# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0481 numbered 1 through 154 Created new target T0481 from T0481.a2m # command:CPU_time= 6.654 sec, elapsed time= 6.787 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qe9A/T0481-2qe9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qe9A expands to /projects/compbio/data/pdb/2qe9.pdb.gz 2qe9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 994, because occupancy 0.5 <= existing 0.500 in 2qe9A Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2qe9A Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2qe9A # T0481 read from 2qe9A/T0481-2qe9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qe9A read from 2qe9A/T0481-2qe9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qe9A to template set # found chain 2qe9A in template set Warning: unaligning (T0481)L96 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qe9A)E100 Warning: unaligning (T0481)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qe9A)E100 T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQ 2qe9A 0 :GMMKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQT # choosing archetypes in rotamer library T0481 104 :EIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFY 2qe9A 101 :LVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSAS T0481 151 :QQRM 2qe9A 149 :IGRT Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qe9A/T0481-2qe9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2qe9A/T0481-2qe9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qe9A read from 2qe9A/T0481-2qe9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qe9A in template set Warning: unaligning (T0481)L96 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qe9A)E100 Warning: unaligning (T0481)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qe9A)E100 T0481 1 :MCQSNQIVSHFL 2qe9A -5 :NLYFQGMMKFFE T0481 13 :SHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQ 2qe9A 10 :QVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQT T0481 104 :EIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFY 2qe9A 101 :LVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSAS T0481 151 :QQR 2qe9A 149 :IGR Number of specific fragments extracted= 4 number of extra gaps= 0 total=7 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 2qe9A/T0481-2qe9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2qe9A/T0481-2qe9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qe9A read from 2qe9A/T0481-2qe9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qe9A in template set Warning: unaligning (T0481)L96 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qe9A)E100 Warning: unaligning (T0481)R103 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qe9A)E100 T0481 4 :SNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNVLAKTYTEKTVAILEQ 2qe9A 1 :MMKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQT T0481 104 :EIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELP 2qe9A 101 :LVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVS Number of specific fragments extracted= 2 number of extra gaps= 0 total=9 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hkvA/T0481-2hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hkvA expands to /projects/compbio/data/pdb/2hkv.pdb.gz 2hkvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 30, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2hkvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 2hkvA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 2hkvA # T0481 read from 2hkvA/T0481-2hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hkvA read from 2hkvA/T0481-2hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hkvA to template set # found chain 2hkvA in template set Warning: unaligning (T0481)T50 because of BadResidue code BAD_PEPTIDE in next template residue (2hkvA)L52 Warning: unaligning (T0481)S51 because of BadResidue code BAD_PEPTIDE at template residue (2hkvA)L52 T0481 1 :M 2hkvA 1 :M T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHIL 2hkvA 3 :DWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLA T0481 52 :FHLFANVIKEGNASPFQNKQEET 2hkvA 53 :LEADLRIATGATADEMAQFYAVP T0481 75 :ETDLNVLAKTYTEKTVAILEQ 2hkvA 78 :PEQLVDRLDQSWQYYQDRLMA T0481 104 :EIDL 2hkvA 99 :DFST T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFY 2hkvA 104 :TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKLDL Number of specific fragments extracted= 6 number of extra gaps= 1 total=15 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 2hkvA/T0481-2hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2hkvA/T0481-2hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hkvA read from 2hkvA/T0481-2hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hkvA in template set Warning: unaligning (T0481)T50 because of BadResidue code BAD_PEPTIDE in next template residue (2hkvA)L52 Warning: unaligning (T0481)S51 because of BadResidue code BAD_PEPTIDE at template residue (2hkvA)L52 Warning: unaligning (T0481)Q151 because last residue in template chain is (2hkvA)F147 T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHIL 2hkvA 3 :DWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLA T0481 52 :FHLFANVIKEGNA 2hkvA 53 :LEADLRIATGATA T0481 70 :K 2hkvA 66 :D T0481 71 :QEETETDLNVLAKTYTEKTVAILEQ 2hkvA 74 :VPVLPEQLVDRLDQSWQYYQDRLMA T0481 104 :EIDL 2hkvA 99 :DFST T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFY 2hkvA 104 :TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKLDL Number of specific fragments extracted= 6 number of extra gaps= 1 total=21 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 2hkvA/T0481-2hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2hkvA/T0481-2hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hkvA read from 2hkvA/T0481-2hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hkvA in template set Warning: unaligning (T0481)T50 because of BadResidue code BAD_PEPTIDE in next template residue (2hkvA)L52 Warning: unaligning (T0481)S51 because of BadResidue code BAD_PEPTIDE at template residue (2hkvA)L52 T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHIL 2hkvA 3 :DWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLA T0481 52 :FHLFANVIKEGNASPFQN 2hkvA 53 :LEADLRIATGATADEMAQ T0481 70 :KQEETETDLNVLAKTYTEKTVAILE 2hkvA 73 :AVPVLPEQLVDRLDQSWQYYQDRLM T0481 105 :IDLT 2hkvA 100 :FSTE T0481 109 :SAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELP 2hkvA 105 :TYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=26 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 2ou6A/T0481-2ou6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ou6A expands to /projects/compbio/data/pdb/2ou6.pdb.gz 2ou6A:Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 2ou6A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 451, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2ou6A Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2ou6A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0481 read from 2ou6A/T0481-2ou6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ou6A read from 2ou6A/T0481-2ou6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ou6A to template set # found chain 2ou6A in template set Warning: unaligning (T0481)M142 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2ou6A)A184 Warning: unaligning (T0481)G143 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2ou6A)A184 T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNA 2ou6A 31 :PHIGALVEMLTYARLTTLQAVEGLPEDQLWATAPGFANSIGTLLAHIAAVERVYHVLSFQGRD T0481 65 :SPFQNKQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 2ou6A 111 :EGTAPARLPTLDELRAELADARAETLRVFAAKDDAWLAEPL T0481 111 :FGRKVTGRALLQLAMEHEIHHKGNLFVYVRE 2ou6A 152 :GPGWANQHWAWFHVMEDEVNHRGQLRLLRQV Number of specific fragments extracted= 3 number of extra gaps= 1 total=29 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 2ou6A/T0481-2ou6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2ou6A/T0481-2ou6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ou6A read from 2ou6A/T0481-2ou6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ou6A in template set Warning: unaligning (T0481)M142 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2ou6A)A184 Warning: unaligning (T0481)G143 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2ou6A)A184 T0481 2 :CQ 2ou6A 30 :TP T0481 4 :SNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNK 2ou6A 33 :IGALVEMLTYARLTTLQAVEGLPEDQLWATAPGFANSIGTLLAHIAAVERVYHVLSFQGRDVTPEDD T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREID 2ou6A 117 :RLPTLDELRAELADARAETLRVFAAKDDAWLAEPLG T0481 111 :FG 2ou6A 153 :PG T0481 114 :KVTGRALLQLAMEHEIHHKGNLFVYVRE 2ou6A 155 :WANQHWAWFHVMEDEVNHRGQLRLLRQV Number of specific fragments extracted= 5 number of extra gaps= 1 total=34 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 2ou6A/T0481-2ou6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2ou6A/T0481-2ou6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ou6A read from 2ou6A/T0481-2ou6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ou6A in template set Warning: unaligning (T0481)M142 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2ou6A)A184 T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQN 2ou6A 32 :HIGALVEMLTYARLTTLQAVEGLPEDQLWATAPGFANSIGTLLAHIAAVERVYHVLSFQGRDVTPED T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 2ou6A 116 :ARLPTLDELRAELADARAETLRVFAAKDDAWLAEPL T0481 111 :FGRKVTGRALLQLAMEHEIHHKGNLFVYVRE 2ou6A 152 :GPGWANQHWAWFHVMEDEVNHRGQLRLLRQV Number of specific fragments extracted= 3 number of extra gaps= 1 total=37 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 3cexA/T0481-3cexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cexA expands to /projects/compbio/data/pdb/3cex.pdb.gz 3cexA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 39, because occupancy 0.500 <= existing 0.500 in 3cexA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3cexA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 3cexA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 3cexA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 3cexA Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 3cexA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0481 read from 3cexA/T0481-3cexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cexA read from 3cexA/T0481-3cexA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cexA to template set # found chain 3cexA in template set T0481 1 :MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNA 3cexA 1 :MKVTQLSSETLDRAHERFEETLAQMTVAEANTMPAPLIKSVTWLMWHTARELDLQISALNHSDP T0481 65 :SPFQNKQEET 3cexA 80 :PDETEDWHHT T0481 75 :ETDLNVLAKTYTEKTVAILEQLTEEQLDREID 3cexA 101 :KQLLSDYLAASVALTKSYLDQIKEEQLSDVID T0481 108 :TSAFG 3cexA 133 :KNWTP T0481 114 :KVTGRALLQLAMEHEIHHKGNLFVYVREMGH 3cexA 138 :PVTRQVRLVSAIDDAVMHSGQAVYTRRLVIG Number of specific fragments extracted= 5 number of extra gaps= 0 total=42 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 3cexA/T0481-3cexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 3cexA/T0481-3cexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cexA read from 3cexA/T0481-3cexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cexA in template set Warning: unaligning (T0481)T145 because last residue in template chain is (3cexA)K169 T0481 1 :MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNAS 3cexA 1 :MKVTQLSSETLDRAHERFEETLAQMTVAEANTMPAPLIKSVTWLMWHTARELDLQISALNHSDPL T0481 66 :PFQ 3cexA 80 :PDE T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 3cexA 97 :VVAEKQLLSDYLAASVALTKSYLDQIKEEQLSDVIDK T0481 110 :AFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGH 3cexA 134 :NWTPPVTRQVRLVSAIDDAVMHSGQAVYTRRLVIG Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 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 3cexA/T0481-3cexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 3cexA/T0481-3cexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cexA read from 3cexA/T0481-3cexA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cexA in template set T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 3cexA 2 :KVTQLSSETLDRAHERFEETLAQMTVAEANTMPAPLIKSVTWLMWHTARELDLQISAL T0481 60 :KEGNASPFQN 3cexA 74 :KFALDLPDET T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 3cexA 96 :VVVAEKQLLSDYLAASVALTKSYLDQIKEEQLSDVI T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYV 3cexA 132 :DKNWTPPVTRQVRLVSAIDDAVMHSGQAVYTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 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 1rxqA/T0481-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rxqA expands to /projects/compbio/data/pdb/1rxq.pdb.gz 1rxqA:Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1rxqA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 571, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0481 read from 1rxqA/T0481-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0481-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rxqA to template set # found chain 1rxqA in template set Warning: unaligning (T0481)T145 because last residue in template chain is (1rxqA)S178 T0481 1 :M 1rxqA 20 :S T0481 2 :CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 1rxqA 22 :EQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRF T0481 60 :KEGNASPFQNKQEET 1rxqA 84 :TEETPAIRPYDEKAW T0481 75 :ETDLNVLAKTYTEKTVAILEQLTEEQLDREID 1rxqA 109 :PSGSLALLQELHGRWTALLRTLTDQQFKRGFY T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGH 1rxqA 141 :HPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 5 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxqA/T0481-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 1rxqA/T0481-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0481-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxqA in template set Warning: unaligning (T0481)T145 because last residue in template chain is (1rxqA)S178 T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 1rxqA 23 :QKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRF T0481 60 :KEGNASPFQNK 1rxqA 83 :LTEETPAIRPY T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREID 1rxqA 105 :KTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFY T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGH 1rxqA 141 :HPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxqA/T0481-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 1rxqA/T0481-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0481-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxqA in template set Warning: unaligning (T0481)T145 because last residue in template chain is (1rxqA)S178 T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 1rxqA 23 :QKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRF T0481 61 :EGNASPFQN 1rxqA 84 :TEETPAIRP T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREID 1rxqA 104 :SKTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFY T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGH 1rxqA 141 :HPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 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 2f22A/T0481-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f22A expands to /projects/compbio/data/pdb/2f22.pdb.gz 2f22A:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 11, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 15, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 19, because occupancy 0.350 <= existing 0.400 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 102, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 107, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 110, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 112, because occupancy 0.250 <= existing 0.250 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 113, because occupancy 0.250 <= existing 0.250 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 116, because occupancy 0.330 <= existing 0.340 in 2f22A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 634, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 638, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 640, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 642, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 644, because occupancy 0.400 <= existing 0.600 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1083, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2f22A # T0481 read from 2f22A/T0481-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0481-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f22A to template set # found chain 2f22A in template set T0481 11 :FLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNA 2f22A 6 :VLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSI T0481 65 :SPFQNKQEET 2f22A 62 :PGRLASDEHR T0481 78 :LNVLAKTYTEKTVAILEQLT 2f22A 72 :LLDELERSMEELVFEFKQTT T0481 102 :DREIDL 2f22A 92 :FNSIKM T0481 111 :FGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFY 2f22A 98 :GENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLPKQW Number of specific fragments extracted= 5 number of extra gaps= 0 total=68 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 2f22A/T0481-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2f22A/T0481-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0481-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f22A in template set T0481 6 :QI 2f22A 5 :GV T0481 12 :LSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNK 2f22A 7 :LYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRL T0481 71 :QEET 2f22A 68 :DEHR T0481 78 :LNVLAKTYTEKTVAILEQLT 2f22A 72 :LLDELERSMEELVFEFKQTT T0481 102 :DREIDL 2f22A 92 :FNSIKM T0481 111 :FGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELP 2f22A 98 :GENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLPK Number of specific fragments extracted= 6 number of extra gaps= 0 total=74 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 2f22A/T0481-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2f22A/T0481-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0481-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f22A in template set T0481 10 :HFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQN 2f22A 5 :GVLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGR T0481 70 :KQEET 2f22A 67 :SDEHR T0481 78 :LNVLAKTYTEKTVAILEQLT 2f22A 72 :LLDELERSMEELVFEFKQTT T0481 108 :T 2f22A 93 :N T0481 109 :SAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTEL 2f22A 96 :KMGENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLP Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 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 2p1aA/T0481-2p1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2p1aA expands to /projects/compbio/data/pdb/2p1a.pdb.gz 2p1aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 124, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2p1aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 2p1aA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2p1aA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1086, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2p1aA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2p1aA # T0481 read from 2p1aA/T0481-2p1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p1aA read from 2p1aA/T0481-2p1aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2p1aA to template set # found chain 2p1aA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNA 2p1aA 2 :FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAPIQSKRSLFEMYAHLSLICHADLLILNGSTE T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2p1aA 73 :QTPETIAQMQKTMIQGYDLLSKTFLSYSNEQLAEMKTA T0481 110 :AFGRKVTGRALLQLAMEHEIHHKGNLFVY 2p1aA 111 :YWGISYSRFEWLLEIVAHFYHHRGQIHIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=82 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 2p1aA/T0481-2p1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2p1aA/T0481-2p1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p1aA read from 2p1aA/T0481-2p1aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p1aA in template set T0481 1 :MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNAS 2p1aA 0 :GMFVQSALHQLKVAVDTSIQMLDQYTEIDLKIAPIQSKRSLFEMYAHLSLICHADLLILNGSTEK T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2p1aA 74 :TPETIAQMQKTMIQGYDLLSKTFLSYSNEQLAEMKTA T0481 110 :AFGRKVTGRALLQLAMEHEIHHKGNLFVY 2p1aA 111 :YWGISYSRFEWLLEIVAHFYHHRGQIHIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 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 2p1aA/T0481-2p1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2p1aA/T0481-2p1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p1aA read from 2p1aA/T0481-2p1aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p1aA in template set T0481 1 :MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQN 2p1aA 0 :GMFVQSALHQLKVAVDTSIQMLDQYTEIDLKIAPIQSKRSLFEMYAHLSLICHADLLILNGSTEKELHT T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 2p1aA 73 :QTPETIAQMQKTMIQGYDLLSKTFLSYSNEQLAEMK T0481 108 :TSAFGRKVTGRALLQLAMEHEIHHKGNLFVY 2p1aA 109 :TAYWGISYSRFEWLLEIVAHFYHHRGQIHIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=88 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 2yqyA/T0481-2yqyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2yqyA expands to /projects/compbio/data/pdb/2yqy.pdb.gz 2yqyA:# T0481 read from 2yqyA/T0481-2yqyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yqyA read from 2yqyA/T0481-2yqyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2yqyA to template set # found chain 2yqyA in template set Warning: unaligning (T0481)Q3 because first residue in template chain is (2yqyA)T9 Warning: unaligning (T0481)E73 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2yqyA)L104 Warning: unaligning (T0481)Q122 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2yqyA)A151 Warning: unaligning (T0481)L123 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A151 Warning: unaligning (T0481)A124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A152 T0481 4 :SNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2yqyA 10 :WDEALKRLEASRKALLALLREADPAWLSAPLREGAWTPLMVAEHVALVEDSTARVL T0481 74 :TETDLNVLAKTYTEKTVAILEQLTEEQ 2yqyA 105 :SLEEVLALLDRARAFLLEEVAKADPQN T0481 102 :DREID 2yqyA 132 :PATFP T0481 108 :TSAFG 2yqyA 137 :HPFFG T0481 114 :KVTGRALL 2yqyA 142 :ELNPLGWL T0481 125 :MEHEIHHKGNLFV 2yqyA 153 :AYHEAHHLKALQA Number of specific fragments extracted= 6 number of extra gaps= 1 total=94 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 2yqyA/T0481-2yqyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2yqyA/T0481-2yqyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yqyA read from 2yqyA/T0481-2yqyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yqyA in template set Warning: unaligning (T0481)Q3 because first residue in template chain is (2yqyA)T9 Warning: unaligning (T0481)E73 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2yqyA)L104 Warning: unaligning (T0481)Q122 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2yqyA)A151 Warning: unaligning (T0481)L123 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A151 Warning: unaligning (T0481)A124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A152 T0481 4 :SNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2yqyA 10 :WDEALKRLEASRKALLALLREADPAWLSAPLREGAWTPLMVAEHVALVEDSTARVL T0481 74 :TETDLNVLAKTYTEKTVAILEQLTEEQ 2yqyA 105 :SLEEVLALLDRARAFLLEEVAKADPQN T0481 102 :DREID 2yqyA 132 :PATFP T0481 108 :TSAFG 2yqyA 137 :HPFFG T0481 114 :KVTGRALL 2yqyA 142 :ELNPLGWL T0481 125 :MEHEIHHKGNLFV 2yqyA 153 :AYHEAHHLKALQA Number of specific fragments extracted= 6 number of extra gaps= 1 total=100 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 2yqyA/T0481-2yqyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2yqyA/T0481-2yqyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yqyA read from 2yqyA/T0481-2yqyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yqyA in template set Warning: unaligning (T0481)Q3 because first residue in template chain is (2yqyA)T9 Warning: unaligning (T0481)E73 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2yqyA)L104 Warning: unaligning (T0481)Q122 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2yqyA)A151 Warning: unaligning (T0481)L123 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A151 Warning: unaligning (T0481)A124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2yqyA)A152 T0481 4 :SNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2yqyA 10 :WDEALKRLEASRKALLALLREADPAWLSAPLREGAWTPLMVAEHVALVEDSTARVL T0481 74 :TETDLNVLAKTYTEKTVAILEQLTEEQ 2yqyA 105 :SLEEVLALLDRARAFLLEEVAKADPQN T0481 102 :DR 2yqyA 132 :PA T0481 106 :DLTSAFGRKVTGRALL 2yqyA 134 :TFPHPFFGELNPLGWL T0481 125 :MEHEIHHKGNL 2yqyA 153 :AYHEAHHLKAL Number of specific fragments extracted= 5 number of extra gaps= 1 total=105 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 2nsfA/T0481-2nsfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2nsfA expands to /projects/compbio/data/pdb/2nsf.pdb.gz 2nsfA:# T0481 read from 2nsfA/T0481-2nsfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsfA read from 2nsfA/T0481-2nsfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nsfA to template set # found chain 2nsfA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2nsfA 8 :PLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAHVAYNAIALCNLM T0481 60 :KEGNASPFQNKQEET 2nsfA 69 :TGEETPMYVSPEARN T0481 75 :ETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2nsfA 94 :PDALRNLHEHSVARLDVAWRETSEDAWSHEVLT T0481 110 :AFGRKV 2nsfA 127 :AQGRTV T0481 116 :TGRALLQLAMEHEIH 2nsfA 137 :TLWMRSREVWIHAVD T0481 132 :KGNLFVYVREM 2nsfA 167 :RTLAAEITQKW Number of specific fragments extracted= 6 number of extra gaps= 0 total=111 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 2nsfA/T0481-2nsfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2nsfA/T0481-2nsfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsfA read from 2nsfA/T0481-2nsfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nsfA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2nsfA 8 :PLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAHVAYNAIALCNLM T0481 60 :KEGNASPFQNK 2nsfA 69 :TGEETPMYVSP T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2nsfA 90 :STLNPDALRNLHEHSVARLDVAWRETSEDAWSHEVLT T0481 110 :AFGRKV 2nsfA 127 :AQGRTV T0481 116 :TGRALLQLAMEHEI 2nsfA 137 :TLWMRSREVWIHAV Number of specific fragments extracted= 5 number of extra gaps= 0 total=116 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 2nsfA/T0481-2nsfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2nsfA/T0481-2nsfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nsfA read from 2nsfA/T0481-2nsfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nsfA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2nsfA 8 :PLEERLTLARLGTSHYSRQLSLVDNAEFGEHSLLEGWTRSHLIAHVAYNAIALCNLM T0481 60 :KEGNASPFQN 2nsfA 68 :NTGEETPMYV T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 2nsfA 89 :GSTLNPDALRNLHEHSVARLDVAWRETSEDAWSHEV T0481 108 :TSAFGRKVTGRALLQLAMEHEIHH 2nsfA 125 :LTAQGRTVPASETLWMRSREVWIH Number of specific fragments extracted= 4 number of extra gaps= 0 total=120 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 2qnlA/T0481-2qnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qnlA expands to /projects/compbio/data/pdb/2qnl.pdb.gz 2qnlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 62, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2qnlA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 526, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 564, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 566, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 568, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 570, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 572, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 574, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 576, because occupancy 0.300 <= existing 0.700 in 2qnlA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2qnlA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2qnlA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0481 read from 2qnlA/T0481-2qnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qnlA read from 2qnlA/T0481-2qnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qnlA to template set # found chain 2qnlA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNA 2qnlA 8 :FVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDAMLPLLELGDT T0481 65 :SPFQNKQEET 2qnlA 81 :NPDKSGLEKP T0481 75 :ETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2qnlA 92 :INDLRLYWSLVQERLANQFNQLQPADWFNKHAA T0481 108 :TSA 2qnlA 133 :EPH T0481 115 :VTGRALLQLAMEHEIHHKGNL 2qnlA 136 :RNKLSVLINRTNHMAYHLGQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=125 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 2qnlA/T0481-2qnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2qnlA/T0481-2qnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qnlA read from 2qnlA/T0481-2qnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qnlA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVI 2qnlA 8 :FVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDAMLPLL T0481 60 :KEGNAS 2qnlA 66 :LGDTLY T0481 66 :PFQNK 2qnlA 82 :PDKSG T0481 71 :QEETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDL 2qnlA 88 :EKPEINDLRLYWSLVQERLANQFNQLQPADWFNKHAA T0481 108 :TSAF 2qnlA 133 :EPHR T0481 116 :TGRALLQLAMEHEIHHKGNL 2qnlA 137 :NKLSVLINRTNHMAYHLGQL 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=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qnlA/T0481-2qnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0481 read from 2qnlA/T0481-2qnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qnlA read from 2qnlA/T0481-2qnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qnlA in template set T0481 3 :QSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPF 2qnlA 8 :FVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDAMLPLLELGDTLYP T0481 69 :N 2qnlA 73 :Q T0481 70 :KQEETETDLNVLAKTYTEKTVAILEQLTEEQLDREI 2qnlA 87 :LEKPEINDLRLYWSLVQERLANQFNQLQPADWFNKH T0481 109 :SAF 2qnlA 123 :AAI T0481 112 :GRKVTGRALLQLAMEHEIHHKGNL 2qnlA 133 :EPHRNKLSVLINRTNHMAYHLGQL 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=30 # command:CPU_time= 13.973 sec, elapsed time= 15.444 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 627 constraints to all_contacts Done adding distance constraints # command:CPU_time= 14.006 sec, elapsed time= 15.481 sec. # command:Reading probabilities from T0481.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 25.109 Optimizing... Probability sum: -245.301, CN propb: -245.301 weights: 0.494 constraints: 185 # command:CPU_time= 16.164 sec, elapsed time= 17.639 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 185 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 185 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 442 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 442 # 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= 16.173 sec, elapsed time= 18.377 sec. # command: