# 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 T0586 numbered 1 through 125 Created new target T0586 from T0586.a2m # command:CPU_time= 5.791 sec, elapsed time= 8.152 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wv0A/T0586-2wv0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wv0A expands to /projects/compbio/data/pdb/2wv0.pdb.gz 2wv0A:Skipped atom 242, because occupancy 0.5 <= existing 0.500 in 2wv0A Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 244, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2wv0A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2wv0A # T0586 read from 2wv0A/T0586-2wv0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wv0A read from 2wv0A/T0586-2wv0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wv0A to template set # found chain 2wv0A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (2wv0A)M1 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITE 2wv0A 2 :NINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQALQGLTSFTEDMK # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 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 2wv0A/T0586-2wv0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2wv0A/T0586-2wv0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wv0A read from 2wv0A/T0586-2wv0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wv0A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (2wv0A)M1 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 2wv0A 2 :NINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSK T0586 80 :DKALFDQLKK 2wv0A 78 :KMEQALQGLT T0586 99 :FLEEAKSIGLD 2wv0A 89 :FTEDMKSRGMT T0586 110 :DQTAIELLI 2wv0A 113 :TEELAAILG T0586 120 :RSRNH 2wv0A 122 :CGHPS Number of specific fragments extracted= 5 number of extra gaps= 0 total=6 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2wv0A/T0586-2wv0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2wv0A/T0586-2wv0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wv0A read from 2wv0A/T0586-2wv0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wv0A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (2wv0A)M1 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQL 2wv0A 2 :NINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQALQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 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 3by6A/T0586-3by6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3by6A expands to /projects/compbio/data/pdb/3by6.pdb.gz 3by6A:# T0586 read from 3by6A/T0586-3by6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3by6A read from 3by6A/T0586-3by6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3by6A to template set # found chain 3by6A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (3by6A)Q-1 Warning: unaligning (T0586)R122 because last residue in template chain is (3by6A)G117 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRS 3by6A 0 :AMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDIL Number of specific fragments extracted= 1 number of extra gaps= 0 total=8 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 3by6A/T0586-3by6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3by6A/T0586-3by6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3by6A read from 3by6A/T0586-3by6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3by6A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (3by6A)Q-1 Warning: unaligning (T0586)S121 because last residue in template chain is (3by6A)G117 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIK 3by6A 0 :AMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVND Number of specific fragments extracted= 1 number of extra gaps= 0 total=9 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 3by6A/T0586-3by6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3by6A/T0586-3by6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3by6A read from 3by6A/T0586-3by6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3by6A in template set Warning: unaligning (T0586)M4 because first residue in template chain is (3by6A)Q-1 Warning: unaligning (T0586)R122 because last residue in template chain is (3by6A)G117 T0586 5 :NPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRS 3by6A 0 :AMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDIL Number of specific fragments extracted= 1 number of extra gaps= 0 total=10 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 3eetA/T0586-3eetA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3eetA expands to /projects/compbio/data/pdb/3eet.pdb.gz 3eetA:Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 3eetA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1135, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 3eetA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1521, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1529, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1531, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1533, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 3eetA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 3eetA # T0586 read from 3eetA/T0586-3eetA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eetA read from 3eetA/T0586-3eetA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3eetA to template set # found chain 3eetA in template set Warning: unaligning (T0586)D11 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)E5 Warning: unaligning (T0586)K70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3eetA)S67 Warning: unaligning (T0586)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)S67 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3eetA 6 :QPAYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEG T0586 72 :G 3eetA 68 :G T0586 75 :SFVTSDKAL 3eetA 69 :TYVRERPVP Number of specific fragments extracted= 3 number of extra gaps= 1 total=13 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 3eetA/T0586-3eetA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3eetA/T0586-3eetA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eetA read from 3eetA/T0586-3eetA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eetA in template set Warning: unaligning (T0586)D11 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)E5 Warning: unaligning (T0586)K70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3eetA)S67 Warning: unaligning (T0586)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)S67 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3eetA 6 :QPAYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEG T0586 72 :G 3eetA 68 :G T0586 75 :SFVTSDKA 3eetA 69 :TYVRERPV Number of specific fragments extracted= 3 number of extra gaps= 1 total=16 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 3eetA/T0586-3eetA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3eetA/T0586-3eetA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eetA read from 3eetA/T0586-3eetA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eetA in template set Warning: unaligning (T0586)D11 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)E5 Warning: unaligning (T0586)K70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3eetA)S67 Warning: unaligning (T0586)R71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3eetA)S67 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3eetA 6 :QPAYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEG T0586 72 :G 3eetA 68 :G T0586 75 :SFVTSDKA 3eetA 69 :TYVRERPV Number of specific fragments extracted= 3 number of extra gaps= 1 total=19 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 3edpA/T0586-3edpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3edpA expands to /projects/compbio/data/pdb/3edp.pdb.gz 3edpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1315, because occupancy 0.370 <= existing 0.630 in 3edpA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 3edpA Skipped atom 1332, because occupancy 0.410 <= existing 0.590 in 3edpA Skipped atom 1338, because occupancy 0.320 <= existing 0.680 in 3edpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 3edpA/T0586-3edpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3edpA read from 3edpA/T0586-3edpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3edpA to template set # found chain 3edpA in template set Warning: unaligning (T0586)D11 because first residue in template chain is (3edpA)K4 Warning: unaligning (T0586)E34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3edpA)M30 Warning: unaligning (T0586)D35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3edpA)M30 T0586 12 :KPIYSQISDWMKKQMITGEWKG 3edpA 5 :KPLFEVIASKIKDSINRDEYKT T0586 38 :PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKA 3edpA 31 :PNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVGLYVQPKLT T0586 89 :KELADAIT 3edpA 76 :AQNILEMT Number of specific fragments extracted= 3 number of extra gaps= 1 total=22 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 3edpA/T0586-3edpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3edpA/T0586-3edpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3edpA read from 3edpA/T0586-3edpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3edpA in template set Warning: unaligning (T0586)D11 because first residue in template chain is (3edpA)K4 Warning: unaligning (T0586)E34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3edpA)M30 Warning: unaligning (T0586)D35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3edpA)M30 T0586 12 :KPIYSQISDWMKKQMITGEWKG 3edpA 5 :KPLFEVIASKIKDSINRDEYKT T0586 38 :PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKA 3edpA 31 :PNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVGLYVQPKLT T0586 85 :DQLKKE 3edpA 76 :AQNILE Number of specific fragments extracted= 3 number of extra gaps= 1 total=25 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 3edpA/T0586-3edpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3edpA/T0586-3edpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3edpA read from 3edpA/T0586-3edpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3edpA in template set Warning: unaligning (T0586)D11 because first residue in template chain is (3edpA)K4 Warning: unaligning (T0586)E34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3edpA)M30 Warning: unaligning (T0586)D35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3edpA)M30 T0586 12 :KPIYSQISDWMKKQMITGEWKG 3edpA 5 :KPLFEVIASKIKDSINRDEYKT T0586 38 :PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFD 3edpA 31 :PNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVGLYVQPKLTAQN T0586 100 :LEE 3edpA 79 :ILE Number of specific fragments extracted= 3 number of extra gaps= 1 total=28 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 1hw1A/T0586-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hw1A expands to /projects/compbio/data/pdb/1hw1.pdb.gz 1hw1A:# T0586 read from 1hw1A/T0586-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0586-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hw1A to template set # found chain 1hw1A in template set Warning: unaligning (T0586)D11 because first residue in template chain is (1hw1A)A5 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1hw1A 6 :QSPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNN T0586 80 :DKALFDQLKKELADAITERFLEEA 1hw1A 90 :DHESVPQLIDNLLSVRTNISTIFI T0586 104 :KSIGLDDQTAIE 1hw1A 115 :TAFRQHPDKAQE T0586 117 :LIKRSRNHE 1hw1A 127 :VLATANEVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 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 1hw1A/T0586-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1hw1A/T0586-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0586-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set Warning: unaligning (T0586)D11 because first residue in template chain is (1hw1A)A5 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1hw1A 6 :QSPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNN T0586 81 :KALFDQLKKELADAITERFLEEAKSI 1hw1A 91 :HESVPQLIDNLLSVRTNISTIFIRTA T0586 107 :GLDDQTAIELLIK 1hw1A 118 :RQHPDKAQEVLAT T0586 120 :RSRN 1hw1A 133 :EVAD Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 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 1hw1A/T0586-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1hw1A/T0586-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0586-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set Warning: unaligning (T0586)D11 because first residue in template chain is (1hw1A)A5 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFD 1hw1A 6 :QSPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNNFWETSG T0586 86 :QLKKELADAITERFLEEAKSI 1hw1A 88 :RLDHESVPQLIDNLLSVRTNI T0586 107 :GLDDQTAIELL 1hw1A 118 :RQHPDKAQEVL T0586 119 :KRSRN 1hw1A 129 :ATANE Number of specific fragments extracted= 4 number of extra gaps= 0 total=40 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 2ek5A/T0586-2ek5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ek5A expands to /projects/compbio/data/pdb/2ek5.pdb.gz 2ek5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 2ek5A/T0586-2ek5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ek5A read from 2ek5A/T0586-2ek5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ek5A to template set # found chain 2ek5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2ek5A)V3 Warning: unaligning (T0586)H124 because last residue in template chain is (2ek5A)R117 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLK 2ek5A 4 :PLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRER T0586 89 :KELADAITERFLEEAKSIGLDDQTAIELLIKRSRN 2ek5A 82 :AAFAATYVAPLIDESIHLGFTRARIHALLDQVAES Number of specific fragments extracted= 2 number of extra gaps= 0 total=42 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 2ek5A/T0586-2ek5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2ek5A/T0586-2ek5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ek5A read from 2ek5A/T0586-2ek5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ek5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2ek5A)V3 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 2ek5A 4 :PLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQ T0586 81 :KALFDQLKKELADAIT 2ek5A 73 :PALIRERRDAAFAATY T0586 97 :ERFLEEAKSIGLDDQTAIELLIK 2ek5A 90 :APLIDESIHLGFTRARIHALLDQ T0586 121 :S 2ek5A 116 :S 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=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ek5A/T0586-2ek5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2ek5A/T0586-2ek5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ek5A read from 2ek5A/T0586-2ek5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ek5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2ek5A)V3 Warning: unaligning (T0586)H124 because last residue in template chain is (2ek5A)R117 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAIT 2ek5A 4 :PLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAAT T0586 97 :ERFLEEAKSIGLDDQTAIELLIKRSRN 2ek5A 90 :APLIDESIHLGFTRARIHALLDQVAES Number of specific fragments extracted= 2 number of extra gaps= 0 total=48 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 2di3A/T0586-2di3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2di3A expands to /projects/compbio/data/pdb/2di3.pdb.gz 2di3A:# T0586 read from 2di3A/T0586-2di3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2di3A read from 2di3A/T0586-2di3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2di3A to template set # found chain 2di3A in template set T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 2di3A 3 :VKAHESVMDWVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTISTATGS T0586 74 :GSFVTSDKALF 2di3A 69 :GTIITAAPGQA T0586 95 :ITERFLEEAKSIGLDDQTAIELLIKRS 2di3A 80 :LSLSVTLQLVTNQVGHHDIYETRQLLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=51 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 2di3A/T0586-2di3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2di3A/T0586-2di3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2di3A read from 2di3A/T0586-2di3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2di3A in template set T0586 14 :IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 2di3A 5 :AHESVMDWVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTISTATG T0586 73 :MGSFVTS 2di3A 68 :SGTIITA T0586 81 :KA 2di3A 77 :GQ T0586 94 :AITERFLEEAKSIGLDDQTAIELLIK 2di3A 79 :ALSLSVTLQLVTNQVGHHDIYETRQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2di3A/T0586-2di3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2di3A/T0586-2di3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2di3A read from 2di3A/T0586-2di3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2di3A in template set T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALF 2di3A 3 :VKAHESVMDWVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTISTATGSGPRSGTIITAA T0586 91 :LADAITERFLEEAKSIGLDDQTAIELLIKRS 2di3A 76 :PGQALSLSVTLQLVTNQVGHHDIYETRQLLE Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 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 3bwgA/T0586-3bwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bwgA expands to /projects/compbio/data/pdb/3bwg.pdb.gz 3bwgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1241, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 3bwgA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 3bwgA # T0586 read from 3bwgA/T0586-3bwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwgA read from 3bwgA/T0586-3bwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bwgA to template set # found chain 3bwgA in template set Warning: unaligning (T0586)I67 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F57 Warning: unaligning (T0586)Y68 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F57 Warning: unaligning (T0586)S75 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F65 Warning: unaligning (T0586)F76 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F65 T0586 17 :QISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGY 3bwgA 6 :QIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGA T0586 69 :AKRGMG 3bwgA 58 :QVRGSG T0586 77 :VTSDKA 3bwgA 66 :VRKHKR Number of specific fragments extracted= 3 number of extra gaps= 2 total=60 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 3bwgA/T0586-3bwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3bwgA/T0586-3bwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwgA read from 3bwgA/T0586-3bwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwgA in template set Warning: unaligning (T0586)I67 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F57 Warning: unaligning (T0586)Y68 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F57 Warning: unaligning (T0586)S75 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F65 Warning: unaligning (T0586)F76 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F65 T0586 17 :QISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGY 3bwgA 6 :QIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGA T0586 69 :AKRGMG 3bwgA 58 :QVRGSG T0586 77 :VTSDK 3bwgA 66 :VRKHK Number of specific fragments extracted= 3 number of extra gaps= 2 total=63 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 3bwgA/T0586-3bwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3bwgA/T0586-3bwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bwgA read from 3bwgA/T0586-3bwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bwgA in template set Warning: unaligning (T0586)I67 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F57 Warning: unaligning (T0586)Y68 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F57 Warning: unaligning (T0586)S75 because of BadResidue code BAD_PEPTIDE in next template residue (3bwgA)F65 Warning: unaligning (T0586)F76 because of BadResidue code BAD_PEPTIDE at template residue (3bwgA)F65 T0586 17 :QISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGY 3bwgA 6 :QIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGA T0586 69 :AKRGMG 3bwgA 58 :QVRGSG T0586 77 :VTSDKA 3bwgA 66 :VRKHKR Number of specific fragments extracted= 3 number of extra gaps= 2 total=66 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 3ic7A/T0586-3ic7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ic7A expands to /projects/compbio/data/pdb/3ic7.pdb.gz 3ic7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 3ic7A/T0586-3ic7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ic7A read from 3ic7A/T0586-3ic7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ic7A to template set # found chain 3ic7A in template set Warning: unaligning (T0586)D35 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)R31 Warning: unaligning (T0586)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)R31 Warning: unaligning (T0586)L37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)I32 Warning: unaligning (T0586)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)V44 Warning: unaligning (T0586)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)V44 Warning: unaligning (T0586)A64 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)E60 Warning: unaligning (T0586)G65 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)E60 Warning: unaligning (T0586)R98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)F96 Warning: unaligning (T0586)F99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)F96 Warning: unaligning (T0586)N123 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)Q121 Warning: unaligning (T0586)H124 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)Q121 T0586 17 :QISDWMKKQMITGEWKGE 3ic7A 12 :QIADRICDDILLGQYEEE T0586 38 :PSVREMGVK 3ic7A 33 :PSVREYASI T0586 50 :NPNTVSRAYQELER 3ic7A 45 :NANTVMRSYEYLQS T0586 66 :YIYAKRGMGSFVTSDKALFDQLK 3ic7A 61 :VIYNKRGIGFFVASGAKMLIHSL T0586 89 :KELADAITE 3ic7A 86 :EQFLKEEVG T0586 100 :LEEAKSIGLDDQTAIELLIKRSR 3ic7A 97 :FRQLYTLGISIKEIEKMYYEFIQ Number of specific fragments extracted= 6 number of extra gaps= 4 total=72 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 3ic7A/T0586-3ic7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3ic7A/T0586-3ic7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ic7A read from 3ic7A/T0586-3ic7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ic7A in template set Warning: unaligning (T0586)D35 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)R31 Warning: unaligning (T0586)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)R31 Warning: unaligning (T0586)L37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)I32 Warning: unaligning (T0586)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)V44 Warning: unaligning (T0586)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)V44 Warning: unaligning (T0586)A64 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)E60 Warning: unaligning (T0586)G65 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)E60 Warning: unaligning (T0586)R98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)F96 Warning: unaligning (T0586)F99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)F96 T0586 17 :QISDWMKKQMITGEWKGE 3ic7A 12 :QIADRICDDILLGQYEEE T0586 38 :PSVREMGVK 3ic7A 33 :PSVREYASI T0586 50 :NPNTVSRAYQELER 3ic7A 45 :NANTVMRSYEYLQS T0586 66 :YIYAKRGMGSFVTSD 3ic7A 61 :VIYNKRGIGFFVASG T0586 81 :KALFDQLKKELADAIT 3ic7A 77 :KMLIHSLRKEQFLKEE T0586 97 :E 3ic7A 94 :G T0586 100 :LEEAKSIGLDDQTAIE 3ic7A 97 :FRQLYTLGISIKEIEK Number of specific fragments extracted= 7 number of extra gaps= 3 total=79 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 3ic7A/T0586-3ic7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3ic7A/T0586-3ic7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ic7A read from 3ic7A/T0586-3ic7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ic7A in template set Warning: unaligning (T0586)D35 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)R31 Warning: unaligning (T0586)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)R31 Warning: unaligning (T0586)L37 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)I32 Warning: unaligning (T0586)L47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)V44 Warning: unaligning (T0586)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)V44 Warning: unaligning (T0586)A64 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)E60 Warning: unaligning (T0586)G65 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)E60 Warning: unaligning (T0586)R98 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3ic7A)F96 Warning: unaligning (T0586)F99 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3ic7A)F96 T0586 17 :QISDWMKKQMITGEWKGE 3ic7A 12 :QIADRICDDILLGQYEEE T0586 38 :PSVREMGVK 3ic7A 33 :PSVREYASI T0586 50 :NPNTVSRAYQELER 3ic7A 45 :NANTVMRSYEYLQS T0586 66 :YIYAKRGMGSFVTSDKALFDQLKKELADAIT 3ic7A 61 :VIYNKRGIGFFVASGAKMLIHSLRKEQFLKE T0586 97 :E 3ic7A 94 :G T0586 100 :LEEAKSIGLDDQTAIE 3ic7A 97 :FRQLYTLGISIKEIEK Number of specific fragments extracted= 6 number of extra gaps= 3 total=85 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 3f8mA/T0586-3f8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3f8mA expands to /projects/compbio/data/pdb/3f8m.pdb.gz 3f8mA:Skipped atom 135, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 139, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 141, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 143, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 145, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 147, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 149, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 151, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 510, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 514, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 516, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 518, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 520, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 524, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 965, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 969, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 971, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 973, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 975, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1027, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1031, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1033, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1035, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1037, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1039, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1085, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1089, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 3f8mA # T0586 read from 3f8mA/T0586-3f8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f8mA read from 3f8mA/T0586-3f8mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f8mA to template set # found chain 3f8mA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3f8mA)L10 T0586 14 :IYSQISDWMKKQMIT 3f8mA 11 :KHQVVRAELDRMLDG T0586 31 :WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3f8mA 26 :MRIGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER T0586 71 :RGMGSFVTSDKALFDQL 3f8mA 65 :RGRTTVVARPKIRQPLG T0586 89 :KELADAIT 3f8mA 82 :MGSYTEAA T0586 104 :KSIGLD 3f8mA 90 :KAQGLS T0586 110 :DQTAIELL 3f8mA 109 :DEVLAGVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=91 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 3f8mA/T0586-3f8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3f8mA/T0586-3f8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f8mA read from 3f8mA/T0586-3f8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f8mA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3f8mA)L10 T0586 14 :IYSQISDWMKKQMIT 3f8mA 11 :KHQVVRAELDRMLDG T0586 31 :WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3f8mA 26 :MRIGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER T0586 71 :RGMGSFVTSDK 3f8mA 65 :RGRTTVVARPK T0586 99 :FLEEAKSIGLD 3f8mA 85 :YTEAAKAQGLS T0586 110 :DQTAIELLI 3f8mA 109 :DEVLAGVLG T0586 120 :RSRNH 3f8mA 118 :VDVGA Number of specific fragments extracted= 6 number of extra gaps= 0 total=97 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 3f8mA/T0586-3f8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3f8mA/T0586-3f8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f8mA read from 3f8mA/T0586-3f8mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3f8mA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3f8mA)L10 T0586 14 :IYSQISDWMKKQMIT 3f8mA 11 :KHQVVRAELDRMLDG T0586 31 :WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 3f8mA 26 :MRIGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER T0586 71 :RGMGSFVTSDK 3f8mA 65 :RGRTTVVARPK T0586 99 :FLEEAKSIGLD 3f8mA 85 :YTEAAKAQGLS Number of specific fragments extracted= 4 number of extra gaps= 0 total=101 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 3c7jA/T0586-3c7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3c7jA expands to /projects/compbio/data/pdb/3c7j.pdb.gz 3c7jA:Skipped atom 3, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 3c7jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 210, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 3c7jA Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 3c7jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 3c7jA/T0586-3c7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c7jA read from 3c7jA/T0586-3c7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3c7jA to template set # found chain 3c7jA in template set T0586 5 :NPTF 3c7jA 18 :QPPA T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKL 3c7jA 22 :HLARTVIEEKLRNAIIDGSLPSGTAL T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKS 3c7jA 48 :RQQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLSIP T0586 107 :GLD 3c7jA 115 :LLD T0586 111 :QTAIELLIKRSR 3c7jA 118 :ADDLAAAASYIE Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 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 3c7jA/T0586-3c7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3c7jA/T0586-3c7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c7jA read from 3c7jA/T0586-3c7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c7jA in template set T0586 14 :IYSQISDWMKKQMITGEWKGEDKLP 3c7jA 24 :ARTVIEEKLRNAIIDGSLPSGTALR T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKA 3c7jA 49 :QQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLIT T0586 86 :QLKKELADAITERFLEEAKSI 3c7jA 92 :EDAVDAYALRILLESEALRLS T0586 107 :GLDDQ 3c7jA 115 :LLDAD T0586 112 :TAIELLIK 3c7jA 123 :AAASYIEQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=111 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 3c7jA/T0586-3c7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3c7jA/T0586-3c7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3c7jA read from 3c7jA/T0586-3c7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3c7jA in template set T0586 6 :PTFHADKPIYSQISDWMKKQMITGEWKGEDKLP 3c7jA 16 :NEQPPAHLARTVIEEKLRNAIIDGSLPSGTALR T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEA 3c7jA 49 :QQELATLFGVSRMPVREALRQLEAQSLLRVETHKGAVVAPLITEDAVDAYALRILLESEALRLS T0586 107 :GL 3c7jA 115 :LL T0586 110 :DQTAIELLIKRSR 3c7jA 117 :DADDLAAAASYIE 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=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hs5A/T0586-2hs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hs5A expands to /projects/compbio/data/pdb/2hs5.pdb.gz 2hs5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 2hs5A/T0586-2hs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hs5A read from 2hs5A/T0586-2hs5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hs5A to template set # found chain 2hs5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2hs5A)T25 Warning: unaligning (T0586)V40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2hs5A)P53 Warning: unaligning (T0586)R41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2hs5A)P53 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKL 2hs5A 26 :SRTTRVAGILRDAIIDGTFRPGARL T0586 39 :S 2hs5A 51 :S T0586 42 :EMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIEL 2hs5A 54 :DICAALDVSRNTVREAFQILIEDRLVAHELNRGVFVRVPTAEDITELYICRRVVECAGVNGFDPATGDLSRVAEA T0586 117 :LIKRSRNH 2hs5A 132 :ADERYAVE Number of specific fragments extracted= 4 number of extra gaps= 1 total=119 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 2hs5A/T0586-2hs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2hs5A/T0586-2hs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hs5A read from 2hs5A/T0586-2hs5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hs5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2hs5A)T25 Warning: unaligning (T0586)V40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2hs5A)P53 Warning: unaligning (T0586)R41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2hs5A)P53 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLP 2hs5A 26 :SRTTRVAGILRDAIIDGTFRPGARLS T0586 42 :EMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 2hs5A 54 :DICAALDVSRNTVREAFQILIEDRLVAHELNRGVFVRV T0586 80 :DKALFDQLK 2hs5A 93 :TAEDITELY T0586 90 :ELADAITERFLEEAKSIGLDDQTAIELLIK 2hs5A 102 :ICRRVVECAGVNGFDPATGDLSRVAEALDL Number of specific fragments extracted= 4 number of extra gaps= 1 total=123 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 2hs5A/T0586-2hs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2hs5A/T0586-2hs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hs5A read from 2hs5A/T0586-2hs5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hs5A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (2hs5A)T25 Warning: unaligning (T0586)V40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2hs5A)P53 Warning: unaligning (T0586)R41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2hs5A)P53 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLP 2hs5A 26 :SRTTRVAGILRDAIIDGTFRPGARLS T0586 42 :EMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKA 2hs5A 54 :DICAALDVSRNTVREAFQILIEDRLVAHELNRGVFVRVPTA T0586 94 :AITERFLEEAKSI 2hs5A 95 :EDITELYICRRVV T0586 107 :GLDDQTAIEL 2hs5A 119 :TGDLSRVAEA Number of specific fragments extracted= 4 number of extra gaps= 1 total=127 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 3fmsA/T0586-3fmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3fmsA expands to /projects/compbio/data/pdb/3fms.pdb.gz 3fmsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 3fmsA/T0586-3fmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fmsA read from 3fmsA/T0586-3fmsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fmsA to template set # found chain 3fmsA in template set T0586 13 :PIYSQISDWMKKQMITGEWKGEDKL 3fmsA 8 :LVRTKVYNLLKEMILNHELKLGEKL T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK 3fmsA 33 :NVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVD T0586 89 :KELADAITERFLEEAKSI 3fmsA 76 :EKFIRETIETRIMMEVFC T0586 107 :GLDDQTAI 3fmsA 95 :ENYFDKIA T0586 115 :ELLIKRSR 3fmsA 105 :EELLEIKG Number of specific fragments extracted= 5 number of extra gaps= 0 total=132 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 3fmsA/T0586-3fmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3fmsA/T0586-3fmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fmsA read from 3fmsA/T0586-3fmsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fmsA in template set T0586 14 :IYSQISDWMKKQMITGEWKGEDKL 3fmsA 9 :VRTKVYNLLKEMILNHELKLGEKL T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 3fmsA 33 :NVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTD T0586 80 :DKALFDQLKKELAD 3fmsA 75 :DEKFIRETIETRIM T0586 94 :AITE 3fmsA 105 :EELL T0586 98 :RFLEEAKSIG 3fmsA 112 :GEIDDVAASA T0586 109 :DDQTAIELLI 3fmsA 122 :AREIFDDSDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=138 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 3fmsA/T0586-3fmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3fmsA/T0586-3fmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fmsA read from 3fmsA/T0586-3fmsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fmsA in template set Warning: unaligning (T0586)D11 because first residue in template chain is (3fmsA)V6 T0586 12 :KPIYSQISDWMKKQMITGEWKGEDKLP 3fmsA 7 :DLVRTKVYNLLKEMILNHELKLGEKLN T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK 3fmsA 34 :VRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVD T0586 93 :DAITERFLEEAKSI 3fmsA 76 :EKFIRETIETRIMM Number of specific fragments extracted= 3 number of extra gaps= 0 total=141 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 3ihuA/T0586-3ihuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ihuA expands to /projects/compbio/data/pdb/3ihu.pdb.gz 3ihuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 806, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1175, because occupancy 0.400 <= existing 0.600 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1179, because occupancy 0.400 <= existing 0.600 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1181, because occupancy 0.400 <= existing 0.600 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1183, because occupancy 0.300 <= existing 0.450 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1185, because occupancy 0.400 <= existing 0.600 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1298, because occupancy 0.500 <= existing 0.500 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1302, because occupancy 0.500 <= existing 0.500 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1304, because occupancy 0.500 <= existing 0.500 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1306, because occupancy 0.370 <= existing 0.380 in 3ihuA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 3ihuA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 3ihuA # T0586 read from 3ihuA/T0586-3ihuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ihuA read from 3ihuA/T0586-3ihuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ihuA to template set # found chain 3ihuA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3ihuA)S15 Warning: unaligning (T0586)T78 because of BadResidue code BAD_PEPTIDE in next template residue (3ihuA)R80 Warning: unaligning (T0586)S79 because of BadResidue code BAD_PEPTIDE at template residue (3ihuA)R80 T0586 14 :IYSQISDWMKKQMITGEWKGEDKL 3ihuA 16 :ASDTVFFGIMSGLELGTFVPGQRL T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 3ihuA 40 :VETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGAVI T0586 80 :DK 3ihuA 81 :LS T0586 89 :KELADAITERFLEEAKSI 3ihuA 83 :LQETLDVLDVAERMTGLL T0586 107 :GLDDQTAIELLIKRSR 3ihuA 107 :GSGNQPQVQALRASVQ Number of specific fragments extracted= 5 number of extra gaps= 1 total=146 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 3ihuA/T0586-3ihuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3ihuA/T0586-3ihuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ihuA read from 3ihuA/T0586-3ihuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ihuA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3ihuA)S15 Warning: unaligning (T0586)T78 because of BadResidue code BAD_PEPTIDE in next template residue (3ihuA)R80 Warning: unaligning (T0586)S79 because of BadResidue code BAD_PEPTIDE at template residue (3ihuA)R80 T0586 14 :IYSQISDWMKKQMITGEWKGEDKL 3ihuA 16 :ASDTVFFGIMSGLELGTFVPGQRL T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 3ihuA 40 :VETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGAVI T0586 80 :DKALFDQLKKELAD 3ihuA 82 :SLQETLDVLDVAER T0586 94 :AITERFLEEAKSI 3ihuA 115 :QALRASVQALVAA T0586 107 :G 3ihuA 131 :Q T0586 109 :DDQTAIELLIK 3ihuA 132 :DGETFSNARRH Number of specific fragments extracted= 6 number of extra gaps= 1 total=152 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 3ihuA/T0586-3ihuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3ihuA/T0586-3ihuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ihuA read from 3ihuA/T0586-3ihuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ihuA in template set Warning: unaligning (T0586)P13 because first residue in template chain is (3ihuA)S15 Warning: unaligning (T0586)T78 because of BadResidue code BAD_PEPTIDE in next template residue (3ihuA)R80 Warning: unaligning (T0586)S79 because of BadResidue code BAD_PEPTIDE at template residue (3ihuA)R80 T0586 14 :IYSQISDWMKKQMITGEWKGEDKLP 3ihuA 16 :ASDTVFFGIMSGLELGTFVPGQRLV T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 3ihuA 41 :ETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGAVI T0586 80 :DK 3ihuA 81 :LS T0586 89 :KELADAITERFLEEAKSI 3ihuA 83 :LQETLDVLDVAERMTGLL T0586 111 :QTAIELLIKRS 3ihuA 111 :QPQVQALRASV Number of specific fragments extracted= 5 number of extra gaps= 1 total=157 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 1fx7A/T0586-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fx7A expands to /projects/compbio/data/pdb/1fx7.pdb.gz 1fx7A:Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1fx7A # T0586 read from 1fx7A/T0586-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0586-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fx7A to template set # found chain 1fx7A in template set T0586 14 :IYSQISDWMKKQMIT 1fx7A 7 :TTEMYLRTIYDLEEE T0586 34 :EDKL 1fx7A 22 :GVTP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1fx7A 26 :LRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELTE T0586 86 :QL 1fx7A 67 :KG T0586 89 :KELADAITERFL 1fx7A 69 :RALAIAVMRKHR T0586 101 :EEAKSIGLDDQTAIELLIKRSRNHE 1fx7A 85 :LLVDVIGLPWEEVHAEACRWEHVMS Number of specific fragments extracted= 6 number of extra gaps= 0 total=163 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 1fx7A/T0586-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1fx7A/T0586-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0586-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx7A in template set T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 1fx7A 26 :LRARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIK 1fx7A 66 :EKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACR Number of specific fragments extracted= 2 number of extra gaps= 0 total=165 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 1fx7A/T0586-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1fx7A/T0586-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0586-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx7A in template set T0586 26 :MITGEWK 1fx7A 20 :EEGVTPL T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 1fx7A 27 :RARIAERLDQSGPTVSQTVSRMERDGLLRVAGDRHLELT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRN 1fx7A 66 :EKGRALAIAVMRKHRLAERLLVDVIGLPWEEVHAEACRWEHV Number of specific fragments extracted= 3 number of extra gaps= 0 total=168 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 2qq9A/T0586-2qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qq9A expands to /projects/compbio/data/pdb/2qq9.pdb.gz 2qq9A:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 963, because occupancy 0.300 <= existing 0.700 in 2qq9A Skipped atom 967, because occupancy 0.300 <= existing 0.700 in 2qq9A Skipped atom 969, because occupancy 0.300 <= existing 0.700 in 2qq9A Skipped atom 971, because occupancy 0.300 <= existing 0.700 in 2qq9A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1395, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1399, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 2qq9A Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 2qq9A # T0586 read from 2qq9A/T0586-2qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qq9A read from 2qq9A/T0586-2qq9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qq9A to template set # found chain 2qq9A in template set T0586 13 :PIYSQISDWMKKQMITG 2qq9A 6 :ATTEMYLRTIYELEEEG T0586 35 :DKL 2qq9A 23 :VTP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 2qq9A 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQM T0586 89 :KELADAITERFLEEA 2qq9A 65 :TPTGRTLATAVMRKH T0586 104 :KSIGLDDQTAIELLIKRSRNHE 2qq9A 88 :DIIGLDINKVHDEADRWEHVMS Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qq9A/T0586-2qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2qq9A/T0586-2qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qq9A read from 2qq9A/T0586-2qq9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qq9A in template set T0586 19 :SDWMKKQMITGE 2qq9A 12 :LRTIYELEEEGV T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2qq9A 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKR 2qq9A 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRW Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qq9A/T0586-2qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2qq9A/T0586-2qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qq9A read from 2qq9A/T0586-2qq9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qq9A in template set T0586 21 :WMKKQMITGE 2qq9A 14 :TIYELEEEGV T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2qq9A 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRN 2qq9A 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHV Number of specific fragments extracted= 3 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dtrA/T0586-2dtrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dtrA expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtrA:# T0586 read from 2dtrA/T0586-2dtrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtrA read from 2dtrA/T0586-2dtrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dtrA to template set # found chain 2dtrA in template set T0586 12 :KPIYSQISDWMKKQMITG 2dtrA 5 :VDTTEMYLRTIYELEEEG T0586 35 :DKL 2dtrA 23 :VTP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtrA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRNHE 2dtrA 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMS Number of specific fragments extracted= 4 number of extra gaps= 0 total=183 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 2dtrA/T0586-2dtrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2dtrA/T0586-2dtrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtrA read from 2dtrA/T0586-2dtrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtrA in template set T0586 21 :WMKKQMITGE 2dtrA 14 :TIYELEEEGV T0586 36 :KL 2dtrA 24 :TP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtrA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIK 2dtrA 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACR Number of specific fragments extracted= 4 number of extra gaps= 0 total=187 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 2dtrA/T0586-2dtrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2dtrA/T0586-2dtrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtrA read from 2dtrA/T0586-2dtrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtrA in template set T0586 21 :WMKKQMITGE 2dtrA 14 :TIYELEEEGV T0586 36 :KL 2dtrA 24 :TP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtrA 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRN 2dtrA 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHV Number of specific fragments extracted= 4 number of extra gaps= 0 total=191 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 1on2A/T0586-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1on2A expands to /projects/compbio/data/pdb/1on2.pdb.gz 1on2A:# T0586 read from 1on2A/T0586-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0586-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1on2A to template set # found chain 1on2A in template set T0586 16 :SQIS 1on2A 8 :MYIE T0586 21 :WMKKQMIT 1on2A 12 :QIYMLIEE T0586 35 :DKL 1on2A 21 :GYA T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1on2A 24 :RVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTS T0586 83 :L 1on2A 65 :K T0586 85 :DQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRNHE 1on2A 66 :GKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLS Number of specific fragments extracted= 6 number of extra gaps= 0 total=197 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 1on2A/T0586-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1on2A/T0586-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0586-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on2A in template set T0586 14 :IYSQISDWMKKQ 1on2A 9 :YIEQIYMLIEEK T0586 29 :GEW 1on2A 21 :GYA T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 1on2A 24 :RVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLT T0586 82 :ALFDQLKKELAD 1on2A 64 :SKGKKIGKRLVY T0586 95 :ITERFLEEAKSIGLDDQTAIELLIKRSR 1on2A 76 :RHELLEQFLRIIGVDEEKIYNDVEGIEH Number of specific fragments extracted= 5 number of extra gaps= 0 total=202 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 1on2A/T0586-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1on2A/T0586-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0586-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on2A in template set T0586 13 :PIYSQISDWMKKQ 1on2A 8 :MYIEQIYMLIEEK T0586 29 :GEWK 1on2A 21 :GYAR T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 1on2A 25 :VSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSK T0586 84 :F 1on2A 66 :G T0586 86 :QLKKELADAITERFLEEAKSIGLDDQTAIELLIK 1on2A 67 :KKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=207 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 1ulyA/T0586-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ulyA expands to /projects/compbio/data/pdb/1uly.pdb.gz 1ulyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 1ulyA/T0586-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0586-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ulyA to template set # found chain 1ulyA in template set T0586 12 :KPIYSQISDWM 1ulyA 19 :EDTRRKILKLL T0586 33 :GEDKL 1ulyA 30 :RNKEM T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS 1ulyA 35 :TISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMK T0586 76 :FVTS 1ulyA 74 :LVEK T0586 80 :DKALFDQL 1ulyA 90 :LYLGDEEL T0586 89 :KELADAITERFLEEAKSIG 1ulyA 98 :RYIARSRLKTKIDIFKRLG T0586 108 :LDDQTAIELLIKRS 1ulyA 119 :FEENELLNIMDRMS Number of specific fragments extracted= 7 number of extra gaps= 0 total=214 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 1ulyA/T0586-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1ulyA/T0586-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0586-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ulyA in template set T0586 16 :S 1ulyA 23 :R T0586 21 :WMKKQMITGEW 1ulyA 24 :KILKLLRNKEM T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYA 1ulyA 35 :TISQLSEILGKTPQTIYHHIEKLKEAGLVEV T0586 70 :KRGMGSFVTS 1ulyA 74 :LVEKYYGRTA T0586 81 :KALFDQLKKELADAITERFLEEAKSIG 1ulyA 90 :LYLGDEELRYIARSRLKTKIDIFKRLG T0586 108 :LDDQTAIELLIK 1ulyA 119 :FEENELLNIMDR Number of specific fragments extracted= 6 number of extra gaps= 0 total=220 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 1ulyA/T0586-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1ulyA/T0586-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0586-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ulyA in template set T0586 14 :IYS 1ulyA 21 :TRR T0586 21 :WMKKQMITGEW 1ulyA 24 :KILKLLRNKEM T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 1ulyA 35 :TISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0586 74 :GSFVTSD 1ulyA 76 :EKYYGRT T0586 81 :KALFDQLKKELADAITERFLEEAKSIGL 1ulyA 90 :LYLGDEELRYIARSRLKTKIDIFKRLGY T0586 109 :DDQTAIELLIKRS 1ulyA 120 :EENELLNIMDRMS Number of specific fragments extracted= 6 number of extra gaps= 0 total=226 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 2h09A/T0586-2h09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h09A expands to /projects/compbio/data/pdb/2h09.pdb.gz 2h09A:# T0586 read from 2h09A/T0586-2h09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h09A read from 2h09A/T0586-2h09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h09A to template set # found chain 2h09A in template set T0586 14 :IYSQISDWMKKQMITG 2h09A 37 :LIDDYVELISDLIREV T0586 35 :DKL 2h09A 53 :GEA T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2h09A 56 :RQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPWRGVFLT T0586 82 :ALFDQ 2h09A 96 :AEGEK T0586 88 :KKELADAITERFLEEAKSIGLDDQTAIELLIKRSRNH 2h09A 101 :LAQESRERHQIVENFLLVLGVSPEIARRDAEGMEHHV 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=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h09A/T0586-2h09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2h09A/T0586-2h09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h09A read from 2h09A/T0586-2h09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h09A in template set T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 2h09A 56 :RQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPWRGVFL T0586 81 :KALFDQLKKELAD 2h09A 95 :TAEGEKLAQESRE T0586 95 :ITERFLEEAKSIGLDDQTAIELLIK 2h09A 108 :RHQIVENFLLVLGVSPEIARRDAEG 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=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h09A/T0586-2h09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2h09A/T0586-2h09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h09A read from 2h09A/T0586-2h09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h09A in template set T0586 28 :TGEWK 2h09A 52 :VGEAR T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 2h09A 57 :QVDMAARLGVSQPTVAKMLKRLATMGLIEMIPWRGVFLTA T0586 83 :LFDQLK 2h09A 97 :EGEKLA T0586 90 :ELADAITERFLEEAKSIGLDDQTAIELL 2h09A 103 :QESRERHQIVENFLLVLGVSPEIARRDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=238 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 2qlzA/T0586-2qlzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qlzA expands to /projects/compbio/data/pdb/2qlz.pdb.gz 2qlzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 2qlzA/T0586-2qlzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qlzA read from 2qlzA/T0586-2qlzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qlzA to template set # found chain 2qlzA in template set Warning: unaligning (T0586)P51 because of BadResidue code BAD_PEPTIDE in next template residue (2qlzA)T40 Warning: unaligning (T0586)N52 because of BadResidue code BAD_PEPTIDE at template residue (2qlzA)T40 Warning: unaligning (T0586)T53 because of BadResidue code BAD_PEPTIDE at template residue (2qlzA)A41 Warning: unaligning (T0586)G74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qlzA)T68 T0586 12 :KPIYSQI 2qlzA 11 :NKVRRDL T0586 23 :KKQMITGEWKGEDKL 2qlzA 18 :LSHLTCMECYFSLLS T0586 45 :VKLAVN 2qlzA 33 :SKVSVS T0586 54 :VSRAYQELERAGYIYAKRGM 2qlzA 42 :VAKHLKIMEREGVLQSYEKE T0586 80 :DKALFDQLKKELADAITERFLEEAKSIG 2qlzA 112 :DTEPSTLKEMITDFIKANKELEKVLEAF T0586 108 :LDDQTAIELLIK 2qlzA 144 :SYRSSLMRKIKE Number of specific fragments extracted= 6 number of extra gaps= 1 total=244 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 2qlzA/T0586-2qlzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2qlzA/T0586-2qlzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qlzA read from 2qlzA/T0586-2qlzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qlzA in template set Warning: unaligning (T0586)P51 because of BadResidue code BAD_PEPTIDE in next template residue (2qlzA)T40 Warning: unaligning (T0586)N52 because of BadResidue code BAD_PEPTIDE at template residue (2qlzA)T40 Warning: unaligning (T0586)T53 because of BadResidue code BAD_PEPTIDE at template residue (2qlzA)A41 T0586 17 :Q 2qlzA 16 :D T0586 22 :MKKQMITGEWKGEDKL 2qlzA 17 :LLSHLTCMECYFSLLS T0586 45 :VKLAVN 2qlzA 33 :SKVSVS T0586 54 :VSRAYQELERAGYIYAKRGM 2qlzA 42 :VAKHLKIMEREGVLQSYEKE Number of specific fragments extracted= 4 number of extra gaps= 1 total=248 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 2qlzA/T0586-2qlzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2qlzA/T0586-2qlzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qlzA read from 2qlzA/T0586-2qlzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qlzA in template set T0586 40 :VREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 2qlzA 181 :VEELSDRLNLKEREVREKISEMARFVPVKIIND Number of specific fragments extracted= 1 number of extra gaps= 0 total=249 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 1e2xA/T0586-1e2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e2xA expands to /projects/compbio/data/pdb/1e2x.pdb.gz 1e2xA:Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1738, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1740, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1e2xA Skipped atom 1742, because occupancy 0.500 <= existing 0.500 in 1e2xA # T0586 read from 1e2xA/T0586-1e2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e2xA read from 1e2xA/T0586-1e2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e2xA to template set # found chain 1e2xA in template set Warning: unaligning (T0586)K12 because first residue in template chain is (1e2xA)Q6 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1e2xA 7 :SPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNN T0586 81 :KALFDQLK 1e2xA 91 :HESVPQLI T0586 89 :KELADAITERFLEEAKSI 1e2xA 110 :TIFIRTAFRQHPDKAQEV T0586 107 :GLD 1e2xA 133 :EVA T0586 110 :DQTAIELLIKRS 1e2xA 138 :ADAFAELDYNIF Number of specific fragments extracted= 5 number of extra gaps= 0 total=254 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 1e2xA/T0586-1e2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1e2xA/T0586-1e2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e2xA read from 1e2xA/T0586-1e2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e2xA in template set T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 1e2xA 7 :SPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNN T0586 80 :DKALFD 1e2xA 79 :GLNILE T0586 86 :QL 1e2xA 88 :RL T0586 88 :KKELADAITERFLEEAKSI 1e2xA 94 :VPQLIDNLLSVRTNISTIF T0586 109 :DDQTAIELLIK 1e2xA 120 :HPDKAQEVLAT Number of specific fragments extracted= 5 number of extra gaps= 0 total=259 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 1e2xA/T0586-1e2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 1e2xA/T0586-1e2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e2xA read from 1e2xA/T0586-1e2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e2xA in template set Warning: unaligning (T0586)K12 because first residue in template chain is (1e2xA)Q6 T0586 13 :PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFD 1e2xA 7 :SPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKVNNFWETSG T0586 86 :QLKKELADAITERFLEEAKSI 1e2xA 88 :RLDHESVPQLIDNLLSVRTNI T0586 110 :DQTAIELL 1e2xA 121 :PDKAQEVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=262 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 3l09A/T0586-3l09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3l09A expands to /projects/compbio/data/pdb/3l09.pdb.gz 3l09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0586 read from 3l09A/T0586-3l09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l09A read from 3l09A/T0586-3l09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3l09A to template set # found chain 3l09A in template set T0586 11 :DKPIYSQISDWMKKQMITGEWK 3l09A 20 :PLKLWSVLVTCLGDVSRDGVIE T0586 36 :KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK 3l09A 43 :SGVALSSFVERMGLQPQAMRVALHRLKRDGWVESR T0586 71 :RGMGSFVTS 3l09A 79 :LGRVGFHRL T0586 89 :KELADAITERFLEEAKSIGLD 3l09A 88 :SDSALTQTRAVAGRIYGPGAG Number of specific fragments extracted= 4 number of extra gaps= 0 total=266 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 3l09A/T0586-3l09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3l09A/T0586-3l09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l09A read from 3l09A/T0586-3l09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l09A in template set T0586 14 :IYSQISDWMKKQMITGE 3l09A 23 :LWSVLVTCLGDVSRDGV T0586 36 :KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTS 3l09A 43 :SGVALSSFVERMGLQPQAMRVALHRLKRDGWVESRRLGRVGFHR T0586 81 :K 3l09A 88 :S T0586 97 :ERFLEEAKSI 3l09A 89 :DSALTQTRAV T0586 114 :IELLIK 3l09A 99 :AGRIYG T0586 120 :RSRNHE 3l09A 106 :GAGPAP Number of specific fragments extracted= 6 number of extra gaps= 0 total=272 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 3l09A/T0586-3l09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 3l09A/T0586-3l09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l09A read from 3l09A/T0586-3l09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l09A in template set Warning: unaligning (T0586)K12 because first residue in template chain is (3l09A)S5 Warning: unaligning (T0586)P13 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l09A)D6 T0586 14 :IYSQISDWMKKQ 3l09A 7 :PIRPLVEALNAE T0586 26 :MITGEW 3l09A 35 :SRDGVI T0586 37 :LPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR 3l09A 44 :GVALSSFVERMGLQPQAMRVALHRLKRDGWVESRR T0586 72 :GMGSFVTSDKALFDQLK 3l09A 80 :GRVGFHRLSDSALTQTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=276 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 2dtr/T0586-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dtr expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtr:Warning: there is no chain 2dtr will retry with 2dtrA # T0586 read from 2dtr/T0586-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0586-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dtr to template set # found chain 2dtr in template set Warning: unaligning (T0586)D11 because first residue in template chain is (2dtr)L4 T0586 12 :KPIYSQISDWMKKQMITGEW 2dtr 5 :VDTTEMYLRTIYELEEEGVT T0586 38 :PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtr 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSRNHE 2dtr 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMS Number of specific fragments extracted= 3 number of extra gaps= 0 total=279 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 2dtr/T0586-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2dtr/T0586-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0586-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtr in template set T0586 13 :PIYSQISDWMKKQMITGE 2dtr 6 :DTTEMYLRTIYELEEEGV T0586 36 :KL 2dtr 24 :TP T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtr 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRS 2dtr 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWE Number of specific fragments extracted= 4 number of extra gaps= 0 total=283 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 2dtr/T0586-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0586 read from 2dtr/T0586-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0586-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtr in template set T0586 12 :KPIYSQISDWMKKQMITGE 2dtr 5 :VDTTEMYLRTIYELEEEGV T0586 39 :SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 2dtr 26 :LRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMT T0586 82 :ALFDQLKKELADAITERFLEEAKSIGLDDQTAIELLIKRSR 2dtr 66 :PTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEH Number of specific fragments extracted= 3 number of extra gaps= 0 total=286 Will force an alignment to be made, even if fragment is small Number of alignments=72 # command:CPU_time= 17.115 sec, elapsed time= 38.292 sec. # command:DEBUG: alignment library has 72 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 72 # Adding 701 constraints to all_contacts Done adding distance constraints # command:CPU_time= 17.151 sec, elapsed time= 38.328 sec. # command:Reading probabilities from T0586.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 64.940 Optimizing... Probability sum: -199.979, CN propb: -199.979 weights: 0.323 constraints: 139 # command:CPU_time= 19.926 sec, elapsed time= 41.174 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 139 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 139 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 562 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 562 # 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= 19.936 sec, elapsed time= 42.575 sec. # command: