# 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 T0374 numbered 1 through 160 Created new target T0374 from T0374.a2m # command:CPU_time= 6.516 sec, elapsed time= 6.581 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ge3A/T0374-2ge3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ge3A expands to /projects/compbio/data/pdb/2ge3.pdb.gz 2ge3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2ge3A/T0374-2ge3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ge3A read from 2ge3A/T0374-2ge3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ge3A to template set # found chain 2ge3A in template set Warning: unaligning (T0374)L78 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 Warning: unaligning (T0374)E159 because last residue in template chain is (2ge3A)G169 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERK # choosing archetypes in rotamer library T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQH 2ge3A 37 :FLEAPPLEAVRAFVLDMIENDHPQFVAIADGDVIGWCDIRRQDR T0374 73 :GDFCA 2ge3A 84 :AHCGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQ 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEF T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2ge3A 118 :GLHRIELSVHADNARAIALYEKIGFAHEGRARDA T0374 143 :DPDGRRVALIQMDKPL 2ge3A 153 :SIDGHYIDSLNMAIIF Number of specific fragments extracted= 6 number of extra gaps= 1 total=6 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 2ge3A/T0374-2ge3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2ge3A/T0374-2ge3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ge3A read from 2ge3A/T0374-2ge3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ge3A in template set Warning: unaligning (T0374)G79 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 Warning: unaligning (T0374)E159 because last residue in template chain is (2ge3A)G169 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKYLS T0374 33 :AIWPFSVAQLAAAIA 2ge3A 37 :FLEAPPLEAVRAFVL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 2ge3A 56 :NDHPQFVAIADGDVIGWCDIRRQDRAT T0374 75 :FCAL 2ge3A 85 :HCGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQ 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEF T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2ge3A 118 :GLHRIELSVHADNARAIALYEKIGFAHEG T0374 138 :IAERHDPDGRRVALIQMDKPL 2ge3A 148 :ARDAVSIDGHYIDSLNMAIIF Number of specific fragments extracted= 7 number of extra gaps= 1 total=13 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 2ge3A/T0374-2ge3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2ge3A/T0374-2ge3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ge3A read from 2ge3A/T0374-2ge3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ge3A in template set Warning: unaligning (T0374)L78 because of BadResidue code BAD_PEPTIDE in next template residue (2ge3A)G90 Warning: unaligning (T0374)N80 because of BadResidue code BAD_PEPTIDE at template residue (2ge3A)G90 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 2ge3A 7 :TVTIKPIRAEHVESFHRALDAVSRERKYLSFLEAPPLEAV T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 2ge3A 50 :VLDMIENDHPQFVAIADGDVIGWCDIRRQDRAT T0374 75 :FCA 2ge3A 86 :CGT T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKAR 2ge3A 91 :MGILPAYRNKGLGARLMRRTLDAAHEFGLHR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQ 2ge3A 122 :IELSVHADNARAIALYEKIGFAHEGRARDAVSIDGHYIDSL Number of specific fragments extracted= 5 number of extra gaps= 1 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yvoA/T0374-1yvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yvoA expands to /projects/compbio/data/pdb/1yvo.pdb.gz 1yvoA:Skipped atom 412, because occupancy 0.5 <= existing 0.500 in 1yvoA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1yvoA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1yvoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yvoA/T0374-1yvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvoA read from 1yvoA/T0374-1yvoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yvoA to template set # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFY 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHD 1yvoA 32 :NETPVDLANRQAWFDTRARQGYPILVASDA T0374 59 :GQVLGFANFYQWQH 1yvoA 63 :GEVLGYASYGDWRP T0374 73 :GDFCAL 1yvoA 81 :RGTVEH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1yvoA 87 :SVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yvoA 115 :GLHVMVAAIESGNAASIGLHRRLGFEISGQMPQV T0374 143 :DPDGRRVALIQMDKPLE 1yvoA 150 :QKFGRWLDLTFMQLNLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=25 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yvoA/T0374-1yvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yvoA/T0374-1yvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvoA read from 1yvoA/T0374-1yvoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFYCYPK 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTAIWN T0374 34 :IWPFSVAQLAAAIA 1yvoA 33 :ETPVDLANRQAWFD T0374 48 :ERRGSTVAVHD 1yvoA 51 :QGYPILVASDA T0374 59 :GQVLGFANFYQWQHGD 1yvoA 63 :GEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvoA 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1yvoA 115 :GLHVMVAAIESGNAASIGLHRRLGFEISG T0374 138 :IAERHDPDGRRVALIQMDKPLE 1yvoA 145 :MPQVGQKFGRWLDLTFMQLNLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=32 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 1yvoA/T0374-1yvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yvoA/T0374-1yvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvoA read from 1yvoA/T0374-1yvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yvoA in template set Warning: unaligning (T0374)S4 because first residue in template chain is (1yvoA)S4 T0374 5 :HRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1yvoA 5 :IRDAGVADLPGILAIYNDAVGNTTAIWNETPVDLANRQAWF T0374 46 :IAERRGSTVAVH 1yvoA 49 :ARQGYPILVASD T0374 58 :DGQVLGFANFYQWQHGD 1yvoA 62 :AGEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yvoA 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQGLHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 1yvoA 119 :MVAAIESGNAASIGLHRRLGFEISGQMPQVGQKFGRWLDLTFM Number of specific fragments extracted= 5 number of extra gaps= 0 total=37 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 1vhsA/T0374-1vhsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vhsA expands to /projects/compbio/data/pdb/1vhs.pdb.gz 1vhsA:Skipped atom 20, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 22, because occupancy 0.350 <= existing 0.650 in 1vhsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 652, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 654, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 656, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 658, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 672, because occupancy 0.330 <= existing 0.330 in 1vhsA Skipped atom 673, because occupancy 0.330 <= existing 0.330 in 1vhsA Skipped atom 809, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 811, because occupancy 0.350 <= existing 0.650 in 1vhsA Skipped atom 813, because occupancy 0.350 <= existing 0.650 in 1vhsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1242, because occupancy 0.350 <= existing 0.650 in 1vhsA # T0374 read from 1vhsA/T0374-1vhsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhsA read from 1vhsA/T0374-1vhsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vhsA to template set # found chain 1vhsA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRM T0374 29 :CYPKAIWPFSVAQLAAA 1vhsA 30 :DTEPVTPEDRMEWFSGH T0374 47 :AERRGSTVAVHD 1vhsA 47 :TESRPLYVAEDE T0374 59 :GQVLGFANFYQWQH 1vhsA 60 :GNVAAWISFETFYG T0374 73 :GDFCAL 1vhsA 78 :NKTAEV T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1vhsA 84 :SIYIDEACRGKGVGSYLLQEALRIAPNL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1vhsA 112 :GIRSLMAFIFGHNKPSLKLFEKHGFAEWGLFPGI T0374 143 :DPDGRRVALIQMDKPLEP 1vhsA 147 :EMDGKRYDLKILGRELSE Number of specific fragments extracted= 8 number of extra gaps= 0 total=45 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 1vhsA/T0374-1vhsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1vhsA/T0374-1vhsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhsA read from 1vhsA/T0374-1vhsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhsA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYP 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMVTA T0374 33 :AIWPFSVAQLAAAIA 1vhsA 30 :DTEPVTPEDRMEWFS T0374 48 :ERRGSTVAVHD 1vhsA 48 :ESRPLYVAEDE T0374 59 :GQVLGFANFYQWQHGD 1vhsA 60 :GNVAAWISFETFYGRP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vhsA 79 :KTAEVSIYIDEACRGKGVGSYLLQEALRIAPNL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1vhsA 112 :GIRSLMAFIFGHNKPSLKLFEKHGFAEWG T0374 138 :IAERHDPDGRRVALIQMDKPLEP 1vhsA 142 :FPGIAEMDGKRYDLKILGRELSE Number of specific fragments extracted= 7 number of extra gaps= 0 total=52 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 1vhsA/T0374-1vhsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1vhsA/T0374-1vhsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhsA read from 1vhsA/T0374-1vhsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhsA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vhsA)S0 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1vhsA 1 :LTLRLAEHRDLEAVVAIYNSTIASRMVT T0374 31 :PKAIWPFSVAQLAAA 1vhsA 30 :DTEPVTPEDRMEWFS T0374 46 :IAERRGSTVAVH 1vhsA 46 :HTESRPLYVAED T0374 58 :DGQVLGFANFYQWQHGD 1vhsA 59 :NGNVAAWISFETFYGRP T0374 75 :FCAL 1vhsA 80 :TAEV T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKAR 1vhsA 84 :SIYIDEACRGKGVGSYLLQEALRIAPNLGIRS T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 1vhsA 116 :LMAFIFGHNKPSLKLFEKHGFAEWGLFPGIAEMDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=59 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 1tiqA/T0374-1tiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tiqA expands to /projects/compbio/data/pdb/1tiq.pdb.gz 1tiqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1tiqA/T0374-1tiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tiqA read from 1tiqA/T0374-1tiqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tiqA to template set # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTFKE T0374 32 :KAIWPFSVAQLAAAI 1tiqA 31 :QNSPENMKAYLESAF T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1tiqA 56 :NMSSQFFFIYFDHEIAGYVKVNIDDA T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1tiqA 88 :AESLEIERIYIKNSFQKHGLGKHLLNKAIEIALER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPD 1tiqA 123 :NKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGD T0374 147 :RRVALIQMDKPLE 1tiqA 160 :EEQTDLIMAKTLI Number of specific fragments extracted= 6 number of extra gaps= 0 total=65 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 1tiqA/T0374-1tiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1tiqA/T0374-1tiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tiqA read from 1tiqA/T0374-1tiqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELF 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDT T0374 33 :AIWPFSVAQLAAAIA 1tiqA 28 :FKEQNSPENMKAYLE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1tiqA 57 :MSSQFFFIYFDHEIAGYVKVNIDDAQS T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1tiqA 90 :SLEIERIYIKNSFQKHGLGKHLLNKAIEIALER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 1tiqA 123 :NKKNIWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEE T0374 149 :VALIQMDKPLE 1tiqA 162 :QTDLIMAKTLI Number of specific fragments extracted= 6 number of extra gaps= 0 total=71 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 1tiqA/T0374-1tiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1tiqA/T0374-1tiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tiqA read from 1tiqA/T0374-1tiqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tiqA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1tiqA)S2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAA 1tiqA 3 :VKMKKCSREDLQTLQQLSIETFNDTFKEQNSPENMKAYLESA T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1tiqA 54 :LSNMSSQFFFIYFDHEIAGYVKVNI T0374 70 :W 1tiqA 86 :M T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1tiqA 87 :GAESLEIERIYIKNSFQKHGLGKHLLNKAIEIALERNKKN T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRR 1tiqA 127 :IWLGVWEKNENAIAFYKKMGFVQTGAHSFYMGDEEQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=76 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 2fe7A/T0374-2fe7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fe7A expands to /projects/compbio/data/pdb/2fe7.pdb.gz 2fe7A:# T0374 read from 2fe7A/T0374-2fe7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fe7A read from 2fe7A/T0374-2fe7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fe7A to template set # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWP 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTD T0374 39 :VAQLAAAI 2fe7A 37 :VEGIRRSL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 2fe7A 48 :GSPTRALMCLSEGRPIGYAVFFYSYS T0374 73 :GDFCALGNMMVAPAA 2fe7A 78 :RNGIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQ 2fe7A 97 :AGRRLLRELAREAVAN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 2fe7A 113 :DCGRLEWSVLDWNQPAIDFYRSIGALPQ T0374 137 :AIAER 2fe7A 142 :EWVRY Number of specific fragments extracted= 7 number of extra gaps= 1 total=83 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 2fe7A/T0374-2fe7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fe7A/T0374-2fe7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fe7A read from 2fe7A/T0374-2fe7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCY 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERAR T0374 33 :AIWPFSVAQLAAAIA 2fe7A 31 :HEVVTDVEGIRRSLF T0374 48 :ERRG 2fe7A 47 :EGSP T0374 52 :STVAVHDGQVLGFANFYQWQHGD 2fe7A 53 :ALMCLSEGRPIGYAVFFYSYSTW T0374 75 :FCALGNMMVAPAA 2fe7A 80 :GIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQ 2fe7A 97 :AGRRLLRELAREAVAN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2fe7A 113 :DCGRLEWSVLDWNQPAIDFYRSIGALPQD T0374 138 :IAERH 2fe7A 143 :WVRYR Number of specific fragments extracted= 8 number of extra gaps= 1 total=91 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 2fe7A/T0374-2fe7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fe7A/T0374-2fe7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fe7A read from 2fe7A/T0374-2fe7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fe7A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2fe7A)L3 Warning: unaligning (T0374)R88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fe7A)G96 Warning: unaligning (T0374)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fe7A)G96 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAE 2fe7A 4 :EIRPAVPADAEQILAFIIELADYERARHEVVTDVEGIRRSLFAEG T0374 49 :RRGSTVAVHDGQVLGFANFYQ 2fe7A 50 :PTRALMCLSEGRPIGYAVFFY T0374 74 :D 2fe7A 75 :W T0374 75 :FCALGNMMVAPAA 2fe7A 80 :GIYLEDLYVTPEY T0374 92 :VARYLIGVMENLAREQYKAR 2fe7A 97 :AGRRLLRELAREAVANDCGR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALI 2fe7A 117 :LEWSVLDWNQPAIDFYRSIGALPQDEWVRYRLDGEALRKM Number of specific fragments extracted= 6 number of extra gaps= 1 total=97 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 2ae6A/T0374-2ae6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ae6A expands to /projects/compbio/data/pdb/2ae6.pdb.gz 2ae6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1072, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1074, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1076, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1078, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1080, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1082, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1084, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1086, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1088, because occupancy 0.300 <= existing 0.700 in 2ae6A Skipped atom 1090, because occupancy 0.300 <= existing 0.700 in 2ae6A # T0374 read from 2ae6A/T0374-2ae6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae6A read from 2ae6A/T0374-2ae6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ae6A to template set # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 Warning: unaligning (T0374)I152 because of BadResidue code BAD_PEPTIDE in next template residue (2ae6A)Q156 Warning: unaligning (T0374)Q153 because of BadResidue code BAD_PEPTIDE at template residue (2ae6A)Q156 Warning: unaligning (T0374)L158 because last residue in template chain is (2ae6A)I161 T0374 1 :M 2ae6A 1 :M T0374 2 :QLSHRPAETGDLETVAGFPQD 2ae6A 4 :SLTIRLVAEADWPALHALDQI T0374 35 :WPFSVAQ 2ae6A 40 :LAAYQEK T0374 47 :AERRGSTVAV 2ae6A 47 :MKDETIFVAI T0374 59 :GQVLGFANFYQWQH 2ae6A 59 :QQLAGFIEVHPPTS T0374 73 :GDFCAL 2ae6A 77 :QKQWLL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 2ae6A 83 :SIGVSPDFQDQGIGGSLLSYIKDMAEIS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2ae6A 111 :GIHKLSLRVMATNQEAIRFYEKHGFVQEAHFKEE T0374 143 :DPDGRRVAL 2ae6A 146 :YINGHYCDD T0374 154 :MDKP 2ae6A 157 :YAYF Number of specific fragments extracted= 10 number of extra gaps= 2 total=107 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 2ae6A/T0374-2ae6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2ae6A/T0374-2ae6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae6A read from 2ae6A/T0374-2ae6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 Warning: unaligning (T0374)I152 because of BadResidue code BAD_PEPTIDE in next template residue (2ae6A)Q156 Warning: unaligning (T0374)Q153 because of BadResidue code BAD_PEPTIDE at template residue (2ae6A)Q156 Warning: unaligning (T0374)L158 because last residue in template chain is (2ae6A)I161 T0374 1 :MQ 2ae6A 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQD 2ae6A 5 :LTIRLVAEADWPALHALDQI T0374 35 :WP 2ae6A 40 :LA T0374 44 :AAIA 2ae6A 42 :AYQE T0374 48 :ERRGSTVAV 2ae6A 48 :KDETIFVAI T0374 59 :GQVLGFANFYQWQHGD 2ae6A 59 :QQLAGFIEVHPPTSLA T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2ae6A 78 :KQWLLSIGVSPDFQDQGIGGSLLSYIKDMAEIS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2ae6A 111 :GIHKLSLRVMATNQEAIRFYEKHGFVQEA T0374 138 :IAERHDPDGRRVAL 2ae6A 141 :FKEEFYINGHYCDD T0374 154 :MDKP 2ae6A 157 :YAYF Number of specific fragments extracted= 10 number of extra gaps= 2 total=117 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 2ae6A/T0374-2ae6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2ae6A/T0374-2ae6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae6A read from 2ae6A/T0374-2ae6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ae6A in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ae6A)S39 Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ae6A)S39 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ae6A)G58 Warning: unaligning (T0374)D58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ae6A)G58 T0374 1 :MQLSHRPAETGDLETVAGFPQD 2ae6A 3 :TSLTIRLVAEADWPALHALDQI T0374 33 :AIWPFSV 2ae6A 40 :LAAYQEK T0374 47 :AERRGSTVAV 2ae6A 47 :MKDETIFVAI T0374 59 :GQVLGFANFYQ 2ae6A 59 :QQLAGFIEVHP T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2ae6A 74 :AAHQKQWLLSIGVSPDFQDQGIGGSLLSYIKDMAEISGIHK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGR 2ae6A 115 :LSLRVMATNQEAIRFYEKHGFVQEAHFKEEFYING Number of specific fragments extracted= 6 number of extra gaps= 1 total=123 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 2cy2A/T0374-2cy2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cy2A expands to /projects/compbio/data/pdb/2cy2.pdb.gz 2cy2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2cy2A/T0374-2cy2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cy2A read from 2cy2A/T0374-2cy2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cy2A to template set # found chain 2cy2A in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 2cy2A 2 :RIRRAGLEDLPGVARVLVDTWRATY T0374 29 :CYPKAIWPFSVAQLAAAI 2cy2A 34 :FLEGLSYEGQAERWAQRL T0374 47 :AERRGSTVAVHD 2cy2A 55 :TWPGRLFVAESE T0374 59 :GQVLGFANFYQWQH 2cy2A 68 :GEVVGFAAFGPDRA T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2cy2A 86 :GYTAELWAIYVLPTWQRKGLGRALFHEGARLLQAE T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2cy2A 121 :GYGRMLVWVLKENPKGRGFYEHLGGVLLGEREIELG T0374 146 :GRRVALIQMDKPLE 2cy2A 157 :GAKLWEVAYGFDLG Number of specific fragments extracted= 7 number of extra gaps= 0 total=130 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 2cy2A/T0374-2cy2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2cy2A/T0374-2cy2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cy2A read from 2cy2A/T0374-2cy2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cy2A in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 2cy2A 2 :RIRRAGLEDLPGVARVLVDTWRATY T0374 29 :CYPKAIWPFSVAQLAAAIA 2cy2A 30 :VPEAFLEGLSYEGQAERWA T0374 48 :E 2cy2A 54 :P T0374 49 :RRGSTVAVHD 2cy2A 57 :PGRLFVAESE T0374 59 :GQVLGFANFYQWQHGD 2cy2A 68 :GEVVGFAAFGPDRASG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2cy2A 88 :TAELWAIYVLPTWQRKGLGRALFHEGARLLQAE T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2cy2A 121 :GYGRMLVWVLKENPKGRGFYEHLGGVLLGEREIELG T0374 146 :GRRVALIQMDKPLEP 2cy2A 157 :GAKLWEVAYGFDLGG Number of specific fragments extracted= 8 number of extra gaps= 0 total=138 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 2cy2A/T0374-2cy2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2cy2A/T0374-2cy2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cy2A read from 2cy2A/T0374-2cy2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cy2A in template set T0374 5 :HRPAETGDLETVAGFPQDRDELFYCY 2cy2A 3 :IRRAGLEDLPGVARVLVDTWRATYRG T0374 31 :PKAIWPFSVAQLAAAIAE 2cy2A 38 :LSYEGQAERWAQRLKTPT T0374 49 :RRGSTVAVH 2cy2A 57 :PGRLFVAES T0374 58 :DGQVLGFANFYQ 2cy2A 67 :SGEVVGFAAFGP T0374 70 :WQHGD 2cy2A 82 :SGFPG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2cy2A 88 :TAELWAIYVLPTWQRKGLGRALFHEGARLLQAEGYGR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPD 2cy2A 125 :MLVWVLKENPKGRGFYEHLGGVLLGEREIELGG Number of specific fragments extracted= 7 number of extra gaps= 0 total=145 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 2beiA/T0374-2beiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2beiA expands to /projects/compbio/data/pdb/2bei.pdb.gz 2beiA:Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2beiA Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2beiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2beiA/T0374-2beiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2beiA read from 2beiA/T0374-2beiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2beiA to template set # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0374)A47 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 37 :FSVAQLAAAI 2beiA 36 :ISEEALRADG T0374 48 :ERRGSTVAV 2beiA 50 :PFYHCLVAE T0374 60 :QVLGFANFYQWQH 2beiA 70 :CVVGYGIYYFIYS T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2beiA 86 :GRTIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 2beiA 121 :GCSQFRLAVLDWNQRAMDLYKALGAQDL T0374 137 :AIAERH 2beiA 153 :GWHFFC Number of specific fragments extracted= 7 number of extra gaps= 1 total=152 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 2beiA/T0374-2beiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2beiA/T0374-2beiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2beiA read from 2beiA/T0374-2beiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 37 :FSVAQLAAAIA 2beiA 36 :ISEEALRADGF T0374 48 :ERRGSTVAVH 2beiA 50 :PFYHCLVAEI T0374 61 :VLGFANFYQWQHGD 2beiA 71 :VVGYGIYYFIYSTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2beiA 88 :TIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2beiA 121 :GCSQFRLAVLDWNQRAMDLYKALGAQD T0374 136 :RAIAERHDPD 2beiA 152 :EGWHFFCFQG Number of specific fragments extracted= 7 number of extra gaps= 0 total=159 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 2beiA/T0374-2beiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2beiA/T0374-2beiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2beiA read from 2beiA/T0374-2beiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2beiA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (2beiA)S3 Warning: unaligning (T0374)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2beiA)K35 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)K35 Warning: unaligning (T0374)A47 because of BadResidue code BAD_PEPTIDE in next template residue (2beiA)N49 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE at template residue (2beiA)N49 Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2beiA)G68 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 2beiA 4 :VRIREAKEGDCGDILRLIRELAEFEK T0374 35 :WPFSVAQLAAAI 2beiA 36 :ISEEALRADGFG T0374 49 :RRGSTVAVH 2beiA 51 :FYHCLVAEI T0374 59 :GQVLGFANFYQWQHGD 2beiA 69 :PCVVGYGIYYFIYSTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2beiA 88 :TIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDKGCSQ T0374 113 :MKISCFNANAAGLLLYTQLGYQP 2beiA 125 :FRLAVLDWNQRAMDLYKALGAQD Number of specific fragments extracted= 6 number of extra gaps= 1 total=165 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 1z4eA/T0374-1z4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z4eA expands to /projects/compbio/data/pdb/1z4e.pdb.gz 1z4eA:# T0374 read from 1z4eA/T0374-1z4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4eA read from 1z4eA/T0374-1z4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z4eA to template set # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRK T0374 29 :CYPKAIWPFSVAQLAAAI 1z4eA 33 :RYEKPLPVSYVRAFKEIK T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1z4eA 52 :DKNNELIVACNGEEIVGMLQVTFTPY T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4eA 83 :SWRATIEGVRTHSAARGQGIGSQLVCWAIERAKER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1z4eA 118 :GCHLIQLTTDKQRPDALRFYEQLGFKASHEGLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 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 1z4eA/T0374-1z4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1z4eA/T0374-1z4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4eA read from 1z4eA/T0374-1z4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYP 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRKRER T0374 33 :AIWPFSVAQLAAAIA 1z4eA 34 :YEKPLPVSYVRAFKE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1z4eA 53 :KNNELIVACNGEEIVGMLQVTFTPYLT T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4eA 85 :RATIEGVRTHSAARGQGIGSQLVCWAIERAKER T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1z4eA 118 :GCHLIQLTTDKQRPDALRFYEQLGFKASH T0374 138 :IAERH 1z4eA 148 :GLKMH Number of specific fragments extracted= 6 number of extra gaps= 0 total=176 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 1z4eA/T0374-1z4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1z4eA/T0374-1z4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4eA read from 1z4eA/T0374-1z4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z4eA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1z4eA)H4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1z4eA 5 :VTIREATEGDLEQMVHMLADDVLGRKRE T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 1z4eA 36 :KPLPVSYVRAFKEIKKDKNNELIVACNGEEIVGMLQVTFTPYLT T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1z4eA 85 :RATIEGVRTHSAARGQGIGSQLVCWAIERAKERGCHL T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIA 1z4eA 122 :IQLTTDKQRPDALRFYEQLGFKASHEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=180 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 1wwzA/T0374-1wwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wwzA expands to /projects/compbio/data/pdb/1wwz.pdb.gz 1wwzA:# T0374 read from 1wwzA/T0374-1wwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwzA read from 1wwzA/T0374-1wwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wwzA to template set # found chain 1wwzA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1wwzA)Q157 T0374 1 :M 1wwzA 1 :M T0374 2 :QLSHRPAE 1wwzA 3 :EIKIEKLK T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAI 1wwzA 14 :KKALNELIDVYMSGYEGLEEYGGEGRDYARNYIKWCW T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1wwzA 52 :KASDGFFVAKVGDKIVGFIVCDKDWF T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1wwzA 83 :RIVGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKY T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1wwzA 118 :NDTIELWVGEKNYGAMNLYEKFGFKKVGKSGI T0374 151 :LIQMDKP 1wwzA 150 :WVRMIKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=187 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 1wwzA/T0374-1wwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1wwzA/T0374-1wwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwzA read from 1wwzA/T0374-1wwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwzA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1wwzA)Q157 T0374 1 :MQ 1wwzA 1 :MD T0374 3 :LSHRPAE 1wwzA 4 :IKIEKLK T0374 10 :TGDLETVAGFPQDRDELF 1wwzA 14 :KKALNELIDVYMSGYEGL T0374 31 :P 1wwzA 32 :E T0374 33 :AIWPFSVAQLAAAIA 1wwzA 33 :EYGGEGRDYARNYIK T0374 49 :RRGSTVAVHDGQVLGFANF 1wwzA 54 :SDGFFVAKVGDKIVGFIVC T0374 68 :YQWQHGD 1wwzA 76 :WFSKYEG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1wwzA 85 :VGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKY T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1wwzA 118 :NDTIELWVGEKNYGAMNLYEKFGFKKVGKSGI T0374 151 :LIQMDKP 1wwzA 150 :WVRMIKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=197 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 1wwzA/T0374-1wwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1wwzA/T0374-1wwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwzA read from 1wwzA/T0374-1wwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwzA in template set T0374 2 :QLSHRPAE 1wwzA 3 :EIKIEKLK T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1wwzA 14 :KKALNELIDVYMSGYEGLEEYGGEGRDYARNYIKWC T0374 46 :IAE 1wwzA 53 :ASD T0374 51 :GSTVAVHDGQVLGFANFYQ 1wwzA 56 :GFFVAKVGDKIVGFIVCDK T0374 70 :WQHGD 1wwzA 78 :SKYEG T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKA 1wwzA 85 :VGAIHEFVVDKKFQGKGIGRKLLITCLDFLGKYNDT T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERH 1wwzA 121 :IELWVGEKNYGAMNLYEKFGFKKVGKSGIW Number of specific fragments extracted= 7 number of extra gaps= 0 total=204 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 1s3zA/T0374-1s3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s3zA expands to /projects/compbio/data/pdb/1s3z.pdb.gz 1s3zA:# T0374 read from 1s3zA/T0374-1s3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3zA read from 1s3zA/T0374-1s3zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s3zA to template set # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLWP T0374 32 :KAIWPFSVAQLAAAI 1s3zA 24 :GHPDDAHLADGEEIL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1s3zA 40 :ADHLASFIAMADGVAIGFADASIRHD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1s3zA 73 :SPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s3zA 108 :GCREMASDTSPENTISQKVHQALGFEETERVIFY T0374 155 :DKP 1s3zA 142 :RKR Number of specific fragments extracted= 6 number of extra gaps= 0 total=210 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 1s3zA/T0374-1s3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1s3zA/T0374-1s3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3zA read from 1s3zA/T0374-1s3zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDR 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQL T0374 34 :IWPFSVAQLAAAIA 1s3zA 22 :WPGHPDDAHLADGE T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHG 1s3zA 41 :DHLASFIAMADGVAIGFADASIRHDY T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1s3zA 75 :VVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNK T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s3zA 108 :GCREMASDTSPENTISQKVHQALGFEETERVIFY Number of specific fragments extracted= 5 number of extra gaps= 0 total=215 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 1s3zA/T0374-1s3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1s3zA/T0374-1s3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3zA read from 1s3zA/T0374-1s3zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3zA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRD 1s3zA 0 :HMDIRQMNKTHLEHWRGLRKQLW T0374 32 :KAIWPFSVAQ 1s3zA 23 :PGHPDDAHLA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 1s3zA 35 :EEILQADHLASFIAMADGVAIGFADASI T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1s3zA 70 :CDSSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCRE T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1s3zA 112 :MASDTSPENTISQKVHQALGFEETERVIFYRK Number of specific fragments extracted= 5 number of extra gaps= 0 total=220 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 1gheA/T0374-1gheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gheA expands to /projects/compbio/data/pdb/1ghe.pdb.gz 1gheA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1gheA/T0374-1gheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gheA read from 1gheA/T0374-1gheA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gheA to template set # found chain 1gheA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 Warning: unaligning (T0374)L158 because last residue in template chain is (1gheA)L173 T0374 4 :SHRPAETGDLET 1gheA 5 :QLRRVTAESFAH T0374 16 :VAGFPQDRDE 1gheA 21 :LAQLLFETVH T0374 29 :CYPKAIWPFSVAQLAAAI 1gheA 37 :FMADLDMQQAYAWCDGLK T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1gheA 59 :AGSLLLWVVAEDDNVLASAQLSLCQK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1gheA 88 :LNRAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKH T0374 109 :KARLMKISCFNANA 1gheA 123 :KRGLLHLDTEAGSV T0374 124 :GLLLYTQLGYQPRAIAERH 1gheA 137 :AEAFYSALAYTRVGELPGY T0374 143 :DPDGRRVALIQMDKP 1gheA 158 :TPDGRLHPTAIYFKT Number of specific fragments extracted= 8 number of extra gaps= 0 total=228 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 1gheA/T0374-1gheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1gheA/T0374-1gheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gheA read from 1gheA/T0374-1gheA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gheA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 Warning: unaligning (T0374)L158 because last residue in template chain is (1gheA)L173 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1gheA 5 :QLRRVTAESFAHYRHGLAQLLFETV T0374 29 :CYPKAIWPFSVAQLAAAIA 1gheA 33 :ASVGFMADLDMQQAYAWCD T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1gheA 60 :GSLLLWVVAEDDNVLASAQLSLCQKPN T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1gheA 90 :RAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKH T0374 109 :KARLMKISCFNAN 1gheA 123 :KRGLLHLDTEAGS T0374 123 :AGLLLYTQLGYQPRAIAERHD 1gheA 136 :VAEAFYSALAYTRVGELPGYC T0374 144 :PDGRRVALIQMDKP 1gheA 159 :PDGRLHPTAIYFKT Number of specific fragments extracted= 7 number of extra gaps= 0 total=235 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 1gheA/T0374-1gheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1gheA/T0374-1gheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gheA read from 1gheA/T0374-1gheA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gheA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1gheA)A4 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCY 1gheA 5 :QLRRVTAESFAHYRHGLAQLLFETVHG T0374 31 :PKAIWPFSVAQLAA 1gheA 37 :FMADLDMQQAYAWC T0374 46 :IAERRGSTVAVHDGQVLGFANFYQWQHGD 1gheA 58 :AAGSLLLWVVAEDDNVLASAQLSLCQKPN T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1gheA 90 :RAEVQKLMVLPSARGRGLGRQLMDEVEQVAVKHKRGL T0374 113 :MKISCFNANAA 1gheA 127 :LHLDTEAGSVA T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1gheA 138 :EAFYSALAYTRVGELPGYCATPD Number of specific fragments extracted= 6 number of extra gaps= 0 total=241 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 1yr0A/T0374-1yr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yr0A expands to /projects/compbio/data/pdb/1yr0.pdb.gz 1yr0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yr0A/T0374-1yr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yr0A read from 1yr0A/T0374-1yr0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yr0A to template set # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 Warning: unaligning (T0374)L158 because last residue in template chain is (1yr0A)L166 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQH 1yr0A 34 :NEVVVDLENRKDWFAARTSRGFPVIVAILDGKVAGYASYGDWRA T0374 73 :GDFCAL 1yr0A 82 :RHTREH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 1yr0A 88 :SVYVHKDARGHGIGKRLMQALIDHAGGN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yr0A 116 :DVHVLIAAIEAENTASIRLHESLGFRVVGRFSEV T0374 143 :DPDGRRVALIQMDKP 1yr0A 151 :TKFGRWLDLTCMELK Number of specific fragments extracted= 6 number of extra gaps= 0 total=247 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 1yr0A/T0374-1yr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yr0A/T0374-1yr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yr0A read from 1yr0A/T0374-1yr0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 Warning: unaligning (T0374)L158 because last residue in template chain is (1yr0A)L166 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTTAIWN T0374 34 :IWPFSVAQLAAAIA 1yr0A 35 :EVVVDLENRKDWFA T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1yr0A 53 :RGFPVIVAILDGKVAGYASYGDWRAFD T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yr0A 83 :HTREHSVYVHKDARGHGIGKRLMQALIDHAGGN T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1yr0A 116 :DVHVLIAAIEAENTASIRLHESLGFRVVG T0374 138 :IAERHDPDGRRVALIQMDKP 1yr0A 146 :FSEVGTKFGRWLDLTCMELK Number of specific fragments extracted= 6 number of extra gaps= 0 total=253 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 1yr0A/T0374-1yr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yr0A/T0374-1yr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yr0A read from 1yr0A/T0374-1yr0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yr0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yr0A)S4 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 1yr0A 5 :VELRDATVDDLSGIMEIYNDAVVNTTAIWNEVVVDLENR T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 1yr0A 47 :FAARTSRGFPVIVAILDGKVAGYASYGDWRAFD T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yr0A 83 :HTREHSVYVHKDARGHGIGKRLMQALIDHAGGNDVHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 1yr0A 120 :LIAAIEAENTASIRLHESLGFRVVGRFSEVGTKFGRWLDLTCM Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 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 2b5gA/T0374-2b5gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b5gA expands to /projects/compbio/data/pdb/2b5g.pdb.gz 2b5gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2b5gA/T0374-2b5gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b5gA read from 2b5gA/T0374-2b5gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b5gA to template set # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 32 :KAIWP 2b5gA 33 :QVILT T0374 39 :VAQLAAAI 2b5gA 38 :EKDLLEDG T0374 47 :AERRGSTVAV 2b5gA 49 :HPFYHCLVAE T0374 58 :DG 2b5gA 66 :PE T0374 60 :QVLGFANFYQWQH 2b5gA 70 :SIVGFAMYYFTYD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2b5gA 86 :GKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRC T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2b5gA 121 :RCSSMHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 8 number of extra gaps= 1 total=265 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 2b5gA/T0374-2b5gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2b5gA/T0374-2b5gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b5gA read from 2b5gA/T0374-2b5gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 34 :IWPFSVAQLAAAIA 2b5gA 33 :QVILTEKDLLEDGF T0374 48 :ERRGSTVAVH 2b5gA 50 :PFYHCLVAEV T0374 58 :DG 2b5gA 66 :PE T0374 60 :QVLGFANFYQWQHGD 2b5gA 70 :SIVGFAMYYFTYDPW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2b5gA 88 :LLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRC T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQP 2b5gA 121 :RCSSMHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 7 number of extra gaps= 1 total=272 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 2b5gA/T0374-2b5gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2b5gA/T0374-2b5gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b5gA read from 2b5gA/T0374-2b5gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b5gA in template set Warning: unaligning (T0374)L26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b5gA)E32 Warning: unaligning (T0374)F27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b5gA)E32 T0374 2 :QLSHRPAETGDLETVAGFPQDRDE 2b5gA 3 :KFVIRPATAADCSDILRLIKELAK T0374 32 :KAIWPFSVAQLAAA 2b5gA 33 :QVILTEKDLLEDGF T0374 46 :IAERRGSTVAVH 2b5gA 48 :EHPFYHCLVAEV T0374 58 :DGQVLGFANFYQWQHGD 2b5gA 68 :GHSIVGFAMYYFTYDPW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2b5gA 88 :LLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSS T0374 113 :MKISCFNANAAGLLLYTQLGYQP 2b5gA 125 :MHFLVAEWNEPSINFYKRRGASD Number of specific fragments extracted= 6 number of extra gaps= 1 total=278 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 1s7kA/T0374-1s7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s7kA expands to /projects/compbio/data/pdb/1s7k.pdb.gz 1s7kA:# T0374 read from 1s7kA/T0374-1s7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s7kA read from 1s7kA/T0374-1s7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s7kA to template set # found chain 1s7kA in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 3 :LSHRPAETGDLETVAGFPQD 1s7kA 11 :LELRAADESHVPALHQLVLK T0374 39 :VAQLAAAI 1s7kA 52 :RKHVQGNI T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1s7kA 64 :RGYAKMYLIFCQNEMAGVLSFNAIEP T0374 73 :GDFCAL 1s7kA 91 :NKAAYI T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1s7kA 97 :GYWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEGCMKQA T0374 143 :DPDGRRVALIQMDKPLEP 1s7kA 161 :YLNGDYHDVNMYARIIDA Number of specific fragments extracted= 6 number of extra gaps= 0 total=284 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 1s7kA/T0374-1s7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1s7kA/T0374-1s7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s7kA read from 1s7kA/T0374-1s7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s7kA in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 3 :LSHRPAETGDLETVAGFPQD 1s7kA 11 :LELRAADESHVPALHQLVLK T0374 39 :VAQLAAAIA 1s7kA 52 :RKHVQGNIL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 1s7kA 65 :GYAKMYLIFCQNEMAGVLSFNAIEPINKAAYIGYWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEG T0374 138 :IAERHDPDGRRVALIQMDKPLEP 1s7kA 156 :MKQAEYLNGDYHDVNMYARIIDA Number of specific fragments extracted= 4 number of extra gaps= 0 total=288 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 1s7kA/T0374-1s7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1s7kA/T0374-1s7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s7kA read from 1s7kA/T0374-1s7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s7kA in template set Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7kA)T51 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7kA)T51 T0374 2 :QLSHRPAETGDLETVAGFPQD 1s7kA 10 :TLELRAADESHVPALHQLVLK T0374 35 :WPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQ 1s7kA 52 :RKHVQGNILLHQRGYAKMYLIFCQNEMAGVLSFNA T0374 70 :WQHGDFCALG 1s7kA 88 :EPINKAAYIG T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRV 1s7kA 98 :YWLDESFQGQGIMSQSLQALMTHYARRGDIRRFVIKCRVDNQASNAVARRNHFTLEGCMKQAEYLNGDY Number of specific fragments extracted= 4 number of extra gaps= 0 total=292 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 2fckA/T0374-2fckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fckA expands to /projects/compbio/data/pdb/2fck.pdb.gz 2fckA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 189, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 666, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 668, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 670, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 672, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 674, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 676, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 678, because occupancy 0.300 <= existing 0.700 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 680, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fckA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1043, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1045, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1047, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1049, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1051, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1053, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1055, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fckA Skipped atom 1199, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1201, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1203, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1205, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1207, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1209, because occupancy 0.300 <= existing 0.700 in 2fckA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1309, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2fckA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2fckA # T0374 read from 2fckA/T0374-2fckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fckA read from 2fckA/T0374-2fckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fckA to template set # found chain 2fckA in template set Warning: unaligning (T0374)A33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 Warning: unaligning (T0374)L158 because last residue in template chain is (2fckA)P178 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 34 :IWPFSVAQLAAAI 2fckA 47 :SQQEAEQFIQATR T0374 47 :AERRGSTVAVHDG 2fckA 64 :KAEAYGFGVFERQ T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQWQH 2fckA 87 :NEFYH T0374 73 :GDFCAL 2fckA 93 :FNMASL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 99 :GYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERH 2fckA 158 :APNR T0374 143 :DPDGRRVALIQMDKP 2fckA 163 :LYAGEPKAGIVFSLI Number of specific fragments extracted= 9 number of extra gaps= 2 total=301 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 2fckA/T0374-2fckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fckA/T0374-2fckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fckA read from 2fckA/T0374-2fckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fckA in template set Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fckA)F46 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 Warning: unaligning (T0374)L158 because last residue in template chain is (2fckA)P178 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 38 :SVAQLAAAIA 2fckA 47 :SQQEAEQFIQ T0374 48 :ERRGSTVAVHDG 2fckA 65 :AEAYGFGVFERQ T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 87 :NEFYHTFNMASLGYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERHDP 2fckA 158 :APNRFL T0374 145 :DGRRVALIQMDKP 2fckA 165 :AGEPKAGIVFSLI Number of specific fragments extracted= 7 number of extra gaps= 2 total=308 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 2fckA/T0374-2fckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fckA/T0374-2fckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fckA read from 2fckA/T0374-2fckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fckA in template set Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fckA)F46 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fckA)F46 Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)I86 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)I86 Warning: unaligning (T0374)A137 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fckA)L157 Warning: unaligning (T0374)I138 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fckA)L157 T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYP 2fckA 11 :RLQLRLITADEAEELVQCIRQSQTLHQWVD T0374 38 :SVAQLAAA 2fckA 47 :SQQEAEQF T0374 46 :IAERRGSTVAVHDG 2fckA 64 :KAEAYGFGVFERQT T0374 60 :QVLGFA 2fckA 79 :TLVGMV T0374 68 :YQ 2fckA 87 :NE T0374 70 :WQHGDFCAL 2fckA 90 :YHTFNMASL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPR 2fckA 99 :GYWIGDRYQRQGYGKEALTALILFCFERLELTRLEIVCDPENVPSQALALRCGANRE T0374 139 :AERHDPDG 2fckA 158 :APNRFLYA Number of specific fragments extracted= 8 number of extra gaps= 2 total=316 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 1yreA/T0374-1yreA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yreA expands to /projects/compbio/data/pdb/1yre.pdb.gz 1yreA:# T0374 read from 1yreA/T0374-1yreA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yreA read from 1yreA/T0374-1yreA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yreA to template set # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAI 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQYMDGPTRPDWYRQSLAEQ T0374 47 :AERRGSTVAVHDGQVLGFA 1yreA 65 :EGRALPLAVRLGVQLVGTT T0374 68 :YQWQH 1yreA 86 :AEFLP T0374 73 :GDFCALGN 1yreA 92 :LPACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREGVLRNH T0374 143 :DPDGRRVALIQMDKP 1yreA 164 :LAGGRLDDTFVYSIT Number of specific fragments extracted= 6 number of extra gaps= 2 total=322 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 1yreA/T0374-1yreA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yreA/T0374-1yreA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yreA read from 1yreA/T0374-1yreA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYC 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQY T0374 33 :AIWPFSVAQLAAAIA 1yreA 47 :MDGPTRPDWYRQSLA T0374 48 :ERRGSTVAVHDGQVLGFA 1yreA 66 :GRALPLAVRLGVQLVGTT T0374 68 :YQWQHGD 1yreA 86 :AEFLPAL T0374 75 :FCALGN 1yreA 94 :ACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREG T0374 138 :IAERHD 1yreA 158 :LRNHRR T0374 144 :PDGRRVALIQMDKP 1yreA 165 :AGGRLDDTFVYSIT Number of specific fragments extracted= 8 number of extra gaps= 2 total=330 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 1yreA/T0374-1yreA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yreA/T0374-1yreA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yreA read from 1yreA/T0374-1yreA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yreA in template set Warning: unaligning (T0374)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)F85 Warning: unaligning (T0374)F67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)F85 Warning: unaligning (T0374)M81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yreA)W101 Warning: unaligning (T0374)M82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yreA)W101 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1yreA 20 :LRLEPLVEADIPELVSLAEANREALQYMDGPTRPDWYRQSLAE T0374 46 :IAERRGSTVAVHDGQVLGFA 1yreA 64 :REGRALPLAVRLGVQLVGTT T0374 68 :YQ 1yreA 86 :AE T0374 70 :WQHGDFCALGN 1yreA 89 :LPALPACEIGW T0374 83 :VAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1yreA 102 :LDQAQHGSGLNRMIKYLMLKHAFDNLRMVRVQLSTAASNLRAQGAIDKLGAQREGVLRNHRR Number of specific fragments extracted= 5 number of extra gaps= 2 total=335 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 1qsmA/T0374-1qsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qsmA expands to /projects/compbio/data/pdb/1qsm.pdb.gz 1qsmA:# T0374 read from 1qsmA/T0374-1qsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsmA read from 1qsmA/T0374-1qsmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qsmA to template set # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFYE T0374 32 :KAIWPFSVAQLAAAI 1qsmA 35 :VSFPDDLDDFNFGRF T0374 47 :AERRGSTVAVHD 1qsmA 53 :NIKMWAAVAVES T0374 59 :GQVLGFANFYQWQH 1qsmA 67 :EKIIGMINFFNHMT T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsmA 85 :KDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsmA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsmA 144 :YKAPKILYKRKG Number of specific fragments extracted= 7 number of extra gaps= 0 total=342 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 1qsmA/T0374-1qsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qsmA/T0374-1qsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsmA read from 1qsmA/T0374-1qsmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELF 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFY T0374 34 :IWPFSVAQLAAAIA 1qsmA 34 :EVSFPDDLDDFNFG T0374 48 :ERRG 1qsmA 52 :PNIK T0374 52 :STVAVH 1qsmA 58 :AAVAVE T0374 58 :DGQVLGFANFYQWQHGD 1qsmA 66 :SEKIIGMINFFNHMTTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsmA 87 :KIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsmA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsmA 144 :YKAPKILYKRKG Number of specific fragments extracted= 8 number of extra gaps= 0 total=350 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 1qsmA/T0374-1qsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qsmA/T0374-1qsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsmA read from 1qsmA/T0374-1qsmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qsmA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVH 1qsmA 8 :NITVRFVTENDKEGWQRLWKSYQDFYEVSFPDDLDDFNFGRFLDPNIKMWAAVAVE T0374 58 :DGQVLGFANFYQ 1qsmA 66 :SEKIIGMINFFN T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qsmA 82 :WDFKDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKLGTPS T0374 113 :MKISCFNANAAGLLLYTQLG 1qsmA 124 :VYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIA 1qsmA 144 :YKAPKI T0374 142 :HDP 1qsmA 150 :LYK Number of specific fragments extracted= 6 number of extra gaps= 0 total=356 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 1i12A/T0374-1i12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i12A expands to /projects/compbio/data/pdb/1i12.pdb.gz 1i12A:Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 1i12A Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 1i12A # T0374 read from 1i12A/T0374-1i12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i12A read from 1i12A/T0374-1i12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i12A to template set # found chain 1i12A in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i12A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAAI 1i12A 29 :TVGTITPESFCKLIKYWN T0374 47 :A 1i12A 60 :M T0374 49 :RRGSTVAVHD 1i12A 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQH 1i12A 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i12A 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i12A 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAI 1i12A 142 :FYEKCGFSNAGV T0374 153 :QMDKP 1i12A 154 :EMQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=365 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 1i12A/T0374-1i12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i12A/T0374-1i12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i12A read from 1i12A/T0374-1i12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i12A in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i12A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i12A 29 :TVGTITPESFCKLIK T0374 48 :ERRGSTVAVH 1i12A 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQHG 1i12A 73 :ETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i12A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i12A 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i12A 140 :VKFYEKCGFSNAG T0374 138 :I 1i12A 154 :E T0374 154 :MDKP 1i12A 155 :MQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=374 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 1i12A/T0374-1i12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i12A/T0374-1i12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i12A read from 1i12A/T0374-1i12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i12A in template set Warning: unaligning (T0374)P144 because last residue in template chain is (1i12A)K159 T0374 3 :LSHRPAETGDLETVAGFPQDR 1i12A 7 :FYIRRMEEGDLEQVTETLKVL T0374 28 :YCYPKAIWPFSVAQLAA 1i12A 28 :TTVGTITPESFCKLIKY T0374 46 :IAERRGSTVAVHDGQVLGFANFYQWQHG 1i12A 60 :MQYNPMVIVDKRTETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i12A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i12A 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERHD 1i12A 140 :VKFYEKCGFSNAGVEMQIR Number of specific fragments extracted= 6 number of extra gaps= 0 total=380 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 2bl1A/T0374-2bl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bl1A expands to /projects/compbio/data/pdb/2bl1.pdb.gz 2bl1A:Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2bl1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1037, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2bl1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2bl1A/T0374-2bl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bl1A read from 2bl1A/T0374-2bl1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bl1A to template set # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFY 2bl1A 15 :GILAIYNDAVGNTT T0374 29 :CYPKAIWPFSVAQLAAAIAERRGSTVAVHD 2bl1A 32 :NETPVDLANRQAWFDARARQGYPILVASDA T0374 59 :GQVLGFANFYQWQH 2bl1A 63 :GEVLGYASYGDWRP T0374 73 :GDFCAL 2bl1A 81 :RGTVEH T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQ 2bl1A 87 :SVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 2bl1A 115 :GLHVMVAAIESGNAASIGLHRRLGFEISGQMPQV T0374 143 :DPDGRRVALIQMDKPLE 2bl1A 150 :QKFGRWLDLTFMQLNLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=388 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 2bl1A/T0374-2bl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2bl1A/T0374-2bl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bl1A read from 2bl1A/T0374-2bl1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFYCYPK 2bl1A 15 :GILAIYNDAVGNTTAIWN T0374 34 :IWPFSVAQLAAAIA 2bl1A 33 :ETPVDLANRQAWFD T0374 48 :ERRGSTVAVHD 2bl1A 51 :QGYPILVASDA T0374 59 :GQVLGFANFYQWQHGD 2bl1A 63 :GEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bl1A 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQ T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 2bl1A 115 :GLHVMVAAIESGNAASIGLHRRLGFEISG T0374 138 :IAERHDPDGRRVALIQMDKPLE 2bl1A 145 :MPQVGQKFGRWLDLTFMQLNLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=396 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 2bl1A/T0374-2bl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2bl1A/T0374-2bl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bl1A read from 2bl1A/T0374-2bl1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bl1A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bl1A)A3 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE in next template residue (2bl1A)P14 Warning: unaligning (T0374)E14 because of BadResidue code BAD_PEPTIDE at template residue (2bl1A)P14 T0374 4 :SHRPAETGD 2bl1A 4 :SIRDAGVAD T0374 15 :TVAGFPQDRDELFYCY 2bl1A 15 :GILAIYNDAVGNTTAI T0374 31 :PKAIWPFS 2bl1A 32 :NETPVDLA T0374 39 :VAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGD 2bl1A 43 :AWFDARARQGYPILVASDAAGEVLGYASYGDWRPFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2bl1A 82 :GTVEHSVYVRDDQRGKGLGVQLLQALIERARAQGLHV T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVALIQMD 2bl1A 119 :MVAAIESGNAASIGLHRRLGFEISGQMPQVGQKFGRWLDLTFM Number of specific fragments extracted= 6 number of extra gaps= 1 total=402 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 2fl4A/T0374-2fl4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fl4A expands to /projects/compbio/data/pdb/2fl4.pdb.gz 2fl4A:# T0374 read from 2fl4A/T0374-2fl4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl4A read from 2fl4A/T0374-2fl4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fl4A to template set # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)Q71 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)G73 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 Warning: unaligning (T0374)E159 because last residue in template chain is (2fl4A)Q146 T0374 1 :MQLSHRPAETGDLETVAGFP 2fl4A 1 :MEIHFEKVTSDNRKAVENLQ T0374 31 :PKAIWPFSVAQLAAAI 2fl4A 21 :VFAEQQAFIESMAENL T0374 47 :AERRGSTVA 2fl4A 42 :FPEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 2fl4A 68 :GRVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNG T0374 141 :RHDPDGR 2fl4A 132 :ELDTNGE T0374 152 :IQMDKPL 2fl4A 139 :RVMEWTH Number of specific fragments extracted= 7 number of extra gaps= 2 total=409 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 2fl4A/T0374-2fl4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fl4A/T0374-2fl4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl4A read from 2fl4A/T0374-2fl4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)Q71 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)H72 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 Warning: unaligning (T0374)E159 because last residue in template chain is (2fl4A)Q146 T0374 1 :MQLSHRPAETGDLE 2fl4A 1 :MEIHFEKVTSDNRK T0374 25 :ELFYCYPKAIWPFSVAQLAAAIA 2fl4A 15 :AVENLQVFAEQQAFIESMAENLK T0374 48 :ERRGSTVA 2fl4A 43 :PEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 73 :G 2fl4A 68 :G T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRA 2fl4A 69 :RVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNG T0374 141 :RHDPDGR 2fl4A 132 :ELDTNGE T0374 152 :IQMDKPL 2fl4A 139 :RVMEWTH Number of specific fragments extracted= 8 number of extra gaps= 2 total=417 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 2fl4A/T0374-2fl4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fl4A/T0374-2fl4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fl4A read from 2fl4A/T0374-2fl4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fl4A in template set Warning: unaligning (T0374)V56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fl4A)D52 Warning: unaligning (T0374)H57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fl4A)D52 Warning: unaligning (T0374)H72 because of BadResidue code BAD_PEPTIDE in next template residue (2fl4A)D67 Warning: unaligning (T0374)G73 because of BadResidue code BAD_PEPTIDE at template residue (2fl4A)D67 T0374 1 :MQLSHRPAETGDLET 2fl4A 1 :MEIHFEKVTSDNRKA T0374 25 :ELFYCYPKAIWPFSVAQLAA 2fl4A 16 :VENLQVFAEQQAFIESMAEN T0374 45 :AIAERRGSTVA 2fl4A 40 :DQFPEWESAGI T0374 58 :DGQVLGFANFYQW 2fl4A 53 :GNQLIGYAMYGRW T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIA 2fl4A 68 :GRVWLDRFLIDQRFQGQGYGKAACRLLMLKLIEKYQTNKLYLSVYDTNSSAIRLYQQLGFVFNGEL T0374 143 :DPDGR 2fl4A 134 :DTNGE Number of specific fragments extracted= 6 number of extra gaps= 2 total=423 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 1on0A/T0374-1on0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1on0A expands to /projects/compbio/data/pdb/1on0.pdb.gz 1on0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1on0A/T0374-1on0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on0A read from 1on0A/T0374-1on0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1on0A to template set # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWP 1on0A 33 :TWLPEDAQ T0374 37 :FSVAQLAAAI 1on0A 42 :LSKQVFTDLL T0374 47 :AERRGSTVAVHD 1on0A 57 :TPHHHLWSLKLN T0374 59 :GQVLGFANFYQWQH 1on0A 70 :KDIVGWLWIHAEPE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1on0A 86 :QQEAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAE 1on0A 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDVVM Number of specific fragments extracted= 7 number of extra gaps= 0 total=430 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 1on0A/T0374-1on0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1on0A/T0374-1on0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on0A read from 1on0A/T0374-1on0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVKAGTWLPEDA T0374 40 :AQLAAAIA 1on0A 45 :QVFTDLLP T0374 48 :ERRGSTVAVHD 1on0A 58 :PHHHLWSLKLN T0374 59 :GQVLGFANFYQWQHGD 1on0A 70 :KDIVGWLWIHAEPEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1on0A 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1on0A 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETD T0374 138 :IA 1on0A 151 :VM Number of specific fragments extracted= 7 number of extra gaps= 0 total=437 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 1on0A/T0374-1on0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1on0A/T0374-1on0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on0A read from 1on0A/T0374-1on0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on0A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1on0A)T2 Warning: unaligning (T0374)D145 because last residue in template chain is (1on0A)L157 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1on0A 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVK T0374 31 :PKAIWPFSVAQ 1on0A 35 :LPEDAQLLSKQ T0374 42 :LAA 1on0A 47 :FTD T0374 46 :IAERRGSTVAVH 1on0A 56 :ETPHHHLWSLKL T0374 58 :DGQVLGFANFYQ 1on0A 69 :EKDIVGWLWIHA T0374 72 :HGD 1on0A 83 :EHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1on0A 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSMGIRK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHDP 1on0A 125 :LSLHVFAHNQTARKLYEQTGFQETDVVMSKKL Number of specific fragments extracted= 8 number of extra gaps= 0 total=445 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 1vkcA/T0374-1vkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vkcA expands to /projects/compbio/data/pdb/1vkc.pdb.gz 1vkcA:Skipped atom 421, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 423, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 425, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 427, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 429, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 431, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 988, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 990, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 992, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 1137, because occupancy 0.350 <= existing 0.650 in 1vkcA Skipped atom 1139, because occupancy 0.350 <= existing 0.650 in 1vkcA # T0374 read from 1vkcA/T0374-1vkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkcA read from 1vkcA/T0374-1vkcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vkcA to template set # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)L112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDELF 1vkcA 9 :EEYIEEIKKLDREISYSF T0374 29 :CYPKAIWPFSVAQLAAAI 1vkcA 27 :VRFPISYEEYEERHEELF T0374 47 :AERRGSTVAVHD 1vkcA 50 :QGEHKFFVALNE T0374 59 :GQVLGFANFYQWQH 1vkcA 63 :SELLGHVWICITLD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vkcA 81 :VKIAYIYDIEVVKWARGLGIGSALLRKAEEWAKER T0374 109 :KAR 1vkcA 116 :GAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANA 1vkcA 127 :DNP T0374 124 :GLLLYTQLGYQPR 1vkcA 130 :AVKWYEERGYKAR Number of specific fragments extracted= 10 number of extra gaps= 2 total=455 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 1vkcA/T0374-1vkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1vkcA/T0374-1vkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkcA read from 1vkcA/T0374-1vkcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)L112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDELF 1vkcA 9 :EEYIEEIKKLDREISYSF T0374 33 :AIWPFSVAQLAAAIA 1vkcA 27 :VRFPISYEEYEERHE T0374 48 :ERRGSTVAVHDG 1vkcA 51 :GEHKFFVALNER T0374 60 :QVLGFANFYQWQHGD 1vkcA 64 :ELLGHVWICITLDTV T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1vkcA 83 :IAYIYDIEVVKWARGLGIGSALLRKAEEWAKER T0374 109 :KAR 1vkcA 116 :GAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANAA 1vkcA 127 :DNPA T0374 125 :LLLYTQLGYQPRAIA 1vkcA 131 :VKWYEERGYKARALI Number of specific fragments extracted= 10 number of extra gaps= 2 total=465 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 1vkcA/T0374-1vkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1vkcA/T0374-1vkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vkcA read from 1vkcA/T0374-1vkcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vkcA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1vkcA)E2 Warning: unaligning (T0374)R111 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I120 Warning: unaligning (T0374)M113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I120 Warning: unaligning (T0374)F118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vkcA)I126 Warning: unaligning (T0374)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vkcA)I126 T0374 3 :LSHRPA 1vkcA 3 :YTIVDG T0374 10 :TGDLETVAGFPQDRDE 1vkcA 9 :EEYIEEIKKLDREISY T0374 28 :YCYPKAIWPFSVAQ 1vkcA 25 :SFVRFPISYEEYEE T0374 42 :LAAAIAERRGSTVAVHDG 1vkcA 45 :ESLLSQGEHKFFVALNER T0374 60 :QVLGFANFYQWQHGD 1vkcA 64 :ELLGHVWICITLDTV T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKA 1vkcA 83 :IAYIYDIEVVKWARGLGIGSALLRKAEEWAKERGAK T0374 114 :KISC 1vkcA 121 :VLRV T0374 120 :ANAA 1vkcA 127 :DNPA T0374 125 :LLLYTQLGYQPRAIAER 1vkcA 131 :VKWYEERGYKARALIME Number of specific fragments extracted= 9 number of extra gaps= 2 total=474 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 1mk4A/T0374-1mk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mk4A expands to /projects/compbio/data/pdb/1mk4.pdb.gz 1mk4A:# T0374 read from 1mk4A/T0374-1mk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mk4A read from 1mk4A/T0374-1mk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mk4A to template set # found chain 1mk4A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1mk4A)H0 Warning: unaligning (T0374)L158 because last residue in template chain is (1mk4A)I156 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRLFFE T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1mk4A 38 :HFQDTSFITSEHNSMTGFLIGFQSQS T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1mk4A 65 :PETAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPR 1mk4A 100 :GCTRVKCVTSPVNKVSIAYHTKLGFDIE T0374 137 :AIA 1mk4A 131 :KTV T0374 140 :ERH 1mk4A 137 :SVF T0374 143 :DPDG 1mk4A 143 :DGPG T0374 149 :VALIQMDKP 1mk4A 147 :QDRVLFVKN Number of specific fragments extracted= 8 number of extra gaps= 0 total=482 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 1mk4A/T0374-1mk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1mk4A/T0374-1mk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mk4A read from 1mk4A/T0374-1mk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mk4A in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1mk4A)I156 T0374 3 :LSHRPAETGDLETVAGFPQD 1mk4A 1 :MDIRTITSSDYEMVTSVLNE T0374 29 :CYPK 1mk4A 21 :WWGG T0374 33 :AIWPFSVAQLAAA 1mk4A 27 :LKEKLPRLFFEHF T0374 49 :RRGSTVAVHDGQVLGFANFYQWQHGD 1mk4A 40 :QDTSFITSEHNSMTGFLIGFQSQSDP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1mk4A 67 :TAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRA 1mk4A 100 :GCTRVKCVTSPVNKVSIAYHTKLGFDIEK T0374 138 :IAER 1mk4A 130 :TKTV T0374 142 :HDPDGR 1mk4A 142 :YDGPGQ T0374 150 :ALIQMDKP 1mk4A 148 :DRVLFVKN Number of specific fragments extracted= 9 number of extra gaps= 0 total=491 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 1mk4A/T0374-1mk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1mk4A/T0374-1mk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mk4A read from 1mk4A/T0374-1mk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mk4A in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1mk4A 1 :MDIRTITSSDYEMVTSVLNEWW T0374 29 :CYPKAIWPFSVAQLAAAIAE 1mk4A 23 :GGRQLKEKLPRLFFEHFQDT T0374 52 :STVAVHDGQVLGFANFYQWQHGD 1mk4A 43 :SFITSEHNSMTGFLIGFQSQSDP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1mk4A 67 :TAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQRGCTR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRA 1mk4A 104 :VKCVTSPVNKVSIAYHTKLGFDIEK T0374 138 :IAERHDPDGRRVA 1mk4A 138 :VFANYDGPGQDRV Number of specific fragments extracted= 6 number of extra gaps= 0 total=497 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 1cjwA/T0374-1cjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cjwA expands to /projects/compbio/data/pdb/1cjw.pdb.gz 1cjwA:# T0374 read from 1cjwA/T0374-1cjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjwA read from 1cjwA/T0374-1cjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cjwA to template set # found chain 1cjwA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1cjwA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVSGNCPLNLDEVQHFLTLC T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1cjwA 78 :PELSLGWFVEGRLVAFIIGSLWDE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNA 1cjwA 116 :GHSAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDA T0374 124 :GLLLYTQLGYQPRAIAERHDPD 1cjwA 164 :LVPFYQRFGFHPAGPCAIVVGS T0374 149 :VALIQMDKP 1cjwA 186 :LTFTEMHCS Number of specific fragments extracted= 5 number of extra gaps= 0 total=502 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 1cjwA/T0374-1cjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1cjwA/T0374-1cjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjwA read from 1cjwA/T0374-1cjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjwA in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 33 :AIWPFSVAQLAAAIA 1cjwA 61 :GNCPLNLDEVQHFLT T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1cjwA 77 :CPELSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1cjwA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVA 1cjwA 165 :VPFYQRFGFHPAGPCAIVVGSLTFTE T0374 152 :IQM 1cjwA 191 :MHC Number of specific fragments extracted= 6 number of extra gaps= 0 total=508 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 1cjwA/T0374-1cjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1cjwA/T0374-1cjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cjwA read from 1cjwA/T0374-1cjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cjwA in template set T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1cjwA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 31 :PKAIWPFSVAQLAAAIAER 1cjwA 61 :GNCPLNLDEVQHFLTLCPE T0374 51 :GSTVAVHDGQVLGFANFYQWQHGD 1cjwA 80 :LSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1cjwA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHD 1cjwA 165 :VPFYQRFGFHPAGPCAIVV Number of specific fragments extracted= 5 number of extra gaps= 0 total=513 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 1n71A/T0374-1n71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n71A expands to /projects/compbio/data/pdb/1n71.pdb.gz 1n71A:# T0374 read from 1n71A/T0374-1n71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n71A read from 1n71A/T0374-1n71A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n71A to template set # found chain 1n71A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1n71A)M1 T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1n71A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1n71A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 1n71A 103 :GGITIYLGT T0374 118 :FNANA 1n71A 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 1n71A 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 1n71A 163 :GWD T0374 149 :VALIQMDKPL 1n71A 166 :KPDIWMAKTI T0374 159 :EP 1n71A 178 :RP Number of specific fragments extracted= 9 number of extra gaps= 0 total=522 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 1n71A/T0374-1n71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1n71A/T0374-1n71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n71A read from 1n71A/T0374-1n71A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n71A in template set T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 1n71A 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1n71A 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISCF 1n71A 103 :GGITIYLGTD T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1n71A 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 1n71A 167 :PDIWMAKTIIP Number of specific fragments extracted= 6 number of extra gaps= 0 total=528 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 1n71A/T0374-1n71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1n71A/T0374-1n71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n71A read from 1n71A/T0374-1n71A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n71A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1n71A)M1 T0374 4 :SHRPAETGD 1n71A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1n71A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1n71A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 1n71A 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 1n71A 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=533 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 2c27A/T0374-2c27A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c27A expands to /projects/compbio/data/pdb/2c27.pdb.gz 2c27A:# T0374 read from 2c27A/T0374-2c27A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c27A read from 2c27A/T0374-2c27A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c27A to template set # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 T0374 2 :QLSHRPAE 2c27A 151 :GVVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPKAI 2c27A 160 :TSDDAELLRVNNAAFAGHPEQGGWT T0374 39 :VAQLAAAI 2c27A 185 :AVQLAERR T0374 47 :AERRGSTVAVHD 2c27A 198 :DPDGLILAFGDS T0374 59 :GQVLGFANFYQWQH 2c27A 215 :GRLLGFHWTKVHPD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 230 :PGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 111 :RLMKISCFNANAAGLLLYTQLGYQPRAIAE 2c27A 277 :PAVLLYVESDNVAAVRTYQSLGFTTYSVDT T0374 153 :QMDK 2c27A 307 :AYAL Number of specific fragments extracted= 8 number of extra gaps= 0 total=541 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 2c27A/T0374-2c27A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2c27A/T0374-2c27A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c27A read from 2c27A/T0374-2c27A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 Warning: unaligning (T0374)K156 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c27A)G312 T0374 3 :LSHRPA 2c27A 152 :VVIRTY T0374 9 :ETGDLETVAGFPQDRDELFY 2c27A 159 :GTSDDAELLRVNNAAFAGHP T0374 33 :AIWPFSVAQLAAAIA 2c27A 179 :EQGGWTAVQLAERRG T0374 48 :ERRGSTVAVHD 2c27A 199 :PDGLILAFGDS T0374 59 :GQVLGFANFYQWQHGD 2c27A 215 :GRLLGFHWTKVHPDHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 232 :LGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 112 :LMKISCFNANAAGLLLYTQLGYQPRAI 2c27A 278 :AVLLYVESDNVAAVRTYQSLGFTTYSV T0374 150 :ALIQMD 2c27A 305 :DTAYAL Number of specific fragments extracted= 8 number of extra gaps= 1 total=549 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 2c27A/T0374-2c27A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2c27A/T0374-2c27A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c27A read from 2c27A/T0374-2c27A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c27A in template set Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c27A)K269 Warning: unaligning (T0374)D145 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c27A)G312 Warning: unaligning (T0374)G146 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c27A)G312 T0374 3 :LSHRPA 2c27A 152 :VVIRTY T0374 9 :ETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAA 2c27A 159 :GTSDDAELLRVNNAAFAGHPEQGGWTAVQLAERRGE T0374 45 :AIAERRGSTVAVHD 2c27A 196 :WFDPDGLILAFGDS T0374 59 :GQVLGFANFYQ 2c27A 215 :GRLLGFHWTKV T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2c27A 227 :PDHPGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDP 2c27A 275 :VEPAVLLYVESDNVAAVRTYQSLGFTTYSVDTAYAL Number of specific fragments extracted= 6 number of extra gaps= 1 total=555 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 1p0hA/T0374-1p0hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p0hA expands to /projects/compbio/data/pdb/1p0h.pdb.gz 1p0hA:Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 503, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1859, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1861, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1863, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1865, because occupancy 0.500 <= existing 0.500 in 1p0hA Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 1p0hA # T0374 read from 1p0hA/T0374-1p0hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p0hA read from 1p0hA/T0374-1p0hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p0hA to template set # found chain 1p0hA in template set Warning: unaligning (T0374)G59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 T0374 2 :QLSHRPAE 1p0hA 151 :GVVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPK 1p0hA 160 :TSDDAELLRVNNAAFAGHPEQGG T0374 37 :FSVAQLAAAI 1p0hA 183 :WTAVQLAERR T0374 47 :AERRGSTVAV 1p0hA 197 :FDPDGLILAF T0374 60 :QVLGFANFYQWQH 1p0hA 216 :RLLGFHWTKVHPD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 230 :PGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 110 :ARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1p0hA 276 :EPAVLLYVESDNVAAVRTYQSLGFTTYSVDTAY Number of specific fragments extracted= 7 number of extra gaps= 0 total=562 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 1p0hA/T0374-1p0hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1p0hA/T0374-1p0hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p0hA read from 1p0hA/T0374-1p0hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p0hA in template set Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 T0374 3 :LSHRPAE 1p0hA 152 :VVIRTYA T0374 10 :TGDLETVAGFPQDRDELF 1p0hA 160 :TSDDAELLRVNNAAFAGH T0374 32 :KAIWPFSVAQLAAAIA 1p0hA 178 :PEQGGWTAVQLAERRG T0374 52 :STVAVH 1p0hA 202 :LILAFG T0374 61 :VLGFANFYQWQHGD 1p0hA 217 :LLGFHWTKVHPDHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 232 :LGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 111 :RLMKISCFNANAAGLLLYTQLGYQPRAIAERHD 1p0hA 277 :PAVLLYVESDNVAAVRTYQSLGFTTYSVDTAYA Number of specific fragments extracted= 7 number of extra gaps= 0 total=569 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 1p0hA/T0374-1p0hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1p0hA/T0374-1p0hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p0hA read from 1p0hA/T0374-1p0hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p0hA in template set Warning: unaligning (T0374)D58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)G215 Warning: unaligning (T0374)G59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1p0hA)G215 Warning: unaligning (T0374)Y108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1p0hA)V275 Warning: unaligning (T0374)P144 because last residue in template chain is (1p0hA)L310 T0374 3 :LSHRPAE 1p0hA 152 :VVIRTYA T0374 10 :TGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVH 1p0hA 160 :TSDDAELLRVNNAAFAGHPEQGGWTAVQLAERRGEAWFDPDGLILAFG T0374 60 :QVLGFANFYQ 1p0hA 216 :RLLGFHWTKV T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1p0hA 227 :PDHPGLGEVYVLGVDPAAQRRGLGQMLTSIGIVSLARR T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERHD 1p0hA 279 :VLLYVESDNVAAVRTYQSLGFTTYSVDTAYA Number of specific fragments extracted= 5 number of extra gaps= 0 total=574 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 2bswA/T0374-2bswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bswA expands to /projects/compbio/data/pdb/2bsw.pdb.gz 2bswA:Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2bswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 867, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 2bswA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2bswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2bswA/T0374-2bswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bswA read from 2bswA/T0374-2bswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bswA to template set # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 Warning: unaligning (T0374)E159 because last residue in template chain is (2bswA)T146 T0374 4 :SHRPAETGD 2bswA 3 :EVKPINAED T0374 13 :LETVAGFPQDRDELFY 2bswA 13 :YELRHRILRPNQPIEA T0374 29 :CYPKAI 2bswA 30 :MFESDL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 2bswA 36 :LRGAFHLGGYYGGKLISIASFHQAEH T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bswA 67 :QKQYQLRGMATLEGYREQKAGSSLIKHAEEILRKR T0374 109 :KARLMK 2bswA 102 :GADLLW T0374 117 :CFNA 2bswA 110 :ARTS T0374 124 :GLLLYTQLGYQPRAIAER 2bswA 114 :ASGYYKKLGFSEQGEVFD T0374 143 :DPDGR 2bswA 132 :TPPVG T0374 150 :ALIQMDKPL 2bswA 137 :PHILMYKRI Number of specific fragments extracted= 10 number of extra gaps= 1 total=584 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 2bswA/T0374-2bswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2bswA/T0374-2bswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bswA read from 2bswA/T0374-2bswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 Warning: unaligning (T0374)E159 because last residue in template chain is (2bswA)T146 T0374 4 :SHRPAETGD 2bswA 3 :EVKPINAED T0374 13 :LETVAGFPQDR 2bswA 13 :YELRHRILRPN T0374 24 :DELFYCYPKAI 2bswA 25 :PIEACMFESDL T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 2bswA 37 :RGAFHLGGYYGGKLISIASFHQAEHSE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2bswA 69 :QYQLRGMATLEGYREQKAGSSLIKHAEEILRKR T0374 109 :KARLMK 2bswA 102 :GADLLW T0374 117 :CFNAN 2bswA 110 :ARTSA T0374 125 :LLLYTQLGYQPRA 2bswA 115 :SGYYKKLGFSEQG T0374 139 :AERHDPDGR 2bswA 128 :EVFDTPPVG T0374 150 :ALIQMDKPL 2bswA 137 :PHILMYKRI Number of specific fragments extracted= 10 number of extra gaps= 1 total=594 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 2bswA/T0374-2bswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2bswA/T0374-2bswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bswA read from 2bswA/T0374-2bswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bswA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2bswA)I2 Warning: unaligning (T0374)I115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bswA)N109 Warning: unaligning (T0374)S116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bswA)N109 T0374 4 :SHRPAETGDL 2bswA 3 :EVKPINAEDT T0374 14 :ETVAGFPQ 2bswA 14 :ELRHRILR T0374 28 :YCYPKAIWPFSV 2bswA 22 :PNQPIEACMFES T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 2bswA 34 :DLLRGAFHLGGYYGGKLISIASFHQ T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2bswA 64 :LQGQKQYQLRGMATLEGYREQKAGSSLIKHAEEILRKRGADL T0374 113 :MK 2bswA 106 :LW T0374 117 :CFNAN 2bswA 110 :ARTSA T0374 125 :LLLYTQLGYQPRAIAERHDPDG 2bswA 115 :SGYYKKLGFSEQGEVFDTPPVG Number of specific fragments extracted= 8 number of extra gaps= 1 total=602 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 1yx0A/T0374-1yx0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yx0A expands to /projects/compbio/data/pdb/1yx0.pdb.gz 1yx0A:# T0374 read from 1yx0A/T0374-1yx0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx0A read from 1yx0A/T0374-1yx0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yx0A to template set # found chain 1yx0A in template set T0374 1 :MQLSHRPAE 1yx0A 1 :MHIKIDDLT T0374 14 :ETVAGFPQDRDELFY 1yx0A 11 :RQVVSLVNEHLHSMT T0374 29 :CYPKAIWPF 1yx0A 27 :MSPPESIHA T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQ 1yx0A 43 :GPEITFWSAWEGDELAGCGALKELD T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yx0A 68 :TRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKR T0374 109 :KARLMKISC 1yx0A 103 :GYERLSLET T0374 118 :FNANAAGLLLYTQLGYQPRAIAERH 1yx0A 114 :MASFEPARKLYESFGFQYCEPFADY T0374 143 :DPDGRR 1yx0A 141 :DPNSVF T0374 150 :AL 1yx0A 147 :MT Number of specific fragments extracted= 9 number of extra gaps= 0 total=611 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 1yx0A/T0374-1yx0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yx0A/T0374-1yx0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx0A read from 1yx0A/T0374-1yx0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx0A in template set T0374 1 :MQLSHRPAE 1yx0A 1 :MHIKIDDLT T0374 14 :ETVAGFPQDRDELFY 1yx0A 11 :RQVVSLVNEHLHSMT T0374 29 :CYPKAIWPFSVAQL 1yx0A 28 :SPPESIHALGLEKL T0374 47 :A 1yx0A 42 :R T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHG 1yx0A 44 :PEITFWSAWEGDELAGCGALKELDTR T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yx0A 70 :HGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKR T0374 109 :KARLMKISC 1yx0A 103 :GYERLSLET T0374 118 :FNANAAGLLLYTQLGYQPRA 1yx0A 114 :MASFEPARKLYESFGFQYCE T0374 138 :IAERHD 1yx0A 135 :FADYGE T0374 144 :PDGRRVA 1yx0A 142 :PNSVFMT T0374 152 :I 1yx0A 149 :K Number of specific fragments extracted= 11 number of extra gaps= 0 total=622 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 1yx0A/T0374-1yx0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yx0A/T0374-1yx0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx0A read from 1yx0A/T0374-1yx0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx0A in template set T0374 14 :ETVAGFPQDRDELFYCYPKAIWPFS 1yx0A 11 :RQVVSLVNEHLHSMTLMSPPESIHA T0374 44 :AAIAERRGSTVAVHDGQVLGFANFYQW 1yx0A 40 :KLRGPEITFWSAWEGDELAGCGALKEL T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yx0A 67 :DTRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKRGYER T0374 113 :MKISCFN 1yx0A 107 :LSLETGS T0374 120 :ANAAGLLLYTQLGYQPRAIAERHDPDGRR 1yx0A 116 :SFEPARKLYESFGFQYCEPFADYGEDPNS Number of specific fragments extracted= 5 number of extra gaps= 0 total=627 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 1q2yA/T0374-1q2yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q2yA expands to /projects/compbio/data/pdb/1q2y.pdb.gz 1q2yA:# T0374 read from 1q2yA/T0374-1q2yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q2yA read from 1q2yA/T0374-1q2yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q2yA to template set # found chain 1q2yA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1q2yA)M1 Warning: unaligning (T0374)P157 because last residue in template chain is (1q2yA)D140 T0374 4 :SHRPAE 1q2yA 2 :KAVIAK T0374 10 :TGDLETVAGFPQDRDELFY 1q2yA 9 :EEQLKDAFYVREEVFVKEQ T0374 29 :CYPKA 1q2yA 29 :VPAEE T0374 34 :IWPF 1q2yA 35 :IDEL T0374 47 :AERRGSTVAVHDGQVLGFANFYQW 1q2yA 39 :ENESEHIVVYDGEKPVGAGRWRMK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1q2yA 63 :DGYGKLERICVLKSHRSAGVGGIIMKALEKAAADG T0374 109 :KARLMKISCFNA 1q2yA 98 :GASGFILNAQTQ T0374 124 :GLLLYTQLGYQP 1q2yA 110 :AVPFYKKHGYRV T0374 136 :RAIAERH 1q2yA 124 :EKEFLDA T0374 149 :VALIQMDK 1q2yA 132 :IPHLQMMK Number of specific fragments extracted= 10 number of extra gaps= 0 total=637 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 1q2yA/T0374-1q2yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1q2yA/T0374-1q2yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q2yA read from 1q2yA/T0374-1q2yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q2yA in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1q2yA)D140 T0374 1 :MQ 1q2yA 1 :MK T0374 5 :HRPAE 1q2yA 3 :AVIAK T0374 10 :TGDLETVAGFPQDRDELFY 1q2yA 9 :EEQLKDAFYVREEVFVKEQ T0374 29 :CYPKAIWP 1q2yA 29 :VPAEEEID T0374 48 :ERRGSTVAVHDGQVLGFANF 1q2yA 40 :NESEHIVVYDGEKPVGAGRW T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1q2yA 60 :RMKDGYGKLERICVLKSHRSAGVGGIIMKALEKAAADG T0374 109 :KARLMKISCFNA 1q2yA 98 :GASGFILNAQTQ T0374 124 :GLLLYTQLGYQPRAIAERHDP 1q2yA 110 :AVPFYKKHGYRVLSEKEFLDA T0374 148 :RVALIQMDK 1q2yA 131 :GIPHLQMMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=646 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 1q2yA/T0374-1q2yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1q2yA/T0374-1q2yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q2yA read from 1q2yA/T0374-1q2yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q2yA in template set T0374 9 :ETGDLETVAGFPQDRDELFYCYPKAIWPFSV 1q2yA 8 :NEEQLKDAFYVREEVFVKEQNVPAEEEIDEL T0374 47 :AERRGSTVAVHDGQVLGFANFYQ 1q2yA 39 :ENESEHIVVYDGEKPVGAGRWRM T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1q2yA 62 :KDGYGKLERICVLKSHRSAGVGGIIMKALEKAAADGGASG T0374 113 :MKISCFNA 1q2yA 102 :FILNAQTQ T0374 124 :GLLLYTQLGYQPRAI 1q2yA 110 :AVPFYKKHGYRVLSE Number of specific fragments extracted= 5 number of extra gaps= 0 total=651 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 1nslA/T0374-1nslA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nslA expands to /projects/compbio/data/pdb/1nsl.pdb.gz 1nslA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1nslA/T0374-1nslA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nslA read from 1nslA/T0374-1nslA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nslA to template set # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 3 :LSHRPAETG 1nslA 10 :ITIRLLEPK T0374 14 :ETVAGFPQDRDELFY 1nslA 21 :ERLAELIIQNQQRLG T0374 31 :P 1nslA 39 :F T0374 32 :KAIWPFSVAQLAAAI 1nslA 48 :DTYRETIIPDWRRQY T0374 47 :A 1nslA 64 :D T0374 50 :RGSTVAVHDGQVLGFANFYQWQH 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQ T0374 73 :GDFCAL 1nslA 91 :NRKAEI T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 97 :GYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRAIAERH 1nslA 148 :IGFLEEGKARDG T0374 143 :DPDGRRVALIQMDKP 1nslA 161 :YVNGMHHDLVYYSLL Number of specific fragments extracted= 11 number of extra gaps= 4 total=662 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 1nslA/T0374-1nslA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1nslA/T0374-1nslA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nslA read from 1nslA/T0374-1nslA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)K32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nslA)S45 Warning: unaligning (T0374)F37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nslA)S45 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 3 :LSHRPAETG 1nslA 10 :ITIRLLEPK T0374 14 :ETVAGFPQDRDELFY 1nslA 21 :ERLAELIIQNQQRLG T0374 29 :CYP 1nslA 37 :WLF T0374 38 :SVAQLA 1nslA 46 :SADTYR T0374 44 :AAIA 1nslA 57 :DWRR T0374 50 :RGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRA 1nslA 148 :IGFLEEG T0374 138 :IAERHDPDGRRVALIQMDKP 1nslA 156 :ARDGLYVNGMHHDLVYYSLL Number of specific fragments extracted= 9 number of extra gaps= 4 total=671 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 1nslA/T0374-1nslA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1nslA/T0374-1nslA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nslA read from 1nslA/T0374-1nslA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nslA in template set Warning: unaligning (T0374)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A20 Warning: unaligning (T0374)L13 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A20 Warning: unaligning (T0374)E48 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)N66 Warning: unaligning (T0374)R49 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)N66 Warning: unaligning (T0374)M113 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)A131 Warning: unaligning (T0374)K114 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)A131 Warning: unaligning (T0374)T129 because of BadResidue code BAD_PEPTIDE in next template residue (1nslA)R147 Warning: unaligning (T0374)Q130 because of BadResidue code BAD_PEPTIDE at template residue (1nslA)R147 T0374 2 :QLSHRPAETG 1nslA 9 :HITIRLLEPK T0374 14 :ETVAGFPQDRDELFYCY 1nslA 21 :ERLAELIIQNQQRLGKW T0374 31 :PKAIWPFSVAQLAAAIA 1nslA 48 :DTYRETIIPDWRRQYAD T0374 50 :RGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARL 1nslA 67 :GIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNR T0374 115 :ISCFNANAAGLLLY 1nslA 132 :ICAAVGNEKSRAVP T0374 131 :LGYQPRAIAERHDP 1nslA 148 :IGFLEEGKARDGLY Number of specific fragments extracted= 6 number of extra gaps= 4 total=677 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 1qstA/T0374-1qstA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qstA expands to /projects/compbio/data/pdb/1qst.pdb.gz 1qstA:# T0374 read from 1qstA/T0374-1qstA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qstA read from 1qstA/T0374-1qstA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qstA to template set # found chain 1qstA in template set T0374 2 :QLSHRPAE 1qstA 50 :DFDILTND T0374 10 :TGD 1qstA 60 :HRN T0374 13 :LETVAGFPQ 1qstA 66 :LIDLKNIFS T0374 32 :KAIWPFSVAQLAAAI 1qstA 75 :RQLPKMPKEYIVKLV T0374 47 :AERRGSTVAVHD 1qstA 91 :DRHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQ T0374 109 :KARLMKISCFNA 1qstA 153 :NIEYLLTYADNF T0374 124 :GLLLYTQLGYQPRAIAE 1qstA 165 :AIGYFKKQGFTKEHRMP T0374 141 :RH 1qstA 187 :GY T0374 143 :DPDGRRVAL 1qstA 192 :YDGGTLMEC T0374 157 :P 1qstA 201 :Y Number of specific fragments extracted= 11 number of extra gaps= 0 total=688 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 1qstA/T0374-1qstA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qstA/T0374-1qstA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qstA read from 1qstA/T0374-1qstA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qstA in template set T0374 13 :LETVAGFPQD 1qstA 66 :LIDLKNIFSR T0374 33 :AIWPFSVAQLAAAIA 1qstA 76 :QLPKMPKEYIVKLVF T0374 48 :ERRGSTVAVHD 1qstA 92 :RHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQ T0374 109 :KARLMKISCFNAN 1qstA 153 :NIEYLLTYADNFA T0374 125 :LLLYTQLGYQPRA 1qstA 166 :IGYFKKQGFTKEH T0374 138 :IA 1qstA 180 :MP T0374 140 :ERHDP 1qstA 186 :KGYIK T0374 145 :DGRR 1qstA 193 :DGGT T0374 153 :QMDKPLE 1qstA 197 :LMECYIH Number of specific fragments extracted= 10 number of extra gaps= 0 total=698 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 1qstA/T0374-1qstA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qstA/T0374-1qstA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qstA read from 1qstA/T0374-1qstA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qstA in template set T0374 13 :LETVAGFPQDRDELF 1qstA 66 :LIDLKNIFSRQLPKM T0374 36 :P 1qstA 81 :P T0374 38 :SVAQLAAAIAERRGSTVAVHD 1qstA 82 :KEYIVKLVFDRHHESMVILKN T0374 59 :GQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qstA 104 :QKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQNIEY T0374 113 :MKISCFNAN 1qstA 157 :LLTYADNFA T0374 125 :LLLYTQLGYQPRAIAE 1qstA 166 :IGYFKKQGFTKEHRMP Number of specific fragments extracted= 6 number of extra gaps= 0 total=704 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 2fsrA/T0374-2fsrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fsrA expands to /projects/compbio/data/pdb/2fsr.pdb.gz 2fsrA:Skipped atom 26, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 28, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 138, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 140, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 142, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 144, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 146, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 148, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 150, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 154, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 333, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 444, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 897, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1061, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1063, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1065, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1067, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1069, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1071, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1284, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1286, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1288, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1290, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1292, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1294, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1296, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1379, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1381, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1383, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1385, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1387, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1389, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1391, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1393, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1395, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1457, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 2fsrA # T0374 read from 2fsrA/T0374-2fsrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fsrA read from 2fsrA/T0374-2fsrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fsrA to template set # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFY 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTGV T0374 29 :CYPKAIWPFSVAQLAAAI 2fsrA 41 :PYDLPSTWGVFCHDLANW T0374 47 :AERRGSTVAVHD 2fsrA 60 :FFGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFCAL 2fsrA 74 :GECIGQIGINHGPLFPEKEL T0374 80 :NMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRR 2fsrA 94 :GWLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAPRSDPEDLV T0374 152 :IQ 2fsrA 163 :YR Number of specific fragments extracted= 6 number of extra gaps= 0 total=710 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 2fsrA/T0374-2fsrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fsrA/T0374-2fsrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fsrA read from 2fsrA/T0374-2fsrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELF 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTG T0374 33 :AIWPFSVAQLAAAIA 2fsrA 38 :VGGPYDLPSTWGVFC T0374 48 :ERRGSTVAVHD 2fsrA 61 :FGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFC 2fsrA 74 :GECIGQIGINHGPLFPEK T0374 78 :LGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAERHDPDGRRVA 2fsrA 92 :ELGWLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAPRSDPEDLVYR T0374 155 :D 2fsrA 165 :Y Number of specific fragments extracted= 6 number of extra gaps= 0 total=716 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 2fsrA/T0374-2fsrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2fsrA/T0374-2fsrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fsrA read from 2fsrA/T0374-2fsrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fsrA in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQ 2fsrA 12 :RLTLRPLAMADFPAYRDFMASPRSTGVGGPYDLPSTWGVF T0374 42 :LAAAIAERRGSTVAVHD 2fsrA 55 :LANWHFFGHGALMIDLG T0374 59 :GQVLGFANFYQWQHGDFCALG 2fsrA 74 :GECIGQIGINHGPLFPEKELG T0374 81 :MMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNANAAGLLLYTQLGYQPRAIAE 2fsrA 95 :WLLYEGHEGRGYAAEAAVALRDWAFETLNLPTLVSYVSPQNRKSAAVAERIGGTLDPLAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=720 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 1u6mA/T0374-1u6mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u6mA expands to /projects/compbio/data/pdb/1u6m.pdb.gz 1u6mA:# T0374 read from 1u6mA/T0374-1u6mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6mA read from 1u6mA/T0374-1u6mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u6mA to template set # found chain 1u6mA in template set Warning: unaligning (T0374)D24 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)E25 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)L26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 Warning: unaligning (T0374)E159 because last residue in template chain is (1u6mA)E190 T0374 4 :SHRPAETGDLETVAGFPQDR 1u6mA 3 :LIRSATKEDGQAIARLVLVI T0374 27 :FY 1u6mA 26 :ME T0374 29 :CYPKAIWPFSVAQLAAAI 1u6mA 30 :ILEEVSEEQMIDLLAEAT T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1u6mA 54 :YGYQRILVYEHAGEVAGIAVGYPAED T0374 73 :GD 1u6mA 110 :PN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQ 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKAS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1u6mA 145 :GKQALGLNVDFDNPGARKLYASKGFKDVTTMTIS T0374 146 :G 1u6mA 179 :G T0374 149 :VALIQMDKPL 1u6mA 180 :HLYNHMQKEV Number of specific fragments extracted= 9 number of extra gaps= 2 total=729 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 1u6mA/T0374-1u6mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1u6mA/T0374-1u6mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6mA read from 1u6mA/T0374-1u6mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u6mA in template set Warning: unaligning (T0374)L26 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)F27 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)Y28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 Warning: unaligning (T0374)E159 because last residue in template chain is (1u6mA)E190 T0374 4 :SHRPAETGDLETVAGFPQ 1u6mA 3 :LIRSATKEDGQAIARLVL T0374 24 :DE 1u6mA 21 :VI T0374 29 :CYPKAIWPFSVAQLAAAIA 1u6mA 26 :MELPILEEVSEEQMIDLLA T0374 48 :ERRG 1u6mA 50 :PTYR T0374 52 :STVAVHDGQVLGFANF 1u6mA 59 :ILVYEHAGEVAGIAVG T0374 68 :YQWQHGD 1u6mA 105 :EEETLPN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQ 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKAS T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAER 1u6mA 145 :GKQALGLNVDFDNPGARKLYASKGFKDVTTMTI T0374 145 :DGRR 1u6mA 178 :SGHL T0374 151 :LIQMDKPL 1u6mA 182 :YNHMQKEV Number of specific fragments extracted= 10 number of extra gaps= 2 total=739 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 1u6mA/T0374-1u6mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1u6mA/T0374-1u6mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6mA read from 1u6mA/T0374-1u6mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u6mA in template set Warning: unaligning (T0374)D24 because of BadResidue code BAD_PEPTIDE in next template residue (1u6mA)K24 Warning: unaligning (T0374)E25 because of BadResidue code BAD_PEPTIDE at template residue (1u6mA)K24 Warning: unaligning (T0374)L26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)D25 Warning: unaligning (T0374)F75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1u6mA)W113 Warning: unaligning (T0374)C76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1u6mA)W113 T0374 4 :SHRPAETGDLETVAGFPQDR 1u6mA 3 :LIRSATKEDGQAIARLVLVI T0374 27 :FYCYPKAIWPFSVAQLAA 1u6mA 26 :MELPILEEVSEEQMIDLL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1u6mA 52 :YRYGYQRILVYEHAGEVAGIAVGYP T0374 70 :WQHGD 1u6mA 107 :ETLPN T0374 77 :ALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1u6mA 114 :YLDTISVDERFRGMGIGSKLLDALPEVAKASGKQA T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1u6mA 149 :LGLNVDFDNPGARKLYASKGFKDVTTMTI Number of specific fragments extracted= 6 number of extra gaps= 2 total=745 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 1z4rA/T0374-1z4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z4rA expands to /projects/compbio/data/pdb/1z4r.pdb.gz 1z4rA:# T0374 read from 1z4rA/T0374-1z4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4rA read from 1z4rA/T0374-1z4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z4rA to template set # found chain 1z4rA in template set T0374 9 :ETGDLETVAGFPQDRDELFYCYP 1z4rA 513 :NRRVLLWLVGLQNVFSHQLPRMP T0374 39 :VAQLAAAI 1z4rA 536 :KEYIARLV T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4rA 545 :DPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKH T0374 109 :KARLMKISCFNA 1z4rA 606 :NILYFLTYADEY T0374 124 :GLLLYTQLGYQPR 1z4rA 618 :AIGYFKKQGFSKD T0374 141 :RH 1z4rA 640 :GY T0374 143 :DPD 1z4rA 645 :YEG T0374 151 :LIQMDKPLEP 1z4rA 648 :ATLMECELNP Number of specific fragments extracted= 8 number of extra gaps= 0 total=753 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 1z4rA/T0374-1z4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1z4rA/T0374-1z4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4rA read from 1z4rA/T0374-1z4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z4rA in template set T0374 13 :LETVAGFPQDR 1z4rA 520 :LVGLQNVFSHQ T0374 34 :IWPFSVAQLAAAIA 1z4rA 531 :LPRMPKEYIARLVF T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1z4rA 546 :PKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKH T0374 109 :KARLMKISCFNA 1z4rA 606 :NILYFLTYADEY T0374 124 :GLLLYTQLGYQPR 1z4rA 618 :AIGYFKKQGFSKD T0374 137 :A 1z4rA 640 :G T0374 141 :RHD 1z4rA 641 :YIK T0374 145 :DGR 1z4rA 646 :EGA T0374 152 :IQMDKPLEP 1z4rA 649 :TLMECELNP Number of specific fragments extracted= 9 number of extra gaps= 0 total=762 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 1z4rA/T0374-1z4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1z4rA/T0374-1z4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z4rA read from 1z4rA/T0374-1z4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z4rA in template set T0374 13 :LETVAGFPQDRDELF 1z4rA 520 :LVGLQNVFSHQLPRM T0374 36 :PFS 1z4rA 535 :PKE T0374 40 :AQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1z4rA 538 :YIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILY T0374 113 :MKISCFNA 1z4rA 610 :FLTYADEY T0374 124 :GLLLYTQLGYQP 1z4rA 618 :AIGYFKKQGFSK Number of specific fragments extracted= 5 number of extra gaps= 0 total=767 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 2atrA/T0374-2atrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2atrA expands to /projects/compbio/data/pdb/2atr.pdb.gz 2atrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 2atrA/T0374-2atrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2atrA read from 2atrA/T0374-2atrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2atrA to template set # found chain 2atrA in template set Warning: unaligning (T0374)P20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)Q21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)Y30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)E32 Warning: unaligning (T0374)P31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)M33 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 1 :M 2atrA 1 :M T0374 3 :LSHRP 2atrA 2 :ITIKK T0374 8 :AETGDLETVAGF 2atrA 10 :VKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQWQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVGDG T0374 73 :GDFCALGNM 2atrA 64 :FSSVFVQDL T0374 84 :APAARGLGVARYLIGVME 2atrA 75 :LPSYQRQGIGSSLMKEAL T0374 109 :KARLMKISCFNA 2atrA 97 :EAYQVQLATEET T0374 122 :AAGLLLYTQLGYQPRAI 2atrA 109 :EKNVGFYRSMGFEILST Number of specific fragments extracted= 8 number of extra gaps= 2 total=775 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 2atrA/T0374-2atrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2atrA/T0374-2atrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2atrA read from 2atrA/T0374-2atrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2atrA in template set Warning: unaligning (T0374)P20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)A33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)W35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)P36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 1 :M 2atrA 1 :M T0374 3 :LSHRP 2atrA 2 :ITIKK T0374 8 :AETGDLETVAGF 2atrA 10 :VKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVG T0374 71 :QHGDFCALGNM 2atrA 62 :DGFSSVFVQDL T0374 84 :APAARGLGVARYLIGVMEN 2atrA 75 :LPSYQRQGIGSSLMKEALG T0374 106 :EQYKARLMKISCFNANAA 2atrA 94 :NFKEAYQVQLATEETEKN T0374 125 :LLLYTQLGYQPRAIAERHD 2atrA 112 :VGFYRSMGFEILSTYDCTG Number of specific fragments extracted= 8 number of extra gaps= 2 total=783 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 2atrA/T0374-2atrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2atrA/T0374-2atrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2atrA read from 2atrA/T0374-2atrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2atrA in template set Warning: unaligning (T0374)R23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2atrA)G23 Warning: unaligning (T0374)P31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)G23 Warning: unaligning (T0374)K32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)W24 Warning: unaligning (T0374)A33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)T25 Warning: unaligning (T0374)I34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)N26 Warning: unaligning (T0374)A40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2atrA)E32 Warning: unaligning (T0374)Q41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2atrA)M33 Warning: unaligning (T0374)M82 because of BadResidue code BAD_PEPTIDE in next template residue (2atrA)V74 Warning: unaligning (T0374)V83 because of BadResidue code BAD_PEPTIDE at template residue (2atrA)V74 T0374 3 :LSHRPAETGDLETVAGFPQD 2atrA 2 :ITIKKQEIVKLEDVLHLYQA T0374 42 :LAAAIAERRGSTVAVHDGQVLGFANFYQ 2atrA 34 :LEQALSHSLVIYLALDGDAVVGLIRLVG T0374 71 :QHGDFCALGNM 2atrA 62 :DGFSSVFVQDL T0374 84 :APAARGLGVARYLIGVME 2atrA 75 :LPSYQRQGIGSSLMKEAL T0374 108 :YKAR 2atrA 97 :EAYQ T0374 113 :MKISCFNA 2atrA 101 :VQLATEET T0374 122 :AAGLLLYTQLGYQPRAIAERHD 2atrA 109 :EKNVGFYRSMGFEILSTYDCTG Number of specific fragments extracted= 7 number of extra gaps= 2 total=790 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 1xebA/T0374-1xebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xebA expands to /projects/compbio/data/pdb/1xeb.pdb.gz 1xebA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1xebA/T0374-1xebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xebA read from 1xebA/T0374-1xebA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xebA to template set # found chain 1xebA in template set T0374 2 :QLSHRP 1xebA 4 :DWTCKH T0374 8 :AETGDLETVAGFPQDRDELFY 1xebA 13 :LTLKELYALLQLRTEVFVVEQ T0374 29 :CYPKAIWPF 1xebA 35 :CPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQWQH 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLDPVR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1xebA 73 :EGQVVIGRVVSSSAARGQGLGHQLMERALQAAERL T0374 108 :YKAR 1xebA 109 :LDTP T0374 113 :MKISCFNA 1xebA 113 :VYLSAQAH T0374 124 :GLLLYTQLGYQPRAIAERHDP 1xebA 121 :LQAYYGRYGFVAVTEVYLEDD T0374 149 :VALIQMDK 1xebA 142 :IPHIGMRR Number of specific fragments extracted= 9 number of extra gaps= 0 total=799 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 1xebA/T0374-1xebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1xebA/T0374-1xebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xebA read from 1xebA/T0374-1xebA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xebA in template set T0374 3 :LSHRP 1xebA 5 :WTCKH T0374 8 :AETGDLETVAGFPQDRDELFY 1xebA 13 :LTLKELYALLQLRTEVFVVEQ T0374 29 :CYPKAIWPF 1xebA 35 :CPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQWQHGD 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLDPVRHE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1xebA 75 :QVVIGRVVSSSAARGQGLGHQLMERALQAAERLWLDTPVYLSAQAHL T0374 125 :LLLYTQLGYQPRA 1xebA 122 :QAYYGRYGFVAVT T0374 138 :IAER 1xebA 136 :VYLE T0374 145 :DG 1xebA 140 :DD T0374 149 :VALIQMDK 1xebA 142 :IPHIGMRR Number of specific fragments extracted= 9 number of extra gaps= 0 total=808 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 1xebA/T0374-1xebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1xebA/T0374-1xebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xebA read from 1xebA/T0374-1xebA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xebA in template set T0374 8 :AETGDLETVAGFPQDRDELFYCYPKAIWPFS 1xebA 13 :LTLKELYALLQLRTEVFVVEQKCPYQEVDGL T0374 45 :AIAERRGSTVAVHDGQVLGFANFYQ 1xebA 44 :DLVGDTHHLMAWRDGQLLAYLRLLD T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKARLMKISCFNAN 1xebA 70 :VRHEGQVVIGRVVSSSAARGQGLGHQLMERALQAAERLWLDTPVYLSAQAHL T0374 125 :LLLYTQLGYQPRAIAE 1xebA 122 :QAYYGRYGFVAVTEVY Number of specific fragments extracted= 4 number of extra gaps= 0 total=812 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 1y9wA/T0374-1y9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y9wA expands to /projects/compbio/data/pdb/1y9w.pdb.gz 1y9wA:# T0374 read from 1y9wA/T0374-1y9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9wA read from 1y9wA/T0374-1y9wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y9wA to template set # found chain 1y9wA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1y9wA)L140 T0374 4 :SHRPAETGDLETVAG 1y9wA 5 :HIENGTRIEGEYIKN T0374 22 :DRDELFY 1y9wA 20 :KVIQYNM T0374 29 :CYPKAIWPF 1y9wA 29 :LTDEVKQPM T0374 49 :RRGSTVAVHD 1y9wA 38 :EEVSLVVKNE T0374 59 :GQVLGFANFYQW 1y9wA 49 :GKIFGGVTGTMY T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9wA 61 :FYHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEK T0374 109 :KARLMKISCFNAN 1y9wA 96 :GCRLILLDSFSFQ T0374 124 :GLLLYTQLGYQPRAIAER 1y9wA 109 :APEFYKKHGYREYGVVED T0374 143 :DPDG 1y9wA 127 :HPKG T0374 149 :VALIQMDKP 1y9wA 131 :HSQHFFEKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=822 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 1y9wA/T0374-1y9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1y9wA/T0374-1y9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9wA read from 1y9wA/T0374-1y9wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9wA in template set Warning: unaligning (T0374)L158 because last residue in template chain is (1y9wA)L140 T0374 1 :MQ 1y9wA 3 :MK T0374 4 :SHRPAETGDLETVAGFPQ 1y9wA 5 :HIENGTRIEGEYIKNKVI T0374 23 :RDELFYCYPKAIWPF 1y9wA 23 :QYNMSILTDEVKQPM T0374 49 :RRGSTVAVHD 1y9wA 38 :EEVSLVVKNE T0374 59 :GQVLGFANFYQWQ 1y9wA 49 :GKIFGGVTGTMYF T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9wA 62 :YHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEK T0374 109 :KARLMKISCFNA 1y9wA 96 :GCRLILLDSFSF T0374 121 :N 1y9wA 110 :P T0374 126 :LLYTQLGYQPRAIAERHDPDG 1y9wA 111 :EFYKKHGYREYGVVEDHPKGH T0374 150 :ALIQMDKP 1y9wA 132 :SQHFFEKR Number of specific fragments extracted= 10 number of extra gaps= 0 total=832 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 1y9wA/T0374-1y9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1y9wA/T0374-1y9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9wA read from 1y9wA/T0374-1y9wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9wA in template set T0374 4 :SHRPAETGDLETVAGFPQDRDEL 1y9wA 5 :HIENGTRIEGEYIKNKVIQYNMS T0374 46 :IAERRGSTVAVH 1y9wA 35 :QPMEEVSLVVKN T0374 58 :DGQVLGFANFYQ 1y9wA 48 :EGKIFGGVTGTM T0374 72 :HGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1y9wA 60 :YFYHLHIDFLWVDESVRHDGYGSQLLHEIEGIAKEKGCRL T0374 113 :MKISCFNA 1y9wA 100 :ILLDSFSF T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1y9wA 110 :PEFYKKHGYREYGVVEDHPKGHS Number of specific fragments extracted= 6 number of extra gaps= 0 total=838 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 1bo4A/T0374-1bo4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bo4A expands to /projects/compbio/data/pdb/1bo4.pdb.gz 1bo4A:# T0374 read from 1bo4A/T0374-1bo4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bo4A read from 1bo4A/T0374-1bo4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bo4A to template set # found chain 1bo4A in template set T0374 2 :QLSHRPAETGDLETVAGFP 1bo4A 26 :IIRTCRLGPDQVKSMRAAL T0374 21 :QDRDELFYCYPK 1bo4A 52 :GDVATYSQHQPD T0374 39 :VAQLAAAI 1bo4A 64 :SDYLGNLL T0374 47 :AERRGSTVAVHDGQVLGFANFYQWQH 1bo4A 73 :SKTFIALAAFDQEAVVGALAAYVLPK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1bo4A 103 :RSEIYIYDLAVSGEHRRQGIATALINLLKHEANAL T0374 109 :KARLMKISCFNA 1bo4A 138 :GAYVIYVQADYG T0374 144 :PDGRRVALI 1bo4A 150 :DDPAVALYT Number of specific fragments extracted= 7 number of extra gaps= 0 total=845 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 1bo4A/T0374-1bo4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1bo4A/T0374-1bo4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bo4A read from 1bo4A/T0374-1bo4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bo4A in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1bo4A)G25 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1bo4A 27 :IRTCRLGPDQVKSMRAALDLFGREFGDVAT T0374 33 :AIWPFSVAQLAAAIA 1bo4A 58 :SQHQPDSDYLGNLLR T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1bo4A 74 :KTFIALAAFDQEAVVGALAAYVLPKFE T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1bo4A 105 :EIYIYDLAVSGEHRRQGIATALINLLKHEANAL T0374 109 :KARLMKI 1bo4A 138 :GAYVIYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=850 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 1bo4A/T0374-1bo4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1bo4A/T0374-1bo4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bo4A read from 1bo4A/T0374-1bo4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bo4A in template set T0374 2 :QLSHRPAETGDLETVAGFPQDRDELFYCY 1bo4A 26 :IIRTCRLGPDQVKSMRAALDLFGREFGDV T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQ 1bo4A 57 :YSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYV T0374 70 :WQHGD 1bo4A 99 :FEQPR T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1bo4A 105 :EIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYV T0374 113 :MKIS 1bo4A 142 :IYVQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=855 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 1qsoA/T0374-1qsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qsoA expands to /projects/compbio/data/pdb/1qso.pdb.gz 1qsoA:# T0374 read from 1qsoA/T0374-1qsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsoA read from 1qsoA/T0374-1qsoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qsoA to template set # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYE T0374 29 :CYPKAIWPFSVAQLA 1qsoA 36 :SFPDDLDDFNFGRFL T0374 47 :AERRGSTVAVHDG 1qsoA 53 :NIKMWAAVAVESS T0374 60 :QVLGFANFYQWQH 1qsoA 68 :KIIGMINFFNHMT T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsoA 85 :KDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsoA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDP 1qsoA 144 :YKAPKILYKRK Number of specific fragments extracted= 7 number of extra gaps= 0 total=862 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 1qsoA/T0374-1qsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qsoA/T0374-1qsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsoA read from 1qsoA/T0374-1qsoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPK 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYEVSFP T0374 36 :PFSVAQLAAAIA 1qsoA 39 :DDLDDFNFGRFL T0374 48 :ERRG 1qsoA 52 :PNIK T0374 52 :STVAVHDG 1qsoA 58 :AAVAVESS T0374 60 :QVLGFANFYQWQHGD 1qsoA 68 :KIIGMINFFNHMTTW T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1qsoA 87 :KIYINDLYVDENSRVKGAGGKLIQFVYDEADKL T0374 109 :KARLMKISCFNANAAGLLLYTQLG 1qsoA 120 :GTPSVYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDP 1qsoA 144 :YKAPKILYKRK Number of specific fragments extracted= 8 number of extra gaps= 0 total=870 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 1qsoA/T0374-1qsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1qsoA/T0374-1qsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qsoA read from 1qsoA/T0374-1qsoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qsoA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1qsoA)N8 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAAIAERRGSTVAVHDG 1qsoA 9 :ITVRFVTENDKEGWQRLWKSYQDFYEVSFPDDLDDFNFGRFLDPNIKMWAAVAVESS T0374 60 :QVLGFANFYQ 1qsoA 68 :KIIGMINFFN T0374 70 :WQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1qsoA 82 :WDFKDKIYINDLYVDENSRVKGAGGKLIQFVYDEADKLGTPS T0374 113 :MKISCFNANAAGLLLYTQLG 1qsoA 124 :VYWCTDESNHRAQLLYVKVG T0374 134 :QPRAIAERHDPD 1qsoA 144 :YKAPKILYKRKG Number of specific fragments extracted= 5 number of extra gaps= 0 total=875 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 1y9kA/T0374-1y9kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y9kA expands to /projects/compbio/data/pdb/1y9k.pdb.gz 1y9kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1099, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1y9kA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1y9kA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1y9kA/T0374-1y9kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9kA read from 1y9kA/T0374-1y9kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y9kA to template set # found chain 1y9kA in template set Warning: unaligning (T0374)E159 because last residue in template chain is (1y9kA)N152 T0374 1 :MQLSHRPAETG 1y9kA 1 :MSVVIERIPKE T0374 18 :GFPQDRDELF 1y9kA 12 :AIPKSLLLLA T0374 32 :KAIWPFSVAQLA 1y9kA 22 :DPSERQIATYVQ T0374 49 :RRGSTVAVHDGQVLGFANFYQWQ 1y9kA 34 :RGLTYVAKQGGSVIGVYVLLETR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9kA 57 :PKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGY T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 92 :GMSKLEVGTGNSSVSQLALYQKCGFRIFSIDFDY T0374 143 :DPDGRRV 1y9kA 130 :YEEEIIE T0374 150 :ALIQMDKPL 1y9kA 143 :DMIRLAMEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=883 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 1y9kA/T0374-1y9kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1y9kA/T0374-1y9kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9kA read from 1y9kA/T0374-1y9kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9kA in template set Warning: unaligning (T0374)E159 because last residue in template chain is (1y9kA)N152 T0374 1 :MQLSHRPAETG 1y9kA 1 :MSVVIERIPKE T0374 18 :GFPQDRDELF 1y9kA 12 :AIPKSLLLLA T0374 36 :PFSVAQLAAAIA 1y9kA 22 :DPSERQIATYVQ T0374 49 :RRGSTVAVHDGQVLGFANFYQWQ 1y9kA 34 :RGLTYVAKQGGSVIGVYVLLETR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1y9kA 57 :PKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGY T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 92 :GMSKLEVGTGNSSVSQLALYQKCGFRIFSIDFDY T0374 143 :DP 1y9kA 130 :YE T0374 145 :DG 1y9kA 137 :NG T0374 147 :RRVALIQMDKPL 1y9kA 140 :VCRDMIRLAMEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=892 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 1y9kA/T0374-1y9kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1y9kA/T0374-1y9kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9kA read from 1y9kA/T0374-1y9kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9kA in template set T0374 1 :MQLSHRPAETGD 1y9kA 1 :MSVVIERIPKEA T0374 17 :AGFPQDR 1y9kA 15 :KSLLLLA T0374 33 :AIWPFSVAQLA 1y9kA 22 :DPSERQIATYV T0374 48 :ERRGSTVAVHDGQVLGFANFYQ 1y9kA 33 :QRGLTYVAKQGGSVIGVYVLLE T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1y9kA 55 :TRPKTMEIMNIAVAEHLQGKGIGKKLLRHAVETAKGYGMSK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAERH 1y9kA 96 :LEVGTGNSSVSQLALYQKCGFRIFSIDFDY Number of specific fragments extracted= 6 number of extra gaps= 0 total=898 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 1i1dA/T0374-1i1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i1dA expands to /projects/compbio/data/pdb/1i1d.pdb.gz 1i1dA:Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 1i1dA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 1i1dA # T0374 read from 1i1dA/T0374-1i1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1dA read from 1i1dA/T0374-1i1dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i1dA to template set # found chain 1i1dA in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAAI 1i1dA 29 :TVGTITPESFCKLIKYWN T0374 47 :AERR 1i1dA 60 :MQYN T0374 52 :STVAVHD 1i1dA 64 :PMVIVDK T0374 59 :GQVLGFANFYQWQH 1i1dA 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i1dA 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i1dA 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAIAER 1i1dA 142 :FYEKCGFSNAGVEMQ T0374 156 :KP 1i1dA 157 :IR Number of specific fragments extracted= 9 number of extra gaps= 0 total=907 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 1i1dA/T0374-1i1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i1dA/T0374-1i1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1dA read from 1i1dA/T0374-1i1dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1dA in template set T0374 1 :MQ 1i1dA 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i1dA 29 :TVGTITPESFCKLIK T0374 49 :RRGSTVAVHD 1i1dA 61 :QYNPMVIVDK T0374 59 :GQVLGFANFYQWQHG 1i1dA 73 :ETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i1dA 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i1dA 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i1dA 140 :VKFYEKCGFSNAG T0374 138 :I 1i1dA 154 :E T0374 154 :MDKP 1i1dA 155 :MQIR Number of specific fragments extracted= 10 number of extra gaps= 0 total=917 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 1i1dA/T0374-1i1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i1dA/T0374-1i1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1dA read from 1i1dA/T0374-1i1dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1dA in template set Warning: unaligning (T0374)P144 because last residue in template chain is (1i1dA)K159 T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i1dA 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :C 1i1dA 29 :T T0374 31 :PKAIWPFSVAQ 1i1dA 30 :VGTITPESFCK T0374 42 :LAA 1i1dA 42 :IKY T0374 46 :IAERRGSTVAVH 1i1dA 59 :IMQYNPMVIVDK T0374 58 :DGQVLGFANFYQWQHG 1i1dA 72 :TETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i1dA 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i1dA 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERHD 1i1dA 140 :VKFYEKCGFSNAGVEMQIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=926 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 1yvkA/T0374-1yvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yvkA expands to /projects/compbio/data/pdb/1yvk.pdb.gz 1yvkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1yvkA/T0374-1yvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvkA read from 1yvkA/T0374-1yvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yvkA to template set # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 Warning: unaligning (T0374)E159 because last residue in template chain is (1yvkA)L156 T0374 3 :LSHRPAE 1yvkA 6 :LRIELGE T0374 14 :ETVAGFPQDR 1yvkA 16 :DELYDLLLLA T0374 32 :KAIWPFSVAQLAA 1yvkA 26 :DPSKDIVDEYLER T0374 50 :RGSTVAVHDGQVLGFANFYQWQ 1yvkA 39 :GECYTAWAGDELAGVYVLLKTR T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvkA 61 :PQTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAERH 1yvkA 96 :GADTIEIGTGNSSIHQLSLYQKCGFRIQAIDHDF T0374 143 :DPDG 1yvkA 133 :HYDE T0374 147 :RRVALIQMDKPL 1yvkA 144 :QCRDMVRLYLDL Number of specific fragments extracted= 8 number of extra gaps= 0 total=934 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 1yvkA/T0374-1yvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yvkA/T0374-1yvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvkA read from 1yvkA/T0374-1yvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 Warning: unaligning (T0374)E159 because last residue in template chain is (1yvkA)L156 T0374 3 :LSHRPAET 1yvkA 6 :LRIELGEE T0374 14 :ETVAGFPQD 1yvkA 16 :DELYDLLLL T0374 35 :WPFSVAQLAAAIA 1yvkA 25 :ADPSKDIVDEYLE T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1yvkA 38 :RGECYTAWAGDELAGVYVLLKTRP T0374 74 :DFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1yvkA 62 :QTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKL T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIA 1yvkA 96 :GADTIEIGTGNSSIHQLSLYQKCGFRIQAID T0374 140 :ERHDPDGRRVALIQMDKPL 1yvkA 137 :DIFENGIQCRDMVRLYLDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=941 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 1yvkA/T0374-1yvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1yvkA/T0374-1yvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yvkA read from 1yvkA/T0374-1yvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yvkA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1yvkA)K5 T0374 3 :LSHRPAET 1yvkA 6 :LRIELGEE T0374 14 :ETVAGFPQDRD 1yvkA 16 :DELYDLLLLAD T0374 33 :AIWPFSVAQLAA 1yvkA 27 :PSKDIVDEYLER T0374 50 :RGSTVAVHDGQVLGFANFYQ 1yvkA 39 :GECYTAWAGDELAGVYVLLK T0374 71 :QHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1yvkA 59 :TRPQTVEIVNIAVKESLQKKGFGKQLVLDAIEKAKKLGADT T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1yvkA 100 :IEIGTGNSSIHQLSLYQKCGFRIQAIDHD Number of specific fragments extracted= 6 number of extra gaps= 0 total=947 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 2a4nA/T0374-2a4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a4nA expands to /projects/compbio/data/pdb/2a4n.pdb.gz 2a4nA:# T0374 read from 2a4nA/T0374-2a4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a4nA read from 2a4nA/T0374-2a4nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a4nA to template set # found chain 2a4nA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2a4nA)M1 T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 2a4nA 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2a4nA 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 2a4nA 103 :GGITIYLGT T0374 118 :FNANA 2a4nA 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 2a4nA 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 2a4nA 163 :GWD T0374 149 :VALIQMDKPL 2a4nA 166 :KPDIWMAKTI T0374 159 :E 2a4nA 179 :P Number of specific fragments extracted= 9 number of extra gaps= 0 total=956 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 2a4nA/T0374-2a4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2a4nA/T0374-2a4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a4nA read from 2a4nA/T0374-2a4nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a4nA in template set T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFP 2a4nA 14 :KDQLSDLL T0374 27 :FYCYPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 2a4nA 22 :RLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 2a4nA 103 :GGITIYLGT T0374 118 :F 2a4nA 114 :L T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 2a4nA 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 2a4nA 167 :PDIWMAKTIIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=963 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 2a4nA/T0374-2a4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 2a4nA/T0374-2a4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a4nA read from 2a4nA/T0374-2a4nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a4nA in template set Warning: unaligning (T0374)L3 because first residue in template chain is (2a4nA)M1 T0374 4 :SHRPAETGD 2a4nA 2 :IISEFDRNN T0374 13 :LETVAGFPQDRD 2a4nA 14 :KDQLSDLLRLTW T0374 31 :PKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 2a4nA 26 :PEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 2a4nA 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 2a4nA 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=968 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 1b87A/T0374-1b87A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b87A expands to /projects/compbio/data/pdb/1b87.pdb.gz 1b87A:# T0374 read from 1b87A/T0374-1b87A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b87A read from 1b87A/T0374-1b87A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b87A to template set # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1b87A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1b87A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKISC 1b87A 103 :GGITIYLGT T0374 118 :FNANA 1b87A 139 :LREHP T0374 125 :LLLYTQLGYQPRAIAERH 1b87A 144 :YEFYEKLGYKIVGVLPNA T0374 143 :DPD 1b87A 163 :GWD T0374 149 :VALIQMDKPL 1b87A 166 :KPDIWMAKTI T0374 159 :EP 1b87A 178 :RP Number of specific fragments extracted= 9 number of extra gaps= 0 total=977 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 1b87A/T0374-1b87A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1b87A/T0374-1b87A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b87A read from 1b87A/T0374-1b87A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDR 1b87A 14 :KDQLSDLLRLT T0374 30 :YPKAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1b87A 25 :WPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASR T0374 109 :KARLMKIS 1b87A 103 :GGITIYLG T0374 118 :FNA 1b87A 114 :LDH T0374 125 :LLLYTQLGYQPRAIAERHDPDGR 1b87A 144 :YEFYEKLGYKIVGVLPNANGWDK T0374 150 :ALIQMDKPLEP 1b87A 167 :PDIWMAKTIIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=984 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 1b87A/T0374-1b87A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1b87A/T0374-1b87A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b87A read from 1b87A/T0374-1b87A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b87A in template set Warning: unaligning (T0374)L3 because first residue in template chain is (1b87A)M1 T0374 4 :SHRPAETGD 1b87A 2 :IISEFDRNN T0374 13 :LETVAGFPQDRDE 1b87A 14 :KDQLSDLLRLTWP T0374 32 :KAIWPFSVAQLAAAIAERRGSTVAVHDGQVLGFANFYQWQHGDFCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1b87A 27 :EEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGIT T0374 113 :MKISCFNA 1b87A 107 :IYLGTDDL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRVALIQMDKPLEP 1b87A 144 :YEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRP Number of specific fragments extracted= 5 number of extra gaps= 0 total=989 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 1ufhA/T0374-1ufhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ufhA expands to /projects/compbio/data/pdb/1ufh.pdb.gz 1ufhA:# T0374 read from 1ufhA/T0374-1ufhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufhA read from 1ufhA/T0374-1ufhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ufhA to template set # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWP 1ufhA 33 :TWLPEDAQ T0374 37 :FSVAQLAAAI 1ufhA 42 :LSKQVFTDLL T0374 47 :AERRGSTVAVHD 1ufhA 57 :TPHHHLWSLKLN T0374 59 :GQVLGFANFYQWQH 1ufhA 70 :KDIVGWLWIHAEPE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1ufhA 86 :QQEAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAI 1ufhA 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDV Number of specific fragments extracted= 7 number of extra gaps= 0 total=996 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 1ufhA/T0374-1ufhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1ufhA/T0374-1ufhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufhA read from 1ufhA/T0374-1ufhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEK T0374 29 :CYPKAIWPFSVAQLAAAIA 1ufhA 34 :WLPEDAQLLSKQVFTDLLP T0374 48 :ERRGSTVAVHD 1ufhA 58 :PHHHLWSLKLN T0374 59 :GQVLGFANFYQWQHGD 1ufhA 70 :KDIVGWLWIHAEPEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1ufhA 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSM T0374 109 :KARLMKISCFNANAAGLLLYTQLGYQPRAIAE 1ufhA 121 :GIRKLSLHVFAHNQTARKLYEQTGFQETDVVM Number of specific fragments extracted= 6 number of extra gaps= 0 total=1002 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 1ufhA/T0374-1ufhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1ufhA/T0374-1ufhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ufhA read from 1ufhA/T0374-1ufhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ufhA in template set Warning: unaligning (T0374)Q2 because first residue in template chain is (1ufhA)T2 T0374 3 :LSHRPAETGDLETVAGFPQDRDELFYCY 1ufhA 3 :IMLTPMQTEEFRSYLTYTTKHYAEEKVK T0374 31 :PKAIWPFSVAQLAA 1ufhA 35 :LPEDAQLLSKQVFT T0374 45 :AIAERRGSTVAVHDG 1ufhA 55 :LETPHHHLWSLKLNE T0374 60 :QVLGFANFYQ 1ufhA 71 :DIVGWLWIHA T0374 70 :WQHG 1ufhA 82 :PEHP T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1ufhA 88 :EAFIYDFGLYEPYRGKGYAKQALAALDQAARSMGIRK T0374 113 :MKISCFNANAAGLLLYTQLGYQPRAIAER 1ufhA 125 :LSLHVFAHNQTARKLYEQTGFQETDVVMS Number of specific fragments extracted= 7 number of extra gaps= 0 total=1009 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 1i21A/T0374-1i21A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i21A expands to /projects/compbio/data/pdb/1i21.pdb.gz 1i21A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0374 read from 1i21A/T0374-1i21A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i21A read from 1i21A/T0374-1i21A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i21A to template set # found chain 1i21A in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1i21A)R158 T0374 3 :LSHRPAETGDLETVAGFPQDRDE 1i21A 7 :FYIRRMEEGDLEQVTETLKVLTT T0374 30 :YPKAIWPFSVAQLAAAI 1i21A 30 :VGTITPESFCKLIKYWN T0374 47 :AERRGSTVAVHD 1i21A 60 :MQYNPMVIVDKR T0374 59 :GQVLGFANFYQWQH 1i21A 73 :ETVAATGNIIIERK T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i21A 92 :GLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNANAA 1i21A 127 :GCYKIILDCDEKNVK T0374 127 :LYTQLGYQPRAIAE 1i21A 142 :FYEKCGFSNAGVEM T0374 155 :DK 1i21A 156 :QI Number of specific fragments extracted= 8 number of extra gaps= 0 total=1017 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 1i21A/T0374-1i21A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i21A/T0374-1i21A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i21A read from 1i21A/T0374-1i21A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i21A in template set Warning: unaligning (T0374)P157 because last residue in template chain is (1i21A)R158 T0374 1 :MQ 1i21A 1 :MS T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i21A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 33 :AIWPFSVAQLAAAIA 1i21A 29 :TVGTITPESFCKLIK T0374 49 :RRGSTVAVH 1i21A 61 :QYNPMVIVD T0374 58 :DGQVLGFANFYQWQHGD 1i21A 72 :TETVAATGNIIIERKII T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQ 1i21A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDY T0374 109 :KARLMKISCFNAN 1i21A 127 :GCYKIILDCDEKN T0374 125 :LLLYTQLGYQPRA 1i21A 140 :VKFYEKCGFSNAG T0374 152 :IQMDK 1i21A 153 :VEMQI Number of specific fragments extracted= 9 number of extra gaps= 0 total=1026 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 1i21A/T0374-1i21A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1i21A/T0374-1i21A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i21A read from 1i21A/T0374-1i21A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i21A in template set T0374 3 :LSHRPAETGDLETVAGFPQDRD 1i21A 7 :FYIRRMEEGDLEQVTETLKVLT T0374 29 :CYPKAIWPFSVAQLAAA 1i21A 29 :TVGTITPESFCKLIKYW T0374 46 :IAERRGSTVAVH 1i21A 59 :IMQYNPMVIVDK T0374 58 :DGQVLGFANFYQWQHG 1i21A 72 :TETVAATGNIIIERKI T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLAREQYKAR 1i21A 94 :CGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYK T0374 113 :MKISCFNAN 1i21A 131 :IILDCDEKN T0374 125 :LLLYTQLGYQPRAIAERH 1i21A 140 :VKFYEKCGFSNAGVEMQI Number of specific fragments extracted= 7 number of extra gaps= 0 total=1033 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 1kuxA/T0374-1kuxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kuxA expands to /projects/compbio/data/pdb/1kux.pdb.gz 1kuxA:# T0374 read from 1kuxA/T0374-1kuxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kuxA read from 1kuxA/T0374-1kuxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kuxA to template set # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 Warning: unaligning (T0374)L158 because last residue in template chain is (1kuxA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFYCYPKAIWPFSVAQLAAA 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVSGNCPLNLDEVQHFLTLC T0374 49 :RRGSTVAVHDGQVLGFANFYQWQH 1kuxA 78 :PELSLGWFVEGRLVAFIIGSLWDE T0374 73 :GDFCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 116 :GHSAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNA 1kuxA 152 :AVRRAVLMCEDA T0374 124 :GLLLYTQLGYQPRAIAERHDPD 1kuxA 164 :LVPFYQRFGFHPAGPCAIVVGS T0374 149 :VALIQMDKP 1kuxA 186 :LTFTEMHCS Number of specific fragments extracted= 6 number of extra gaps= 1 total=1039 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 1kuxA/T0374-1kuxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1kuxA/T0374-1kuxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kuxA read from 1kuxA/T0374-1kuxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 Warning: unaligning (T0374)L158 because last residue in template chain is (1kuxA)L195 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 33 :AIWPFSVAQLAAAIA 1kuxA 61 :GNCPLNLDEVQHFLT T0374 48 :ERRGSTVAVHDGQVLGFANFYQWQHGD 1kuxA 77 :CPELSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNAN 1kuxA 152 :AVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAERHDPDGRRV 1kuxA 165 :VPFYQRFGFHPAGPCAIVVGSLTFT T0374 153 :QMDKP 1kuxA 190 :EMHCS Number of specific fragments extracted= 7 number of extra gaps= 1 total=1046 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 1kuxA/T0374-1kuxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0374 read from 1kuxA/T0374-1kuxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kuxA read from 1kuxA/T0374-1kuxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kuxA in template set Warning: unaligning (T0374)Q107 because of BadResidue code BAD_PEPTIDE in next template residue (1kuxA)P151 Warning: unaligning (T0374)Y108 because of BadResidue code BAD_PEPTIDE at template residue (1kuxA)P151 T0374 4 :SHRPAETGDLETVAGFPQDRDELFY 1kuxA 36 :EFRCLTPEDAAGVFEIEREAFISVS T0374 31 :PKAIWPFSVAQLAAAIAER 1kuxA 61 :GNCPLNLDEVQHFLTLCPE T0374 51 :GSTVAVHDGQVLGFANFYQWQHGD 1kuxA 80 :LSLGWFVEGRLVAFIIGSLWDEER T0374 75 :FCALGNMMVAPAARGLGVARYLIGVMENLARE 1kuxA 118 :SAHLHALAVHRSFRQQGKGSVLLWRYLHHVGA T0374 109 :KARLMKISCFNAN 1kuxA 152 :AVRRAVLMCEDAL T0374 125 :LLLYTQLGYQPRAIAER 1kuxA 165 :VPFYQRFGFHPAGPCAI Number of specific fragments extracted= 6 number of extra gaps= 1 total=1052 Will force an alignment to be made, even if fragment is small Number of alignments=147 # command:CPU_time= 31.195 sec, elapsed time= 34.060 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 147 Adding 12720 constraints to all_contacts Done adding distance constraints # command:CPU_time= 31.305 sec, elapsed time= 34.175 sec. # command:Reading probabilities from T0374.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 79.689 Optimizing... Probability sum: -279.577, CN propb: -279.577 weights: 0.428 constraints: 379 # command:CPU_time= 41.137 sec, elapsed time= 44.037 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 379 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 379 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1104 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1104 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 9993 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 9993 # command:CPU_time= 41.339 sec, elapsed time= 44.419 sec. # command: