# 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 T0330 numbered 1 through 233 Created new target T0330 from T0330.a2m # command:CPU_time= 6.332 sec, elapsed time= 6.378 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/T0330-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ah5A expands to /projects/compbio/data/pdb/2ah5.pdb.gz 2ah5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2ah5A/T0330-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0330-2ah5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFS 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGF # choosing archetypes in rotamer library T0330 49 :DGAIIYEVLSNVG 2ah5A 47 :MGPPLESSFATCL T0330 63 :ER 2ah5A 60 :SK T0330 69 :DKFDKAKETYIALFRER 2ah5A 62 :DQISEAVQIYRSYYKAK T0330 87 :RREDITLLEGVRELLDALSSR 2ah5A 79 :GIYEAQLFPQIIDLLEELSSS T0330 110 :VLLGLLT 2ah5A 100 :YPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARRM 2ah5A 140 :ADVIHQALQTH T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 151 :QLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 9 number of extra gaps= 1 total=9 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 2ah5A/T0330-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2ah5A/T0330-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0330-2ah5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADAL 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTF T0330 31 :EVYGTE 2ah5A 31 :KELGVP T0330 37 :GSTGS 2ah5A 38 :PDAKT T0330 42 :HDFSGKMDGAIIY 2ah5A 44 :RGFMGPPLESSFA T0330 60 :VGLERAEI 2ah5A 57 :TCLSKDQI T0330 72 :DKAKETYIALFRERAR 2ah5A 65 :SEAVQIYRSYYKAKGI T0330 89 :EDITLLEGVRELLDALSSR 2ah5A 81 :YEAQLFPQIIDLLEELSSS T0330 110 :VLLGLLT 2ah5A 100 :YPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARRM 2ah5A 140 :ADVIHQALQTH T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 151 :QLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 11 number of extra gaps= 1 total=20 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 2ah5A/T0330-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2ah5A/T0330-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ah5A read from 2ah5A/T0330-2ah5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEV 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFAT T0330 66 :EIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 2ah5A 58 :CLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSS T0330 109 :DVLLGLLT 2ah5A 99 :SYPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARR 2ah5A 140 :ADVIHQALQT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 150 :HQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 6 number of extra gaps= 1 total=26 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 2fdrA/T0330-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fdrA expands to /projects/compbio/data/pdb/2fdr.pdb.gz 2fdrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 0.5 <= existing 0.500 in 2fdrA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1330, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2fdrA/T0330-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0330-2fdrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEA T0330 62 :LERAE 2fdrA 64 :IPLSA T0330 69 :DKFDKAKETYIALFRE 2fdrA 69 :SLLDKSEKLLDMRLER T0330 90 :DITLLEGVRELLDAL 2fdrA 85 :DVKIIDGVKFALSRL T0330 108 :S 2fdrA 100 :T T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADDALDR 2fdrA 129 :PHIYSAKDLGAD T0330 149 :NELPHIALERARRM 2fdrA 143 :KPKPDIFLHGAAQF T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 157 :GVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 11 number of extra gaps= 1 total=37 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 2fdrA/T0330-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2fdrA/T0330-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0330-2fdrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADAL 2fdrA 11 :CDGVLVDSEIIAAQVESRLL T0330 31 :EVYGTEGSTGS 2fdrA 31 :TEAGYPISVEE T0330 42 :HDFSGKMDGAIIYEVLSNVGLERA 2fdrA 44 :ERFAGMTWKNILLQVESEASIPLS T0330 72 :DKAKETYIALFRERAR 2fdrA 68 :ASLLDKSEKLLDMRLE T0330 89 :EDITLLEGVRELLDAL 2fdrA 84 :RDVKIIDGVKFALSRL T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADDALD 2fdrA 129 :PHIYSAKDLGA T0330 148 :RNELPHIALERARRM 2fdrA 142 :VKPKPDIFLHGAAQF T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 157 :GVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 11 number of extra gaps= 1 total=48 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 2fdrA/T0330-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2fdrA/T0330-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fdrA read from 2fdrA/T0330-2fdrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEA T0330 64 :RAEIADKFDKAKETYIALFRER 2fdrA 63 :SIPLSASLLDKSEKLLDMRLER T0330 90 :DITLLEGVRELLDAL 2fdrA 85 :DVKIIDGVKFALSRL T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADD 2fdrA 129 :PHIYSAKD T0330 145 :ALDRNELPHIALERARR 2fdrA 139 :ADRVKPKPDIFLHGAAQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 156 :FGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 9 number of extra gaps= 1 total=57 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 1te2A/T0330-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1te2A expands to /projects/compbio/data/pdb/1te2.pdb.gz 1te2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 79, because occupancy 0.470 <= existing 0.530 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 83, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 87, because occupancy 0.440 <= existing 0.560 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.420 <= existing 0.580 in 1te2A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 213, because occupancy 0.450 <= existing 0.550 in 1te2A Skipped atom 215, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 217, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 412, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 420, because occupancy 0.480 <= existing 0.520 in 1te2A Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 426, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 538, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 544, because occupancy 0.490 <= existing 0.510 in 1te2A Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1te2A Skipped atom 552, because occupancy 0.480 <= existing 0.520 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 996, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 998, because occupancy 0.490 <= existing 0.510 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1te2A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1te2A/T0330-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0330-1te2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1te2A to template set # found chain 1te2A in template set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQ T0330 62 :LERA 1te2A 70 :PSRQ T0330 69 :DKFDKAKETYIALFRER 1te2A 74 :EVVERVIARAISLVEET T0330 91 :ITLLEGVRELLDALSSRS 1te2A 91 :RPLLPGVREAVALCKEQG T0330 110 :VLLGLLTGNFEASGRHKLK 1te2A 109 :LLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARRM 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1te2A 162 :GVDPLTCVALEDSVNGMIASKAARMRSIVVPAP T0330 210 :PGTLFKNFAET 1te2A 205 :ANVKLSSLTEL T0330 221 :DEVLA 1te2A 217 :AKDLL Number of specific fragments extracted= 9 number of extra gaps= 1 total=66 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 1te2A/T0330-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1te2A/T0330-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0330-1te2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADAL 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVM T0330 31 :EVYGTEGSTGS 1te2A 34 :ASLGVDISRRN T0330 42 :HDFSGKMDGAIIYEVLSNVGLERAEI 1te2A 47 :PDTLGLRIDMVVDLWYARQPWNGPSR T0330 72 :DKAKETYIALFRERAR 1te2A 73 :QEVVERVIARAISLVE T0330 89 :EDITLLEGVRELLDALSSRS 1te2A 89 :ETRPLLPGVREAVALCKEQG T0330 110 :VLLGLLTGNFEASGRHKLK 1te2A 109 :LLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARRM 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1te2A 162 :GVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEA T0330 201 :TMEELAR 1te2A 198 :NDPRFVL T0330 210 :PGTLFKNFAET 1te2A 205 :ANVKLSSLTEL T0330 221 :DEVLA 1te2A 217 :AKDLL Number of specific fragments extracted= 11 number of extra gaps= 1 total=77 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 1te2A/T0330-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1te2A/T0330-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1te2A read from 1te2A/T0330-1te2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1te2A in template set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQPWN T0330 68 :ADKFDKAKETYIALFRERARRED 1te2A 69 :GPSRQEVVERVIARAISLVEETR T0330 92 :TLLEGVRELLDALSS 1te2A 92 :PLLPGVREAVALCKE T0330 108 :SDVLLGLLTGNFEASGRHKLK 1te2A 107 :QGLLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARR 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1te2A 161 :LGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEA T0330 201 :TMEELA 1te2A 198 :NDPRFV T0330 209 :KPGTLFKNFAET 1te2A 204 :LANVKLSSLTEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=85 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 2gfhA/T0330-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gfhA expands to /projects/compbio/data/pdb/2gfh.pdb.gz 2gfhA:Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2gfhA # T0330 read from 2gfhA/T0330-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0330-2gfhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDF 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEI T0330 49 :DGAIIYEVLSNVG 2gfhA 48 :ICDKVQVKLSKEC T0330 62 :LERAEIADKFDKAKETYIALFRER 2gfhA 84 :KGGADNRKLAEECYFLWKSTRLQH T0330 91 :ITLLEGVRELLDALSSR 2gfhA 108 :MILADDVKAMLTELRKE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLL T0330 166 :NYSPSQIVIIGDTE 2gfhA 178 :GVQPGDCVMVGDTL T0330 180 :HDIRCARELDAR 2gfhA 193 :TDIQGGLNAGLK T0330 192 :SIAVATG 2gfhA 206 :TVWINKS T0330 199 :NFT 2gfhA 220 :SPM T0330 210 :PGTLFKNFAETDEVLASILTP 2gfhA 223 :PHYMVSSVLELPALLQSIDCK Number of specific fragments extracted= 11 number of extra gaps= 1 total=96 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 2gfhA/T0330-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2gfhA/T0330-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0330-2gfhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0330)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADAL 2gfhA 13 :LDNTLIDTAGASRRGMLEVI T0330 31 :EVY 2gfhA 33 :KLL T0330 34 :GT 2gfhA 38 :KY T0330 36 :EG 2gfhA 60 :CF T0330 44 :FSGKMDGAIIYEVLSNVGLERA 2gfhA 68 :ITDVRTSHWEEAIQETKGGADN T0330 72 :DKAKETYIALFRERAR 2gfhA 90 :RKLAEECYFLWKSTRL T0330 89 :EDITLLEGVRELLDALSSR 2gfhA 106 :QHMILADDVKAMLTELRKE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLL T0330 166 :NYSPSQIVIIGDTE 2gfhA 178 :GVQPGDCVMVGDTL T0330 180 :HDIRCARELDA 2gfhA 193 :TDIQGGLNAGL T0330 191 :RSIAVATGNFT 2gfhA 205 :ATVWINKSGRV T0330 207 :RHKPGTLFKNFAETDEVLASILTP 2gfhA 220 :SPMPHYMVSSVLELPALLQSIDCK Number of specific fragments extracted= 13 number of extra gaps= 1 total=109 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 2gfhA/T0330-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2gfhA/T0330-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gfhA read from 2gfhA/T0330-2gfhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADALIEV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0330 37 :GSTGSHDFS 2gfhA 40 :HYKEEAEII T0330 46 :GKMDGAIIYEVLSNVGL 2gfhA 69 :TDVRTSHWEEAIQETKG T0330 68 :ADKFDKAKETYIALFRERARR 2gfhA 86 :GADNRKLAEECYFLWKSTRLQ T0330 90 :DITLLEGVRELLDALSS 2gfhA 107 :HMILADDVKAMLTELRK T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2gfhA 124 :EVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDL T0330 165 :ANYSPSQIVIIGDTE 2gfhA 177 :LGVQPGDCVMVGDTL T0330 180 :HDIRCARELDARSIAVATGNFT 2gfhA 193 :TDIQGGLNAGLKATVWINKSGR T0330 208 :HKPGTLFKNFAETDEVLASILT 2gfhA 221 :PMPHYMVSSVLELPALLQSIDC Number of specific fragments extracted= 10 number of extra gaps= 1 total=119 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 1o08A/T0330-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1o08A/T0330-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0330-1o08A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 T0330 1 :M 1o08A 1001 :M T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 62 :LER 1o08A 1064 :VSA T0330 69 :DKFDKAKETYIALFRERA 1o08A 1067 :EEFKELAKRKNDNYVKMI T0330 87 :RREDITLLEGVRELLDALSSRS 1o08A 1086 :DVSPADVYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1o08A 1108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1o08A 1189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1o08A 1197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 12 number of extra gaps= 2 total=131 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 1o08A/T0330-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1o08A/T0330-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0330-1o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 T0330 1 :M 1o08A 1001 :M T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADAL 1o08A 1009 :LDGVITDTAEYHFRAWKALA T0330 31 :EVYGTE 1o08A 1029 :EEIGIN T0330 37 :GSTGS 1o08A 1036 :VDRQF T0330 42 :HDFSGKMDGAIIYEVLSNVG 1o08A 1042 :EQLKGVSREDSLQKILDLAD T0330 62 :LERAEI 1o08A 1064 :VSAEEF T0330 72 :DKAKETYIALFRERA 1o08A 1070 :KELAKRKNDNYVKMI T0330 89 :EDIT 1o08A 1085 :QDVS T0330 93 :LLEGVRELLDALSSRS 1o08A 1092 :VYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1o08A 1108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1o08A 1189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1o08A 1197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 16 number of extra gaps= 2 total=147 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 1o08A/T0330-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1o08A/T0330-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o08A read from 1o08A/T0330-1o08A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o08A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 Warning: unaligning (T0330)S233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)K1221 T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 64 :RAEIADKFDKAKETYIALFRERARRE 1o08A 1061 :DKKVSAEEFKELAKRKNDNYVKMIQD T0330 90 :DITLLEGVRELLDALSS 1o08A 1089 :PADVYPGILQLLKDLRS T0330 108 :SDVLLGLLTGN 1o08A 1106 :NKIKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1158 :VGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELA 1o08A 1189 :GRPEDLG T0330 209 :KPGTLFKNFAET 1o08A 1196 :DDIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 10 number of extra gaps= 2 total=157 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 1x42A/T0330-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x42A expands to /projects/compbio/data/pdb/1x42.pdb.gz 1x42A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1x42A/T0330-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0330-1x42A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x42A to template set # found chain 1x42A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 1 :M 1x42A 1 :M T0330 3 :RTLVLFDIDGTLLKVES 1x42A 2 :IRAVFFDFVGTLLSVEG T0330 21 :NRRVLADALIEVYGTEGS 1x42A 19 :EAKTHLKIMEEVLGDYPL T0330 49 :DGAIIYEVLSNVG 1x42A 37 :NPKTLLDEYEKLT T0330 62 :LERAEI 1x42A 62 :RPIRDI T0330 68 :ADKFDKAKETY 1x42A 69 :EEVMRKLAEKY T0330 79 :IALFRER 1x42A 88 :WEIHLRM T0330 87 :RREDITLLEGVRELLDALSSR 1x42A 95 :HQRYGELYPEVVEVLKSLKGK T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKA T0330 166 :NYSPSQIVIIGDTE 1x42A 169 :GVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDK T0330 210 :PGTLFKNFAETDEVLASI 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=169 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 1x42A/T0330-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1x42A/T0330-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0330-1x42A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 1 :M 1x42A 1 :M T0330 3 :RTLVLFDIDGTLLK 1x42A 2 :IRAVFFDFVGTLLS T0330 17 :VESMNRRVLADALIEVYGTEGST 1x42A 41 :LLDEYEKLTREAFSNYAGKPYRP T0330 49 :DGAIIYEVLSNVGLERA 1x42A 68 :EEEVMRKLAEKYGFKYP T0330 72 :DKAKETYIALFR 1x42A 85 :ENFWEIHLRMHQ T0330 89 :EDITLLEGVRELLDALSSR 1x42A 97 :RYGELYPEVVEVLKSLKGK T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKA T0330 166 :NYSPSQIVIIGDTE 1x42A 169 :GVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEEL 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFW T0330 207 :RH 1x42A 210 :DK T0330 210 :PGTLFKNFAETDEVLASI 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=180 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 1x42A/T0330-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1x42A/T0330-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x42A read from 1x42A/T0330-1x42A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x42A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1x42A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 3 :RTLVLFDIDGTLLKVE 1x42A 2 :IRAVFFDFVGTLLSVE T0330 20 :MNRRVLADALIEV 1x42A 18 :GEAKTHLKIMEEV T0330 33 :YGTEGSTGSHDFSGKMDGAI 1x42A 33 :DYPLNPKTLLDEYEKLTREA T0330 57 :LSNV 1x42A 53 :FSNY T0330 61 :GLERAEIADKFDKAKETY 1x42A 58 :GKPYRPIRDIEEEVMRKL T0330 79 :IALFRERARREDITLLEGVRELLDALSS 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKG T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1x42A 115 :KYHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKK T0330 165 :ANYSPSQIVIIGDTE 1x42A 168 :AGVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEELA 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWD T0330 209 :KPGTLFKNFAETDEVLASI 1x42A 211 :KCDFIVSDLREVIKIVDEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=190 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 1zrn/T0330-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0330 read from 1zrn/T0330-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0330-1zrn-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zrn to template set # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNR 1zrn 4 :IKGIAFDLYGTLFDVHSVVG T0330 23 :RVLADALIEVYGTEGSTGSHDF 1zrn 42 :QKQLEYTWLRSLMNRYVNFQQA T0330 49 :DGAIIYEVLSNVGLERAE 1zrn 64 :TEDALRFTCRHLGLDLDA T0330 69 :DKFDKAKE 1zrn 82 :RTRSTLCD T0330 87 :RREDITLLEGVRELLDALSSRS 1zrn 90 :AYLRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1zrn 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1zrn 165 :GLDRSAILFVASNAWDATGARYFGFPTCWINRT T0330 199 :NFT 1zrn 205 :GQT T0330 210 :PGTLFKNFAETDE 1zrn 208 :PDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=199 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 1zrn/T0330-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zrn/T0330-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0330-1zrn-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRC T0330 25 :LADALIEVY 1zrn 40 :WRQKQLEYT T0330 34 :GT 1zrn 55 :NR T0330 42 :HDFSGKMDGAIIYEVLSNVGLERA 1zrn 57 :YVNFQQATEDALRFTCRHLGLDLD T0330 72 :DKAKETYIALF 1zrn 81 :ARTRSTLCDAY T0330 89 :EDITLLEGVRELLDALSSRS 1zrn 92 :LRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1zrn 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1zrn 165 :GLDRSAILFVASNAWDATGARYFGFPTCWINRTGNV T0330 207 :RHKPGTLFKNFAETDE 1zrn 205 :GQTPDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=208 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 1zrn/T0330-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zrn/T0330-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zrn read from 1zrn/T0330-1zrn-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1zrn 29 :FPGRGREISALWRQKQLEYTWLRSLMNR T0330 68 :ADKFDKAKETYIALFRERA 1zrn 57 :YVNFQQATEDALRFTCRHL T0330 87 :R 1zrn 88 :C T0330 89 :EDITLLEGVRELLDALSS 1zrn 92 :LRLAPFSEVPDSLRELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1zrn 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1zrn 164 :LGLDRSAILFVASNAWDATGARYFGFPTCWINRTGN T0330 201 :TME 1zrn 203 :EMG T0330 208 :HKPGTLFKNFAETDE 1zrn 206 :QTPDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=217 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 2go7A/T0330-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2go7A expands to /projects/compbio/data/pdb/2go7.pdb.gz 2go7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2go7A/T0330-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0330-2go7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVL 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRV T0330 58 :SNVGLERAE 2go7A 59 :EDRNLDVEV T0330 74 :AKETYIALFRE 2go7A 68 :LNQVRAQSLAE T0330 87 :RREDITLLEGVRELLDALSSRS 2go7A 79 :KNAQVVLMPGAREVLAWADESG T0330 110 :VLLG 2go7A 101 :IQQF T0330 116 :TGNFE 2go7A 107 :THKGN T0330 122 :SGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2go7A 112 :NAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKY T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 2go7A 153 :QLNSDNTYYIGDRTLDVEFAQNSGIQSINFLESTY T0330 209 :KPGTLFKNFAETD 2go7A 188 :EGNHRIQALADIS T0330 226 :SILTP 2go7A 201 :RIFET Number of specific fragments extracted= 11 number of extra gaps= 2 total=228 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 2go7A/T0330-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2go7A/T0330-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0330-2go7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADAL 2go7A 10 :LDGTLLDSYEAILSGIEETF T0330 31 :EVYGTEGSTGS 2go7A 30 :AQFSIPYDKEK T0330 42 :HDFS 2go7A 42 :REFI T0330 46 :GKMDGAIIYEVLSNVGLER 2go7A 47 :KYSVQDLLVRVAEDRNLDV T0330 72 :DKAKETYIALFRERA 2go7A 66 :EVLNQVRAQSLAEKN T0330 89 :EDITLLEGVRELLDALSSRS 2go7A 81 :AQVVLMPGAREVLAWADESG T0330 110 :VLLG 2go7A 101 :IQQF T0330 116 :TG 2go7A 107 :TH T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2go7A 109 :KGNNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKY T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 2go7A 153 :QLNSDNTYYIGDRTLDVEFAQNSGIQSINFL T0330 199 :NFTME 2go7A 184 :ESTYE T0330 210 :PGTLFKNFAETDEV 2go7A 189 :GNHRIQALADISRI Number of specific fragments extracted= 13 number of extra gaps= 2 total=241 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 2go7A/T0330-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2go7A/T0330-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2go7A read from 2go7A/T0330-2go7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAEDRNLD T0330 68 :ADKFDKAKETYI 2go7A 65 :VEVLNQVRAQSL T0330 85 :RARREDITLLEGVRELLDALSS 2go7A 77 :AEKNAQVVLMPGAREVLAWADE T0330 108 :SDVLLG 2go7A 99 :SGIQQF T0330 116 :TGN 2go7A 107 :THK T0330 120 :EASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2go7A 110 :GNNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 2go7A 152 :YQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0330 197 :TGNFTM 2go7A 182 :FLESTY T0330 209 :KPGTLFKNFAETDEV 2go7A 188 :EGNHRIQALADISRI Number of specific fragments extracted= 10 number of extra gaps= 2 total=251 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 1swvA/T0330-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0330 read from 1swvA/T0330-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0330-1swvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1swvA to template set # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1swvA 6 :IEAVIFAWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGK 1swvA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGL T0330 49 :DGAIIYEVLSNVG 1swvA 52 :LKIDHVRALTEMP T0330 62 :LER 1swvA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1swvA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1swvA 98 :LPRYASPINGVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1swvA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1swvA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1swvA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1swvA 212 :GLTEEEVENMD T0330 210 :PGTLFKNFAETDEVLASIL 1swvA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 13 number of extra gaps= 0 total=264 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 1swvA/T0330-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1swvA/T0330-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0330-1swvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLK 1swvA 6 :IEAVIFAWAGTTVD T0330 17 :V 1swvA 25 :P T0330 22 :RRVLADAL 1swvA 26 :LEVFMEIF T0330 31 :EVYGTEGSTGS 1swvA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1swvA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1swvA 70 :WNRVFR T0330 62 :LERAEI 1swvA 78 :PTEADI T0330 72 :DKAKETYIALFRERAR 1swvA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1swvA 100 :RYASPINGVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGR 1swvA 120 :IKIGSTTGYTREMMD T0330 125 :HKLKLPGID 1swvA 138 :KEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1swvA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1swvA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1swvA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 16 number of extra gaps= 0 total=280 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 1swvA/T0330-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1swvA/T0330-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1swvA read from 1swvA/T0330-1swvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLK 1swvA 6 :IEAVIFAWAGTTVD T0330 22 :RRVLADALIEVYGTEGSTGSHDFSGKM 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLL T0330 50 :GAIIYEVLSNV 1swvA 53 :KIDHVRALTEM T0330 61 :GLERAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1swvA 72 :RVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRE T0330 108 :SDVLLGLLTGNFEA 1swvA 118 :RGIKIGSTTGYTRE T0330 122 :SGRHKLKLPGID 1swvA 135 :IVAKEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARR 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1swvA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1swvA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1swvA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 11 number of extra gaps= 0 total=291 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 1qq5A/T0330-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq5A expands to /projects/compbio/data/pdb/1qq5.pdb.gz 1qq5A:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 646, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 648, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 650, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 652, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 654, because occupancy 0.450 <= existing 0.550 in 1qq5A Skipped atom 764, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 766, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 768, because occupancy 0.440 <= existing 0.560 in 1qq5A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1qq5A Skipped atom 1361, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1363, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1463, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1465, because occupancy 0.510 <= existing 0.530 in 1qq5A Skipped atom 1752, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1754, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1756, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1758, because occupancy 0.280 <= existing 0.720 in 1qq5A Skipped atom 1793, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1795, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1797, because occupancy 0.490 <= existing 0.510 in 1qq5A Skipped atom 1820, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1822, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1824, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1826, because occupancy 0.460 <= existing 0.540 in 1qq5A Skipped atom 1828, because occupancy 0.460 <= existing 0.540 in 1qq5A # T0330 read from 1qq5A/T0330-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0330-1qq5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq5A to template set # found chain 1qq5A in template set T0330 1 :M 1qq5A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNR 1qq5A 2 :IKAVVFDAYGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1qq5A 40 :QKQLEYSWLRALMGRYADFWSV T0330 49 :DGAIIYEVLSNVGLERAE 1qq5A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1qq5A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1qq5A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1qq5A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq5A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq5A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1qq5A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLASI 1qq5A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 11 number of extra gaps= 0 total=302 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 1qq5A/T0330-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qq5A/T0330-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0330-1qq5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1qq5A)A245 T0330 1 :M 1qq5A 1 :M T0330 3 :RTLVLFDIDGTLLK 1qq5A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1qq5A 19 :VADATERA T0330 25 :LADAL 1qq5A 39 :RQKQL T0330 31 :EVY 1qq5A 44 :EYS T0330 34 :GTEGSTG 1qq5A 53 :GRYADFW T0330 47 :KMDGAIIYEVLSNVGLERAE 1qq5A 60 :SVTREALAYTLGTLGLEPDE T0330 72 :DKAK 1qq5A 80 :SFLA T0330 84 :ERAR 1qq5A 84 :DMAQ T0330 88 :REDITLLEGVRELLDALS 1qq5A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1qq5A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq5A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq5A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1qq5A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1qq5A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=317 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 1qq5A/T0330-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qq5A/T0330-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq5A read from 1qq5A/T0330-1qq5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1qq5A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq5A)A245 T0330 3 :RTLVLFDIDGTLLK 1qq5A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1qq5A 19 :VADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1qq5A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 64 :RAEIADKFDKAKETYIAL 1qq5A 55 :YADFWSVTREALAYTLGT T0330 82 :FRERARR 1qq5A 81 :FLADMAQ T0330 89 :EDITLLEGVRELLDAL 1qq5A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1qq5A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1qq5A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1qq5A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 10 number of extra gaps= 0 total=327 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 1rdfA/T0330-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0330 read from 1rdfA/T0330-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0330-1rdfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLKVE 1rdfA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEG 1rdfA 23 :FAPLEVFMEIFHKRGVAIT T0330 38 :STGSHDFSGKMDGAIIYEVLSNVG 1rdfA 51 :LLKIDHVRALTEMPRIASEWNRVF T0330 62 :LER 1rdfA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1rdfA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1rdfA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rdfA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rdfA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rdfA 174 :GV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVATG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1rdfA 220 :NMDSVELREKI T0330 210 :PGTLFKNFAET 1rdfA 242 :AHFTIETMQEL T0330 221 :DEVLASILTP 1rdfA 256 :MEHIEKQELI Number of specific fragments extracted= 14 number of extra gaps= 1 total=341 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 1rdfA/T0330-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rdfA/T0330-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0330-1rdfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLK 1rdfA 6 :IEAVIFDWAGTTVD T0330 19 :SMNRRVLADAL 1rdfA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1rdfA 34 :HKRGVAITAEE T0330 42 :HDFSGK 1rdfA 46 :RKPMPL T0330 48 :MDGAIIYEVLSNVG 1rdfA 62 :EMPRIASEWNRVFR T0330 62 :LERAEI 1rdfA 78 :PTEADI T0330 72 :DKAKETYIALFRERAR 1rdfA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1rdfA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHY 1rdfA 120 :IKIGSTTGYTREMMDIVAKEAALQGY T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rdfA 174 :GV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVAT 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0330 199 :NFTMEE 1rdfA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASILT 1rdfA 237 :FVENGAHFTIETMQELESVMEHIEK Number of specific fragments extracted= 14 number of extra gaps= 1 total=355 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 1rdfA/T0330-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rdfA/T0330-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rdfA read from 1rdfA/T0330-1rdfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLK 1rdfA 6 :IEAVIFDWAGTTVD T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFS 1rdfA 24 :APLEVFMEIFHKRGVAITAEEARKPM T0330 46 :GKMDGAIIYEVLSNVG 1rdfA 59 :ALTEMPRIASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1rdfA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1rdfA 118 :RGIKIGSTTGYTREMMDIVAKEAALQGYK T0330 137 :PFGAFADDALDRNELPHIALERARR 1rdfA 148 :DFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1rdfA 173 :LGV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVATGNF 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 201 :TMEE 1rdfA 214 :TEEE T0330 205 :LARHKPGTLFKNFAETDEVLASILTPKH 1rdfA 237 :FVENGAHFTIETMQELESVMEHIEKQEL Number of specific fragments extracted= 10 number of extra gaps= 1 total=365 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 2fi1A/T0330-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0330 read from 2fi1A/T0330-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0330-2fi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fi1A to template set # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTE 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQ T0330 49 :DGAIIYEVLSN 2fi1A 40 :DHDSVYQALKV T0330 63 :ERAEIADKF 2fi1A 51 :STPFAIETF T0330 72 :DKAKETYIALFRE 2fi1A 64 :ENFLEKYKENEAR T0330 87 :RREDITLLEGVRELLDALSSRS 2fi1A 77 :ELEHPILFEGVSDLLEDISNQG T0330 110 :VLLGLLTGNFEA 2fi1A 99 :GRHFLVSHRNDQ T0330 123 :GRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKY T0330 166 :NY 2fi1A 151 :QI T0330 170 :SQIVIIGDTEHDIRCARELDARS 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=375 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 2fi1A/T0330-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2fi1A/T0330-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0330-2fi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADAL 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETL T0330 31 :EVYGTEGSTGS 2fi1A 33 :ALYGITQDHDS T0330 56 :VLSNVGLERAEIADKF 2fi1A 44 :VYQALKVSTPFAIETF T0330 72 :DKAKETYIALFRERA 2fi1A 64 :ENFLEKYKENEAREL T0330 89 :EDITLLEGVRELLDALSSRS 2fi1A 79 :EHPILFEGVSDLLEDISNQG T0330 110 :VLLGLLTGNF 2fi1A 99 :GRHFLVSHRN T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2fi1A 109 :DQVLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKY T0330 166 :NY 2fi1A 151 :QI T0330 170 :SQIVIIGDTEHDIRCARELDARS 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=385 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 2fi1A/T0330-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2fi1A/T0330-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fi1A read from 2fi1A/T0330-2fi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFS 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQAL T0330 47 :KMDGAIIYEVLSNV 2fi1A 49 :KVSTPFAIETFAPN T0330 68 :ADKFDKAKETYIALF 2fi1A 63 :LENFLEKYKENEARE T0330 88 :REDITLLEGVRELLDALSS 2fi1A 78 :LEHPILFEGVSDLLEDISN T0330 108 :SDVLLGLLTGNFEA 2fi1A 97 :QGGRHFLVSHRNDQ T0330 123 :GRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREK T0330 165 :ANYS 2fi1A 150 :YQIS T0330 171 :QIVIIGDTEHDIRCARELDARS 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=394 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 1qyiA/T0330-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qyiA expands to /projects/compbio/data/pdb/1qyi.pdb.gz 1qyiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1qyiA/T0330-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0330-1qyiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0330 1 :M 1qyiA 1 :M T0330 4 :TLVLFDIDGTLLKVESMNR 1qyiA 2 :KKILFDVDGVFLSEERCFD T0330 23 :RVLADALI 1qyiA 24 :LTVYELLM T0330 31 :EVYGTEGSTGSHDF 1qyiA 34 :CYLGLHSHIDWETL T0330 49 :DGAIIYEVLSNVG 1qyiA 48 :TDNDIQDIRNRIF T0330 62 :LERAEIADKFDKAKETY 1qyiA 142 :VGKNNIYAALEEFATTE T0330 79 :IALFRERA 1qyiA 188 :SKLYEDVE T0330 87 :RREDITLLEGVRELLDALSSRS 1qyiA 210 :QEIILRPVDEVKVLLNDLKGAG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 232 :FELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADDALD 1qyiA 261 :DFIATASDVLE T0330 148 :RNELPHIALERARRMT 1qyiA 283 :GKPNPFSYIAALYGNN T0330 164 :GANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 310 :DNIVNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=407 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 1qyiA/T0330-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qyiA/T0330-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0330-1qyiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0330 1 :M 1qyiA 1 :M T0330 4 :TLVLFDIDGTLLKVESMN 1qyiA 2 :KKILFDVDGVFLSEERCF T0330 22 :RRVLADALI 1qyiA 23 :ALTVYELLM T0330 31 :EVYGTEGSTGSHDFSGKMDGAIIYE 1qyiA 34 :CYLGLHSHIDWETLTDNDIQDIRNR T0330 56 :VLSNVGLERAEIADKF 1qyiA 136 :FLDNVKVGKNNIYAAL T0330 79 :IALFRERARREDITL 1qyiA 152 :EEFATTELHVSDATL T0330 94 :LEGVRELLDALSSRS 1qyiA 217 :VDEVKVLLNDLKGAG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 232 :FELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADDAL 1qyiA 261 :DFIATASDVL T0330 148 :RNELPHIALERAR 1qyiA 283 :GKPNPFSYIAALY T0330 166 :NYSPSQ 1qyiA 296 :GNNRDK T0330 172 :IVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 318 :VFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=420 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 1qyiA/T0330-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qyiA/T0330-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qyiA read from 1qyiA/T0330-1qyiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qyiA in template set T0330 4 :TLVLFDIDGTLLKVESM 1qyiA 2 :KKILFDVDGVFLSEERC T0330 22 :RRVLADALIEV 1qyiA 19 :FDVSALTVYEL T0330 34 :GT 1qyiA 44 :WE T0330 41 :SHDFSGKMDGAI 1qyiA 89 :LIDILKKLSHDE T0330 53 :IYEVLSNV 1qyiA 147 :IYAALEEF T0330 61 :GLERAEIADKFDKAKETYIALFRERA 1qyiA 163 :DATLFSLKGALWTLAQEVYQEWYLGS T0330 87 :R 1qyiA 195 :E T0330 91 :ITLLEGVRELLDALSS 1qyiA 214 :LRPVDEVKVLLNDLKG T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 230 :AGFELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADD 1qyiA 261 :DFIATASD T0330 145 :ALDRNELPHIALERARR 1qyiA 278 :QARPLGKPNPFSYIAAL T0330 165 :ANYSPSQ 1qyiA 295 :YGNNRDK T0330 172 :IVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 318 :VFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=434 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 1l7mA/T0330-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l7mA expands to /projects/compbio/data/pdb/1l7m.pdb.gz 1l7mA:Skipped atom 73, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 75, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 465, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 1l7mA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1526, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1l7mA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1l7mA # T0330 read from 1l7mA/T0330-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0330-1l7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l7mA to template set # found chain 1l7mA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVY 1l7mA 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1l7mA 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1l7mA 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1l7mA 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1l7mA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDAL 1l7mA 131 :TGDVEGEVLK T0330 147 :DRN 1l7mA 142 :NAK T0330 152 :PHIALERARRM 1l7mA 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1l7mA 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1l7mA 185 :CAKPILKEK T0330 210 :PGTLF 1l7mA 194 :ADICI T0330 215 :KNFAETD 1l7mA 201 :RDLREIL Number of specific fragments extracted= 13 number of extra gaps= 0 total=447 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 1l7mA/T0330-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1l7mA/T0330-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0330-1l7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADAL 1l7mA 22 :IDEIA T0330 31 :EVYGT 1l7mA 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1l7mA 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1l7mA 62 :DLPIEKV T0330 72 :DKA 1l7mA 69 :EKA T0330 86 :A 1l7mA 72 :I T0330 89 :EDITLLEGVRELLDALSSRS 1l7mA 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1l7mA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1l7mA 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1l7mA 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1l7mA 180 :LKIAFCA T0330 202 :MEELARH 1l7mA 187 :KPILKEK T0330 210 :PGTLFK 1l7mA 194 :ADICIE T0330 216 :NFAETD 1l7mA 202 :DLREIL Number of specific fragments extracted= 15 number of extra gaps= 0 total=462 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 1l7mA/T0330-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1l7mA/T0330-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l7mA read from 1l7mA/T0330-1l7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l7mA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVYGTEGSTGSHDFS 1l7mA 22 :IDEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVGL 1l7mA 45 :GKLNFEQSLRKRVSLLK T0330 66 :EIA 1l7mA 62 :DLP T0330 72 :DKAKETYIA 1l7mA 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1l7mA 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1l7mA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1l7mA 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1l7mA 155 :EGINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELAR 1l7mA 185 :CAKPILKE T0330 209 :KPGTLFKN 1l7mA 193 :KADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=473 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 2b0cA/T0330-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0330 read from 2b0cA/T0330-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0330-2b0cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b0cA to template set # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKVES 2b0cA 7 :KMLYIFDLGNVIVDIDF T0330 23 :RVLADALIEVYGTEGSTGSHDF 2b0cA 24 :NRVLGAWSDLTRIPLASLKKSF T0330 49 :DGAIIYEVLSNVGLERAEIA 2b0cA 46 :HMGEAFHQHERGEISDEAFA T0330 72 :DKAKETY 2b0cA 66 :EALCHEM T0330 79 :IALFRERARREDITLLEGVRELLDALSSRS 2b0cA 78 :YEQFSHGWQAVFVALRPEVIAIMHKLREQG T0330 110 :VLLGLLTGNF 2b0cA 108 :HRVVVLSNTN T0330 120 :EASGRHK 2b0cA 128 :YPEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARRM 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 162 :GFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=483 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 2b0cA/T0330-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b0cA/T0330-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0330-2b0cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKV 2b0cA 7 :KMLYIFDLGNVIVDI T0330 18 :ESMNRRVLA 2b0cA 23 :FNRVLGAWS T0330 31 :EVYGT 2b0cA 32 :DLTRI T0330 36 :EGSTGS 2b0cA 46 :HMGEAF T0330 42 :HDFSGKMDGAIIYEVLSNVGLERAE 2b0cA 54 :HERGEISDEAFAEALCHEMALPLSY T0330 72 :DKAKETYI 2b0cA 79 :EQFSHGWQ T0330 88 :REDITLLEGVRELLDALSSRS 2b0cA 87 :AVFVALRPEVIAIMHKLREQG T0330 110 :VLLGLLTGNFE 2b0cA 108 :HRVVVLSNTNR T0330 121 :ASGRHK 2b0cA 129 :PEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARRM 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 162 :GFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 12 number of extra gaps= 0 total=495 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 2b0cA/T0330-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b0cA/T0330-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0cA read from 2b0cA/T0330-2b0cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKV 2b0cA 7 :KMLYIFDLGNVIVDI T0330 18 :ESMNRRVLADA 2b0cA 23 :FNRVLGAWSDL T0330 36 :EGSTGSHDFSGKMDGAIIYEVLSNV 2b0cA 35 :RIPLASLKKSFHMGEAFHQHERGEI T0330 67 :IADKFDKAKETY 2b0cA 60 :SDEAFAEALCHE T0330 79 :IALFRERARREDITLLEGVRELLDALSS 2b0cA 78 :YEQFSHGWQAVFVALRPEVIAIMHKLRE T0330 108 :SDVLLGLLTGNF 2b0cA 106 :QGHRVVVLSNTN T0330 120 :EASGRHK 2b0cA 128 :YPEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARR 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 161 :EGFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=505 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 1rqlA/T0330-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0330 read from 1rqlA/T0330-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0330-1rqlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rqlA to template set # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGKM 1rqlA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLL T0330 49 :DGAIIYEVLSNVG 1rqlA 62 :EMPRIASEWNRVF T0330 62 :LER 1rqlA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1rqlA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1rqlA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rqlA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rqlA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rqlA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1rqlA 220 :NMDSVELREKI T0330 210 :PGTLFKNFAETDEVLASIL 1rqlA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 13 number of extra gaps= 0 total=518 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 1rqlA/T0330-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rqlA/T0330-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0330-1rqlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADAL 1rqlA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1rqlA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1rqlA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1rqlA 70 :WNRVFR T0330 62 :LERAEIA 1rqlA 77 :LPTEADI T0330 72 :DKAKETYIALFRERAR 1rqlA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1rqlA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rqlA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rqlA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rqlA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1rqlA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1rqlA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 15 number of extra gaps= 0 total=533 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 1rqlA/T0330-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rqlA/T0330-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rqlA read from 1rqlA/T0330-1rqlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFSGKMDGAI 1rqlA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDH T0330 53 :IYEVLSNVG 1rqlA 66 :IASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1rqlA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1rqlA 118 :RGIKIGSTTGYTREMMDIVAKEAALQGYK T0330 137 :PFGAFADDALDRNELPHIALERARR 1rqlA 148 :DFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1rqlA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 201 :TMEE 1rqlA 214 :TEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1rqlA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 10 number of extra gaps= 0 total=543 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 1fezA/T0330-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0330 read from 1fezA/T0330-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0330-1fezA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fezA to template set # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLKVE 1fezA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGKM 1fezA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLL T0330 49 :DGAIIYEVLSNVG 1fezA 62 :EMPRIASEWNRVF T0330 62 :LER 1fezA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1fezA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1fezA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1fezA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1fezA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1fezA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1fezA 220 :NMDSVE T0330 205 :LARHKPGTLFKNFAETDEVLASI 1fezA 237 :FVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 13 number of extra gaps= 0 total=556 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 1fezA/T0330-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1fezA/T0330-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0330-1fezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLK 1fezA 6 :IEAVIFDWAGTTVD T0330 19 :SMNRRVLADAL 1fezA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1fezA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1fezA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1fezA 70 :WNRVFR T0330 71 :FDKAKETYIALFRERAR 1fezA 83 :IQEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1fezA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGR 1fezA 120 :IKIGSTTGYTREMMD T0330 125 :HKLKLPGID 1fezA 138 :KEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1fezA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVAT 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0330 198 :GNFTMEE 1fezA 219 :ENMDSVE T0330 205 :LARHKPGTLFKNFAETDEVLASI 1fezA 237 :FVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 14 number of extra gaps= 0 total=570 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 1fezA/T0330-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1fezA/T0330-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fezA read from 1fezA/T0330-1fezA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLK 1fezA 6 :IEAVIFDWAGTTVD T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFSGKMDGAI 1fezA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDH T0330 53 :IYEVLSNVG 1fezA 66 :IASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1fezA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEA 1fezA 118 :RGIKIGSTTGYTRE T0330 122 :SGRHKLKLPGID 1fezA 135 :IVAKEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARR 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1fezA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 202 :MEELARHKPGTLFKNFAETDEVLASI 1fezA 234 :RNRFVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 10 number of extra gaps= 0 total=580 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 1zjjA/T0330-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0330 read from 1zjjA/T0330-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0330-1zjjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0330 1 :M 1zjjA 1 :M T0330 4 :TLVLFDIDGTLLKVES 1zjjA 2 :VAIIFDMDGVLYRGNR T0330 93 :LLEGVRELLDALSSRS 1zjjA 18 :AIPGVRELIEFLKERG T0330 110 :VLLGLLTGNF 1zjjA 34 :IPFAFLTNNS T0330 120 :EASGRHKLKLPGID 1zjjA 47 :PEMYREKLLKMGID T0330 136 :F 1zjjA 61 :V T0330 137 :PFGAFADDALD 1zjjA 64 :SIIITSGLATR T0330 148 :RNE 1zjjA 186 :GKP T0330 152 :PHIALERARRMTG 1zjjA 189 :NEPMYEVVREMFP T0330 166 :NY 1zjjA 202 :GE T0330 171 :QIVIIGDTE 1zjjA 204 :ELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKKSE T0330 210 :PGTLFKNFAETD 1zjjA 246 :PDLVLPSVYELI Number of specific fragments extracted= 13 number of extra gaps= 0 total=593 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 1zjjA/T0330-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zjjA/T0330-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0330-1zjjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0330 4 :TLVLFDIDGTLLK 1zjjA 2 :VAIIFDMDGVLYR T0330 90 :DITLLEGVRELLDALSSRS 1zjjA 15 :GNRAIPGVRELIEFLKERG T0330 110 :VLLGLLTG 1zjjA 34 :IPFAFLTN T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDAL 1zjjA 45 :KTPEMYREKLLKMGIDVSSSIIITSGLAT T0330 148 :RNELPHIALERARRMTGA 1zjjA 186 :GKPNEPMYEVVREMFPGE T0330 171 :QIVIIGDTE 1zjjA 204 :ELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK T0330 208 :HKPGTLFKNFAETD 1zjjA 244 :YKPDLVLPSVYELI Number of specific fragments extracted= 8 number of extra gaps= 0 total=601 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 1zjjA/T0330-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zjjA/T0330-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjjA read from 1zjjA/T0330-1zjjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjjA in template set T0330 4 :TLVLFDIDGTLLK 1zjjA 2 :VAIIFDMDGVLYR T0330 90 :DITLLEGVRELLDALSS 1zjjA 15 :GNRAIPGVRELIEFLKE T0330 108 :SDVLLGLLTGNF 1zjjA 32 :RGIPFAFLTNNS T0330 120 :EASGRHKLKLPGID 1zjjA 47 :PEMYREKLLKMGID T0330 134 :HYFP 1zjjA 64 :SIII T0330 138 :FGAFADD 1zjjA 122 :VVVGLDP T0330 149 :NE 1zjjA 187 :KP T0330 152 :PHIALERARRM 1zjjA 189 :NEPMYEVVREM T0330 167 :YSPSQIVIIGDTE 1zjjA 200 :FPGEELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK T0330 208 :HKPGTLFKNFAET 1zjjA 244 :YKPDLVLPSVYEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=612 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 1qq7A/T0330-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qq7A expands to /projects/compbio/data/pdb/1qq7.pdb.gz 1qq7A:Bad short name: C2 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1qq7A # T0330 read from 1qq7A/T0330-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0330-1qq7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0330 1 :M 1qq7A 1 :M T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLKVESMNR 1qq7A 10 :YGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1qq7A 40 :QKQLEYSWLRALMGRYADFWSV T0330 49 :DGAIIYEVLSNVGLERAE 1qq7A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1qq7A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1qq7A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1qq7A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq7A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq7A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1qq7A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLASI 1qq7A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 12 number of extra gaps= 0 total=624 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 1qq7A/T0330-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qq7A/T0330-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0330-1qq7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq7A)A245 T0330 1 :M 1qq7A 1 :M T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLK 1qq7A 10 :YGTLFD T0330 17 :VESMNRRV 1qq7A 19 :VADATERA T0330 25 :LADALIEVY 1qq7A 38 :WRQKQLEYS T0330 34 :GTEGS 1qq7A 53 :GRYAD T0330 45 :SGKMDGAIIYEVLSNVGLERAE 1qq7A 58 :FWSVTREALAYTLGTLGLEPDE T0330 72 :DKA 1qq7A 80 :SFL T0330 83 :RERAR 1qq7A 83 :ADMAQ T0330 88 :REDITLLEGVRELLDALS 1qq7A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1qq7A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq7A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq7A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1qq7A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1qq7A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=639 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 1qq7A/T0330-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1qq7A/T0330-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qq7A read from 1qq7A/T0330-1qq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qq7A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq7A)A245 T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLKV 1qq7A 10 :YGTLFDV T0330 18 :ESMNRRV 1qq7A 20 :ADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1qq7A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 68 :ADKFDKAKETYIALFR 1qq7A 55 :YADFWSVTREALAYTL T0330 84 :ERARR 1qq7A 83 :ADMAQ T0330 89 :EDITLLEGVRELLDAL 1qq7A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1qq7A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1qq7A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1qq7A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 11 number of extra gaps= 0 total=650 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 2c4nA/T0330-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0330 read from 2c4nA/T0330-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0330-2c4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 17 :VESMNRRV 2c4nA 17 :DNVAVPGA T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 2c4nA 25 :AEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDV T0330 87 :RREDITLL 2c4nA 64 :PDSVFYTS T0330 97 :VRELLDALSSRSDVLLGLL 2c4nA 72 :AMATADFLRRQEGKKAYVV T0330 119 :FEASGRHKLKLPGID 2c4nA 91 :GEGALIHELYKAGFT T0330 136 :F 2c4nA 106 :I T0330 137 :PFGAFADDALD 2c4nA 112 :DFVIVGETRSY T0330 148 :RNELPHIALERARRM 2c4nA 175 :GKPSPWIIRAALNKM T0330 166 :NYSPSQIVIIGDTE 2c4nA 190 :QAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDSMP T0330 210 :PGTLFKNFAET 2c4nA 237 :PSWIYPSVAEI Number of specific fragments extracted= 12 number of extra gaps= 1 total=662 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 2c4nA/T0330-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2c4nA/T0330-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0330-2c4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 17 :VESMNRRVLADAL 2c4nA 20 :AVPGAAEFLHGIM T0330 32 :VYGT 2c4nA 33 :DKGL T0330 47 :K 2c4nA 46 :S T0330 62 :LER 2c4nA 47 :QTG T0330 72 :DKAKETYIA 2c4nA 50 :QDLANRFAT T0330 89 :EDITLLE 2c4nA 59 :AGVDVPD T0330 96 :GVRELLDALSSRSDVLLGLLTGN 2c4nA 71 :SAMATADFLRRQEGKKAYVVGEG T0330 122 :SGRHKLKLPGID 2c4nA 94 :ALIHELYKAGFT T0330 136 :FPFGAFADDAL 2c4nA 111 :PDFVIVGETRS T0330 147 :DRNELPHIALERARRM 2c4nA 174 :VGKPSPWIIRAALNKM T0330 166 :NYSPSQIVIIGDTE 2c4nA 190 :QAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEEL 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0330 207 :RHKPGTLFKNFAET 2c4nA 234 :PFRPSWIYPSVAEI Number of specific fragments extracted= 14 number of extra gaps= 1 total=676 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 2c4nA/T0330-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2c4nA/T0330-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4nA read from 2c4nA/T0330-2c4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 90 :DITLLEGVRELLDALSS 2c4nA 17 :DNVAVPGAAEFLHGIMD T0330 108 :SDVLLGLLTGNF 2c4nA 34 :KGLPLVLLTNYP T0330 120 :EASGRHKLKLPGI 2c4nA 49 :GQDLANRFATAGV T0330 133 :DHYFP 2c4nA 65 :DSVFY T0330 138 :FGAFADD 2c4nA 113 :FVIVGET T0330 147 :DRNELPHIALERARR 2c4nA 174 :VGKPSPWIIRAALNK T0330 165 :ANYSPSQIVIIGDTE 2c4nA 189 :MQAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEE 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDD T0330 208 :HKPGTLFKNFAE 2c4nA 235 :FRPSWIYPSVAE Number of specific fragments extracted= 10 number of extra gaps= 1 total=686 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 1nnlA/T0330-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nnlA expands to /projects/compbio/data/pdb/1nnl.pdb.gz 1nnlA:# T0330 read from 1nnlA/T0330-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0330-1nnlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nnlA to template set # found chain 1nnlA in template set Warning: unaligning (T0330)I53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVES 1nnlA 15 :DAVCFDVDSTVIREEG T0330 25 :LADALIEVY 1nnlA 31 :IDELAKICG T0330 49 :DGAI 1nnlA 40 :VEDA T0330 67 :IADKFDKAKETY 1nnlA 58 :FKAALTERLALI T0330 79 :IALFRERARREDITLLEGVRELLDALSSRS 1nnlA 73 :REQVQRLIAEQPPHLTPGIRELVSRLQERN T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1nnlA 103 :VQVFLISGGFRSIVEHVASKLNIP T0330 134 :HYFPFGAFADDALD 1nnlA 129 :NVFANRLKFYFNGE T0330 148 :RN 1nnlA 157 :GK T0330 152 :PHIALERARRM 1nnlA 159 :GKVIKLLKEKF T0330 168 :SPSQIVIIGDTEHDIRCA 1nnlA 170 :HFKKIIMIGDGATDMEAC T0330 189 :DARSIAVATGNFTMEELARH 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0330 210 :PGTLFKNFAET 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=698 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 1nnlA/T0330-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nnlA/T0330-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0330-1nnlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0330)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)M48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVES 1nnlA 15 :DAVCFDVDSTVIREEG T0330 25 :LADAL 1nnlA 31 :IDELA T0330 31 :EVYGTE 1nnlA 36 :KICGVE T0330 49 :DGAIIYEVLSNVGLERA 1nnlA 58 :FKAALTERLALIQPSRE T0330 81 :LFRERARREDITLLEGVRELLDALSSRS 1nnlA 75 :QVQRLIAEQPPHLTPGIRELVSRLQERN T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1nnlA 103 :VQVFLISGGFRSIVEHVASKLNIPATNVFANRL T0330 147 :DRNELPHIALERARRM 1nnlA 154 :ESGGKGKVIKLLKEKF T0330 168 :SPSQIVIIGDTEHDIRC 1nnlA 170 :HFKKIIMIGDGATDMEA T0330 189 :DA 1nnlA 189 :PA T0330 191 :RSIAV 1nnlA 192 :AFIGF T0330 197 :TGNFTMEELARH 1nnlA 197 :GGNVIRQQVKDN T0330 210 :PGTLFKNFAET 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=710 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 1nnlA/T0330-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nnlA/T0330-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nnlA read from 1nnlA/T0330-1nnlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nnlA in template set Warning: unaligning (T0330)A51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVESM 1nnlA 15 :DAVCFDVDSTVIREEGI T0330 39 :TGSHDFSGKMDG 1nnlA 32 :DELAKICGVEDA T0330 67 :IADKFDKAKETY 1nnlA 58 :FKAALTERLALI T0330 79 :IALFRERARREDITLLEGVRELLDALSS 1nnlA 73 :REQVQRLIAEQPPHLTPGIRELVSRLQE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFAD 1nnlA 101 :RNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLK T0330 145 :ALDRNELPHIALERARR 1nnlA 152 :TAESGGKGKVIKLLKEK T0330 165 :ANY 1nnlA 169 :FHF T0330 170 :SQIVIIGDTEHDIRC 1nnlA 172 :KKIIMIGDGATDMEA T0330 189 :DARSIAVATGNFTMEELAR 1nnlA 189 :PADAFIGFGGNVIRQQVKD T0330 209 :KPGTLFKNFAET 1nnlA 208 :NAKWYITDFVEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=720 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 1zs9A/T0330-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zs9A expands to /projects/compbio/data/pdb/1zs9.pdb.gz 1zs9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1zs9A/T0330-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0330-1zs9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zs9A to template set # found chain 1zs9A in template set T0330 3 :RTLVLFDIDGTLLKVESM 1zs9A 10 :VTVILLDIEGTTTPIAFV T0330 21 :NRRVLADALIEVYGTEGSTGSHDF 1zs9A 31 :LFPYIEENVKEYLQTHWEEEECQQ T0330 49 :DGAIIYEVLSNVG 1zs9A 55 :DVSLLRKQAEEDA T0330 62 :LERAEIADKFDKAKETY 1zs9A 81 :NGVDDLQQMIQAVVDNV T0330 79 :IALFRE 1zs9A 119 :RAAFTA T0330 87 :RREDITLLEGVRELLDALSSRS 1zs9A 125 :GRMKAEFFADVVPAVRKWREAG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1zs9A 147 :MKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGAFADDAL 1zs9A 171 :DILELVDGHFDTKIGH T0330 149 :NELPHIALERARRM 1zs9A 187 :KVESESYRKIADSI T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1zs9A 201 :GCSTNNILFLTDVTREASAAEEADVHVAVVVRP T0330 199 :NFTMEELARHK 1zs9A 237 :GLTDDEKTYYS T0330 213 :LFKNFAET 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=732 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 1zs9A/T0330-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zs9A/T0330-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0330-1zs9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set Warning: unaligning (T0330)G61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0330)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0330 3 :RTLVLFDIDGTLLK 1zs9A 10 :VTVILLDIEGTTTP T0330 17 :VESMNRRVLADALIEVYGT 1zs9A 31 :LFPYIEENVKEYLQTHWEE T0330 36 :EGSTGS 1zs9A 68 :HLDGAV T0330 42 :HDFSGKMDGAIIYE 1zs9A 75 :IPAASGNGVDDLQQ T0330 56 :VLSNV 1zs9A 97 :VCWQM T0330 64 :R 1zs9A 107 :T T0330 72 :DKAKETYIALFRERAR 1zs9A 108 :TALKQLQGHMWRAAFT T0330 88 :REDITLLEGVRELLDALSSRS 1zs9A 126 :RMKAEFFADVVPAVRKWREAG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1zs9A 147 :MKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGAF 1zs9A 171 :DILELVDGHFD T0330 144 :DALDRNELPHIALERARRM 1zs9A 182 :TKIGHKVESESYRKIADSI T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGN 1zs9A 201 :GCSTNNILFLTDVTREASAAEEADVHVAVVVRPG T0330 200 :FTMEELARHK 1zs9A 238 :LTDDEKTYYS T0330 213 :LFKNFAET 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=746 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 1zs9A/T0330-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zs9A/T0330-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zs9A read from 1zs9A/T0330-1zs9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zs9A in template set Warning: unaligning (T0330)A65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0330)I67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0330 3 :RTLVLFDIDGTLLK 1zs9A 10 :VTVILLDIEGTTTP T0330 17 :VESMNRRVLADALIEV 1zs9A 31 :LFPYIEENVKEYLQTH T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLS 1zs9A 77 :AASGNGVDDLQQMIQAVVDNVCWQMS T0330 64 :R 1zs9A 103 :L T0330 68 :ADKFDKAKETYIALFRER 1zs9A 107 :TTALKQLQGHMWRAAFTA T0330 87 :RREDITLLEGVRELLDALSS 1zs9A 125 :GRMKAEFFADVVPAVRKWRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLP 1zs9A 145 :AGMKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGA 1zs9A 171 :DILELVDGHF T0330 143 :DDALDRNELPHIALERARR 1zs9A 181 :DTKIGHKVESESYRKIADS T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1zs9A 200 :IGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGN T0330 201 :TMEELARH 1zs9A 239 :TDDEKTYY T0330 212 :TLFKNFAET 1zs9A 247 :SLITSFSEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=758 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 1zd3A/T0330-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0330 read from 1zd3A/T0330-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0330-1zd3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zd3A to template set # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLLKVE 1zd3A 3 :LRAAVFDLDGVLALPA T0330 21 :NRRVLADALIEVYGTEGSTGSHDFSG 1zd3A 19 :VFGVLGRTEEALALPRGLLNDAFQKG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1zd3A 45 :GPEGATTRLMKGEITLSQWIPLMEENCRKC T0330 79 :IALFRE 1zd3A 89 :KEIFDK T0330 87 :RREDITLLEGVRELLDALSSRS 1zd3A 95 :AISARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTGNF 1zd3A 117 :FTTAILTNTW T0330 120 :EASGRHKLKLPGID 1zd3A 133 :RDGLAQLMCELKMH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1zd3A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1zd3A 174 :KASPSEVVFLDDIGANLKPARDLGMVTIL T0330 214 :FKNFAETDEVLASILTPK 1zd3A 203 :VQDTDTALKELEKVTGIQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=768 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 1zd3A/T0330-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zd3A/T0330-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0330-1zd3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLL 1zd3A 3 :LRAAVFDLDGVLA T0330 17 :VESMNRRV 1zd3A 19 :VFGVLGRT T0330 29 :L 1zd3A 27 :E T0330 31 :EVYGTEG 1zd3A 28 :EALALPR T0330 51 :AIIYE 1zd3A 35 :GLLND T0330 56 :VLSNVGLER 1zd3A 52 :RLMKGEITL T0330 72 :DKAKETYIALFRERARREDITL 1zd3A 61 :SQWIPLMEENCRKCSETAKVCL T0330 94 :LEGVRELLDALSSRS 1zd3A 102 :NRPMLQAALMLRKKG T0330 110 :VLLGLLTG 1zd3A 117 :FTTAILTN T0330 118 :NFEASGRHKLKLPG 1zd3A 131 :AERDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARRM 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSI 1zd3A 174 :KASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASILTPK 1zd3A 202 :LVQDTDTALKELEKVTGIQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=781 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 1zd3A/T0330-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1zd3A/T0330-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zd3A read from 1zd3A/T0330-1zd3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLL 1zd3A 3 :LRAAVFDLDGVLA T0330 16 :KVESMNRRV 1zd3A 18 :AVFGVLGRT T0330 29 :LIEVYGTEGSTG 1zd3A 27 :EEALALPRGLLN T0330 41 :SHDFSGKMDGAIIYEVLSNV 1zd3A 51 :TRLMKGEITLSQWIPLMEEN T0330 71 :FDKAKETY 1zd3A 71 :CRKCSETA T0330 79 :IALFRERAR 1zd3A 89 :KEIFDKAIS T0330 90 :DITLLEGVRELLDALSS 1zd3A 98 :ARKINRPMLQAALMLRK T0330 108 :SDVLLGLLTGNF 1zd3A 115 :KGFTTAILTNTW T0330 120 :EASGRHKLKLPG 1zd3A 133 :RDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1zd3A 173 :LKASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASIL 1zd3A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=793 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 1u7pA/T0330-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0330 read from 1u7pA/T0330-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0330-1u7pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u7pA to template set # found chain 1u7pA in template set T0330 3 :RTLVLFDIDGTLLKVES 1u7pA 5 :PKLAVFDLDYTLWPFWV T0330 34 :GTEGSTGSHDFSGKM 1u7pA 22 :DTHVDPPFHKSSDGT T0330 87 :RREDITLLEGVRELLDALSSRS 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLG T0330 110 :VLLGLLTG 1u7pA 63 :VPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDA 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPGS T0330 149 :N 1u7pA 100 :K T0330 152 :PHIALERARRM 1u7pA 101 :VTHFERLHHKT T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1u7pA 112 :GVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0330 200 :FTMEELAR 1u7pA 145 :MSLQTLTQ T0330 220 :TDEVLASILT 1u7pA 153 :GLETFAKAQA Number of specific fragments extracted= 10 number of extra gaps= 0 total=803 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 1u7pA/T0330-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1u7pA/T0330-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0330-1u7pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0330 1 :M 1u7pA 1 :M T0330 2 :SRTLVLFDIDGTLLKV 1u7pA 4 :LPKLAVFDLDYTLWPF T0330 36 :EGSTGS 1u7pA 20 :WVDTHV T0330 42 :HDFSGKMDG 1u7pA 27 :PPFHKSSDG T0330 72 :D 1u7pA 40 :R T0330 87 :RREDITLLEGVRELLDALSSRS 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLG T0330 110 :VLLGLLTG 1u7pA 63 :VPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDAL 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPGSK T0330 152 :PHIALERARRM 1u7pA 101 :VTHFERLHHKT T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1u7pA 112 :GVPFSQMVFFDDENRNIIDVGRLGVTCIHI T0330 197 :TGNFTMEELAR 1u7pA 142 :RDGMSLQTLTQ T0330 220 :TDEVLASILTP 1u7pA 153 :GLETFAKAQAG Number of specific fragments extracted= 12 number of extra gaps= 0 total=815 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 1u7pA/T0330-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1u7pA/T0330-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u7pA read from 1u7pA/T0330-1u7pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u7pA in template set T0330 2 :SRTLVLFDIDGTLLKV 1u7pA 4 :LPKLAVFDLDYTLWPF T0330 66 :EIADKFD 1u7pA 20 :WVDTHVD T0330 86 :ARREDITLLEGVRELLDALSS 1u7pA 40 :RRGQNIQLYPEVPEVLGRLQS T0330 108 :SDVLLGLLTG 1u7pA 61 :LGVPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFA 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIY T0330 148 :RNELPHIALERARR 1u7pA 97 :PGSKVTHFERLHHK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1u7pA 111 :TGVPFSQMVFFDDENRNIIDVGRLGVTCIH T0330 196 :ATGNFTMEELAR 1u7pA 141 :IRDGMSLQTLTQ T0330 220 :TDEVLASILTP 1u7pA 153 :GLETFAKAQAG Number of specific fragments extracted= 9 number of extra gaps= 0 total=824 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 1j97A/T0330-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j97A expands to /projects/compbio/data/pdb/1j97.pdb.gz 1j97A:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0330 read from 1j97A/T0330-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0330-1j97A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL T0330 11 :DGTLLKVES 1j97A 13 :DSTLVNNET T0330 25 :LADALIEVY 1j97A 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1j97A 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1j97A 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1j97A 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1j97A 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDALDR 1j97A 131 :TGDVEGEVLKEN T0330 149 :N 1j97A 144 :K T0330 152 :PHIALERARRM 1j97A 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1j97A 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1j97A 185 :CAKPILKEK T0330 210 :PGTLF 1j97A 194 :ADICI T0330 215 :KNFAETD 1j97A 201 :RDLREIL Number of specific fragments extracted= 14 number of extra gaps= 0 total=838 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 1j97A/T0330-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1j97A/T0330-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0330-1j97A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL T0330 11 :DGTLLKVES 1j97A 13 :DSTLVNNET T0330 25 :LADAL 1j97A 22 :IDEIA T0330 31 :EVYGT 1j97A 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1j97A 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1j97A 62 :DLPIEKV T0330 72 :DKA 1j97A 69 :EKA T0330 86 :A 1j97A 72 :I T0330 89 :EDITLLEGVRELLDALSSRS 1j97A 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1j97A 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1j97A 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1j97A 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1j97A 180 :LKIAFCA T0330 202 :MEELARH 1j97A 187 :KPILKEK T0330 210 :PGTLF 1j97A 194 :ADICI T0330 215 :KNFAETD 1j97A 201 :RDLREIL Number of specific fragments extracted= 16 number of extra gaps= 0 total=854 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 1j97A/T0330-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1j97A/T0330-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j97A read from 1j97A/T0330-1j97A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL T0330 11 :DGTLLKVESM 1j97A 13 :DSTLVNNETI T0330 26 :ADALIEVYGTEGSTGSHDFS 1j97A 23 :DEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVG 1j97A 45 :GKLNFEQSLRKRVSLL T0330 65 :AEIA 1j97A 61 :KDLP T0330 72 :DKAKETYIA 1j97A 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1j97A 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1j97A 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1j97A 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1j97A 155 :EGINLEDTVAVGDGANDISMFKKAGLKIA T0330 195 :V 1j97A 184 :F T0330 200 :FTMEELAR 1j97A 185 :CAKPILKE T0330 209 :KPGTLFKN 1j97A 193 :KADICIEK Number of specific fragments extracted= 13 number of extra gaps= 0 total=867 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 1rkuA/T0330-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkuA expands to /projects/compbio/data/pdb/1rku.pdb.gz 1rkuA:Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1rkuA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1rkuA # T0330 read from 1rkuA/T0330-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0330-1rkuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkuA to template set # found chain 1rkuA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLKV 1rkuA 8 :LEGVLVPE T0330 24 :VLADALIEVYGT 1rkuA 16 :IWIAFAEKTGID T0330 39 :TGSHDFSGKM 1rkuA 28 :ALKATTRDIP T0330 49 :DGAIIYEVLSNVGLERAE 1rkuA 42 :LMKQRLRILDEHGLKLGD T0330 82 :FRE 1rkuA 60 :IQE T0330 87 :RREDITLLEGVRELLDALSSR 1rkuA 63 :VIATLKPLEGAVEFVDWLRER T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALD 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDR T0330 148 :RN 1rkuA 129 :QK T0330 153 :HIALERARRMTGANY 1rkuA 131 :DPKRQSVIAFKSLYY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 13 number of extra gaps= 1 total=880 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 1rkuA/T0330-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rkuA/T0330-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0330-1rkuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLK 1rkuA 8 :LEGVLVP T0330 24 :VLADAL 1rkuA 16 :IWIAFA T0330 31 :EVYGTE 1rkuA 22 :EKTGID T0330 39 :TGSHDFSGK 1rkuA 28 :ALKATTRDI T0330 48 :MDGAIIYE 1rkuA 38 :DYDVLMKQ T0330 56 :VLSNVGLERAE 1rkuA 49 :ILDEHGLKLGD T0330 82 :FRERA 1rkuA 60 :IQEVI T0330 89 :EDITLLEGVRELLDALSSR 1rkuA 65 :ATLKPLEGAVEFVDWLRER T0330 110 :VLLGLLTGNFEASGRHKLKLPGI 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGF T0330 136 :FPFGAF 1rkuA 107 :PTLLCH T0330 142 :ADDA 1rkuA 116 :IDDS T0330 147 :DRNELPHIALERARRM 1rkuA 128 :RQKDPKRQSVIAFKSL T0330 166 :NY 1rkuA 144 :YY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 17 number of extra gaps= 1 total=897 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 1rkuA/T0330-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rkuA/T0330-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkuA read from 1rkuA/T0330-1rkuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkuA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLKV 1rkuA 8 :LEGVLVPE T0330 24 :VLADALIEVYGTEGS 1rkuA 16 :IWIAFAEKTGIDALK T0330 63 :ERAEIADKFDKAKETYIALFRE 1rkuA 31 :ATTRDIPDYDVLMKQRLRILDE T0330 85 :RARREDITLLEGVRELLDALSS 1rkuA 61 :QEVIATLKPLEGAVEFVDWLRE T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1rkuA 83 :RFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDD T0330 146 :LDRNELPHIALERARR 1rkuA 127 :LRQKDPKRQSVIAFKS T0330 165 :ANY 1rkuA 143 :LYY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 11 number of extra gaps= 1 total=908 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 1jud/T0330-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0330 read from 1jud/T0330-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0330-1jud-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jud to template set # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNR 1jud 4 :IKGIAFDLYGTLFDVHSVVG T0330 23 :RVLADALIEVYGTEGSTGSHDF 1jud 42 :QKQLEYTWLRSLMNRYVNFQQA T0330 49 :DGAIIYEVLSNVGLERAE 1jud 64 :TEDALRFTCRHLGLDLDA T0330 69 :DKFDKAKE 1jud 82 :RTRSTLCD T0330 87 :RREDITLLEGVRELLDALSSRS 1jud 90 :AYLRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1jud 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1jud 165 :GLDRSAILFVSSNAWDATGARYFGFPTCWINRT T0330 199 :NFT 1jud 205 :GQT T0330 210 :PGTLFKNFAETDE 1jud 208 :PDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=917 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 1jud/T0330-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1jud/T0330-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0330-1jud-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1jud 4 :IKGIAFDLYGTLFDVHSVVGRC T0330 25 :LADALIEVY 1jud 40 :WRQKQLEYT T0330 40 :GSHDFSGKMDGAIIYEVLSNVGLERA 1jud 55 :NRYVNFQQATEDALRFTCRHLGLDLD T0330 72 :DKAKETYIALF 1jud 81 :ARTRSTLCDAY T0330 89 :EDITLLEGVRELLDALSSRS 1jud 92 :LRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1jud 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1jud 165 :GLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNV T0330 207 :RHKPGTLFKNFAETDE 1jud 205 :GQTPDWEVTSLRAVVE Number of specific fragments extracted= 8 number of extra gaps= 0 total=925 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 1jud/T0330-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1jud/T0330-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jud read from 1jud/T0330-1jud-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1jud 29 :FPGRGREISALWRQKQLEYTWLRSLMNR T0330 68 :ADKFDKAKETYIALFRERA 1jud 57 :YVNFQQATEDALRFTCRHL T0330 88 :REDITLLEGVRELLDALSS 1jud 91 :YLRLAPFSEVPDSLRELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1jud 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1jud 164 :LGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGN T0330 201 :TME 1jud 203 :EMG T0330 208 :HKPGTLFKNFAETDE 1jud 206 :QTPDWEVTSLRAVVE Number of specific fragments extracted= 8 number of extra gaps= 0 total=933 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 1vjrA/T0330-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0330 read from 1vjrA/T0330-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0330-1vjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1vjrA 5 :IELFILDMDGTFYLDDSLLPGS T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 1vjrA 27 :LEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDV T0330 87 :RREDITLLEGV 1vjrA 66 :PDDAVVTSGEI T0330 100 :LLDAL 1vjrA 77 :TAEHM T0330 105 :SSRSDVLLGLL 1vjrA 83 :KRFGRCRIFLL T0330 119 :FEASGRHKLKLPGID 1vjrA 94 :GTPQLKKVFEAYGHV T0330 136 :F 1vjrA 109 :I T0330 137 :PFGAFADDALD 1vjrA 115 :DFVVLGFDKTL T0330 148 :RNELPHIALERARRM 1vjrA 182 :GKPNPLVVDVISEKF T0330 166 :NYSPSQIVIIGDTE 1vjrA 197 :GVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=945 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 1vjrA/T0330-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1vjrA/T0330-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0330-1vjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLLK 1vjrA 5 :IELFILDMDGTFYL T0330 17 :VESMNRRVLADA 1vjrA 22 :LLPGSLEFLETL T0330 31 :EVYGT 1vjrA 34 :KEKNK T0330 46 :GKMDGAIIYE 1vjrA 48 :SLGAQDYVRK T0330 57 :LSNVGLERAE 1vjrA 58 :LRNMGVDVPD T0330 89 :EDITLLEGV 1vjrA 68 :DAVVTSGEI T0330 100 :LLDAL 1vjrA 77 :TAEHM T0330 105 :SSRSDVLLGLLTG 1vjrA 83 :KRFGRCRIFLLGT T0330 121 :ASGRHKLKLPGID 1vjrA 96 :PQLKKVFEAYGHV T0330 134 :HYFPFGAFADDAL 1vjrA 112 :ENPDFVVLGFDKT T0330 147 :DRNELPHIALERARRM 1vjrA 181 :AGKPNPLVVDVISEKF T0330 166 :NYSPSQIVIIGDTE 1vjrA 197 :GVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=959 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 1vjrA/T0330-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1vjrA/T0330-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vjrA read from 1vjrA/T0330-1vjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLL 1vjrA 5 :IELFILDMDGTFY T0330 90 :DITLLEGVRELLDALSS 1vjrA 19 :DDSLLPGSLEFLETLKE T0330 108 :SDVLLGLLTGNF 1vjrA 36 :KNKRFVFFTNNS T0330 120 :EASGRHKLKLPGI 1vjrA 51 :AQDYVRKLRNMGV T0330 133 :DHYFP 1vjrA 67 :DDAVV T0330 148 :RNELPHIALERARR 1vjrA 182 :GKPNPLVVDVISEK T0330 165 :ANYSPSQIVIIGDTE 1vjrA 196 :FGVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 9 number of extra gaps= 0 total=968 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 2feaA/T0330-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2feaA expands to /projects/compbio/data/pdb/2fea.pdb.gz 2feaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 517, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1319, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1323, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1329, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 1566, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1570, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1572, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1574, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1576, because occupancy 0.300 <= existing 0.700 in 2feaA # T0330 read from 2feaA/T0330-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0330-2feaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2feaA to template set # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0330 2 :SRTLVLFDIDGTLLKVES 2feaA 4 :RKPFIICDFDGTITMNDN T0330 25 :LADALIEVYGT 2feaA 22 :IINIMKTFAPP T0330 49 :DGAIIYEVLSNVGLERA 2feaA 33 :EWMALKDGVLSKTLSIK T0330 69 :DKFDKAK 2feaA 50 :EGVGRMF T0330 76 :ETYIALFRER 2feaA 65 :EEITSFVLED T0330 91 :ITLLEGVRELLDALSSRS 2feaA 75 :AKIREGFREFVAFINEHE T0330 110 :VLLGL 2feaA 93 :IPFYV T0330 117 :GNFEASGRHKLKLP 2feaA 100 :GGMDFFVYPLLEGI T0330 131 :GIDHYFPFGAFADDALD 2feaA 115 :EKDRIYCNHASFDNDYI T0330 148 :RN 2feaA 150 :CK T0330 156 :LERARRMTGANY 2feaA 152 :PSVIHELSEPNQ T0330 171 :QIVIIGDTEHDIRCARE 2feaA 164 :YIIMIGDSVTDVEAAKL T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLAS 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 15 number of extra gaps= 1 total=983 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 2feaA/T0330-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2feaA/T0330-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0330-2feaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0330 2 :SRTLVLFDIDGTLL 2feaA 4 :RKPFIICDFDGTIT T0330 19 :SM 2feaA 20 :DN T0330 25 :LADAL 2feaA 22 :IINIM T0330 31 :EVY 2feaA 27 :KTF T0330 37 :GSTGSHDF 2feaA 30 :APPEWMAL T0330 45 :SGKMDGAIIYEVLSNVGLERA 2feaA 44 :KTLSIKEGVGRMFGLLPSSLK T0330 72 :DKAKETYIAL 2feaA 65 :EEITSFVLED T0330 91 :ITLLEGVRELLDALSSRS 2feaA 75 :AKIREGFREFVAFINEHE T0330 110 :VLLGL 2feaA 93 :IPFYV T0330 117 :GNFEASGRHKLKLP 2feaA 100 :GGMDFFVYPLLEGI T0330 132 :IDHYFPFG 2feaA 115 :EKDRIYCN T0330 140 :AFADDAL 2feaA 124 :ASFDNDY T0330 155 :ALERARRM 2feaA 151 :KPSVIHEL T0330 167 :YSPS 2feaA 159 :SEPN T0330 171 :QIVIIGDTEHDIRCAR 2feaA 164 :YIIMIGDSVTDVEAAK T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLAS 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 18 number of extra gaps= 1 total=1001 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 2feaA/T0330-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2feaA/T0330-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2feaA read from 2feaA/T0330-2feaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0330)P152 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0330)H153 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0330 2 :SRTLVLFDIDGTLL 2feaA 4 :RKPFIICDFDGTIT T0330 16 :K 2feaA 20 :D T0330 24 :VLADALIEVYGTEGSTGSHDFS 2feaA 21 :NIINIMKTFAPPEWMALKDGVL T0330 46 :GKMDGAIIYEVLSNVG 2feaA 44 :KTLSIKEGVGRMFGLL T0330 64 :RAEIADKFDKAKETY 2feaA 60 :PSSLKEEITSFVLED T0330 91 :ITLLEGVRELLDALSS 2feaA 75 :AKIREGFREFVAFINE T0330 108 :SDVLLGL 2feaA 91 :HEIPFYV T0330 117 :GNFEASGRHKLKLPGIDHYF 2feaA 100 :GGMDFFVYPLLEGIVEKDRI T0330 137 :PFGAFADD 2feaA 121 :CNHASFDN T0330 145 :ALDRNEL 2feaA 141 :GTCSNQC T0330 154 :IALERARRMTGANY 2feaA 150 :CKPSVIHELSEPNQ T0330 171 :QIVIIGDTEHDIRCARE 2feaA 164 :YIIMIGDSVTDVEAAKL T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLASI 2feaA 204 :YQDFYEIRKEIENV Number of specific fragments extracted= 15 number of extra gaps= 2 total=1016 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0330-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0330 read from 1ymqA/T0330-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0330-1ymqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ymqA to template set # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLL 1ymqA 3 :KALFFDIDGTLV T0330 87 :RREDITLLEGVRELLDALSSRS 1ymqA 15 :SFETHRIPSSTIEALEAAHAKG T0330 110 :VLLGLLTGNFEASGR 1ymqA 37 :LKIFIATGRPKAIIN T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADDA 1ymqA 62 :IDGYITMNGA T0330 148 :RNELPHIALERARRM 1ymqA 185 :GDTKQKGIDEIIRHF T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1ymqA 200 :GIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFT 1ymqA 224 :IGVAMGQAK T0330 203 :EELARH 1ymqA 233 :EDVKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1027 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0330-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1ymqA/T0330-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0330-1ymqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLLKV 1ymqA 3 :KALFFDIDGTLVSF T0330 89 :EDITLLEGVRELLDALSSRS 1ymqA 17 :ETHRIPSSTIEALEAAHAKG T0330 110 :VLLGLLTGNFEASGR 1ymqA 37 :LKIFIATGRPKAIIN T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADDAL 1ymqA 62 :IDGYITMNGAY T0330 147 :DRNELPHIALERARRM 1ymqA 184 :KGDTKQKGIDEIIRHF T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1ymqA 200 :GIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFTME 1ymqA 224 :IGVAMGQAKED T0330 205 :LARH 1ymqA 235 :VKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1038 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/T0330-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1ymqA/T0330-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ymqA read from 1ymqA/T0330-1ymqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLLK 1ymqA 3 :KALFFDIDGTLVS T0330 88 :REDITLLEGVRELLDALSS 1ymqA 16 :FETHRIPSSTIEALEAAHA T0330 108 :SDVLLGLLTGNFEASG 1ymqA 35 :KGLKIFIATGRPKAII T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADD 1ymqA 62 :IDGYITMNG T0330 145 :ALDRNELPHIALERARR 1ymqA 182 :TAKGDTKQKGIDEIIRH T0330 165 :ANYSPSQIVIIGDTEHDIRCARELD 1ymqA 199 :FGIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFTME 1ymqA 224 :IGVAMGQAKED T0330 205 :LARH 1ymqA 235 :VKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1049 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0330-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wr8A expands to /projects/compbio/data/pdb/1wr8.pdb.gz 1wr8A:# T0330 read from 1wr8A/T0330-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0330-1wr8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wr8A to template set # found chain 1wr8A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTL 1wr8A 3 :IKAISIDIDGTI T0330 87 :RREDITLLEGVRELLDALSSRS 1wr8A 15 :TYPNRMIHEKALEAIRRAESLG T0330 110 :VLLGLLTGNF 1wr8A 37 :IPIMLVTGNT T0330 120 :EASGRHKLKLPGID 1wr8A 122 :VETVREIINELNLN T0330 136 :F 1wr8A 136 :L T0330 138 :FGAFADD 1wr8A 137 :VAVDSGF T0330 148 :RNELPHIALERARRM 1wr8A 151 :WINKGSGIEKASEFL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1wr8A 166 :GIKPKEVAHVGDGENDLDAFKVVGYKVAV T0330 199 :NFTMEELARH 1wr8A 195 :AQAPKILKEN T0330 210 :PGTLFKN 1wr8A 205 :ADYVTKK T0330 217 :FAETDEVLASIL 1wr8A 217 :GAEAIYHILEKF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1060 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0330-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1wr8A/T0330-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0330-1wr8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTLLK 1wr8A 3 :IKAISIDIDGTITY T0330 89 :EDITLLEGVRELLDALSSRS 1wr8A 17 :PNRMIHEKALEAIRRAESLG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1wr8A 37 :IPIMLVTGNTVQFAEAASILIGTS T0330 138 :FGAFADDAL 1wr8A 61 :GPVVAEDGG T0330 147 :DRNELPHIALERARRM 1wr8A 150 :PWINKGSGIEKASEFL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1wr8A 166 :GIKPKEVAHVGDGENDLDAFKVVG T0330 191 :RSIAV 1wr8A 190 :YKVAV T0330 198 :GNFT 1wr8A 195 :AQAP T0330 203 :EELARH 1wr8A 199 :KILKEN T0330 210 :PGTLFKN 1wr8A 205 :ADYVTKK T0330 217 :FAETDEVLAS 1wr8A 217 :GAEAIYHILE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1071 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/T0330-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1wr8A/T0330-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wr8A read from 1wr8A/T0330-1wr8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wr8A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTLL 1wr8A 3 :IKAISIDIDGTIT T0330 88 :REDITLLEGVRELLDALSS 1wr8A 16 :YPNRMIHEKALEAIRRAES T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFP 1wr8A 35 :LGIPIMLVTGNTVQFAEAASILIGTSGPVV T0330 145 :ALDRNELPHIALERARR 1wr8A 148 :KKPWINKGSGIEKASEF T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1wr8A 165 :LGIKPKEVAHVGDGENDLDAFKVVGYKVA T0330 197 :TGNF 1wr8A 194 :VAQA T0330 202 :MEELAR 1wr8A 198 :PKILKE T0330 209 :KPGTLFKN 1wr8A 204 :NADYVTKK T0330 217 :FAETDEVLAS 1wr8A 214 :GEGGAEAIYH Number of specific fragments extracted= 9 number of extra gaps= 0 total=1080 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0330-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b8eA expands to /projects/compbio/data/pdb/2b8e.pdb.gz 2b8eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2b8eA/T0330-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0330-2b8eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b8eA to template set # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)F200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLKVESMNR 2b8eA 419 :TAVIFDKTGTLTKGKPEVT T0330 23 :RVLADALIEVYGTEGSTGSHDFSGKM 2b8eA 466 :EAIVKKALEHGIELGEPEKVEVIAGE T0330 54 :YEVLSNVGLERAE 2b8eA 503 :KRLMEDFGVAVSN T0330 73 :KAKETYIALFRERA 2b8eA 516 :EVELALEKLEREAK T0330 91 :ITLLEGVRELLDALSSRS 2b8eA 548 :DTLKESAKPAVQELKRMG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2b8eA 566 :IKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADDALDRN 2b8eA 590 :LVIAEVLPHQK T0330 156 :LERARRMTGA 2b8eA 601 :SEEVKKLQAK T0330 170 :SQIVIIGDT 2b8eA 611 :EVVAFVGDG T0330 182 :IRCARELDARSIA 2b8eA 623 :APALAQADLGIAV T0330 202 :M 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 13 number of extra gaps= 2 total=1093 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0330-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b8eA/T0330-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0330-2b8eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLK 2b8eA 419 :TAVIFDKTGTLTK T0330 17 :VESMNRRVLADAL 2b8eA 460 :SEHPIAEAIVKKA T0330 31 :EVYGTEGSTGS 2b8eA 473 :LEHGIELGEPE T0330 42 :HDFSGK 2b8eA 486 :EVIAGE T0330 54 :YEVLSNVGLERA 2b8eA 503 :KRLMEDFGVAVS T0330 72 :DKAKETYIALFRERA 2b8eA 515 :NEVELALEKLEREAK T0330 91 :ITLLEGVRELLDALSSRS 2b8eA 548 :DTLKESAKPAVQELKRMG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2b8eA 566 :IKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADDA 2b8eA 590 :LVIAEVL T0330 152 :PHIALERARRMTGA 2b8eA 597 :PHQKSEEVKKLQAK T0330 171 :QIVIIGDT 2b8eA 612 :VVAFVGDG T0330 182 :IRCARELD 2b8eA 623 :APALAQAD T0330 191 :RSIAV 2b8eA 631 :LGIAV T0330 198 :G 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 16 number of extra gaps= 2 total=1109 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/T0330-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b8eA/T0330-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b8eA read from 2b8eA/T0330-2b8eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLK 2b8eA 419 :TAVIFDKTGTLTK T0330 22 :RRVLADALIEVYGTEGS 2b8eA 447 :RELLRLAAIAERRSEHP T0330 49 :DGAIIY 2b8eA 464 :IAEAIV T0330 55 :EVLSNVGL 2b8eA 504 :RLMEDFGV T0330 66 :EIADKFDKAKETYIA 2b8eA 512 :AVSNEVELALEKLER T0330 91 :ITLLEGVRELLDALSS 2b8eA 548 :DTLKESAKPAVQELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGID 2b8eA 564 :MGIKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADD 2b8eA 590 :LVIAEV T0330 151 :LPHIALERARRMTGA 2b8eA 596 :LPHQKSEEVKKLQAK T0330 170 :SQIVIIGDT 2b8eA 611 :EVVAFVGDG T0330 182 :IRCARELD 2b8eA 623 :APALAQAD T0330 191 :RSIAV 2b8eA 631 :LGIAV T0330 202 :M 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 15 number of extra gaps= 2 total=1124 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0330-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0330 read from 1aq6A/T0330-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0330-1aq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aq6A to template set # found chain 1aq6A in template set T0330 1 :M 1aq6A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNR 1aq6A 2 :IKAVVFDAYGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1aq6A 40 :QKQLEYSWLRALMGRYADFWGV T0330 49 :DGAIIYEVLSNVGLERAE 1aq6A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1aq6A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1aq6A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1aq6A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1aq6A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1aq6A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1aq6A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLAS 1aq6A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1135 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0330-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1aq6A/T0330-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0330-1aq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1aq6A)A245 T0330 1 :M 1aq6A 1 :M T0330 3 :RTLVLFDIDGTLLK 1aq6A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1aq6A 19 :VADATERA T0330 25 :LADALIEVY 1aq6A 38 :WRQKQLEYS T0330 34 :GT 1aq6A 53 :GR T0330 47 :KMDGAIIYEVLSNVGLERAE 1aq6A 60 :GVTREALAYTLGTLGLEPDE T0330 72 :DKA 1aq6A 80 :SFL T0330 76 :E 1aq6A 83 :A T0330 84 :ERAR 1aq6A 84 :DMAQ T0330 88 :REDITLLEGVRELLDALS 1aq6A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1aq6A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1aq6A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1aq6A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1aq6A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1aq6A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1150 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/T0330-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1aq6A/T0330-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aq6A read from 1aq6A/T0330-1aq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aq6A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1aq6A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1aq6A)A245 T0330 3 :RTLVLFDIDGTLLK 1aq6A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1aq6A 19 :VADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1aq6A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 64 :RAEIADKFDKAKETYIAL 1aq6A 55 :YADFWGVTREALAYTLGT T0330 82 :FRERARR 1aq6A 81 :FLADMAQ T0330 89 :EDITLLEGVRELLDAL 1aq6A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1aq6A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1aq6A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1aq6A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 10 number of extra gaps= 0 total=1160 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0330-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0330 read from 1wviA/T0330-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0330-1wviA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wviA to template set # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAG T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1wviA 1025 :EDFVKRLQERQLPYILVTNNTTRTPEMVQEMLATSF T0330 62 :LERAE 1wviA 1064 :TPLET T0330 74 :AKETYIALFRERARREDITLL 1wviA 1072 :ATLATIDYMNDMKRGKTAYVI T0330 95 :EGVRELL 1wviA 1095 :TGLKKAV T0330 105 :SSRS 1wviA 1102 :AEAG T0330 109 :DVLLGLLTGNF 1wviA 1112 :NPAYVVVGLDT T0330 120 :EASGRHKLKLP 1wviA 1129 :LTLATLAIQKG T0330 136 :FPFGAFADDAL 1wviA 1140 :AVFIGTNPDLN T0330 148 :RNELPHIALERARRM 1wviA 1180 :GKPEAVIMNKALDRL T0330 166 :NYSPSQIVIIGDTE 1wviA 1195 :GVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0330 210 :PGTLFKNFAE 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1173 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0330-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1wviA/T0330-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0330-1wviA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLLK 1wviA 1003 :YKGYLIDLDGTIYK T0330 17 :VESMNRRVLADAL 1wviA 1020 :RIPAGEDFVKRLQ T0330 31 :EV 1wviA 1033 :ER T0330 34 :GT 1wviA 1035 :QL T0330 46 :GKMDGAIIYE 1wviA 1045 :TTRTPEMVQE T0330 56 :VLSNVGLERAE 1wviA 1056 :LATSFNIKTPL T0330 72 :D 1wviA 1067 :E T0330 74 :AKET 1wviA 1072 :ATLA T0330 97 :VRELLDA 1wviA 1076 :TIDYMND T0330 105 :SSRS 1wviA 1083 :MKRG T0330 110 :VLLGLLTG 1wviA 1087 :KTAYVIGE T0330 121 :ASGRHKLKLPGID 1wviA 1095 :TGLKKAVAEAGYR T0330 134 :HYFPFGAFADDAL 1wviA 1111 :ENPAYVVVGLDTN T0330 147 :DRNELPHIALERARRM 1wviA 1179 :IGKPEAVIMNKALDRL T0330 166 :NYSPSQIVIIGDTE 1wviA 1195 :GVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0330 210 :PGTLFKNFAE 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 17 number of extra gaps= 0 total=1190 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/T0330-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1wviA/T0330-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wviA read from 1wviA/T0330-1wviA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLL 1wviA 1003 :YKGYLIDLDGTIY T0330 92 :TLLEGVRELLDALSS 1wviA 1019 :DRIPAGEDFVKRLQE T0330 108 :SDVLLGLLTGNF 1wviA 1034 :RQLPYILVTNNT T0330 120 :EASGRHKLKL 1wviA 1049 :PEMVQEMLAT T0330 130 :PGI 1wviA 1060 :FNI T0330 133 :DHYFP 1wviA 1066 :LETIY T0330 138 :FGAFADD 1wviA 1116 :VVVGLDT T0330 148 :RNELPHIALERARR 1wviA 1180 :GKPEAVIMNKALDR T0330 165 :ANYSPSQIVIIGDTE 1wviA 1194 :LGVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPA T0330 208 :HKPGTLFKNFAE 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1201 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0330-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lvhA expands to /projects/compbio/data/pdb/1lvh.pdb.gz 1lvhA:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0330 read from 1lvhA/T0330-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0330-1lvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 1 :M 1lvhA 1 :M T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 62 :LERAE 1lvhA 62 :KKVSA T0330 69 :DKFDKAKETYIALFRERA 1lvhA 67 :EEFKELAKRKNDNYVKMI T0330 87 :RREDITLLEGVRELLDALSSRS 1lvhA 86 :DVSPADVYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1lvhA 108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1lvhA 189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1lvhA 197 :DIVIVPDTSHY T0330 221 :DEVLASILTP 1lvhA 209 :LEFLKEVWLQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=1213 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0330-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1lvhA/T0330-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0330-1lvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 1 :M 1lvhA 1 :M T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADAL 1lvhA 10 :DGVITDTAEYHFRAWKALA T0330 31 :EVYGTE 1lvhA 29 :EEIGIN T0330 37 :GSTGS 1lvhA 36 :VDRQF T0330 42 :HDFSGKMDGAIIYEVLSNVG 1lvhA 42 :EQLKGVSREDSLQKILDLAD T0330 62 :LERAEI 1lvhA 64 :VSAEEF T0330 72 :DKAKETYIALFRERA 1lvhA 70 :KELAKRKNDNYVKMI T0330 89 :EDIT 1lvhA 85 :QDVS T0330 93 :LLEGVRELLDALSSRS 1lvhA 92 :VYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1lvhA 108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1lvhA 189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1lvhA 197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1lvhA 209 :LEFLKEVWL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1229 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/T0330-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1lvhA/T0330-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvhA read from 1lvhA/T0330-1lvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvhA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 64 :RAEIADKFDKAKETYIALFRERARREDIT 1lvhA 61 :DKKVSAEEFKELAKRKNDNYVKMIQDVSP T0330 93 :LLEGVRELLDALSS 1lvhA 92 :VYPGILQLLKDLRS T0330 108 :SDVLLGLLTGN 1lvhA 106 :NKIKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 158 :VGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELA 1lvhA 189 :GRPEDLG T0330 209 :KPGTLFKNFAE 1lvhA 196 :DDIVIVPDTSH T0330 221 :DEVLASILTPKH 1lvhA 209 :LEFLKEVWLQKQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=1239 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0330-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nrwA expands to /projects/compbio/data/pdb/1nrw.pdb.gz 1nrwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 122, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 630, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2199, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2205, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2207, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2209, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2211, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2213, because occupancy 0.500 <= existing 0.500 in 1nrwA Skipped atom 2215, because occupancy 0.500 <= existing 0.500 in 1nrwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1nrwA/T0330-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0330-1nrwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nrwA to template set # found chain 1nrwA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 T0330 4 :TLVLFDIDGTLLKVE 1nrwA 2 :KLIAIDLDGTLLNSK T0330 91 :ITLLEGVRELLDALSSRS 1nrwA 17 :HQVSLENENALRQAQRDG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1nrwA 35 :IEVVVSTGRAHFDVMSIFEPLGIK T0330 137 :PFGAFA 1nrwA 59 :TWVISA T0330 144 :DAL 1nrwA 65 :NGA T0330 148 :RN 1nrwA 213 :SK T0330 152 :PHIALERARRM 1nrwA 215 :GQALKRLAKQL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1nrwA 226 :NIPLEETAAVGDSLNDKSMLEAAG T0330 191 :RSIAV 1nrwA 250 :KGVAM T0330 199 :NFTMEELARH 1nrwA 255 :GNAREDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE T0330 220 :TDEVLASI 1nrwA 277 :VAHMMKHL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1251 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0330-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nrwA/T0330-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0330-1nrwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nrwA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1nrwA)L285 T0330 4 :TLVLFDIDGTLLK 1nrwA 2 :KLIAIDLDGTLLN T0330 17 :VESMNRRVLADAL 1nrwA 19 :VSLENENALRQAQ T0330 31 :EV 1nrwA 32 :RD T0330 34 :GT 1nrwA 34 :GI T0330 38 :STGSHDFSGK 1nrwA 71 :DPEGRLYHHE T0330 48 :MDGAIIYE 1nrwA 86 :RAYDILSW T0330 56 :VLSNV 1nrwA 125 :RFRSA T0330 61 :GLERAEIADKFDKAKET 1nrwA 132 :EADLSVLKQAAEVQYSQ T0330 89 :EDITLLE 1nrwA 149 :SGFAYIN T0330 104 :LSSRSD 1nrwA 160 :LFEADE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDA 1nrwA 169 :FYNILGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHN T0330 147 :DRNELPHIALERARRM 1nrwA 210 :RKASKGQALKRLAKQL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1nrwA 226 :NIPLEETAAVGDSLNDKSMLEAAG T0330 191 :RSIAV 1nrwA 250 :KGVAM T0330 199 :NFTMEELARH 1nrwA 255 :GNAREDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE T0330 220 :TDEVLASI 1nrwA 277 :VAHMMKHL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1268 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/T0330-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nrwA/T0330-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nrwA read from 1nrwA/T0330-1nrwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nrwA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 T0330 4 :TLVLFDIDGTLLKV 1nrwA 2 :KLIAIDLDGTLLNS T0330 90 :DITLLEGVRELLDALSS 1nrwA 16 :KHQVSLENENALRQAQR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1nrwA 33 :DGIEVVVSTGRAHFDVMSIFEPLGIKTWV T0330 138 :FGAFADD 1nrwA 196 :TLVSSAE T0330 147 :DRNELPHIALERARR 1nrwA 210 :RKASKGQALKRLAKQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARELD 1nrwA 225 :LNIPLEETAAVGDSLNDKSMLEAAG T0330 191 :R 1nrwA 250 :K T0330 194 :AVATGNFT 1nrwA 251 :GVAMGNAR T0330 203 :EELARH 1nrwA 259 :EDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 10 number of extra gaps= 0 total=1278 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0330-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rkqA expands to /projects/compbio/data/pdb/1rkq.pdb.gz 1rkqA:Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 1rkqA Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 1rkqA # T0330 read from 1rkqA/T0330-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0330-1rkqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rkqA to template set # found chain 1rkqA in template set Warning: unaligning (T0330)P230 because last residue in template chain is (1rkqA)N271 T0330 2 :SRTLVLFDIDGTL 1rkqA 3 :AIKLIAIDMDGTL T0330 87 :RREDITLLEGVRELLDALSSRS 1rkqA 16 :LLPDHTISPAVKNAIAAARARG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1rkqA 38 :VNVVLTTGRPYAGVHNYLKELHMEQPGDYCITY T0330 145 :ALD 1rkqA 71 :NGA T0330 148 :RN 1rkqA 197 :NK T0330 152 :PHIALERARRM 1rkqA 199 :GTGVKSLADVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1rkqA 210 :GIKPEEIMAIGDQENDIAMIEYAGVGVAV T0330 199 :NFTMEELARH 1rkqA 239 :DNAIPSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE T0330 220 :TDEVLASILT 1rkqA 261 :VAFAIEKYVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1288 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0330-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rkqA/T0330-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0330-1rkqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkqA in template set Warning: unaligning (T0330)P230 because last residue in template chain is (1rkqA)N271 T0330 2 :SRTLVLFDI 1rkqA 3 :AIKLIAIDM T0330 26 :ADAL 1rkqA 12 :DGTL T0330 86 :A 1rkqA 16 :L T0330 88 :REDITLLEGVRELLDALSSRS 1rkqA 17 :LPDHTISPAVKNAIAAARARG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDAL 1rkqA 38 :VNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGAL T0330 150 :ELPHIALERARRM 1rkqA 197 :NKGTGVKSLADVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1rkqA 210 :GIKPEEIMAIGDQENDIAMIEYAG T0330 193 :IAVATGNFT 1rkqA 234 :VGVAVDNAI T0330 203 :EELARH 1rkqA 243 :PSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE T0330 220 :TDEVLASILT 1rkqA 261 :VAFAIEKYVL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1299 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/T0330-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1rkqA/T0330-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rkqA read from 1rkqA/T0330-1rkqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rkqA in template set T0330 2 :SRTLVLFDIDGTLL 1rkqA 3 :AIKLIAIDMDGTLL T0330 88 :REDITLLEGVRELLDALSS 1rkqA 17 :LPDHTISPAVKNAIAAARA T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFP 1rkqA 36 :RGVNVVLTTGRPYAGVHNYLKELHMEQPGD T0330 146 :LDRNELPHIALERARR 1rkqA 193 :DKRVNKGTGVKSLADV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARS 1rkqA 209 :LGIKPEEIMAIGDQENDIAMIEYAGVGV T0330 196 :ATGNF 1rkqA 237 :AVDNA T0330 202 :MEELARH 1rkqA 242 :IPSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1307 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0330-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k1eA expands to /projects/compbio/data/pdb/1k1e.pdb.gz 1k1eA:# T0330 read from 1k1eA/T0330-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0330-1k1eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k1eA to template set # found chain 1k1eA in template set T0330 3 :RTLVLFDIDGTLLKVES 1k1eA 8 :IKFVITDVDGVLTDGQL T0330 41 :SHDFS 1k1eA 25 :HYDAN T0330 87 :RREDITLLEGVRELLDALSSRS 1k1eA 30 :GEAIKSFHVRDGLGIKMLMDAD T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1k1eA 52 :IQVAVLSGRDSPILRRRIADLGIK T0330 138 :FGAFA 1k1eA 76 :LFFLG T0330 144 :DA 1k1eA 81 :KL T0330 148 :RN 1k1eA 83 :EK T0330 152 :PHIALERARRM 1k1eA 85 :ETACFDLMKQA T0330 166 :NYSPSQIVIIGDTEHDIRCARE 1k1eA 96 :GVTAEQTAYIGDDSVDLPAFAA T0330 190 :ARSIAVATG 1k1eA 118 :CGTSFAVAD T0330 200 :FTME 1k1eA 127 :APIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST T0330 217 :FAETDEVLASILT 1k1eA 148 :FREMSDMILQAQG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1321 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0330-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1k1eA/T0330-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0330-1k1eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1eA in template set T0330 3 :RTLVLFDIDGTLLK 1k1eA 8 :IKFVITDVDGVLTD T0330 39 :TGS 1k1eA 28 :ANG T0330 89 :EDITLLEGVRELLDALSSRS 1k1eA 32 :AIKSFHVRDGLGIKMLMDAD T0330 110 :VLLGLLTGNFEASGRHKLKLPGI 1k1eA 52 :IQVAVLSGRDSPILRRRIADLGI T0330 137 :PFGAFADD 1k1eA 75 :KLFFLGKL T0330 148 :RN 1k1eA 83 :EK T0330 152 :PHIALERARRM 1k1eA 85 :ETACFDLMKQA T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1k1eA 96 :GVTAEQTAYIGDDSVDLPAFAACG T0330 191 :RSIAV 1k1eA 120 :TSFAV T0330 198 :GNFTME 1k1eA 125 :ADAPIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST T0330 217 :FAETDEVL 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 13 number of extra gaps= 0 total=1334 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/T0330-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1k1eA/T0330-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k1eA read from 1k1eA/T0330-1k1eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k1eA in template set T0330 3 :RTLVLFDIDGTLLKV 1k1eA 8 :IKFVITDVDGVLTDG T0330 95 :EGVRELLDALSS 1k1eA 38 :VRDGLGIKMLMD T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGI 1k1eA 50 :ADIQVAVLSGRDSPILRRRIADLGI T0330 137 :PFGAFA 1k1eA 75 :KLFFLG T0330 148 :RNELPHIALERARR 1k1eA 81 :KLEKETACFDLMKQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARE 1k1eA 95 :AGVTAEQTAYIGDDSVDLPAFAA T0330 190 :ARSIAV 1k1eA 118 :CGTSFA T0330 197 :TGNFTME 1k1eA 124 :VADAPIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST Number of specific fragments extracted= 10 number of extra gaps= 0 total=1344 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0330-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0330 read from 1nf2A/T0330-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0330-1nf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nf2A to template set # found chain 1nf2A in template set T0330 1 :M 1nf2A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEG 1nf2A 2 :YRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCY T0330 39 :TGSHDFS 1nf2A 37 :VVFASGR T0330 49 :DGAIIYEVLSNVG 1nf2A 44 :MLVSTLNVEKKYF T0330 62 :LERAE 1nf2A 83 :IPPEV T0330 97 :VRELLDALSSRS 1nf2A 88 :AKDIIEYIKPLN T0330 110 :VLLG 1nf2A 100 :VHWQ T0330 114 :LLTGNFEASGRHKLKLPGID 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0330 136 :FPF 1nf2A 130 :YRV T0330 142 :ADDALD 1nf2A 133 :EPNLSE T0330 148 :RN 1nf2A 190 :DK T0330 152 :PHIALERARRM 1nf2A 192 :GKALRFLRERM T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1nf2A 203 :NWKKEEIVVFGDNENDLFMFEEAGLRVAM T0330 199 :NFTMEELARH 1nf2A 232 :ENAIEKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLAS 1nf2A 254 :VSYVLER Number of specific fragments extracted= 16 number of extra gaps= 0 total=1360 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0330-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nf2A/T0330-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0330-1nf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf2A in template set T0330 1 :M 1nf2A 1 :M T0330 3 :RTLVLFDIDGTLLK 1nf2A 2 :YRVFVFDLDGTLLN T0330 17 :VESMNRRVLADAL 1nf2A 20 :ISEKDRRNIEKLS T0330 31 :EVY 1nf2A 33 :RKC T0330 46 :GKMDGAIIYEVLSNVGLER 1nf2A 41 :SGRMLVSTLNVEKKYFKRT T0330 94 :LEGVRELLDALSSRS 1nf2A 85 :PEVAKDIIEYIKPLN T0330 110 :VLLG 1nf2A 100 :VHWQ T0330 114 :LLTGNFEASGRHKLKLPGID 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0330 136 :FP 1nf2A 130 :YR T0330 141 :FADDA 1nf2A 132 :VEPNL T0330 147 :DRNELPHIALERARRM 1nf2A 187 :KNVDKGKALRFLRERM T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1nf2A 203 :NWKKEEIVVFGDNENDLFMFEEAGLR T0330 195 :VATGNFT 1nf2A 229 :VAMENAI T0330 203 :EELARH 1nf2A 236 :EKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLASI 1nf2A 254 :VSYVLERI Number of specific fragments extracted= 16 number of extra gaps= 0 total=1376 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/T0330-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1nf2A/T0330-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nf2A read from 1nf2A/T0330-1nf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nf2A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1nf2A)M1 T0330 3 :RTLVLFDIDGTLLK 1nf2A 2 :YRVFVFDLDGTLLN T0330 33 :YGTEGSTGSHDFS 1nf2A 16 :DNLEISEKDRRNI T0330 46 :GKMDGAIIYEVLSNVGLERAE 1nf2A 41 :SGRMLVSTLNVEKKYFKRTFP T0330 95 :EGVRELLDALSS 1nf2A 86 :EVAKDIIEYIKP T0330 108 :SDVLLG 1nf2A 98 :LNVHWQ T0330 114 :LLTGNFEASGRHKLKLPGIDHYFP 1nf2A 110 :LYSEKDNEEIKSYARHSNVDYRVE T0330 145 :ALDRNELPHIALERARR 1nf2A 185 :VPKNVDKGKALRFLRER T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1nf2A 202 :MNWKKEEIVVFGDNENDLFMFEEAGLRVA T0330 197 :TGNFT 1nf2A 231 :MENAI T0330 203 :EELARH 1nf2A 236 :EKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLAS 1nf2A 254 :VSYVLER Number of specific fragments extracted= 12 number of extra gaps= 0 total=1388 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b82A/T0330-2b82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b82A expands to /projects/compbio/data/pdb/2b82.pdb.gz 2b82A:# T0330 read from 2b82A/T0330-2b82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b82A read from 2b82A/T0330-2b82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b82A to template set # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRRVLAD 2b82A 45 :IDDTVLFSSPGFWRGKKT T0330 33 :YG 2b82A 63 :FS T0330 36 :EGSTGSHDFS 2b82A 65 :PESEDYLKNP T0330 69 :D 2b82A 75 :V T0330 78 :YIALFRER 2b82A 76 :FWEKMNNG T0330 87 :RREDITLLEGVRELLDALSSRS 2b82A 84 :WDEFSIPKEVARQLIDMHVRRG T0330 110 :VLLGLLTGNF 2b82A 106 :DAIFFVTGRS T0330 123 :GRHKLKLPGID 2b82A 123 :SKTLADNFHIP T0330 134 :HYFPFGAFADDAL 2b82A 136 :NMNPVIFAGDKPG T0330 147 :DRN 2b82A 150 :NTK T0330 156 :LERARRM 2b82A 153 :SQWLQDK T0330 166 :NYS 2b82A 160 :NIR T0330 173 :VIIGDTEHDIRCARELDARSIAVATG 2b82A 163 :IFYGDSDNDITAARDVGARGIRILRA Number of specific fragments extracted= 14 number of extra gaps= 1 total=1402 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b82A/T0330-2b82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b82A/T0330-2b82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b82A read from 2b82A/T0330-2b82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRRVL 2b82A 45 :IDDTVLFSSPGFWRGK T0330 31 :EVYG 2b82A 61 :KTFS T0330 39 :TGSHDFSG 2b82A 65 :PESEDYLK T0330 49 :DGAIIYEVLS 2b82A 73 :NPVFWEKMNN T0330 61 :GL 2b82A 83 :GW T0330 89 :EDITLLEGVRELLDALSSRS 2b82A 86 :EFSIPKEVARQLIDMHVRRG T0330 110 :VLLGLLTG 2b82A 106 :DAIFFVTG T0330 118 :NFEASGRHKLKLPG 2b82A 121 :TVSKTLADNFHIPA T0330 133 :DHYFPFGAFADDALD 2b82A 135 :TNMNPVIFAGDKPGQ T0330 148 :RN 2b82A 151 :TK T0330 156 :LERARRM 2b82A 153 :SQWLQDK T0330 166 :NYS 2b82A 160 :NIR T0330 173 :VIIGDTEHDIRCARELDARSIAVAT 2b82A 163 :IFYGDSDNDITAARDVGARGIRILR T0330 199 :N 2b82A 189 :S Number of specific fragments extracted= 15 number of extra gaps= 1 total=1417 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b82A/T0330-2b82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2b82A/T0330-2b82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b82A read from 2b82A/T0330-2b82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRR 2b82A 45 :IDDTVLFSSPGFWR T0330 53 :IYEVLSNVG 2b82A 59 :GKKTFSPES T0330 66 :EIADKFDKAKETY 2b82A 68 :EDYLKNPVFWEKM T0330 87 :RREDITLLEGVRELLDALSS 2b82A 84 :WDEFSIPKEVARQLIDMHVR T0330 108 :SDVLLGLLTGNF 2b82A 104 :RGDAIFFVTGRS T0330 122 :SGRHKL 2b82A 121 :TVSKTL T0330 128 :KLPGID 2b82A 128 :DNFHIP T0330 134 :HYFPFGAFADDALDRNEL 2b82A 135 :TNMNPVIFAGDKPGQNTK T0330 156 :LERARR 2b82A 153 :SQWLQD T0330 165 :ANYS 2b82A 159 :KNIR T0330 173 :VIIGDTEHDIRCARELDARSIAVA 2b82A 163 :IFYGDSDNDITAARDVGARGIRIL Number of specific fragments extracted= 12 number of extra gaps= 1 total=1429 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0330-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0330 read from 1vj5A/T0330-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0330-1vj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vj5A to template set # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLLKVE 1vj5A 3 :LRAAVFDLDGVLALPA T0330 21 :NRRVLADALIEVYG 1vj5A 19 :VFGVLGRTEEALAL T0330 49 :DGAIIYEVLSNVG 1vj5A 33 :PRGLLNDAFQKGG T0330 62 :LERAEIADKFDKAKETY 1vj5A 58 :ITLSQWIPLMEENCRKC T0330 79 :IALFRE 1vj5A 89 :KEIFDK T0330 87 :RREDITLLEGVRELLDALSSRS 1vj5A 95 :AISARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTGNF 1vj5A 117 :FTTAILTNTW T0330 120 :EASGRHKLKLPGID 1vj5A 133 :RDGLAQLMCELKMH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1vj5A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1vj5A 174 :KASPSEVVFLDDIGANLKPARDLGMVTIL T0330 214 :FKNFAETDEVLASILTPK 1vj5A 203 :VQDTDTALKELEKVTGIQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=1440 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0330-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1vj5A/T0330-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0330-1vj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLL 1vj5A 3 :LRAAVFDLDGVLA T0330 17 :VESMNRRV 1vj5A 19 :VFGVLGRT T0330 29 :L 1vj5A 27 :E T0330 31 :EVYGTEGS 1vj5A 28 :EALALPRG T0330 52 :IIYE 1vj5A 36 :LLND T0330 56 :VLSNVGLERAEIADKFDKAKET 1vj5A 52 :RLMKGEITLSQWIPLMEENCRK T0330 78 :YIALFRERA 1vj5A 88 :IKEIFDKAI T0330 89 :EDITLLEGVRELLDALSSRS 1vj5A 97 :SARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTG 1vj5A 117 :FTTAILTN T0330 118 :NFEASGRHKLKLPGI 1vj5A 131 :AERDGLAQLMCELKM T0330 135 :YFPFGAFADDALDRNELPHIALERARRM 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSI 1vj5A 174 :KASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASILTP 1vj5A 202 :LVQDTDTALKELEKVTGI Number of specific fragments extracted= 13 number of extra gaps= 0 total=1453 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/T0330-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1vj5A/T0330-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vj5A read from 1vj5A/T0330-1vj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLL 1vj5A 3 :LRAAVFDLDGVLA T0330 16 :KVESMNRRV 1vj5A 18 :AVFGVLGRT T0330 25 :LADALI 1vj5A 37 :LNDAFQ T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLS 1vj5A 43 :KGGPEGATTRLMKGEITLSQWIPLME T0330 69 :DKFDKAKETY 1vj5A 69 :ENCRKCSETA T0330 79 :IALFRERAR 1vj5A 88 :IKEIFDKAI T0330 89 :EDITLLEGVRELLDALSS 1vj5A 97 :SARKINRPMLQAALMLRK T0330 108 :SDVLLGLLTGNF 1vj5A 115 :KGFTTAILTNTW T0330 120 :EASGRHKLKLPG 1vj5A 133 :RDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1vj5A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1vj5A 173 :LKASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASIL 1vj5A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=1465 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0330-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q92A expands to /projects/compbio/data/pdb/1q92.pdb.gz 1q92A:# T0330 read from 1q92A/T0330-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0330-1q92A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q92A to template set # found chain 1q92A in template set Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)Y33 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)S41 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)H42 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)D49 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0330)G50 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0330)S58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)N59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 2 :SRTLVLFDIDGTLLKVESMNRRV 1q92A 34 :RALRVLVDMDGVLADFEGGFLRK T0330 29 :LIE 1q92A 57 :FRA T0330 34 :GTEGSTG 1q92A 62 :PDQPFIA T0330 43 :D 1q92A 71 :D T0330 45 :S 1q92A 72 :R T0330 51 :AIIYEVL 1q92A 75 :FWVSEQY T0330 60 :VGLERAE 1q92A 84 :LRPGLSE T0330 81 :LFRERA 1q92A 91 :KAISIW T0330 87 :RREDITL 1q92A 101 :FFFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTGNF 1q92A 120 :SLQNTDVFICTSPI T0330 120 :EASGRHKLKL 1q92A 140 :PYEKYAWVEK T0330 131 :G 1q92A 152 :G T0330 133 :DHYFPFGAFADDAL 1q92A 153 :PDFLEQIVLTRDKT T0330 166 :NYSPS 1q92A 167 :VVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 206 :ARH 1q92A 200 :QHL T0330 210 :PGT 1q92A 207 :PRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 23 number of extra gaps= 10 total=1488 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0330-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1q92A/T0330-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0330-1q92A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0330)E31 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)G40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)H42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0330)S58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)N59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLAD 1q92A 34 :RALRVLVDMDGVLADFEGGFLRKFRA T0330 33 :YGTE 1q92A 62 :PDQP T0330 37 :GS 1q92A 67 :IA T0330 41 :S 1q92A 71 :D T0330 44 :FS 1q92A 75 :FW T0330 53 :IYEVL 1q92A 77 :VSEQY T0330 60 :VGLERA 1q92A 84 :LRPGLS T0330 76 :E 1q92A 90 :E T0330 81 :LFRERAR 1q92A 91 :KAISIWE T0330 88 :REDITL 1q92A 102 :FFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTG 1q92A 120 :SLQNTDVFICTS T0330 118 :NFEASGRHKLKL 1q92A 138 :YCPYEKYAWVEK T0330 133 :DHYFPFGAFADDAL 1q92A 153 :PDFLEQIVLTRDKT T0330 166 :NYSPS 1q92A 167 :VVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 180 :H 1q92A 181 :T T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 206 :ARHK 1q92A 200 :QHLQ T0330 210 :PGT 1q92A 207 :PRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 24 number of extra gaps= 10 total=1512 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/T0330-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1q92A/T0330-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q92A read from 1q92A/T0330-1q92A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q92A in template set Warning: unaligning (T0330)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)G40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)F44 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)G131 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1q92A 35 :ALRVLVDMDGVLADFEGGFLRKFRA T0330 33 :YGTEGS 1q92A 63 :DQPFIA T0330 41 :SH 1q92A 80 :QY T0330 45 :SGKMDGAIIYEVLSNVG 1q92A 84 :LRPGLSEKAISIWESKN T0330 87 :RREDITL 1q92A 101 :FFFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTGNF 1q92A 120 :SLQNTDVFICTSPI T0330 120 :EASGRHKLKL 1q92A 140 :PYEKYAWVEK T0330 132 :IDHYFPFGAFADDALDRNEL 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 209 :KPGT 1q92A 206 :PPRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 16 number of extra gaps= 9 total=1528 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0330-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bdeA expands to /projects/compbio/data/pdb/2bde.pdb.gz 2bdeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2bdeA/T0330-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0330-2bdeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bdeA to template set # found chain 2bdeA in template set T0330 3 :RTLVLFDIDGTLLKVESMNRRVL 2bdeA 17 :IKLIGLDMDHTLIRYNSKNFESL T0330 49 :DGAIIYEVLSNVG 2bdeA 40 :VYDLVKERLAESF T0330 62 :LERAEIADKFDKAKETY 2bdeA 151 :PSYQAIAQDVQYCVDKV T0330 81 :LFRERA 2bdeA 172 :TLKNII T0330 87 :RREDITLLEGVRELLDALSSRS 2bdeA 181 :LKKYVIREKEVVEGLKHFIRYG T0330 110 :VLLGLLTGNFEASGRHKLKLP 2bdeA 203 :KKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADDALD 2bdeA 233 :HWQGLFEFVITLANKPR T0330 155 :ALERARRM 2bdeA 284 :AKKFTEDL T0330 166 :NYSPSQIVIIGDTE 2bdeA 292 :GVGGDEILYIGDHI T0330 180 :HDIRCARELDARSIAVATG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0330 217 :FAETDEVLAS 2bdeA 327 :LGEEIASQIR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1539 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0330-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2bdeA/T0330-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0330-2bdeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdeA in template set T0330 3 :RTLVLFDIDGTLLK 2bdeA 17 :IKLIGLDMDHTLIR T0330 17 :VESMNRRVLADALIEVYGT 2bdeA 36 :FESLVYDLVKERLAESFHY T0330 36 :EGSTGSHDFSGK 2bdeA 113 :YVDLGDPNYMAI T0330 48 :MDGAIIYEVLSNVG 2bdeA 131 :AFCILYGQLVDLKD T0330 62 :LERAEIADKFDKAKETYIAL 2bdeA 151 :PSYQAIAQDVQYCVDKVHSD T0330 82 :FRERAR 2bdeA 173 :LKNIII T0330 88 :REDITLLEGVRELLDALSSRS 2bdeA 182 :KKYVIREKEVVEGLKHFIRYG T0330 110 :VLLGLLTGNFEASGRHKLKLP 2bdeA 203 :KKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADDAL 2bdeA 233 :HWQGLFEFVITLANKP T0330 155 :ALERARRM 2bdeA 284 :AKKFTEDL T0330 166 :NYSPSQIVIIGDTE 2bdeA 292 :GVGGDEILYIGDHI T0330 180 :HDIRCARELDARSIAVATG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0330 202 :MEELARH 2bdeA 327 :LGEEIAS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1552 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/T0330-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2bdeA/T0330-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bdeA read from 2bdeA/T0330-2bdeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bdeA in template set T0330 2 :SRTLVLFDIDGTLL 2bdeA 16 :KIKLIGLDMDHTLI T0330 16 :KVESMNRRVLADALIEV 2bdeA 35 :NFESLVYDLVKERLAES T0330 33 :YGTEGSTGSHDFS 2bdeA 96 :GTKQISFSDQKKI T0330 46 :GKMDGAIIYEVLSNVGLERAEI 2bdeA 132 :FCILYGQLVDLKDTNPDKMPSY T0330 69 :DKFDKAKETYIALFRERA 2bdeA 154 :QAIAQDVQYCVDKVHSDG T0330 87 :RREDITLLEGVRELLDALSS 2bdeA 181 :LKKYVIREKEVVEGLKHFIR T0330 108 :SDVLLGLLTGNFEASGRHKLKLP 2bdeA 201 :YGKKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADD 2bdeA 233 :HWQGLFEFVITLAN T0330 151 :L 2bdeA 283 :N T0330 155 :ALERARR 2bdeA 284 :AKKFTED T0330 165 :ANYSPSQIVIIGDTE 2bdeA 291 :LGVGGDEILYIGDHI T0330 181 :D 2bdeA 307 :G T0330 182 :IRCARELDARSIAVATG 2bdeA 310 :LRLKKDCNWRTALVVEE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1565 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0330-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f5sA expands to /projects/compbio/data/pdb/1f5s.pdb.gz 1f5sA:Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f5sA # T0330 read from 1f5sA/T0330-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0330-1f5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1f5sA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVY 1f5sA 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1f5sA 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1f5sA 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1f5sA 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1f5sA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDAL 1f5sA 131 :TGDVEGEVLK T0330 147 :DRN 1f5sA 142 :NAK T0330 152 :PHIALERARRM 1f5sA 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1f5sA 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1f5sA 185 :CAKPILKEK T0330 210 :PGTLF 1f5sA 194 :ADICI T0330 215 :KNFAETD 1f5sA 201 :RDLREIL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1578 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0330-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1f5sA/T0330-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0330-1f5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1f5sA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADAL 1f5sA 22 :IDEIA T0330 31 :EVYGT 1f5sA 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1f5sA 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1f5sA 62 :DLPIEKV T0330 72 :DKAK 1f5sA 69 :EKAI T0330 89 :EDITLLEGVRELLDALSSRS 1f5sA 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1f5sA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1f5sA 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1f5sA 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1f5sA 180 :LKIAFCA T0330 202 :MEELARH 1f5sA 187 :KPILKEK T0330 210 :PGTLFK 1f5sA 194 :ADICIE T0330 216 :NFAETD 1f5sA 202 :DLREIL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1592 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/T0330-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1f5sA/T0330-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5sA read from 1f5sA/T0330-1f5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVESM 1f5sA 4 :KKKLILFDFDSTLVNNETI T0330 26 :ADALIEVYGTEGSTGSHDFS 1f5sA 23 :DEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVG 1f5sA 45 :GKLNFEQSLRKRVSLL T0330 65 :AEIA 1f5sA 61 :KDLP T0330 72 :DKAKETYIA 1f5sA 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1f5sA 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1f5sA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1f5sA 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1f5sA 155 :EGINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELAR 1f5sA 185 :CAKPILKE T0330 209 :KPGTLFKN 1f5sA 193 :KADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=1603 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0330-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g09A expands to /projects/compbio/data/pdb/2g09.pdb.gz 2g09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1940, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2g09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2g09A/T0330-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0330-2g09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g09A to template set # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKVE 2g09A 46 :IITDFDMTLSRFS T0330 25 :LADALIEV 2g09A 67 :CHNIIDNC T0330 36 :EGSTG 2g09A 76 :LVTDE T0330 49 :DGAIIYEVLSNVG 2g09A 81 :CRRKLLQLKEQYY T0330 62 :LERAEIADKFDKAKETYIALFRERA 2g09A 101 :LTVEEKFPYMVEWYTKSHGLLIEQG T0330 87 :RREDITLLEGVRELLDALSSRS 2g09A 136 :ADSDVMLKEGYENFFGKLQQHG T0330 110 :VLLGLLTGNFEASGRHKLKLPG 2g09A 158 :IPVFIFSAGIGDVLEEVIRQAG T0330 132 :IDHYFPFGAFA 2g09A 181 :YHSNVKVVSNF T0330 143 :DD 2g09A 195 :DE T0330 148 :RN 2g09A 219 :KN T0330 152 :PH 2g09A 221 :TD T0330 158 :RARRMT 2g09A 223 :YFSQLK T0330 166 :NY 2g09A 229 :DN T0330 170 :SQIVIIGDTEHDIRCAR 2g09A 231 :SNIILLGDSQGDLRMAD T0330 189 :DAR 2g09A 248 :GVA T0330 192 :SIAVAT 2g09A 257 :KIGYLN T0330 200 :FTMEELARHK 2g09A 263 :DRVDELLEKY T0330 210 :PGTLF 2g09A 276 :YDIVL T0330 215 :KNFAETDEVLAS 2g09A 284 :ESLEVVNSILQK Number of specific fragments extracted= 19 number of extra gaps= 1 total=1622 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0330-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2g09A/T0330-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0330-2g09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKV 2g09A 46 :IITDFDMTLSRF T0330 25 :LADAL 2g09A 67 :CHNII T0330 31 :E 2g09A 72 :D T0330 34 :GTE 2g09A 73 :NCK T0330 37 :GSTG 2g09A 77 :VTDE T0330 49 :DGAIIYEVLSNV 2g09A 81 :CRRKLLQLKEQY T0330 61 :GLERAEIADKFDKAKETYIALFRE 2g09A 100 :VLTVEEKFPYMVEWYTKSHGLLIE T0330 85 :RARREDITLLEGVRELLDALSSRS 2g09A 134 :IVADSDVMLKEGYENFFGKLQQHG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2g09A 158 :IPVFIFSAGIGDVLEEVIRQAGVY T0330 134 :HYFPFGAFA 2g09A 183 :SNVKVVSNF T0330 143 :D 2g09A 195 :D T0330 152 :PHIAL 2g09A 214 :HDGAL T0330 158 :RARRMTGA 2g09A 223 :YFSQLKDN T0330 170 :SQIVIIGDTEHDIRCA 2g09A 231 :SNIILLGDSQGDLRMA T0330 188 :LDAR 2g09A 247 :DGVA T0330 192 :SIAVATG 2g09A 257 :KIGYLND T0330 201 :TMEE 2g09A 264 :RVDE T0330 205 :LARH 2g09A 272 :YMDS T0330 210 :PGTLF 2g09A 276 :YDIVL T0330 215 :KNFAETDEVLA 2g09A 284 :ESLEVVNSILQ Number of specific fragments extracted= 20 number of extra gaps= 1 total=1642 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/T0330-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 2g09A/T0330-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g09A read from 2g09A/T0330-2g09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKV 2g09A 46 :IITDFDMTLSRF T0330 21 :NRRVLA 2g09A 67 :CHNIID T0330 33 :YGTEGSTGSHDFS 2g09A 73 :NCKLVTDECRRKL T0330 51 :AIIYEVLSNVGLERAEIADKFDKAKETYIALFRERARREDIT 2g09A 86 :LQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIP T0330 93 :LLEGVRELLDALSS 2g09A 142 :LKEGYENFFGKLQQ T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFAD 2g09A 156 :HGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNF T0330 145 :ALDRNELPHIAL 2g09A 207 :LIHVFNKHDGAL T0330 157 :ERARR 2g09A 223 :YFSQL T0330 165 :ANYS 2g09A 228 :KDNS T0330 171 :QIVIIGDTEHDIRC 2g09A 232 :NIILLGDSQGDLRM T0330 187 :ELDAR 2g09A 246 :ADGVA T0330 192 :SIAVATG 2g09A 257 :KIGYLND T0330 201 :TMEELA 2g09A 264 :RVDELL T0330 218 :AETDE 2g09A 270 :EKYMD Number of specific fragments extracted= 14 number of extra gaps= 1 total=1656 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0330-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0330 read from 1ek1A/T0330-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0330-1ek1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)N21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 T0330 5 :LVLFDIDGTLLK 1ek1A 5 :VAAFDLDGVLAL T0330 19 :SM 1ek1A 17 :PS T0330 87 :RREDITLLEGVRELLDALSSRS 1ek1A 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1ek1A 117 :FTTCIVTNNW T0330 120 :EASGRHKLKL 1ek1A 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1ek1A 174 :KAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 7 number of extra gaps= 0 total=1663 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0330-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1ek1A/T0330-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0330-1ek1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0330)F44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0330)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0330 5 :LVLFDIDGTLLK 1ek1A 5 :VAAFDLDGVLAL T0330 17 :V 1ek1A 18 :S T0330 36 :EGSTGS 1ek1A 57 :KITFSQ T0330 42 :HD 1ek1A 64 :VP T0330 88 :REDITLLEGVRELLDALSSRS 1ek1A 96 :MAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTG 1ek1A 117 :FTTCIVTN T0330 118 :NFEASGRHKLKL 1ek1A 131 :DKRDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1ek1A 174 :KAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1672 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/T0330-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1ek1A/T0330-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ek1A read from 1ek1A/T0330-1ek1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0330)K70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0330 5 :LVLFDIDGTLL 1ek1A 5 :VAAFDLDGVLA T0330 40 :GSHDFS 1ek1A 49 :PTEQLM T0330 59 :NVGLERAEIAD 1ek1A 55 :KGKITFSQWVP T0330 87 :RREDITLLEGVRELLDALSS 1ek1A 95 :AMAARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1ek1A 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKLP 1ek1A 133 :RDSLAQMMCEL T0330 133 :DHYFPFGAFADDALDRNELPHIALERARR 1ek1A 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDA 1ek1A 173 :LKAKPNEVVFLDDFGSNLKPARDMGM Number of specific fragments extracted= 8 number of extra gaps= 0 total=1680 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0330-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mh9A expands to /projects/compbio/data/pdb/1mh9.pdb.gz 1mh9A:# T0330 read from 1mh9A/T0330-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0330-1mh9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mh9A to template set # found chain 1mh9A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1mh9A)R34 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRK T0330 29 :LIEVYGT 1mh9A 57 :FRARFPD T0330 37 :GSTGSHDFS 1mh9A 64 :QPFIALEDR T0330 49 :DGAIIYEVLSNVGLERAE 1mh9A 73 :RGFWVSEQYGRLRPGLSE T0330 81 :LFRERA 1mh9A 91 :KAISIW T0330 87 :RREDITLLEGVRELLDALSSRSDVLLGLLTGNF 1mh9A 101 :FFFELEPLPGAVEAVKEMASLQNTDVFICTSPI T0330 120 :EASGRHKLKLP 1mh9A 140 :PYEKYAWVEKY T0330 131 :G 1mh9A 152 :G T0330 133 :DHYFPFGAFADDALDR 1mh9A 153 :PDFLEQIVLTRDKTVV T0330 166 :NYS 1mh9A 169 :SAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 206 :ARH 1mh9A 200 :QHL T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 15 number of extra gaps= 0 total=1695 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0330-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1mh9A/T0330-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0330-1mh9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1mh9A)R34 Warning: unaligning (T0330)T229 because last residue in template chain is (1mh9A)P227 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRKFRA T0330 32 :VY 1mh9A 60 :RF T0330 34 :GTE 1mh9A 63 :DQP T0330 37 :GSTGS 1mh9A 67 :IALED T0330 42 :H 1mh9A 73 :R T0330 46 :GKMDGAIIYE 1mh9A 74 :GFWVSEQYGR T0330 60 :VGLER 1mh9A 84 :LRPGL T0330 75 :K 1mh9A 89 :S T0330 80 :ALFRERAR 1mh9A 90 :EKAISIWE T0330 88 :REDITLLEGVRELLDALSSRSDVLLGLLTGN 1mh9A 102 :FFELEPLPGAVEAVKEMASLQNTDVFICTSP T0330 119 :FEASGRHKLKLP 1mh9A 139 :CPYEKYAWVEKY T0330 133 :DHYFPFGAFADDALD 1mh9A 153 :PDFLEQIVLTRDKTV T0330 166 :NYS 1mh9A 169 :SAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 180 :H 1mh9A 181 :T T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 206 :ARHK 1mh9A 200 :QHLQ T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 19 number of extra gaps= 0 total=1714 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/T0330-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1mh9A/T0330-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mh9A read from 1mh9A/T0330-1mh9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mh9A in template set Warning: unaligning (T0330)K209 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 Warning: unaligning (T0330)T229 because last residue in template chain is (1mh9A)P227 T0330 4 :TLVLFDIDGTLLKVESMNRRVLADA 1mh9A 36 :LRVLVDMDGVLADFEGGFLRKFRAR T0330 32 :V 1mh9A 61 :F T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1mh9A 72 :RRGFWVSEQYGRLRPGLSEKAISIWESKN T0330 87 :RREDITLLEGVRELLDALSSRSDVLLGLLTGNF 1mh9A 101 :FFFELEPLPGAVEAVKEMASLQNTDVFICTSPI T0330 120 :EASGRHKLKLPGIDHYFPFGAFADDALDRNEL 1mh9A 140 :PYEKYAWVEKYFGPDFLEQIVLTRDKTVVSAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 9 number of extra gaps= 1 total=1723 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0330-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0330 read from 1cqzA/T0330-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0330-1cqzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)S19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0330)E36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0330)I52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLLKVE 1cqzA 5 :VAAFDLDGVLALPS T0330 37 :GSTGSHDFSGK 1cqzA 49 :PTEQLMKGKIT T0330 49 :DGA 1cqzA 60 :FSQ T0330 87 :RREDITLLEGVRELLDALSSRS 1cqzA 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1cqzA 117 :FTTCIVTNNW T0330 120 :EASGRHKLKL 1cqzA 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 1cqzA 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVH T0330 215 :KNFAETDEVLASILTPKH 1cqzA 205 :NTASALRELEKVTGTQFP Number of specific fragments extracted= 9 number of extra gaps= 0 total=1732 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0330-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1cqzA/T0330-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0330-1cqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0330)E36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0330)D49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLLK 1cqzA 5 :VAAFDLDGVLAL T0330 37 :GSTGS 1cqzA 49 :PTEQL T0330 42 :HDFSGKM 1cqzA 56 :GKITFSQ T0330 84 :ERA 1cqzA 94 :QAM T0330 89 :EDITLLEGVRELLDALSSRS 1cqzA 97 :AARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTG 1cqzA 117 :FTTCIVTN T0330 118 :NFEASGRHKLKL 1cqzA 131 :DKRDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 1cqzA 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVH T0330 215 :KNFAETDEVLASILTPKHS 1cqzA 205 :NTASALRELEKVTGTQFPE Number of specific fragments extracted= 10 number of extra gaps= 0 total=1742 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/T0330-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1cqzA/T0330-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cqzA read from 1cqzA/T0330-1cqzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)A65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLL 1cqzA 5 :VAAFDLDGVLA T0330 66 :EIADKFD 1cqzA 91 :IFSQAMA T0330 90 :DITLLEGVRELLDALSS 1cqzA 98 :ARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1cqzA 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKL 1cqzA 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARR 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1cqzA 173 :LKAKPNEVVFLDDFGSNLKPARDMGMVTI T0330 212 :TLFKNFAETDEVLASILTPKH 1cqzA 202 :LVHNTASALRELEKVTGTQFP Number of specific fragments extracted= 8 number of extra gaps= 0 total=1750 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0330-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0330 read from 1cr6B/T0330-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0330-1cr6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLLKVES 1cr6B 5 :VAAFDLDGVLALPSI T0330 26 :ADALIEVYGTEG 1cr6B 20 :AGAFRRSEEALA T0330 38 :STGSHDFSGKMDGAIIYEVLSNVGLERAEIADKFDKAKETY 1cr6B 34 :RDFLLGAYQTEFPEGPTEQLMKGKITFSQWVPLMDESYRKS T0330 79 :IALFRE 1cr6B 89 :SQIFSQ T0330 87 :RREDITLLEGVRELLDALSSRS 1cr6B 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1cr6B 117 :FTTCIVTNNW T0330 120 :EASGRHKLKLPGID 1cr6B 133 :RDSLAQMMCELSQH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1cr6B 147 :FDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1cr6B 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=1759 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0330-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1cr6B/T0330-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0330-1cr6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLLK 1cr6B 5 :VAAFDLDGVLAL T0330 19 :SMNRRVLADAL 1cr6B 17 :PSIAGAFRRSE T0330 31 :EVY 1cr6B 28 :EAL T0330 36 :EGSTGS 1cr6B 31 :ALPRDF T0330 42 :HDFSGKMD 1cr6B 38 :LGAYQTEF T0330 50 :GAIIYEVL 1cr6B 47 :EGPTEQLM T0330 59 :NVGLERAEIA 1cr6B 55 :KGKITFSQWV T0330 72 :DKAKETYIA 1cr6B 65 :PLMDESYRK T0330 81 :LFRERA 1cr6B 91 :IFSQAM T0330 89 :EDITLLEGVRELLDALSSRS 1cr6B 97 :AARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGN 1cr6B 117 :FTTCIVTNN T0330 119 :FEASGRHKLKLPG 1cr6B 132 :KRDSLAQMMCELS T0330 134 :HYFPFGAFADDALDRNELPHIALERARRM 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1cr6B 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0330 200 :F 1cr6B 207 :A Number of specific fragments extracted= 15 number of extra gaps= 0 total=1774 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/T0330-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0330 read from 1cr6B/T0330-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cr6B read from 1cr6B/T0330-1cr6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLL 1cr6B 5 :VAAFDLDGVLA T0330 16 :KVESMNRRV 1cr6B 18 :SIAGAFRRS T0330 33 :YGTEGSTGSHDFS 1cr6B 42 :QTEFPEGPTEQLM T0330 46 :GKMDGAIIY 1cr6B 56 :GKITFSQWV T0330 55 :EVLSNV 1cr6B 69 :ESYRKS T0330 63 :ERAEIADK 1cr6B 78 :CGANLPEN T0330 71 :FDKAKETYI 1cr6B 88 :ISQIFSQAM T0330 89 :EDITLLEGVRELLDALSS 1cr6B 97 :AARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1cr6B 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKLPG 1cr6B 133 :RDSLAQMMCELS T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1cr6B 173 :LKAKPNEVVFLDDFGSNLKPARDMGMVTI Number of specific fragments extracted= 12 number of extra gaps= 0 total=1786 Will force an alignment to be made, even if fragment is small Number of alignments=147 # command:CPU_time= 40.858 sec, elapsed time= 43.644 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 147 Adding 27028 constraints to all_contacts Done adding distance constraints # command:CPU_time= 41.034 sec, elapsed time= 43.835 sec. # command:Reading probabilities from T0330.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 70.082 Optimizing... Probability sum: -379.974, CN propb: -379.974 weights: 0.416 constraints: 515 # command:CPU_time= 209.217 sec, elapsed time= 212.342 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 515 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 515 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 3456 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 3456 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 21229 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 21229 # command:CPU_time= 209.666 sec, elapsed time= 213.130 sec. # command: