# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0475 numbered 1 through 122 Created new target T0475 from T0475.a2m # command:CPU_time= 6.269 sec, elapsed time= 6.365 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nwwA/T0475-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1nwwA/T0475-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0475-1nwwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nwwA)N55 T0475 1 :LN 1nwwA 19 :AA # choosing archetypes in rotamer library T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQY 1nwwA 22 :TPDEKIVLEFMDALTSNDAAKLIEYFAEDTMY T0475 37 :FPATLLAG 1nwwA 56 :MPLPPAYG T0475 46 :AAEIRVRHIERFKE 1nwwA 64 :RDAVEQTLAGLFTV T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNF 1nwwA 79 :SIDAVETFHIGSSNGLVYTERVDVLRA T0475 87 :PEGKG 1nwwA 107 :PTGKS T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIVSQ 1nwwA 113 :NLSILGVFQLTEGKITGWRDYFDLREFEEA Number of specific fragments extracted= 7 number of extra gaps= 1 total=7 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 1nwwA/T0475-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1nwwA/T0475-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0475-1nwwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nwwA)N55 T0475 1 :LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQY 1nwwA 20 :ASTPDEKIVLEFMDALTSNDAAKLIEYFAEDTMY T0475 37 :FPAT 1nwwA 56 :MPLP T0475 42 :LAGNAAEIRVRHIERF 1nwwA 60 :PAYGRDAVEQTLAGLF T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNF 1nwwA 77 :VMSIDAVETFHIGSSNGLVYTERVDVLRA T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQ 1nwwA 108 :TGKSYNLSILGVFQLTEGKITGWRDYFDLREFEEA Number of specific fragments extracted= 5 number of extra gaps= 1 total=12 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 1nwwA/T0475-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1nwwA/T0475-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nwwA read from 1nwwA/T0475-1nwwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nwwA in training set Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nwwA)N55 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nwwA)N55 T0475 2 :NSEIELPVQKQLEAYNARDIDAFMAWWADDCQY 1nwwA 21 :STPDEKIVLEFMDALTSNDAAKLIEYFAEDTMY T0475 37 :FPATL 1nwwA 56 :MPLPP T0475 43 :AGNAAEIRVRHIERF 1nwwA 61 :AYGRDAVEQTLAGLF T0475 58 :K 1nwwA 77 :V T0475 62 :LYGELLTRVIVGNVVIDHETVTRNF 1nwwA 81 :DAVETFHIGSSNGLVYTERVDVLRA T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIG 1nwwA 108 :TGKSYNLSILGVFQLTEGKITGWRDYFD Number of specific fragments extracted= 6 number of extra gaps= 1 total=18 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 2bngA/T0475-2bngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bngA expands to /projects/compbio/data/pdb/2bng.pdb.gz 2bngA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 2bngA/T0475-2bngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bngA read from 2bngA/T0475-2bngA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bngA to template set # found chain 2bngA in template set Warning: unaligning (T0475)N2 because first residue in template chain is (2bngA)E13 Warning: unaligning (T0475)C32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)V45 Warning: unaligning (T0475)Q33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)V45 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)N48 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)N48 Warning: unaligning (T0475)E80 because of BadResidue code BAD_PEPTIDE in next template residue (2bngA)T92 Warning: unaligning (T0475)T81 because of BadResidue code BAD_PEPTIDE at template residue (2bngA)T92 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADD 2bngA 15 :TEAIRAVEAFLNALQNEDFDTVDAALGDD T0475 34 :Y 2bngA 46 :Y T0475 37 :FPATLLAG 2bngA 49 :VGFSRIRG T0475 46 :AAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDH 2bngA 57 :GRRTATLLRRMQGRVGFEVKIHRIGADGAAVLTE T0475 82 :VTRN 2bngA 93 :DALI T0475 87 :PEGKG 2bngA 97 :IGPLR T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIVSQ 2bngA 103 :QFWVCGVFEVDDGRITLWRDYFDVYDMFKG Number of specific fragments extracted= 7 number of extra gaps= 3 total=25 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 2bngA/T0475-2bngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2bngA/T0475-2bngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bngA read from 2bngA/T0475-2bngA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bngA in template set Warning: unaligning (T0475)N2 because first residue in template chain is (2bngA)E13 Warning: unaligning (T0475)C32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)V45 Warning: unaligning (T0475)Q33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)V45 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)N48 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)N48 Warning: unaligning (T0475)E80 because of BadResidue code BAD_PEPTIDE in next template residue (2bngA)T92 Warning: unaligning (T0475)T81 because of BadResidue code BAD_PEPTIDE at template residue (2bngA)T92 T0475 3 :SE 2bngA 14 :TT T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADD 2bngA 17 :AIRAVEAFLNALQNEDFDTVDAALGDD T0475 34 :Y 2bngA 46 :Y T0475 37 :FPAT 2bngA 49 :VGFS T0475 42 :LAGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDH 2bngA 53 :RIRGGRRTATLLRRMQGRVGFEVKIHRIGADGAAVLTE T0475 82 :VTRNFPEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVS 2bngA 93 :DALIIGPLRVQFWVCGVFEVDDGRITLWRDYFDVYDMFK Number of specific fragments extracted= 6 number of extra gaps= 3 total=31 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 2bngA/T0475-2bngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2bngA/T0475-2bngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bngA read from 2bngA/T0475-2bngA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bngA in template set Warning: unaligning (T0475)C32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)V45 Warning: unaligning (T0475)Q33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)V45 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bngA)N48 Warning: unaligning (T0475)A36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bngA)N48 Warning: unaligning (T0475)E80 because of BadResidue code BAD_PEPTIDE in next template residue (2bngA)T92 Warning: unaligning (T0475)T81 because of BadResidue code BAD_PEPTIDE at template residue (2bngA)T92 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADD 2bngA 16 :EAIRAVEAFLNALQNEDFDTVDAALGDD T0475 34 :Y 2bngA 46 :Y T0475 38 :PATLLAGNAAEIRVRHIERFKEPDLYGELLTRVIVGNVVIDH 2bngA 49 :VGFSRIRGGRRTATLLRRMQGRVGFEVKIHRIGADGAAVLTE T0475 82 :VTRNFPEGKGEVDVACIYEVENGRIAKAWFKIG 2bngA 93 :DALIIGPLRVQFWVCGVFEVDDGRITLWRDYFD Number of specific fragments extracted= 4 number of extra gaps= 3 total=35 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 1ohpA/T0475-1ohpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ohpA expands to /projects/compbio/data/pdb/1ohp.pdb.gz 1ohpA:# T0475 read from 1ohpA/T0475-1ohpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ohpA read from 1ohpA/T0475-1ohpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ohpA to template set # found chain 1ohpA in template set T0475 1 :LN 1ohpA 1 :MN T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1ohpA 5 :EHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGS T0475 41 :LLAG 1ohpA 44 :PRSG T0475 46 :AAEIRVRHIERFKE 1ohpA 48 :TAAIREFYANSLKL T0475 60 :PDLYGE 1ohpA 63 :LAVELT T0475 67 :LTRVIVGNVVIDHETVTRN 1ohpA 69 :QEVRAVANEAAFAFIVSFE T0475 87 :PEGKG 1ohpA 88 :YQGRK T0475 92 :EVDVACIYEV 1ohpA 94 :VVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVS 1ohpA 105 :GAGKVVSMRALFGEKNIHA Number of specific fragments extracted= 9 number of extra gaps= 0 total=44 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 1ohpA/T0475-1ohpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ohpA/T0475-1ohpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ohpA read from 1ohpA/T0475-1ohpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ohpA in template set T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERF 1ohpA 5 :EHMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSL T0475 58 :KEPDLYGE 1ohpA 61 :LPLAVELT T0475 67 :LTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1ohpA 69 :QEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVSQ 1ohpA 105 :GAGKVVSMRALFGEKNIHAG Number of specific fragments extracted= 4 number of extra gaps= 0 total=48 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 1ohpA/T0475-1ohpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ohpA/T0475-1ohpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ohpA read from 1ohpA/T0475-1ohpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ohpA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERF 1ohpA 6 :HMTAVVQRYVAALNAGDLDGIVALFADDATVENPVGSEPRSGTAAIREFYANSL T0475 58 :KEPDLYGEL 1ohpA 61 :LPLAVELTQ T0475 68 :TRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1ohpA 70 :EVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVSQK 1ohpA 105 :GAGKVVSMRALFGEKNIHAGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=52 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 2geyA/T0475-2geyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2geyA expands to /projects/compbio/data/pdb/2gey.pdb.gz 2geyA:Skipped atom 175, because occupancy 0.5 <= existing 0.500 in 2geyA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 1016, because occupancy 0.300 <= existing 0.700 in 2geyA Skipped atom 1020, because occupancy 0.300 <= existing 0.700 in 2geyA Skipped atom 1022, because occupancy 0.300 <= existing 0.700 in 2geyA Skipped atom 1024, because occupancy 0.300 <= existing 0.700 in 2geyA Skipped atom 1026, because occupancy 0.300 <= existing 0.700 in 2geyA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2geyA Skipped atom 1178, because occupancy 0.000 <= existing 0.000 in 2geyA Skipped atom 1180, because occupancy 0.000 <= existing 0.000 in 2geyA Skipped atom 1182, because occupancy 0.000 <= existing 0.000 in 2geyA # T0475 read from 2geyA/T0475-2geyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2geyA read from 2geyA/T0475-2geyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2geyA to template set # found chain 2geyA in template set Warning: unaligning (T0475)N2 because first residue in template chain is (2geyA)S2 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 2geyA 4 :AERKALCLEMVAAWNRWDLSGIIKHWSPDIVHYSEDNE T0475 43 :AG 2geyA 42 :VS T0475 46 :AAEIRVRHIERFKE 2geyA 44 :SADMVKLMEGGLKA T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNFPE 2geyA 59 :PDLQLEVKSIMAEEDRVALRITVTATHQG T0475 89 :GKG 2geyA 96 :GQR T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIVSQ 2geyA 100 :SWHLVEELRFVDGKVVEHWDVINMRPLLVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=58 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 2geyA/T0475-2geyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2geyA/T0475-2geyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2geyA read from 2geyA/T0475-2geyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2geyA in template set T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2geyA 4 :AERKALCLEMVAAWNRWDLSGIIKHWSPDIVHYS T0475 39 :AT 2geyA 38 :ED T0475 42 :LAGNAAEIRVRHIERF 2geyA 40 :NEVSSADMVKLMEGGL T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNF 2geyA 57 :AFPDLQLEVKSIMAEEDRVALRITVTATH T0475 87 :P 2geyA 87 :G T0475 88 :EGKGEVDVACIYEVENGRIAKAWFKIGEPRIVS 2geyA 96 :GQRVSWHLVEELRFVDGKVVEHWDVINMRPLLV Number of specific fragments extracted= 6 number of extra gaps= 0 total=64 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 2geyA/T0475-2geyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2geyA/T0475-2geyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2geyA read from 2geyA/T0475-2geyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2geyA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2geyA 5 :ERKALCLEMVAAWNRWDLSGIIKHWSPDIVHYS T0475 38 :PA 2geyA 38 :ED T0475 42 :LAGNAAEIRVRHIERF 2geyA 40 :NEVSSADMVKLMEGGL T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNF 2geyA 57 :AFPDLQLEVKSIMAEEDRVALRITVTATH T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIG 2geyA 95 :TGQRVSWHLVEELRFVDGKVVEHWDVIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=69 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 1dmmA/T0475-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dmmA expands to /projects/compbio/data/pdb/1dmm.pdb.gz 1dmmA:# T0475 read from 1dmmA/T0475-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0475-1dmmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dmmA to template set # found chain 1dmmA in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dmmA)K65 Warning: unaligning (T0475)S120 because last residue in template chain is (1dmmA)V127 T0475 1 :LN 1dmmA 4 :PT T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1dmmA 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQ T0475 41 :LLAG 1dmmA 46 :PIHG T0475 46 :AAEIRVRHIER 1dmmA 50 :REQIAAFFRQG T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRN 1dmmA 66 :VRACLTGPVRASHNGCGAMPFRVEMV T0475 87 :PEGKG 1dmmA 92 :WNGQP T0475 92 :EVDVACIYEV 1dmmA 98 :ALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1dmmA 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 8 number of extra gaps= 0 total=77 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 1dmmA/T0475-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1dmmA/T0475-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0475-1dmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dmmA in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dmmA)K65 Warning: unaligning (T0475)E59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dmmA)K65 Warning: unaligning (T0475)S120 because last residue in template chain is (1dmmA)V127 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1dmmA 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFFRQG T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1dmmA 66 :VRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1dmmA 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=80 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 1dmmA/T0475-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1dmmA/T0475-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dmmA read from 1dmmA/T0475-1dmmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dmmA in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dmmA)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dmmA)K65 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1dmmA 9 :VQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFFRQG T0475 62 :LYGELLTRVIV 1dmmA 66 :VRACLTGPVRA T0475 73 :GNVVIDHETVTRNFPEGKGEVDVACIYEVE 1dmmA 79 :NGCGAMPFRVEMVWNGQPCALDVIDVMRFD T0475 103 :NGRIAKAWFKIGEPRI 1dmmA 110 :HGRIQTMQAYWSEVNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=84 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 1oh0A/T0475-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oh0A expands to /projects/compbio/data/pdb/1oh0.pdb.gz 1oh0A:# T0475 read from 1oh0A/T0475-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0475-1oh0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oh0A to template set # found chain 1oh0A in template set Warning: unaligning (T0475)S120 because last residue in template chain is (1oh0A)V127 T0475 1 :LN 1oh0A 3 :LP T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1oh0A 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQ T0475 41 :LLAG 1oh0A 46 :PIHG T0475 46 :AAEIRVRHIERFKE 1oh0A 50 :REQIAAFYRQGLGG T0475 60 :PDLYGELLTRV 1oh0A 65 :KVRACLTGPVR T0475 71 :IVGNVVIDHETVTRN 1oh0A 77 :SHNGCGAMPFRVEMV T0475 87 :PEGKG 1oh0A 92 :WNGQP T0475 92 :EVDVACIYEV 1oh0A 98 :ALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1oh0A 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 9 number of extra gaps= 0 total=93 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 1oh0A/T0475-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1oh0A/T0475-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0475-1oh0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oh0A in template set Warning: unaligning (T0475)S120 because last residue in template chain is (1oh0A)V127 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPDLYGELL 1oh0A 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLT T0475 68 :TRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1oh0A 74 :VRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1oh0A 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 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 1oh0A/T0475-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1oh0A/T0475-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oh0A read from 1oh0A/T0475-1oh0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oh0A in template set Warning: unaligning (T0475)S120 because last residue in template chain is (1oh0A)V127 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPDLYGELLTRVIV 1oh0A 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQGLGGGKVRACLTGPVRA T0475 73 :GNVVIDHETVTRNFPEGKGEVDVACIYEV 1oh0A 79 :NGCGAMPFRVEMVWNGQPCALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1oh0A 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 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 1sjwA/T0475-1sjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sjwA expands to /projects/compbio/data/pdb/1sjw.pdb.gz 1sjwA:Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 1sjwA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 1sjwA # T0475 read from 1sjwA/T0475-1sjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjwA read from 1sjwA/T0475-1sjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sjwA to template set # found chain 1sjwA in template set Warning: unaligning (T0475)S3 because first residue in template chain is (1sjwA)S2 Warning: unaligning (T0475)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)R19 Warning: unaligning (T0475)D20 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)R19 Warning: unaligning (T0475)D30 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)D30 Warning: unaligning (T0475)D31 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)D30 Warning: unaligning (T0475)P38 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)E38 Warning: unaligning (T0475)A39 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)E38 Warning: unaligning (T0475)L41 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)I41 T0475 4 :EIELPVQKQLEAYNA 1sjwA 3 :RQTEIVRRMVSAFNT T0475 21 :IDAFMAWWA 1sjwA 20 :TDDVDEYIH T0475 32 :CQYYAF 1sjwA 31 :YLNPAT T0475 40 :T 1sjwA 39 :H T0475 42 :LAG 1sjwA 42 :HTG T0475 46 :AAEIRVRHIERFKE 1sjwA 45 :PKAFAQLVGWVRAT T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNFPE 1sjwA 61 :EEARLEEVRIEERGPWVKAYLVLYGRHVG T0475 89 :GKG 1sjwA 98 :DRR T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIVSQ 1sjwA 102 :SGEQVHLMRIVDGKIRDHRDWPDFQGTLRQ Number of specific fragments extracted= 9 number of extra gaps= 4 total=108 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 1sjwA/T0475-1sjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1sjwA/T0475-1sjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjwA read from 1sjwA/T0475-1sjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sjwA in template set Warning: unaligning (T0475)S3 because first residue in template chain is (1sjwA)S2 Warning: unaligning (T0475)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)R19 Warning: unaligning (T0475)D20 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)R19 Warning: unaligning (T0475)D30 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)D30 Warning: unaligning (T0475)D31 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)D30 Warning: unaligning (T0475)P38 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)E38 Warning: unaligning (T0475)A39 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)E38 Warning: unaligning (T0475)L41 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)I41 Warning: unaligning (T0475)L42 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)I41 Warning: unaligning (T0475)E59 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)S60 T0475 4 :EIELPVQKQLEAYNA 1sjwA 3 :RQTEIVRRMVSAFNT T0475 21 :IDAFMAWWA 1sjwA 20 :TDDVDEYIH T0475 32 :CQYYAF 1sjwA 31 :YLNPAT T0475 40 :T 1sjwA 39 :H T0475 43 :AGNAAEIRVRHIERF 1sjwA 42 :HTGPKAFAQLVGWVR T0475 58 :K 1sjwA 58 :T T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNF 1sjwA 61 :EEARLEEVRIEERGPWVKAYLVLYGRH T0475 87 :P 1sjwA 89 :G T0475 88 :EGKGEVDVACIYEVENGRIAKAWFKIGEPRIVSQ 1sjwA 98 :DRRFSGEQVHLMRIVDGKIRDHRDWPDFQGTLRQ Number of specific fragments extracted= 9 number of extra gaps= 5 total=117 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 1sjwA/T0475-1sjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1sjwA/T0475-1sjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjwA read from 1sjwA/T0475-1sjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sjwA in template set Warning: unaligning (T0475)S3 because first residue in template chain is (1sjwA)S2 Warning: unaligning (T0475)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)R19 Warning: unaligning (T0475)D20 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)R19 Warning: unaligning (T0475)P38 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)D30 Warning: unaligning (T0475)A39 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)D30 Warning: unaligning (T0475)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)I41 Warning: unaligning (T0475)L41 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)I41 Warning: unaligning (T0475)E59 because of BadResidue code BAD_PEPTIDE in next template residue (1sjwA)S60 Warning: unaligning (T0475)P60 because of BadResidue code BAD_PEPTIDE at template residue (1sjwA)S60 T0475 4 :EIELPVQKQLEAYNA 1sjwA 3 :RQTEIVRRMVSAFNT T0475 21 :ID 1sjwA 20 :TD T0475 31 :DCQYYAF 1sjwA 22 :DVDEYIH T0475 43 :AGNAAEIRVRHIERF 1sjwA 42 :HTGPKAFAQLVGWVR T0475 58 :K 1sjwA 58 :T T0475 61 :D 1sjwA 61 :E T0475 62 :LYGELLTRVIVGNVVIDHETVTRNF 1sjwA 63 :ARLEEVRIEERGPWVKAYLVLYGRH T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIG 1sjwA 97 :TDRRFSGEQVHLMRIVDGKIRDHRDWPD Number of specific fragments extracted= 8 number of extra gaps= 4 total=125 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 1s5aA/T0475-1s5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s5aA expands to /projects/compbio/data/pdb/1s5a.pdb.gz 1s5aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 1s5aA/T0475-1s5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5aA read from 1s5aA/T0475-1s5aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s5aA to template set # found chain 1s5aA in template set T0475 1 :LN 1s5aA 3 :MN T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 1s5aA 7 :EKACETLRKFMAYMLEKDMKSWTELWDENAVFEFP T0475 38 :P 1s5aA 46 :G T0475 42 :LAG 1s5aA 51 :IEG T0475 46 :AAEIRVRHIERFKE 1s5aA 54 :KAAIYDYIKDYPKQ T0475 60 :PDLYGELLTRV 1s5aA 69 :HLSSFTAPTVY T0475 71 :IVGNVVIDHETVTRNF 1s5aA 82 :ADSNTVIAEFQCDGHV T0475 87 :PEGKG 1s5aA 99 :ETGLP T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIVSQ 1s5aA 105 :RQSYISVIETRDGRIVRYRDYWNPLVVKEA Number of specific fragments extracted= 9 number of extra gaps= 0 total=134 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 1s5aA/T0475-1s5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1s5aA/T0475-1s5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5aA read from 1s5aA/T0475-1s5aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5aA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 1s5aA 8 :KACETLRKFMAYMLEKDMKSWTELWDENAVFEFP T0475 38 :PATLLAGNAAEIRVRHIERF 1s5aA 46 :GSPKRIEGKAAIYDYIKDYP T0475 58 :KEPDLYGELLTRV 1s5aA 67 :QIHLSSFTAPTVY T0475 71 :IVGNVVIDHETVTRNF 1s5aA 82 :ADSNTVIAEFQCDGHV T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIGEPRIVS 1s5aA 100 :TGLPYRQSYISVIETRDGRIVRYRDYWNPLVVKE Number of specific fragments extracted= 5 number of extra gaps= 0 total=139 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 1s5aA/T0475-1s5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1s5aA/T0475-1s5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5aA read from 1s5aA/T0475-1s5aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5aA in template set T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPA 1s5aA 9 :ACETLRKFMAYMLEKDMKSWTELWDENAVFEFPYA T0475 41 :LLAGNAAEIRVRHIERF 1s5aA 49 :KRIEGKAAIYDYIKDYP T0475 63 :YGELLTRV 1s5aA 67 :QIHLSSFT T0475 71 :IV 1s5aA 78 :VY T0475 73 :GNVVIDHETVTRNF 1s5aA 84 :SNTVIAEFQCDGHV T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIG 1s5aA 100 :TGLPYRQSYISVIETRDGRIVRYRDYWN Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 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 2a15A/T0475-2a15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a15A expands to /projects/compbio/data/pdb/2a15.pdb.gz 2a15A:Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 140, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 142, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 144, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 146, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 148, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 440, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2a15A Skipped atom 684, because occupancy 0.350 <= existing 0.650 in 2a15A Skipped atom 687, because occupancy 0.350 <= existing 0.650 in 2a15A # T0475 read from 2a15A/T0475-2a15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a15A read from 2a15A/T0475-2a15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a15A to template set # found chain 2a15A in template set T0475 2 :NSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2a15A 6 :QSPALIASQSSWRCVQAHDREGWLALMADDVVIEDP T0475 38 :PATLLAG 2a15A 50 :DGSGIKG T0475 46 :AAEIRVRHIERFKEPDLYGELLTRVIV 2a15A 57 :KEAVGAFFDTHIAANRLTVTCEETFPS T0475 73 :GNVVIDHETVTRNFPEGKG 2a15A 86 :PDEIAHILVLHSEFDGGFT T0475 92 :EVDVACIYEV 2a15A 106 :EVRGVFTYRV T0475 102 :ENGRIAKAWFKIGEPRIV 2a15A 117 :KAGLITNMRGYWNLDMMT Number of specific fragments extracted= 6 number of extra gaps= 0 total=151 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 2a15A/T0475-2a15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2a15A/T0475-2a15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a15A read from 2a15A/T0475-2a15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a15A in template set Warning: unaligning (T0475)Q121 because of BadResidue code BAD_PEPTIDE in next template residue (2a15A)N137 T0475 1 :LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 2a15A 5 :TQSPALIASQSSWRCVQAHDREGWLALMADDVVIEDPIGK T0475 41 :LLAGNAAEIRVRHIERFKEPDLYGELLTRVIV 2a15A 52 :SGIKGKEAVGAFFDTHIAANRLTVTCEETFPS T0475 73 :GNVVIDHETVTRNF 2a15A 86 :PDEIAHILVLHSEF T0475 87 :PEGKGEVDVACIYEV 2a15A 101 :GGFTSEVRGVFTYRV T0475 102 :ENGRIAKAWFKIGEPRIVS 2a15A 117 :KAGLITNMRGYWNLDMMTF Number of specific fragments extracted= 5 number of extra gaps= 1 total=156 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 2a15A/T0475-2a15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2a15A/T0475-2a15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a15A read from 2a15A/T0475-2a15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a15A in template set T0475 1 :LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPA 2a15A 5 :TQSPALIASQSSWRCVQAHDREGWLALMADDVVIEDPIG T0475 41 :LLAGNAAEIRVRHIERFKEPDLYGELLTRVIV 2a15A 52 :SGIKGKEAVGAFFDTHIAANRLTVTCEETFPS T0475 73 :GNVVIDHETVTRNFPEGKGEVDVACIYEV 2a15A 87 :DEIAHILVLHSEFDGGFTSEVRGVFTYRV T0475 102 :ENGRIAKAWFKIGE 2a15A 117 :KAGLITNMRGYWNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=160 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 1tuhA/T0475-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tuhA expands to /projects/compbio/data/pdb/1tuh.pdb.gz 1tuhA:Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 982, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 984, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 1tuhA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1tuhA # T0475 read from 1tuhA/T0475-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0475-1tuhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tuhA to template set # found chain 1tuhA in template set Warning: unaligning (T0475)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1tuhA)C121 Warning: unaligning (T0475)A96 because of BadResidue code BAD_PEPTIDE at template residue (1tuhA)C121 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1tuhA 22 :EQNAETVRRGYAAFNSGDMKTLTELFDENASWHTPGRS T0475 42 :LAG 1tuhA 65 :HKG T0475 46 :AAEIRVRHIERFKE 1tuhA 68 :REAIFAQFGRYGGE T0475 60 :PD 1tuhA 83 :GG T0475 62 :LYGELLTRV 1tuhA 86 :FKAVLLHVL T0475 71 :IVGNVVIDHETVTRN 1tuhA 96 :SDDGRVIGIHRNTAE T0475 87 :PEGKG 1tuhA 111 :RGGKR T0475 92 :EVD 1tuhA 117 :DVG T0475 97 :CIYEVENGRIAKAWFKI 1tuhA 122 :IVFEFKNGRVIDGREHF T0475 114 :GEPRIVSQ 1tuhA 140 :DLYAWDEF Number of specific fragments extracted= 10 number of extra gaps= 1 total=170 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 1tuhA/T0475-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1tuhA/T0475-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0475-1tuhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tuhA in template set Warning: unaligning (T0475)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1tuhA)C121 Warning: unaligning (T0475)A96 because of BadResidue code BAD_PEPTIDE at template residue (1tuhA)C121 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 1tuhA 23 :QNAETVRRGYAAFNSGDMKTLTELFDENASWHTP T0475 38 :PATLLAGNAAEIRVRHIERF 1tuhA 60 :RIAGDHKGREAIFAQFGRYG T0475 58 :KEPD 1tuhA 81 :ETGG T0475 62 :LYGELLTRVIVGN 1tuhA 86 :FKAVLLHVLKSDD T0475 75 :VVIDHETVTRNFPEGKGEVD 1tuhA 100 :RVIGIHRNTAERGGKRLDVG T0475 97 :CIYEVENGRIAKAWFK 1tuhA 122 :IVFEFKNGRVIDGREH T0475 113 :IGEPRIV 1tuhA 139 :YDLYAWD Number of specific fragments extracted= 7 number of extra gaps= 1 total=177 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 1tuhA/T0475-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1tuhA/T0475-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tuhA read from 1tuhA/T0475-1tuhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tuhA in template set Warning: unaligning (T0475)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1tuhA)C121 Warning: unaligning (T0475)A96 because of BadResidue code BAD_PEPTIDE at template residue (1tuhA)C121 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPA 1tuhA 23 :QNAETVRRGYAAFNSGDMKTLTELFDENASWHTPGR T0475 41 :LLAGNAAEIRVRHIERF 1tuhA 63 :GDHKGREAIFAQFGRYG T0475 58 :KEPDLYGELLTRVIVGN 1tuhA 82 :TGGTFKAVLLHVLKSDD T0475 75 :VVIDHETVTRNFPEGKGEVD 1tuhA 100 :RVIGIHRNTAERGGKRLDVG T0475 97 :CIYEVENGRIAKAWFKIGE 1tuhA 122 :IVFEFKNGRVIDGREHFYD Number of specific fragments extracted= 5 number of extra gaps= 1 total=182 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 2gxfA/T0475-2gxfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gxfA expands to /projects/compbio/data/pdb/2gxf.pdb.gz 2gxfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 2gxfA/T0475-2gxfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gxfA read from 2gxfA/T0475-2gxfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gxfA to template set # found chain 2gxfA in template set Warning: unaligning (T0475)N85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gxfA)M98 Warning: unaligning (T0475)S120 because last residue in template chain is (2gxfA)G128 T0475 1 :LNSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAG 2gxfA 1 :MEQQLKDIISACDLAIQNEDFDTLMNYYSEDAVLVVKPGMIARG T0475 46 :AAEIRVRHIERFKE 2gxfA 45 :KEEIKKAFITIANY T0475 60 :PDLYGELLTRV 2gxfA 61 :HHIVPTQGKMI T0475 71 :IVGNVVIDHETVTR 2gxfA 74 :EAGDTVLVLSQTLL T0475 92 :EVDVACIYEV 2gxfA 99 :ERRATYVFKK T0475 102 :ENGRIAKAWFKIGEPRIV 2gxfA 110 :AQGEWLCVIDNSYGTDLI Number of specific fragments extracted= 6 number of extra gaps= 0 total=188 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 2gxfA/T0475-2gxfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2gxfA/T0475-2gxfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gxfA read from 2gxfA/T0475-2gxfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gxfA in template set Warning: unaligning (T0475)N85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gxfA)M98 Warning: unaligning (T0475)G91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gxfA)M98 Warning: unaligning (T0475)S120 because last residue in template chain is (2gxfA)G128 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2gxfA 4 :QLKDIISACDLAIQNEDFDTLMNYYSEDAVLVVK T0475 39 :ATLLAGNAAEIRVRHIERF 2gxfA 38 :PGMIARGKEEIKKAFITIA T0475 58 :KE 2gxfA 58 :YF T0475 60 :PDLYGELLTRV 2gxfA 61 :HHIVPTQGKMI T0475 71 :IVGNVVIDHETVTR 2gxfA 74 :EAGDTVLVLSQTLL T0475 92 :EVDVACIYEV 2gxfA 99 :ERRATYVFKK T0475 102 :ENGRIAKAWFKIGEPRIV 2gxfA 110 :AQGEWLCVIDNSYGTDLI Number of specific fragments extracted= 7 number of extra gaps= 0 total=195 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 2gxfA/T0475-2gxfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2gxfA/T0475-2gxfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gxfA read from 2gxfA/T0475-2gxfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gxfA in template set Warning: unaligning (T0475)F86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gxfA)M98 Warning: unaligning (T0475)K90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gxfA)M98 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 2gxfA 5 :LKDIISACDLAIQNEDFDTLMNYYSEDAVLVVKPGM T0475 42 :LAGNAAEIRVRHIERF 2gxfA 41 :IARGKEEIKKAFITIA T0475 58 :KEPDLYGELLTRVIV 2gxfA 59 :FNHHIVPTQGKMILL T0475 73 :GNVVIDHETVTRN 2gxfA 75 :AGDTVLVLSQTLL T0475 91 :GEVDVACIYEVENGRIAKAWFK 2gxfA 99 :ERRATYVFKKNAQGEWLCVIDN Number of specific fragments extracted= 5 number of extra gaps= 0 total=200 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cu3A/T0475-3cu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cu3A expands to /projects/compbio/data/pdb/3cu3.pdb.gz 3cu3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 811, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 865, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 867, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 869, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 871, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 873, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 875, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 877, because occupancy 0.300 <= existing 0.700 in 3cu3A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 3cu3A Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 3cu3A # T0475 read from 3cu3A/T0475-3cu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cu3A read from 3cu3A/T0475-3cu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cu3A to template set # found chain 3cu3A in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAG 3cu3A 16 :AIRAFHRQMIDAWNRGSGEGFAAPFSETADFITFEGTHLKG T0475 46 :AAEIRVRHIERFKE 3cu3A 57 :RKEIAAFHQQAFDT T0475 60 :PDLY 3cu3A 73 :KGTR T0475 64 :GELLTRV 3cu3A 79 :GEVDFVR T0475 71 :IVGNVVIDHETVTRNF 3cu3A 87 :VNSQLALMLVVIRVIL T0475 87 :PEGKG 3cu3A 105 :QTETS T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPRIV 3cu3A 113 :DSLPLYVVTKGDEGWQIEGLLNTRKLTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=207 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 3cu3A/T0475-3cu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3cu3A/T0475-3cu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cu3A read from 3cu3A/T0475-3cu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cu3A in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 3cu3A 16 :AIRAFHRQMIDAWNRGSGEGFAAPFSETADFITF T0475 39 :ATLLAGNAAEIRVRHIERF 3cu3A 50 :EGTHLKGRKEIAAFHQQAF T0475 58 :KEPDLYGELLTRV 3cu3A 71 :VVKGTRLEGEVDF T0475 71 :IVGNVVIDHETVTRNF 3cu3A 87 :VNSQLALMLVVIRVIL T0475 87 :PEGKGE 3cu3A 106 :TETSAS T0475 93 :VDVACIYEVENGRIAKAWFKIGEPR 3cu3A 114 :SLPLYVVTKGDEGWQIEGLLNTRKL Number of specific fragments extracted= 6 number of extra gaps= 0 total=213 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 3cu3A/T0475-3cu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3cu3A/T0475-3cu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cu3A read from 3cu3A/T0475-3cu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cu3A in template set T0475 6 :ELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATL 3cu3A 18 :RAFHRQMIDAWNRGSGEGFAAPFSETADFITFEGTH T0475 43 :AGNAAEIRVRHIERF 3cu3A 54 :LKGRKEIAAFHQQAF T0475 58 :KEPD 3cu3A 70 :TVVK T0475 62 :LYGELLTRVIV 3cu3A 77 :LEGEVDFVRFV T0475 73 :GNVVIDHETVTRNFPEG 3cu3A 89 :SQLALMLVVIRVILPGQ T0475 90 :KGEVD 3cu3A 113 :DSLPL T0475 97 :CIYEVENGRIAKAWFKIGE 3cu3A 118 :YVVTKGDEGWQIEGLLNTR Number of specific fragments extracted= 7 number of extra gaps= 0 total=220 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 3bb9A/T0475-3bb9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3bb9A expands to /projects/compbio/data/pdb/3bb9.pdb.gz 3bb9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 600, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3bb9A Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 3bb9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 3bb9A/T0475-3bb9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bb9A read from 3bb9A/T0475-3bb9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bb9A to template set # found chain 3bb9A in template set Warning: unaligning (T0475)P87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bb9A)S120 Warning: unaligning (T0475)K90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bb9A)S120 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 3bb9A 30 :AAGNVVKQFHAALQMGNEAIVRQSLAANVQIYEG T0475 39 :ATLLAG 3bb9A 64 :GKVERS T0475 46 :AAEIRV 3bb9A 70 :LTEYAN T0475 52 :RHIERFKE 3bb9A 77 :HMLADMAY T0475 60 :PDLYGELLTRV 3bb9A 86 :KGLTITPKEHQ T0475 71 :IVGNVVIDHETVTRNF 3bb9A 99 :ITGDIAISTSISHAQG T0475 91 :G 3bb9A 121 :I T0475 92 :EVDVACIYEV 3bb9A 124 :MTMETLVLIK T0475 102 :ENGRIAKAWFK 3bb9A 135 :ADGRWKITHVH Number of specific fragments extracted= 9 number of extra gaps= 0 total=229 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 3bb9A/T0475-3bb9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3bb9A/T0475-3bb9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bb9A read from 3bb9A/T0475-3bb9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bb9A in template set Warning: unaligning (T0475)P87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3bb9A)S120 Warning: unaligning (T0475)K90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bb9A)S120 T0475 6 :ELPVQKQLEAYNARDIDAFMAWWADDCQYYA 3bb9A 32 :GNVVKQFHAALQMGNEAIVRQSLAANVQIYE T0475 39 :ATLLAGNAAEIRV 3bb9A 63 :GGKVERSLTEYAN T0475 52 :RHIERF 3bb9A 77 :HMLADM T0475 58 :KEPDLYGELLTRV 3bb9A 84 :YLKGLTITPKEHQ T0475 71 :IVGNVVIDHETVTRNF 3bb9A 99 :ITGDIAISTSISHAQG T0475 91 :GE 3bb9A 121 :ID T0475 93 :VDVACIYEV 3bb9A 125 :TMETLVLIK T0475 102 :ENGRIAKAWFKI 3bb9A 135 :ADGRWKITHVHW Number of specific fragments extracted= 8 number of extra gaps= 0 total=237 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 3bb9A/T0475-3bb9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3bb9A/T0475-3bb9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bb9A read from 3bb9A/T0475-3bb9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3bb9A in template set Warning: unaligning (T0475)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3bb9A)S120 T0475 2 :NSEIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 3bb9A 28 :DSAAGNVVKQFHAALQMGNEAIVRQSLAANVQIYE T0475 38 :PATL 3bb9A 63 :GGKV T0475 43 :AGNAAEIRV 3bb9A 67 :ERSLTEYAN T0475 52 :RHIERF 3bb9A 77 :HMLADM T0475 58 :KEPDLYGELLTRVIV 3bb9A 84 :YLKGLTITPKEHQIT T0475 73 :GNVVIDHETVTRNF 3bb9A 101 :GDIAISTSISHAQG T0475 89 :GKGEV 3bb9A 121 :IDSMT T0475 94 :DVACIYEVENGRIAKAWFK 3bb9A 127 :ETLVLIKQADGRWKITHVH Number of specific fragments extracted= 8 number of extra gaps= 0 total=245 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 3b7cA/T0475-3b7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3b7cA expands to /projects/compbio/data/pdb/3b7c.pdb.gz 3b7cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 64, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 273, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 331, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 718, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 732, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 3b7cA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 3b7cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 3b7cA/T0475-3b7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7cA read from 3b7cA/T0475-3b7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3b7cA to template set # found chain 3b7cA in template set Warning: unaligning (T0475)C97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3b7cA)L104 Warning: unaligning (T0475)I98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3b7cA)L104 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWA 3b7cA 4 :DDIVQLLKGQEEAWNRGDLDAYMQGYW T0475 30 :DDCQYYAF 3b7cA 33 :EQLMLISN T0475 39 :ATLLAG 3b7cA 41 :GKFRNG T0475 46 :AAEIRVRHIERFKE 3b7cA 47 :WDETLAAYKKNYPD T0475 60 :P 3b7cA 62 :E T0475 61 :DLYGELLTRV 3b7cA 66 :ELKFTIKEIK T0475 71 :IVGNVVIDHETVTRNFPEGKGEVDVA 3b7cA 77 :LSNYAAMVVGRWDLKRLKDTPTGVFT T0475 99 :YEVENGRIAKAWFKIG 3b7cA 105 :VEKIDDRWVITMDHSS Number of specific fragments extracted= 8 number of extra gaps= 1 total=253 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 3b7cA/T0475-3b7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3b7cA/T0475-3b7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7cA read from 3b7cA/T0475-3b7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b7cA in template set Warning: unaligning (T0475)C97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3b7cA)L104 Warning: unaligning (T0475)I98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3b7cA)L104 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADD 3b7cA 5 :DIVQLLKGQEEAWNRGDLDAYMQGYWQN T0475 32 :CQYYA 3b7cA 35 :LMLIS T0475 39 :ATLLAGNAAEIRVRHIERF 3b7cA 40 :NGKFRNGWDETLAAYKKNY T0475 58 :KEPD 3b7cA 60 :DKES T0475 62 :LYGELLTRVIV 3b7cA 67 :LKFTIKEIKML T0475 73 :GNVVIDHETVTRNFPEGKGEVDVA 3b7cA 79 :NYAAMVVGRWDLKRLKDTPTGVFT T0475 99 :YEVENGRIAKAWFKIG 3b7cA 105 :VEKIDDRWVITMDHSS Number of specific fragments extracted= 7 number of extra gaps= 1 total=260 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 3b7cA/T0475-3b7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3b7cA/T0475-3b7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7cA read from 3b7cA/T0475-3b7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b7cA in template set Warning: unaligning (T0475)C97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3b7cA)L104 Warning: unaligning (T0475)I98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3b7cA)L104 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADD 3b7cA 6 :IVQLLKGQEEAWNRGDLDAYMQGYWQN T0475 32 :CQYY 3b7cA 35 :LMLI T0475 38 :PATLLAGNAAEIRVRHIERFKEPD 3b7cA 39 :SNGKFRNGWDETLAAYKKNYPDKE T0475 62 :LYGELLTRVIV 3b7cA 67 :LKFTIKEIKML T0475 73 :GNVVIDHETVTRNFPEGKGEVDVA 3b7cA 79 :NYAAMVVGRWDLKRLKDTPTGVFT T0475 99 :YEVENGRIAKAWFK 3b7cA 105 :VEKIDDRWVITMDH Number of specific fragments extracted= 6 number of extra gaps= 1 total=266 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 3cnxA/T0475-3cnxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cnxA expands to /projects/compbio/data/pdb/3cnx.pdb.gz 3cnxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 137, because occupancy 0.500 <= existing 0.500 in 3cnxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 141, because occupancy 0.500 <= existing 0.500 in 3cnxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 3cnxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 145, because occupancy 0.370 <= existing 0.380 in 3cnxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 3cnxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 3cnxA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 3cnxA # T0475 read from 3cnxA/T0475-3cnxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnxA read from 3cnxA/T0475-3cnxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cnxA to template set # found chain 3cnxA in template set Warning: unaligning (T0475)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3cnxA)G125 Warning: unaligning (T0475)P116 because last residue in template chain is (3cnxA)A157 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADD 3cnxA 12 :QVGLANTAFYEAMERGDFETLSSLWLTP T0475 32 :CQYYAFPATLLAG 3cnxA 57 :VSCVHPGWPVLSG T0475 46 :AAEIRVRHIERFKE 3cnxA 70 :RGEVLRSYALIMAN T0475 60 :PDLYGEL 3cnxA 85 :EYIQFFL T0475 67 :LTRVIVGNVVIDHETVTRNFP 3cnxA 94 :VHVSVTGDTALVTCTENILSG T0475 89 :GKG 3cnxA 127 :LVG T0475 92 :EVDVACIYEVENG 3cnxA 131 :LVVATNVFRRTPD T0475 105 :RIAKAWFKIGE 3cnxA 146 :KLWSHHASPVL Number of specific fragments extracted= 8 number of extra gaps= 0 total=274 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 3cnxA/T0475-3cnxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3cnxA/T0475-3cnxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnxA read from 3cnxA/T0475-3cnxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnxA in template set Warning: unaligning (T0475)P87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3cnxA)G125 Warning: unaligning (T0475)P116 because last residue in template chain is (3cnxA)A157 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWAD 3cnxA 12 :QVGLANTAFYEAMERGDFETLSSLWLT T0475 32 :CQYYAF 3cnxA 57 :VSCVHP T0475 39 :ATLLAGNAAEIRVRHIERF 3cnxA 63 :GWPVLSGRGEVLRSYALIM T0475 58 :KEPDLYGELLTRV 3cnxA 83 :NTEYIQFFLTDVH T0475 71 :IVGNVVIDHETVTRNF 3cnxA 98 :VTGDTALVTCTENILS T0475 89 :GKGEVDVACIYEVENG 3cnxA 128 :VGQLVVATNVFRRTPD T0475 105 :RIAKAWFKIGE 3cnxA 146 :KLWSHHASPVL Number of specific fragments extracted= 7 number of extra gaps= 0 total=281 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 3cnxA/T0475-3cnxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3cnxA/T0475-3cnxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cnxA read from 3cnxA/T0475-3cnxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cnxA in template set T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADD 3cnxA 13 :VGLANTAFYEAMERGDFETLSSLWLTP T0475 32 :CQYY 3cnxA 57 :VSCV T0475 37 :FPATLLAGNAAEIRVRHIERF 3cnxA 61 :HPGWPVLSGRGEVLRSYALIM T0475 58 :KEPDLYGEL 3cnxA 83 :NTEYIQFFL T0475 67 :LTRVIVGNVVIDHETVTRNF 3cnxA 94 :VHVSVTGDTALVTCTENILS T0475 87 :PEGKGEVDVACIYEVENGRIAKAWFKIGEPR 3cnxA 126 :PLVGQLVVATNVFRRTPDGWKLWSHHASPVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=287 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 2rfrA/T0475-2rfrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rfrA expands to /projects/compbio/data/pdb/2rfr.pdb.gz 2rfrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 101, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 103, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 105, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 107, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 109, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 111, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 113, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 115, because occupancy 0.380 <= existing 0.620 in 2rfrA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 472, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 474, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 476, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 478, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 480, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 482, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 484, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 486, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 488, because occupancy 0.480 <= existing 0.520 in 2rfrA Skipped atom 579, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 581, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 583, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 585, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 587, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 589, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 591, because occupancy 0.370 <= existing 0.630 in 2rfrA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2rfrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 681, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 683, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 685, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 687, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 689, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 691, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 693, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 695, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 697, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 699, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 701, because occupancy 0.350 <= existing 0.650 in 2rfrA Skipped atom 929, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 931, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 933, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 935, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 937, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 939, because occupancy 0.410 <= existing 0.590 in 2rfrA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2rfrA Skipped atom 991, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 993, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 995, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 997, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 999, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 1001, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 1003, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 1005, because occupancy 0.450 <= existing 0.550 in 2rfrA Skipped atom 1163, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1165, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1167, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1169, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1171, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1173, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1175, because occupancy 0.470 <= existing 0.530 in 2rfrA Skipped atom 1177, because occupancy 0.470 <= existing 0.530 in 2rfrA # T0475 read from 2rfrA/T0475-2rfrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rfrA read from 2rfrA/T0475-2rfrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rfrA to template set # found chain 2rfrA in template set Warning: unaligning (T0475)L67 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2rfrA)T88 Warning: unaligning (T0475)T68 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2rfrA)T88 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAG 2rfrA 20 :IRELIARYGPLADSGDAEALSELWVEDGEYAVVGFATAKG T0475 46 :AAEIRVRHI 2rfrA 60 :RAAIAALID T0475 55 :ERFK 2rfrA 74 :ALMA T0475 60 :PDLYGEL 2rfrA 78 :DGCAHFL T0475 69 :RVIVGNVVIDHETVTRNF 2rfrA 89 :VTVEGDTATARCHSVVFR T0475 87 :PEGKG 2rfrA 109 :SGTFG T0475 92 :EVDVACIYEVENG 2rfrA 117 :VSANRWTFRRTPA T0475 105 :RIAKAWFK 2rfrA 132 :RAVRRENA T0475 113 :IGEPR 2rfrA 141 :LDGSA Number of specific fragments extracted= 9 number of extra gaps= 1 total=296 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 2rfrA/T0475-2rfrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2rfrA/T0475-2rfrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rfrA read from 2rfrA/T0475-2rfrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rfrA in template set Warning: unaligning (T0475)L67 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2rfrA)T88 Warning: unaligning (T0475)T68 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2rfrA)T88 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 2rfrA 20 :IRELIARYGPLADSGDAEALSELWVEDGEYAVVGFA T0475 42 :LAGNAAEIRVRH 2rfrA 56 :TAKGRAAIAALI T0475 54 :IERF 2rfrA 73 :RALM T0475 58 :KEPDLYGEL 2rfrA 78 :DGCAHFLGP T0475 69 :RVIVGNVVIDHETVTRNF 2rfrA 89 :VTVEGDTATARCHSVVFR T0475 87 :PEGKGE 2rfrA 109 :SGTFGS T0475 93 :VDVACIYEVENG 2rfrA 118 :SANRWTFRRTPA T0475 105 :RIAKAWFKIGEPRI 2rfrA 132 :RAVRRENALLDGSA Number of specific fragments extracted= 8 number of extra gaps= 1 total=304 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 2rfrA/T0475-2rfrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2rfrA/T0475-2rfrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rfrA read from 2rfrA/T0475-2rfrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rfrA in template set Warning: unaligning (T0475)T68 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2rfrA)T88 T0475 6 :ELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATL 2rfrA 21 :RELIARYGPLADSGDAEALSELWVEDGEYAVVGFAT T0475 43 :AGNAAEIRVRHI 2rfrA 57 :AKGRAAIAALID T0475 55 :ERFKEPDLYGELL 2rfrA 73 :RALMADGCAHFLG T0475 69 :RVIVGNVVIDHETVTRNF 2rfrA 89 :VTVEGDTATARCHSVVFR T0475 87 :PEGKGEVDVACI 2rfrA 109 :SGTFGSHRVSAN T0475 99 :YEVENG 2rfrA 124 :FRRTPA T0475 105 :RIAKAWFK 2rfrA 132 :RAVRRENA Number of specific fragments extracted= 7 number of extra gaps= 1 total=311 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 2chcA/T0475-2chcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2chcA expands to /projects/compbio/data/pdb/2chc.pdb.gz 2chcA:# T0475 read from 2chcA/T0475-2chcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2chcA read from 2chcA/T0475-2chcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2chcA to template set # found chain 2chcA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2chcA 13 :RIQALCARYCLTINTQDGEGWAGCFTEDGAFEFD T0475 39 :ATLLAG 2chcA 47 :GWVIRG T0475 46 :AAEIRVRHIERFKE 2chcA 53 :RPALREYADAHARV T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNF 2chcA 69 :GRHLTTDLLYEVDGDVATGRSASVVTL T0475 87 :PEGKG 2chcA 98 :AAGYK T0475 92 :EVDVACIYEVENG 2chcA 106 :SGEYQDRLIKQDG T0475 105 :RIAKAWFKIGEPR 2chcA 121 :RIAYRRLRNDRLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=318 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 2chcA/T0475-2chcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2chcA/T0475-2chcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2chcA read from 2chcA/T0475-2chcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2chcA in template set Warning: unaligning (T0475)P60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2chcA)R68 Warning: unaligning (T0475)D61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2chcA)R68 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2chcA 14 :IQALCARYCLTINTQDGEGWAGCFTEDGAFEF T0475 39 :ATLLAGNAAEIRVRHIERFKE 2chcA 46 :DGWVIRGRPALREYADAHARV T0475 62 :LYGEL 2chcA 69 :GRHLT T0475 67 :LTRVIVGNVVIDHETVTRNF 2chcA 76 :LLYEVDGDVATGRSASVVTL T0475 87 :PEGKGEV 2chcA 98 :AAGYKIL T0475 94 :DVACIYEVENG 2chcA 108 :EYQDRLIKQDG T0475 105 :RIAKAWFKIGEPRIVSQ 2chcA 121 :RIAYRRLRNDRLVSDPS Number of specific fragments extracted= 7 number of extra gaps= 1 total=325 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 2chcA/T0475-2chcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2chcA/T0475-2chcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2chcA read from 2chcA/T0475-2chcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2chcA in template set Warning: unaligning (T0475)P60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2chcA)R68 Warning: unaligning (T0475)D61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2chcA)R68 T0475 6 :ELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2chcA 15 :QALCARYCLTINTQDGEGWAGCFTEDGAFEF T0475 39 :ATLLAGNAAEIRVRHIERFKE 2chcA 46 :DGWVIRGRPALREYADAHARV T0475 62 :LYGELLTRV 2chcA 69 :GRHLTTDLL T0475 71 :IVGNVVIDHETVTRNF 2chcA 80 :VDGDVATGRSASVVTL T0475 87 :PEGKGEV 2chcA 98 :AAGYKIL T0475 94 :DVACIYEVENG 2chcA 108 :EYQDRLIKQDG T0475 105 :RIAKAWFKIGEPR 2chcA 121 :RIAYRRLRNDRLV Number of specific fragments extracted= 7 number of extra gaps= 1 total=332 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 2r4iA/T0475-2r4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2r4iA expands to /projects/compbio/data/pdb/2r4i.pdb.gz 2r4iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 23, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 225, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 229, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 231, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 233, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 235, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 237, because occupancy 0.300 <= existing 0.700 in 2r4iA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2r4iA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 901, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2r4iA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2r4iA # T0475 read from 2r4iA/T0475-2r4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2r4iA read from 2r4iA/T0475-2r4iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2r4iA to template set # found chain 2r4iA in template set T0475 1 :LNS 2r4iA 1 :MNQ T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAG 2r4iA 6 :VILDCEKKLLTAIQNNDVESLEVLLHDDLLFIIPSGETVTK T0475 47 :AEIRVRHIERFKE 2r4iA 47 :ETDIAAYSSGKIA T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNF 2r4iA 61 :RAVVPSDYIIRIIHDTVVVSVNIEIKG T0475 87 :PEGKG 2r4iA 89 :YMEHT T0475 92 :EVDVACIYEVENGRIAKAWFKIGEP 2r4iA 97 :TFRYLRVWKLFDGNWKVIAGSCTAI Number of specific fragments extracted= 6 number of extra gaps= 0 total=338 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 2r4iA/T0475-2r4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2r4iA/T0475-2r4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2r4iA read from 2r4iA/T0475-2r4iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2r4iA in template set T0475 1 :LNSE 2r4iA 1 :MNQR T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2r4iA 7 :ILDCEKKLLTAIQNNDVESLEVLLHDDLLFIIP T0475 39 :ATLLAGN 2r4iA 40 :SGETVTK T0475 47 :AEIRVRHIERF 2r4iA 47 :ETDIAAYSSGK T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNF 2r4iA 59 :ALRAVVPSDYIIRIIHDTVVVSVNIEIKG T0475 87 :PEGKGE 2r4iA 90 :MEHTLD T0475 93 :VDVACIYEVENGRIAKAWFKIGEP 2r4iA 98 :FRYLRVWKLFDGNWKVIAGSCTAI Number of specific fragments extracted= 7 number of extra gaps= 0 total=345 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 2r4iA/T0475-2r4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2r4iA/T0475-2r4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2r4iA read from 2r4iA/T0475-2r4iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2r4iA in template set T0475 7 :LPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLL 2r4iA 9 :DCEKKLLTAIQNNDVESLEVLLHDDLLFIIPSGETV T0475 45 :NAAEIRVRHIERF 2r4iA 45 :TKETDIAAYSSGK T0475 62 :LYGELLTRVIVGNVVIDHETVTRNF 2r4iA 63 :VVPSDYIIRIIHDTVVVSVNIEIKG T0475 87 :PEG 2r4iA 90 :MEH T0475 90 :KGEVDVACIYEVENGRIAKAWFKIGE 2r4iA 95 :DNTFRYLRVWKLFDGNWKVIAGSCTA Number of specific fragments extracted= 5 number of extra gaps= 0 total=350 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 2ux0A/T0475-2ux0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ux0A expands to /projects/compbio/data/pdb/2ux0.pdb.gz 2ux0A:# T0475 read from 2ux0A/T0475-2ux0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ux0A read from 2ux0A/T0475-2ux0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ux0A to template set # found chain 2ux0A in template set Warning: unaligning (T0475)Y34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ux0A)F429 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ux0A)F429 Warning: unaligning (T0475)P116 because last residue in template chain is (2ux0A)A521 T0475 1 :LNSE 2ux0A 386 :MTED T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQ 2ux0A 399 :IIKITEQLIEAINNGDFEAYTKICDPGLT T0475 36 :AF 2ux0A 430 :EP T0475 38 :PAT 2ux0A 433 :ALG T0475 41 :LLAG 2ux0A 437 :LVEG T0475 46 :AAEIRVRHIERFKE 2ux0A 441 :MDFHKFYFENLLSK T0475 60 :PDLYGELLTRVIV 2ux0A 457 :KPIHTTILNPHVH T0475 73 :GNVVIDH 2ux0A 473 :EDAACIA T0475 80 :ETVTRNFPEGKG 2ux0A 482 :RLTQYIDGQGRP T0475 92 :EVDVACIYEVENGRIAKAWFKIGE 2ux0A 497 :QSEETRVWHRRDGKWLNVHYHCSG Number of specific fragments extracted= 10 number of extra gaps= 1 total=360 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 2ux0A/T0475-2ux0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2ux0A/T0475-2ux0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ux0A read from 2ux0A/T0475-2ux0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ux0A in template set Warning: unaligning (T0475)Y34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ux0A)F429 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ux0A)F429 Warning: unaligning (T0475)P116 because last residue in template chain is (2ux0A)A521 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQ 2ux0A 398 :EIIKITEQLIEAINNGDFEAYTKICDPGLT T0475 36 :AF 2ux0A 430 :EP T0475 38 :PATLLAGNAAEIRVRHIERF 2ux0A 433 :ALGNLVEGMDFHKFYFENLL T0475 58 :KE 2ux0A 454 :KN T0475 60 :PDLYGELLTRVIV 2ux0A 457 :KPIHTTILNPHVH T0475 73 :GN 2ux0A 473 :ED T0475 75 :VVIDHETVTRNF 2ux0A 477 :CIAYIRLTQYID T0475 87 :PEGKGE 2ux0A 490 :QGRPRT T0475 93 :VDVACIYEVENGRIAKAWFKIGE 2ux0A 498 :SEETRVWHRRDGKWLNVHYHCSG Number of specific fragments extracted= 9 number of extra gaps= 1 total=369 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 2ux0A/T0475-2ux0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2ux0A/T0475-2ux0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ux0A read from 2ux0A/T0475-2ux0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ux0A in template set Warning: unaligning (T0475)Y34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ux0A)F429 Warning: unaligning (T0475)Y35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ux0A)F429 Warning: unaligning (T0475)P116 because last residue in template chain is (2ux0A)A521 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQ 2ux0A 398 :EIIKITEQLIEAINNGDFEAYTKICDPGLT T0475 36 :AFPA 2ux0A 430 :EPEA T0475 40 :TLLAGNAAEIRVRHIERF 2ux0A 435 :GNLVEGMDFHKFYFENLL T0475 58 :KEPDLYGELLTRVIV 2ux0A 455 :NSKPIHTTILNPHVH T0475 73 :GNVVIDHETVTRNFPEG 2ux0A 475 :AACIAYIRLTQYIDGQG T0475 90 :KGEVDVACIYEVENGRIAKAWFKIGE 2ux0A 495 :TSQSEETRVWHRRDGKWLNVHYHCSG Number of specific fragments extracted= 6 number of extra gaps= 1 total=375 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 1hkxA/T0475-1hkxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hkxA expands to /projects/compbio/data/pdb/1hkx.pdb.gz 1hkxA:# T0475 read from 1hkxA/T0475-1hkxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkxA read from 1hkxA/T0475-1hkxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hkxA to template set # found chain 1hkxA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1hkxA 349 :EIIKVTEQLIEAISNGDFESYTKMCDPGMTAFEPEAL T0475 41 :LLAG 1hkxA 388 :LVEG T0475 46 :AAEIRVRHIERFKE 1hkxA 392 :LDFHRFYFENLWSR T0475 60 :PDLYGELLTRVIV 1hkxA 408 :KPVHTTILNPHIH T0475 73 :GNVVIDHETVTRNF 1hkxA 424 :DESACIAYIRITQY T0475 87 :PEGKG 1hkxA 440 :AGGIP T0475 92 :EVDVACIYEVENGRIAKAWFKIGEPR 1hkxA 448 :QSEETRVWHRRDGKWQIVHFHRSGAP Number of specific fragments extracted= 7 number of extra gaps= 0 total=382 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 1hkxA/T0475-1hkxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1hkxA/T0475-1hkxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkxA read from 1hkxA/T0475-1hkxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hkxA in template set Warning: unaligning (T0475)I118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hkxA)V475 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 1hkxA 349 :EIIKVTEQLIEAISNGDFESYTKMCDPGMTAFEP T0475 38 :PATLLAGNAAEIRVRHIERF 1hkxA 384 :ALGNLVEGLDFHRFYFENLW T0475 58 :KEPDLYGELLTRVIV 1hkxA 406 :NSKPVHTTILNPHIH T0475 73 :GNVVIDHETVTRNF 1hkxA 424 :DESACIAYIRITQY T0475 87 :PEGKGE 1hkxA 441 :GGIPRT T0475 93 :VDVACIYEVENGRIAKAWFKIGEPR 1hkxA 449 :SEETRVWHRRDGKWQIVHFHRSGAP Number of specific fragments extracted= 6 number of extra gaps= 1 total=388 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 1hkxA/T0475-1hkxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1hkxA/T0475-1hkxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkxA read from 1hkxA/T0475-1hkxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hkxA in template set T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPA 1hkxA 350 :IIKVTEQLIEAISNGDFESYTKMCDPGMTAFEPEA T0475 40 :TLLAGNAAEIRVRHIERF 1hkxA 386 :GNLVEGLDFHRFYFENLW T0475 58 :KEPDLYGELLTRVIV 1hkxA 406 :NSKPVHTTILNPHIH T0475 73 :GNVVIDHETVTRNFPEG 1hkxA 426 :SACIAYIRITQYLDAGG T0475 90 :KGEVDVACIYEVENGRIAKAWFKIGEPR 1hkxA 446 :TAQSEETRVWHRRDGKWQIVHFHRSGAP Number of specific fragments extracted= 5 number of extra gaps= 0 total=393 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 1ocvA/T0475-1ocvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ocvA expands to /projects/compbio/data/pdb/1ocv.pdb.gz 1ocvA:# T0475 read from 1ocvA/T0475-1ocvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ocvA read from 1ocvA/T0475-1ocvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ocvA to template set # found chain 1ocvA in template set T0475 1 :L 1ocvA 1 :M T0475 2 :N 1ocvA 3 :T T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1ocvA 5 :EHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGS T0475 41 :LLAG 1ocvA 44 :PRSG T0475 46 :AAEIRVRHIERFKE 1ocvA 48 :TAAIREFYANSLKL T0475 61 :DLYGELLT 1ocvA 62 :PLAVELTQ T0475 69 :RVIVGNVVIDHETVTRN 1ocvA 71 :VRAVANEAAFAFIVSFE T0475 87 :PEGKG 1ocvA 88 :YQGRK T0475 92 :EVDVACIYEV 1ocvA 94 :VVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVS 1ocvA 105 :GAGKVVSMRALWGEKNIHA Number of specific fragments extracted= 10 number of extra gaps= 0 total=403 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 1ocvA/T0475-1ocvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ocvA/T0475-1ocvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ocvA read from 1ocvA/T0475-1ocvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ocvA in template set T0475 2 :NSE 1ocvA 3 :TPE T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERF 1ocvA 7 :MTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSL T0475 58 :KEPDLYGE 1ocvA 61 :LPLAVELT T0475 67 :LTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1ocvA 69 :QEVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVSQ 1ocvA 105 :GAGKVVSMRALWGEKNIHAG Number of specific fragments extracted= 5 number of extra gaps= 0 total=408 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 1ocvA/T0475-1ocvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ocvA/T0475-1ocvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ocvA read from 1ocvA/T0475-1ocvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ocvA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERFKEPD 1ocvA 6 :HMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFYANSLKLPL T0475 63 :YGELL 1ocvA 64 :AVELT T0475 68 :TRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEVE 1ocvA 70 :EVRAVANEAAFAFIVSFEYQGRKTVVAPIDHFRFN T0475 103 :NGRIAKAWFKIGEPRIVSQK 1ocvA 106 :AGKVVSMRALWGEKNIHAGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=412 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 1opy/T0475-1opy-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1opy expands to /projects/compbio/data/pdb/1opy.pdb.gz 1opy:Warning: there is no chain 1opy will retry with 1opyA # T0475 read from 1opy/T0475-1opy-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opy read from 1opy/T0475-1opy-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1opy to template set # found chain 1opy in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1opy)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1opy)K65 T0475 2 :N 1opy 5 :T T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1opy 7 :QEVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQ T0475 41 :LLAG 1opy 46 :PIHG T0475 46 :AAEIRVRHIER 1opy 50 :REQIAAFYRQG T0475 62 :LYGELLTRV 1opy 66 :VRACLTGPV T0475 71 :IVGN 1opy 76 :ASHN T0475 75 :VVIDHETVTRN 1opy 81 :CGAMPFRVEMV T0475 87 :PEGKG 1opy 92 :WNGQP T0475 92 :EVDVACIYEV 1opy 98 :ALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRI 1opy 109 :EHGRIQTMQAYWSEVNL Number of specific fragments extracted= 10 number of extra gaps= 0 total=422 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 1opy/T0475-1opy-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1opy/T0475-1opy-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opy read from 1opy/T0475-1opy-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1opy in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1opy)K65 Warning: unaligning (T0475)E59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1opy)K65 Warning: unaligning (T0475)S120 because last residue in template chain is (1opy)V127 T0475 3 :S 1opy 7 :Q T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1opy 9 :VQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQG T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1opy 66 :VRACLTGPVRASHNGCGAMPFRVEMVWNGQPCALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRIV 1opy 109 :EHGRIQTMQAYWSEVNLS Number of specific fragments extracted= 4 number of extra gaps= 0 total=426 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 1opy/T0475-1opy-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1opy/T0475-1opy-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1opy read from 1opy/T0475-1opy-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1opy in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1opy)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1opy)K65 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1opy 8 :EVQGLMARYIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQG T0475 62 :LYGELLTRVIV 1opy 66 :VRACLTGPVRA T0475 73 :GNVVIDHETVTRNFPEGKGEVDVACIYEVE 1opy 79 :NGCGAMPFRVEMVWNGQPCALDVIDVMRFD T0475 103 :NGRIAKAWFKIGEPRIV 1opy 110 :HGRIQTMQAYWSEVNLS Number of specific fragments extracted= 4 number of extra gaps= 0 total=430 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 2f86B/T0475-2f86B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f86B expands to /projects/compbio/data/pdb/2f86.pdb.gz 2f86B:# T0475 read from 2f86B/T0475-2f86B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f86B read from 2f86B/T0475-2f86B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f86B to template set # found chain 2f86B in template set Warning: unaligning (T0475)K58 because of BadResidue code BAD_PEPTIDE in next template residue (2f86B)G404 Warning: unaligning (T0475)E59 because of BadResidue code BAD_PEPTIDE at template residue (2f86B)G404 Warning: unaligning (T0475)E115 because last residue in template chain is (2f86B)T471 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2f86B 351 :QDIVRVTQTLLDAISCKDFETYTRLCDTSMTCFEP T0475 38 :PA 2f86B 388 :LG T0475 41 :LLAG 2f86B 391 :LIEG T0475 46 :AAEI 2f86B 395 :IEFH T0475 54 :IERF 2f86B 399 :RFYF T0475 60 :PDLYGELLTRV 2f86B 408 :NQVHTTMLNPN T0475 71 :IVGN 2f86B 421 :IIGE T0475 75 :VVIDH 2f86B 426 :AACVA T0475 80 :ETVTRNFPEGKG 2f86B 433 :KLTQFLDRNGEA T0475 92 :EVDVACIYEVENGRIAKAWFKIG 2f86B 448 :QSQESRVWSKKQGRWVCVHVHRS Number of specific fragments extracted= 10 number of extra gaps= 1 total=440 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 2f86B/T0475-2f86B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2f86B/T0475-2f86B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f86B read from 2f86B/T0475-2f86B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f86B in template set Warning: unaligning (T0475)E115 because last residue in template chain is (2f86B)T471 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2f86B 352 :DIVRVTQTLLDAISCKDFETYTRLCDTSMTCFEP T0475 38 :PATLLAGNAAEI 2f86B 387 :ALGNLIEGIEFH T0475 54 :IERF 2f86B 399 :RFYF T0475 58 :KEPDLYGELLTRV 2f86B 406 :RKNQVHTTMLNPN T0475 71 :IVGNVVIDHETVTRNF 2f86B 422 :IGEDAACVAYVKLTQF T0475 87 :PEGKGE 2f86B 441 :NGEAHT T0475 93 :VDVACIYEVENGRIAKAWFKIG 2f86B 449 :SQESRVWSKKQGRWVCVHVHRS Number of specific fragments extracted= 7 number of extra gaps= 0 total=447 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 2f86B/T0475-2f86B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2f86B/T0475-2f86B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f86B read from 2f86B/T0475-2f86B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f86B in template set Warning: unaligning (T0475)E115 because last residue in template chain is (2f86B)T471 T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYY 2f86B 352 :DIVRVTQTLLDAISCKDFETYTRLCDTSMTCF T0475 36 :AFPATL 2f86B 386 :EALGNL T0475 43 :AGNAA 2f86B 392 :IEGIE T0475 52 :RHIERF 2f86B 397 :FHRFYF T0475 58 :KEPDLYGELLTRVIV 2f86B 406 :RKNQVHTTMLNPNVH T0475 73 :GN 2f86B 423 :GE T0475 75 :VVIDHETVTRNFPEG 2f86B 428 :CVAYVKLTQFLDRNG T0475 90 :KGEVDVACIYEVENGRIAKAWFKIG 2f86B 446 :TRQSQESRVWSKKQGRWVCVHVHRS Number of specific fragments extracted= 8 number of extra gaps= 0 total=455 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 2imjA/T0475-2imjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2imjA expands to /projects/compbio/data/pdb/2imj.pdb.gz 2imjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 2imjA/T0475-2imjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imjA read from 2imjA/T0475-2imjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2imjA to template set # found chain 2imjA in template set T0475 2 :N 2imjA 15 :T T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2imjA 17 :ESAIEKIRLAEDGWNSRDPERVSLAYTLDTQWRN T0475 39 :AT 2imjA 51 :RA T0475 41 :LLAG 2imjA 54 :FAHN T0475 46 :AAEIRVRHIERFKE 2imjA 58 :REEAKAFLTRKWAK T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRNFPEGKG 2imjA 73 :LDYRLIKELWAFTDNRIAVRYAYEWHDDSGNW T0475 92 :EVDVACIYEV 2imjA 106 :RSYGNENWEF T0475 102 :ENGRIAKAWFKIGEPRIVS 2imjA 117 :EQGLMARRFACINDMPIKA Number of specific fragments extracted= 8 number of extra gaps= 0 total=463 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 2imjA/T0475-2imjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2imjA/T0475-2imjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imjA read from 2imjA/T0475-2imjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2imjA in template set T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2imjA 17 :ESAIEKIRLAEDGWNSRDPERVSLAYTLDTQWRN T0475 39 :ATLLAGNAAEIRVRHIERF 2imjA 51 :RAEFAHNREEAKAFLTRKW T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNF 2imjA 71 :KELDYRLIKELWAFTDNRIAVRYAYEWHD T0475 87 :PEGKGEVDVACIYEV 2imjA 101 :SGNWFRSYGNENWEF T0475 102 :ENGRIAKAWFKIGEPRIVS 2imjA 117 :EQGLMARRFACINDMPIKA Number of specific fragments extracted= 5 number of extra gaps= 0 total=468 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 2imjA/T0475-2imjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2imjA/T0475-2imjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2imjA read from 2imjA/T0475-2imjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2imjA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2imjA 18 :SAIEKIRLAEDGWNSRDPERVSLAYTLDTQWRN T0475 39 :ATLLAGNAAEIRVRHIERF 2imjA 51 :RAEFAHNREEAKAFLTRKW T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNFPEG 2imjA 71 :KELDYRLIKELWAFTDNRIAVRYAYEWHDDSG T0475 90 :KGEVDVACIYEV 2imjA 104 :WFRSYGNENWEF T0475 102 :ENGRIAKAWFKIGEPRIV 2imjA 117 :EQGLMARRFACINDMPIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=473 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3blzA/T0475-3blzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3blzA expands to /projects/compbio/data/pdb/3blz.pdb.gz 3blzA:Skipped atom 71, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 73, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 75, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 77, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 79, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 81, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 83, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 85, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 87, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 89, because occupancy 0.300 <= existing 0.700 in 3blzA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3blzA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 658, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 3blzA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 3blzA # T0475 read from 3blzA/T0475-3blzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3blzA read from 3blzA/T0475-3blzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3blzA to template set # found chain 3blzA in template set Warning: unaligning (T0475)V93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3blzA)T102 Warning: unaligning (T0475)D94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3blzA)T102 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 3blzA 13 :IVEVLSKYNEGGKKADSTIMRPAFSSQATIFGV T0475 38 :PAT 3blzA 48 :DNK T0475 41 :LLAG 3blzA 52 :TGGP T0475 46 :AAEIRVRHIERFKE 3blzA 56 :IQGLFDVIDNVFHP T0475 60 :PDLYGELLTRVIVGNVVIDHETVTRN 3blzA 71 :PEAKAAIARIDIVGTAASARIDTDDI T0475 87 :PEG 3blzA 97 :SGF T0475 92 :E 3blzA 100 :R T0475 95 :VACIYEVENGRIAKAWFKI 3blzA 103 :DFFNLLKVEGKWTVVSKIY Number of specific fragments extracted= 8 number of extra gaps= 1 total=481 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3blzA/T0475-3blzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3blzA/T0475-3blzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3blzA read from 3blzA/T0475-3blzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3blzA in template set Warning: unaligning (T0475)V93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3blzA)T102 Warning: unaligning (T0475)D94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3blzA)T102 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 3blzA 13 :IVEVLSKYNEGGKKADSTIMRPAFSSQATIFGV T0475 38 :PATLLAGNAAEIRVRHIERF 3blzA 48 :DNKLTGGPIQGLFDVIDNVF T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNFP 3blzA 69 :PSPEAKAAIARIDIVGTAASARIDTDDISG T0475 91 :GE 3blzA 99 :FR T0475 95 :VACIYEVENGRIAKAWFKIG 3blzA 103 :DFFNLLKVEGKWTVVSKIYH Number of specific fragments extracted= 5 number of extra gaps= 1 total=486 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3blzA/T0475-3blzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 3blzA/T0475-3blzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3blzA read from 3blzA/T0475-3blzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3blzA in template set Warning: unaligning (T0475)V93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3blzA)T102 Warning: unaligning (T0475)D94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3blzA)T102 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYY 3blzA 13 :IVEVLSKYNEGGKKADSTIMRPAFSSQATIF T0475 36 :AFPAT 3blzA 45 :VDVDN T0475 41 :LLAGNAAEIRVRHIERF 3blzA 51 :LTGGPIQGLFDVIDNVF T0475 58 :KEPDLYGELLTRVIVGNVVIDHETVTRNFP 3blzA 69 :PSPEAKAAIARIDIVGTAASARIDTDDISG T0475 91 :GE 3blzA 99 :FR T0475 95 :VACIYEVENGRIAKAWFKIG 3blzA 103 :DFFNLLKVEGKWTVVSKIYH T0475 119 :VSQ 3blzA 123 :THP Number of specific fragments extracted= 7 number of extra gaps= 1 total=493 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2owpA/T0475-2owpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2owpA expands to /projects/compbio/data/pdb/2owp.pdb.gz 2owpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 99, because occupancy 0.500 <= existing 0.500 in 2owpA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2owpA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 2owpA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2owpA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2owpA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2owpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0475 read from 2owpA/T0475-2owpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2owpA read from 2owpA/T0475-2owpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2owpA to template set # found chain 2owpA in template set T0475 3 :SE 2owpA 6 :PD T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADD 2owpA 12 :VQAAFVEYERALVENDIEAMNALFWHT T0475 32 :CQYYAFPA 2owpA 41 :TVRYGIAE T0475 41 :LLAG 2owpA 49 :VQHG T0475 46 :AAEIRVRHIERFKE 2owpA 53 :GEAIRAWRERCEPV T0475 60 :PDLYGELLTRVIVGN 2owpA 68 :KSRKLHRTVVTTFGT T0475 75 :VVIDHETVT 2owpA 84 :FATVSTEFT T0475 87 :PEGKG 2owpA 93 :SDATP T0475 92 :EVDVACIYEV 2owpA 99 :LGRQMQTWAR T0475 102 :ENG 2owpA 110 :SPA T0475 105 :RIAKAWFKIGEP 2owpA 116 :KIVAAHVSLIAM Number of specific fragments extracted= 11 number of extra gaps= 0 total=504 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2owpA/T0475-2owpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2owpA/T0475-2owpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2owpA read from 2owpA/T0475-2owpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2owpA in template set T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADD 2owpA 12 :VQAAFVEYERALVENDIEAMNALFWHT T0475 32 :CQYYA 2owpA 41 :TVRYG T0475 39 :ATLLAGNAAEIRVRHIERF 2owpA 46 :IAEVQHGGEAIRAWRERCE T0475 58 :KEPDLYGELLTRV 2owpA 66 :VPKSRKLHRTVVT T0475 71 :IVGNVVIDHETVTR 2owpA 80 :FGTDFATVSTEFTS T0475 87 :PEGKGEVDVACIYEV 2owpA 94 :DATPLLGRQMQTWAR T0475 102 :ENG 2owpA 110 :SPA T0475 105 :RIAKAWFKIGE 2owpA 116 :KIVAAHVSLIA Number of specific fragments extracted= 8 number of extra gaps= 0 total=512 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2owpA/T0475-2owpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2owpA/T0475-2owpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2owpA read from 2owpA/T0475-2owpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2owpA in template set Warning: unaligning (T0475)R117 because last residue in template chain is (2owpA)P128 T0475 6 :ELPVQKQLEAYNARDIDAFMAWWAD 2owpA 13 :QAAFVEYERALVENDIEAMNALFWH T0475 37 :FPA 2owpA 38 :TPE T0475 40 :TLLAGNAAEIRVRHI 2owpA 47 :AEVQHGGEAIRAWRE T0475 56 :RFKEPDLYGELLTRVIV 2owpA 62 :RCEPVPKSRKLHRTVVT T0475 73 :GNVVIDHETVTRNFPE 2owpA 82 :TDFATVSTEFTSDATP T0475 91 :GEVDVACIYEVENG 2owpA 98 :LLGRQMQTWARLSP T0475 105 :RIAKAWFKIGEP 2owpA 116 :KIVAAHVSLIAM Number of specific fragments extracted= 7 number of extra gaps= 0 total=519 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgqA/T0475-2rgqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rgqA expands to /projects/compbio/data/pdb/2rgq.pdb.gz 2rgqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 149, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 153, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 157, because occupancy 0.370 <= existing 0.380 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2rgqA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 666, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 670, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 674, because occupancy 0.370 <= existing 0.380 in 2rgqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2rgqA # T0475 read from 2rgqA/T0475-2rgqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgqA read from 2rgqA/T0475-2rgqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rgqA to template set # found chain 2rgqA in template set T0475 3 :S 2rgqA 5 :A T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAF 2rgqA 10 :EIMELAARFEMSLDKEDVENYLATFASDGALQGF T0475 39 :ATLLAG 2rgqA 44 :WGIAKG T0475 46 :AAEIRVRHIERFKE 2rgqA 50 :KEELRQGFYAMLDT T0475 60 :PDLYGELLTRV 2rgqA 66 :RGKRHCSSNAI T0475 71 :IVGNVVIDHETVTRNF 2rgqA 79 :GNYDEATMESYLTVVN T0475 87 :PEGKG 2rgqA 96 :EDLNR T0475 92 :EVDVACIYEVENG 2rgqA 103 :SAFVKDQVRKING T0475 105 :RIAKAWFKIGE 2rgqA 118 :YLILRQIEVDP Number of specific fragments extracted= 9 number of extra gaps= 0 total=528 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgqA/T0475-2rgqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2rgqA/T0475-2rgqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgqA read from 2rgqA/T0475-2rgqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rgqA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2rgqA 10 :EIMELAARFEMSLDKEDVENYLATFASDGALQG T0475 39 :ATLLAGNAAEIRVRHIERF 2rgqA 43 :FWGIAKGKEELRQGFYAML T0475 58 :KEPD 2rgqA 63 :TFAR T0475 62 :LYGELLTRVIVGN 2rgqA 68 :KRHCSSNAIIQGN T0475 75 :VVIDHETVTRNF 2rgqA 83 :EATMESYLTVVN T0475 87 :PEGKGE 2rgqA 97 :DLNRAG T0475 93 :VDVACIYEVENGRI 2rgqA 104 :AFVKDQVRKINGKW T0475 107 :AKAWFKIGEP 2rgqA 120 :ILRQIEVDPS Number of specific fragments extracted= 8 number of extra gaps= 0 total=536 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rgqA/T0475-2rgqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 2rgqA/T0475-2rgqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rgqA read from 2rgqA/T0475-2rgqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rgqA in template set T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYA 2rgqA 11 :IMELAARFEMSLDKEDVENYLATFASDGALQG T0475 39 :ATLLAGNAAEIRVRHIERF 2rgqA 43 :FWGIAKGKEELRQGFYAML T0475 58 :KEPDLYGELLTRVIV 2rgqA 64 :FARGKRHCSSNAIIQ T0475 73 :GNVVIDHETVTRNF 2rgqA 81 :YDEATMESYLTVVN T0475 87 :PEG 2rgqA 96 :EDL T0475 90 :KGEVDVACIYEVENGRIAKAWFKI 2rgqA 101 :AGSAFVKDQVRKINGKWYLILRQI Number of specific fragments extracted= 6 number of extra gaps= 0 total=542 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1buqA/T0475-1buqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1buqA expands to /projects/compbio/data/pdb/1buq.pdb.gz 1buqA:# T0475 read from 1buqA/T0475-1buqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1buqA read from 1buqA/T0475-1buqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1buqA to template set # found chain 1buqA in template set T0475 1 :LN 1buqA 1 :MN T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1buqA 5 :EHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGS T0475 41 :LLAG 1buqA 44 :PRSG T0475 46 :AAEIRVRHIERFKE 1buqA 48 :TAAIREFFANSLKL T0475 60 :PDLYGE 1buqA 63 :LAVELT T0475 68 :TRVIVGNVVIDHETVTRNFP 1buqA 70 :EVRAVANEAAFAFTVSFEFQ T0475 89 :GKG 1buqA 90 :GRK T0475 92 :EVDVACIYEV 1buqA 94 :VVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIV 1buqA 105 :GAGKVVSMRALFGEKNIH Number of specific fragments extracted= 9 number of extra gaps= 0 total=551 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1buqA/T0475-1buqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1buqA/T0475-1buqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1buqA read from 1buqA/T0475-1buqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1buqA in template set T0475 1 :LN 1buqA 1 :MN T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERF 1buqA 5 :EHMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFFANSL T0475 58 :KEPDLYGE 1buqA 61 :LPLAVELT T0475 68 :TRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEV 1buqA 70 :EVRAVANEAAFAFTVSFEFQGRKTVVAPIDHFRF T0475 102 :ENGRIAKAWFKIGEPRIVSQ 1buqA 105 :GAGKVVSMRALFGEKNIHAG Number of specific fragments extracted= 5 number of extra gaps= 0 total=556 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1buqA/T0475-1buqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1buqA/T0475-1buqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1buqA read from 1buqA/T0475-1buqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1buqA in template set T0475 4 :EIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIERF 1buqA 6 :HMTAVVQRYVAALNAGDLDGIVALFADDATVEDPVGSEPRSGTAAIREFFANSL T0475 58 :KEPDLYGE 1buqA 61 :LPLAVELT T0475 68 :TRVIVGNVVIDHETVTRNFPEGKGEVDVACIYEVE 1buqA 70 :EVRAVANEAAFAFTVSFEFQGRKTVVAPIDHFRFN T0475 103 :NGRIAKAWFKIGEPRIVSQK 1buqA 106 :AGKVVSMRALFGEKNIHAGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=560 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ea2A/T0475-1ea2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ea2A expands to /projects/compbio/data/pdb/1ea2.pdb.gz 1ea2A:# T0475 read from 1ea2A/T0475-1ea2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea2A read from 1ea2A/T0475-1ea2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ea2A to template set # found chain 1ea2A in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ea2A)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ea2A)K65 T0475 2 :N 1ea2A 5 :T T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPAT 1ea2A 7 :QEVQGLMARFIELVDVGDIEAIVQMYADDATVEDPFGQ T0475 41 :LLAG 1ea2A 46 :PIHG T0475 46 :AAEIRVRHIER 1ea2A 50 :REQIAAFYRQG T0475 62 :LYGELLTRV 1ea2A 66 :VRACLTGPV T0475 71 :IVGN 1ea2A 76 :ASHN T0475 75 :VVIDHETVTRN 1ea2A 81 :CGAMPFRVEMV T0475 87 :PEGKG 1ea2A 92 :WNGQP T0475 92 :EVDVACIYEV 1ea2A 98 :ALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRI 1ea2A 109 :EHGRIQTMQAYWSEVNL Number of specific fragments extracted= 10 number of extra gaps= 0 total=570 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ea2A/T0475-1ea2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ea2A/T0475-1ea2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea2A read from 1ea2A/T0475-1ea2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ea2A in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ea2A)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ea2A)K65 T0475 3 :SEIELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1ea2A 7 :QEVQGLMARFIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQG T0475 62 :LYGELLTRV 1ea2A 66 :VRACLTGPV T0475 71 :IVGN 1ea2A 76 :ASHN T0475 75 :VVIDHETVTRNFPEGKGEVDVACIYEV 1ea2A 81 :CGAMPFRVEMVWNGQPCALDVIDVMRF T0475 102 :ENGRIAKAWFKIGEPRI 1ea2A 109 :EHGRIQTMQAYWSEVNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=575 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ea2A/T0475-1ea2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0475 read from 1ea2A/T0475-1ea2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea2A read from 1ea2A/T0475-1ea2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ea2A in template set Warning: unaligning (T0475)F57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ea2A)K65 Warning: unaligning (T0475)D61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ea2A)K65 T0475 5 :IELPVQKQLEAYNARDIDAFMAWWADDCQYYAFPATLLAGNAAEIRVRHIER 1ea2A 9 :VQGLMARFIELVDVGDIEAIVQMYADDATVEDPFGQPPIHGREQIAAFYRQG T0475 62 :LYGELLTRVIV 1ea2A 66 :VRACLTGPVRA T0475 73 :GNVVIDHETVTRNFPEGKGEVDVACIYEVE 1ea2A 79 :NGCGAMPFRVEMVWNGQPCALDVIDVMRFD T0475 103 :NGRIAKAWFKIGEPRI 1ea2A 110 :HGRIQTMQAYWSEVNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=579 Will force an alignment to be made, even if fragment is small Number of alignments=87 # command:CPU_time= 20.733 sec, elapsed time= 37.867 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 87 Adding 770 constraints to all_contacts Done adding distance constraints # command:CPU_time= 20.782 sec, elapsed time= 37.920 sec. # command:Reading probabilities from T0475.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 83.614 Optimizing... Probability sum: -220.377, CN propb: -220.377 weights: 0.455 constraints: 275 # command:CPU_time= 24.608 sec, elapsed time= 41.747 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 275 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 275 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 495 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 495 # 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= 24.621 sec, elapsed time= 42.679 sec. # command: