL T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVL 2wkrA 426 :PIIFASDSFLQLTEYSREEILGRNMRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkrA 454 :QGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFE 2wkrA 501 :DQKGDVQYFIGVQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=428 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkrA/T0523-2wkrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkrA/T0523-2wkrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkrA read from 2wkrA/T0523-2wkrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkrA in template set T0523 9 :FHLAPIGLVLSR 2wkrA 408 :LERIEKNFVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 2wkrA 424 :DNPIIFASDSFLQLTEYSREEILGRNMRFLQGP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkrA 457 :ETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRV 2wkrA 501 :DQKGDVQYFIGVQLDGTEHVRD Number of specific fragments extracted= 4 number of extra gaps= 0 total=432 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkrA/T0523-2wkrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkrA/T0523-2wkrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkrA read from 2wkrA/T0523-2wkrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkrA in template set T0523 11 :LAPIGLVLSR 2wkrA 413 :KNFVITDPRL T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 2wkrA 424 :DNPIIFASDSFLQLTEYSREEILGRNMRFLQ T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkrA 455 :GPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRVA 2wkrA 501 :DQKGDVQYFIGVQLDGTEHVRDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=436 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jnuA/T0523-1jnuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jnuA expands to /projects/compbio/data/pdb/1jnu.pdb.gz 1jnuA:# T0523 read from 1jnuA/T0523-1jnuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnuA read from 1jnuA/T0523-1jnuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jnuA to template set # found chain 1jnuA in template set T0523 17 :VLSR 1jnuA 932 :VITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1jnuA 940 :DNPIIFASDRFLELTEYTREEVLGNNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1jnuA 970 :QGRGTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVM T0523 98 :DRTAPLAAGVWTFED 1jnuA 1017 :DENGDVQYFIGVQQE Number of specific fragments extracted= 4 number of extra gaps= 0 total=440 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jnuA/T0523-1jnuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1jnuA/T0523-1jnuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnuA read from 1jnuA/T0523-1jnuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jnuA in template set Warning: unaligning (T0523)L113 because last residue in template chain is (1jnuA)M1032 T0523 15 :GLVLSR 1jnuA 930 :SFVITD T0523 21 :DR 1jnuA 937 :RL T0523 23 :VIEDCNDELAAIFRCARADLIGRSFEVLYPS 1jnuA 942 :PIIFASDRFLELTEYTREEVLGNNCRFLQGR T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1jnuA 973 :GTDRKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVM T0523 98 :DRTAPLAAGVWTFED 1jnuA 1017 :DENGDVQYFIGVQQE Number of specific fragments extracted= 5 number of extra gaps= 0 total=445 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jnuA/T0523-1jnuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1jnuA/T0523-1jnuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnuA read from 1jnuA/T0523-1jnuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jnuA in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1jnuA)K929 Warning: unaligning (T0523)L113 because last residue in template chain is (1jnuA)M1032 T0523 15 :GLVLSR 1jnuA 930 :SFVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDE 1jnuA 940 :DNPIIFASDRFLELTEYTREEVLGNNCRFLQGRGTD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 1jnuA 976 :RKAVQLIRDAVKEQRDVTVQVLNYTKGGRAFWNLFHLQVM T0523 98 :DRTAPLAAGVWTFED 1jnuA 1017 :DENGDVQYFIGVQQE Number of specific fragments extracted= 4 number of extra gaps= 0 total=449 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkpA/T0523-2wkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wkpA expands to /projects/compbio/data/pdb/2wkp.pdb.gz 2wkpA:Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1059, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1089, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1090, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1092, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1094, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1660, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1662, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1664, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1666, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 1668, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2045, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 2046, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 2047, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 2048, because occupancy 0.300 <= existing 0.700 in 2wkpA Skipped atom 2260, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2261, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2262, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2263, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2396, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2398, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2399, because occupancy 0.500 <= existing 0.500 in 2wkpA Skipped atom 2400, because occupancy 0.500 <= existing 0.500 in 2wkpA # T0523 read from 2wkpA/T0523-2wkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkpA read from 2wkpA/T0523-2wkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wkpA to template set # found chain 2wkpA in template set T0523 10 :HLAPIGLVLSR 2wkpA 409 :ERIEKNFVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2wkpA 424 :DNPIIFASDSFLQLTEYSREEILGRNCRFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkpA 454 :QGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFE 2wkpA 501 :DQKGDVQYFIGVQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=453 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkpA/T0523-2wkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkpA/T0523-2wkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkpA read from 2wkpA/T0523-2wkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkpA in template set T0523 9 :FHLAPIGLVLSR 2wkpA 408 :LERIEKNFVITD T0523 21 :DRV 2wkpA 421 :RLP T0523 24 :IEDCNDELAAIFRCARADLIGRSFEVLYPS 2wkpA 427 :IIFASDSFLQLTEYSREEILGRNCRFLQGP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkpA 457 :ETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRR 2wkpA 501 :DQKGDVQYFIGVQLDGTEHVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=458 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkpA/T0523-2wkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkpA/T0523-2wkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkpA read from 2wkpA/T0523-2wkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkpA in template set T0523 11 :LAPIGLVLSR 2wkpA 413 :KNFVITDPRL T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDE 2wkpA 424 :DNPIIFASDSFLQLTEYSREEILGRNCRFLQGPETD T0523 58 :ERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkpA 460 :RATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRVA 2wkpA 501 :DQKGDVQYFIGVQLDGTEHVRDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=462 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lswA/T0523-1lswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lswA expands to /projects/compbio/data/pdb/1lsw.pdb.gz 1lswA:# T0523 read from 1lswA/T0523-1lswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lswA read from 1lswA/T0523-1lswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lswA to template set # found chain 1lswA in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1lswA)D154 T0523 15 :GLVLSR 1lswA 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 1lswA 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNIL T0523 52 :PSSDEFERIGERISPVMIAHGSY 1lswA 192 :MPEPDRSRHDSYISRYRTTSDPH T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAPLA 1lswA 219 :GRIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDLSATRR 1lswA 249 :FTGFVRDLTEHQQ T0523 119 :VA 1lswA 263 :QA Number of specific fragments extracted= 6 number of extra gaps= 0 total=468 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lswA/T0523-1lswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1lswA/T0523-1lswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lswA read from 1lswA/T0523-1lswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lswA in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1lswA)D154 T0523 15 :GLVLSR 1lswA 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLYPS 1lswA 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILMPE T0523 55 :DEFERIGERISPVMIAHGS 1lswA 195 :PDRSRHDSYISRYRTTSDP T0523 74 :YADDRIMKRAGGELFWCHVTGRALDRTAPLA 1lswA 218 :IGRIVTGKRRDGTTFPMHLSIGEMQSGGEPY T0523 106 :GVWTFEDLSATRRV 1lswA 249 :FTGFVRDLTEHQQT Number of specific fragments extracted= 5 number of extra gaps= 0 total=473 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lswA/T0523-1lswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 1lswA/T0523-1lswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lswA read from 1lswA/T0523-1lswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lswA in template set Warning: unaligning (T0523)I14 because first residue in template chain is (1lswA)D154 T0523 15 :GLVLSR 1lswA 155 :AMIVID T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 1lswA 162 :HGIIQLFSTAAERLFGWSELEAIGQNVNILM T0523 53 :SSDEFERIGERISPVMIAHGSY 1lswA 193 :PEPDRSRHDSYISRYRTTSDPH T0523 75 :ADDRIMKRAGGELFWCHVTGRALDRTAP 1lswA 219 :GRIVTGKRRDGTTFPMHLSIGEMQSGGE T0523 104 :AAGVWTFEDLSATRRVA 1lswA 247 :PYFTGFVRDLTEHQQTQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=478 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkqA/T0523-2wkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wkqA expands to /projects/compbio/data/pdb/2wkq.pdb.gz 2wkqA:Skipped atom 530, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 531, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 532, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 533, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 534, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 535, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 536, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 537, because occupancy 0.440 <= existing 0.560 in 2wkqA Skipped atom 600, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 601, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 602, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 603, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 604, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 605, because occupancy 0.410 <= existing 0.590 in 2wkqA Skipped atom 786, because occupancy 0.280 <= existing 0.720 in 2wkqA Skipped atom 787, because occupancy 0.280 <= existing 0.720 in 2wkqA Skipped atom 788, because occupancy 0.280 <= existing 0.720 in 2wkqA Skipped atom 789, because occupancy 0.280 <= existing 0.720 in 2wkqA Skipped atom 790, because occupancy 0.280 <= existing 0.720 in 2wkqA Skipped atom 815, because occupancy 0.420 <= existing 0.580 in 2wkqA Skipped atom 816, because occupancy 0.420 <= existing 0.580 in 2wkqA Skipped atom 817, because occupancy 0.420 <= existing 0.580 in 2wkqA Skipped atom 818, because occupancy 0.420 <= existing 0.580 in 2wkqA Skipped atom 819, because occupancy 0.420 <= existing 0.580 in 2wkqA Skipped atom 1178, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1179, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1180, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1181, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1182, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1183, because occupancy 0.400 <= existing 0.600 in 2wkqA Skipped atom 1481, because occupancy 0.350 <= existing 0.650 in 2wkqA Skipped atom 1482, because occupancy 0.350 <= existing 0.650 in 2wkqA Skipped atom 1483, because occupancy 0.350 <= existing 0.650 in 2wkqA Skipped atom 1657, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1658, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1659, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1660, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1661, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1662, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1663, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1664, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1665, because occupancy 0.310 <= existing 0.690 in 2wkqA Skipped atom 1758, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 1759, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 1760, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 1761, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 1762, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 1763, because occupancy 0.340 <= existing 0.660 in 2wkqA Skipped atom 2155, because occupancy 0.380 <= existing 0.620 in 2wkqA Skipped atom 2156, because occupancy 0.380 <= existing 0.620 in 2wkqA Skipped atom 2157, because occupancy 0.380 <= existing 0.620 in 2wkqA Skipped atom 2158, because occupancy 0.380 <= existing 0.620 in 2wkqA Skipped atom 2159, because occupancy 0.380 <= existing 0.620 in 2wkqA Skipped atom 2292, because occupancy 0.450 <= existing 0.550 in 2wkqA Skipped atom 2293, because occupancy 0.450 <= existing 0.550 in 2wkqA Skipped atom 2294, because occupancy 0.450 <= existing 0.550 in 2wkqA Skipped atom 2295, because occupancy 0.450 <= existing 0.550 in 2wkqA Skipped atom 2296, because occupancy 0.450 <= existing 0.550 in 2wkqA # T0523 read from 2wkqA/T0523-2wkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkqA read from 2wkqA/T0523-2wkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wkqA to template set # found chain 2wkqA in template set T0523 9 :FHLAPIGLVLSR 2wkqA 408 :LERIEKNFVITD T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVL 2wkqA 424 :DNPIIFASDSFLQLTEYSREEILGRNARFL T0523 52 :PSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkqA 454 :QGPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFED 2wkqA 501 :DQKGDVQYFIGVQLD Number of specific fragments extracted= 4 number of extra gaps= 0 total=482 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkqA/T0523-2wkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkqA/T0523-2wkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkqA read from 2wkqA/T0523-2wkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkqA in template set T0523 9 :FHLAPIGLVLSR 2wkqA 408 :LERIEKNFVITD T0523 21 :DRV 2wkqA 421 :RLP T0523 24 :IEDCNDELAAIFRCARADLIGRSFEVLYPS 2wkqA 427 :IIFASDSFLQLTEYSREEILGRNARFLQGP T0523 55 :DEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkqA 457 :ETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRV 2wkqA 501 :DQKGDVQYFIGVQLDGTEHVRD Number of specific fragments extracted= 5 number of extra gaps= 0 total=487 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wkqA/T0523-2wkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0523 read from 2wkqA/T0523-2wkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wkqA read from 2wkqA/T0523-2wkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wkqA in template set T0523 11 :LAPIGLVLSR 2wkqA 413 :KNFVITDPRL T0523 21 :DRVIEDCNDELAAIFRCARADLIGRSFEVLY 2wkqA 424 :DNPIIFASDSFLQLTEYSREEILGRNARFLQ T0523 53 :SSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL 2wkqA 455 :GPETDRATVRKIRDAIDNQTEVTVQLINYTKSGKKFWNLFHLQPM T0523 98 :DRTAPLAAGVWTFEDLSATRRVA 2wkqA 501 :DQKGDVQYFIGVQLDGTEHVRDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=491 Will force an alignment to be made, even if fragment is small Number of alignments=93 # command:CPU_time= 18.853 sec, elapsed time= 35.902 sec. # command:DEBUG: alignment library has 93 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 93 # Adding 618 constraints to all_contacts Done adding distance constraints # command:CPU_time= 18.901 sec, elapsed time= 35.951 sec. # command:Reading probabilities from T0523.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 84.819 Optimizing... Probability sum: -206.132, CN propb: -206.132 weights: 0.487 constraints: 242 # command:CPU_time= 19.912 sec, elapsed time= 36.966 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 242 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 242 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 376 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 376 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 19.922 sec, elapsed time= 37.640 sec. # command: