# 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 T0364 numbered 1 through 156 Created new target T0364 from T0364.a2m # command:CPU_time= 6.267 sec, elapsed time= 6.304 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/T0364-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s5uA expands to /projects/compbio/data/pdb/1s5u.pdb.gz 1s5uA:# T0364 read from 1s5uA/T0364-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0364-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s5uA to template set # found chain 1s5uA in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN # choosing archetypes in rotamer library T0364 99 :GFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 99 :AENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 1s5uA/T0364-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1s5uA/T0364-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0364-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5uA in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVNAE T0364 101 :DEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 101 :NTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 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 1s5uA/T0364-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1s5uA/T0364-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0364-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5uA in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0364)L132 because last residue in template chain is (1s5uA)F132 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0364 99 :GFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCR 1s5uA 99 :AENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 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 1z54A/T0364-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z54A expands to /projects/compbio/data/pdb/1z54.pdb.gz 1z54A:# T0364 read from 1z54A/T0364-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0364-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z54A to template set # found chain 1z54A in template set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVERE T0364 101 :DEVLAASEQMLLHVD 1z54A 97 :GVLLAEGFTRHLCQV T0364 118 :GPQSAPFGHTTVCRLNHL 1z54A 112 :GERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 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 1z54A/T0364-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1z54A/T0364-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0364-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z54A in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1z54A)M1 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVERE T0364 101 :DEVLAASEQMLLHV 1z54A 97 :GVLLAEGFTRHLCQ T0364 117 :AGPQSAPFGHTTVCRLNHL 1z54A 111 :VGERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 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 1z54A/T0364-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1z54A/T0364-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0364-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z54A in template set Warning: unaligning (T0364)A3 because first residue in template chain is (1z54A)M1 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVER T0364 100 :FDEVLAASEQMLLHVD 1z54A 96 :EGVLLAEGFTRHLCQV T0364 118 :GPQSAPFGHTTVCRLNHL 1z54A 112 :GERAARIPEDIYRALSVL Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 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 2cyeA/T0364-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cyeA expands to /projects/compbio/data/pdb/2cye.pdb.gz 2cyeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2cyeA/T0364-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0364-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cyeA to template set # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 Warning: unaligning (T0364)Q139 because last residue in template chain is (2cyeA)P132 T0364 3 :A 2cyeA 3 :G T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0364 46 :ADSRGQ 2cyeA 47 :WLEEGH T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2cyeA 53 :FVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTAN T0364 101 :DEVLAASEQMLLHV 2cyeA 96 :GESAAKGLGVLVWL T0364 117 :AGPQSAPFGHTTVCRLNHLVEQ 2cyeA 110 :EGGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 6 number of extra gaps= 0 total=21 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 2cyeA/T0364-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2cyeA/T0364-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0364-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0364 46 :ADSRGQ 2cyeA 47 :WLEEGH T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2cyeA 53 :FVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTAN T0364 101 :DEVLAASEQMLLHV 2cyeA 96 :GESAAKGLGVLVWL T0364 117 :AGPQSAPFGHTTVCRLNHLVEQ 2cyeA 110 :EGGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 5 number of extra gaps= 0 total=26 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 2cyeA/T0364-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2cyeA/T0364-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0364-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cyeA in template set Warning: unaligning (T0364)I42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0364)D45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0364 46 :ADSR 2cyeA 47 :WLEE T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cyeA 51 :GHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTA T0364 100 :FDEVLAASEQMLLHVD 2cyeA 95 :NGESAAKGLGVLVWLE T0364 118 :GPQSAPFGHTTVCRLNHLV 2cyeA 111 :GGRPAPLPEAIRERIRALE Number of specific fragments extracted= 5 number of extra gaps= 0 total=31 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 2aliA/T0364-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aliA expands to /projects/compbio/data/pdb/2ali.pdb.gz 2aliA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 157, because occupancy 0.5 <= existing 0.500 in 2aliA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 745, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 749, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 757, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 759, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 864, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 866, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 890, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 892, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2aliA # T0364 read from 2aliA/T0364-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0364-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aliA to template set # found chain 2aliA in template set Warning: unaligning (T0364)A46 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0364)D47 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 7 :LHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLE T0364 100 :FDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=34 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 2aliA/T0364-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2aliA/T0364-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0364-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aliA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (2aliA)Q5 Warning: unaligning (T0364)A46 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0364)D47 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLE T0364 100 :FDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=37 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/T0364-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2aliA/T0364-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0364-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aliA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0364 52 :SGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 2aliA 52 :AAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLEDP T0364 102 :EVLAASEQMLLHVDLAGPQSAPFGHTTVCRL 2aliA 103 :GTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 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 2gf6A/T0364-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gf6A expands to /projects/compbio/data/pdb/2gf6.pdb.gz 2gf6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2gf6A/T0364-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0364-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gf6A to template set # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 1 :MPAL 2gf6A 1 :MENI T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2gf6A 6 :YVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKE T0364 42 :IGLDAD 2gf6A 44 :VGIPYP T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2gf6A 52 :NENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKD T0364 101 :DEVLAASEQMLLH 2gf6A 100 :GELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 6 number of extra gaps= 1 total=46 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 2gf6A/T0364-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2gf6A/T0364-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0364-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gf6A 4 :IEYVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFI T0364 40 :DRIGLDA 2gf6A 42 :EKVGIPY T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 2gf6A 52 :NENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKD T0364 101 :DEVLAASEQMLLH 2gf6A 100 :GELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=51 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 2gf6A/T0364-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2gf6A/T0364-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0364-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf6A in template set Warning: unaligning (T0364)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0364)D115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFI T0364 40 :DRIGLDA 2gf6A 42 :EKVGIPY T0364 52 :SGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2gf6A 53 :ENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLK T0364 100 :FDEVLAASEQMLLH 2gf6A 99 :DGELTTEGYVIQIA T0364 116 :LAGPQSAPFGHTTVCRL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=56 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 1lo7A/T0364-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lo7A expands to /projects/compbio/data/pdb/1lo7.pdb.gz 1lo7A:Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 976, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 1lo7A # T0364 read from 1lo7A/T0364-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0364-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lo7A to template set # found chain 1lo7A in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRG 1lo7A 46 :PWRQTV T0364 51 :QSGN 1lo7A 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1lo7A 103 :PGG T0364 102 :EVLAASEQMLLHVDLAGPQSA 1lo7A 108 :QLVMRADEIRVFAMNDGERLR T0364 123 :PFGHTTVCRL 1lo7A 131 :EVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=63 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 1lo7A/T0364-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1lo7A/T0364-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0364-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lo7A in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP T0364 46 :ADSRG 1lo7A 47 :WRQTV T0364 51 :QSGN 1lo7A 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1lo7A 103 :PGG T0364 102 :EVLAASEQMLLHV 1lo7A 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFGHTTVCRL 1lo7A 123 :DGERLRAIEVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=70 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 1lo7A/T0364-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1lo7A/T0364-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0364-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lo7A in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo7A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGNS 1lo7A 46 :PWRQTVVERGI T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 1lo7A 59 :TPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG T0364 102 :EVLAASEQML 1lo7A 108 :QLVMRADEIR T0364 112 :LHVDLAGPQSAPFGHTTVCRL 1lo7A 120 :AMNDGERLRAIEVPADYIELC Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 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 2essA/T0364-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2essA expands to /projects/compbio/data/pdb/2ess.pdb.gz 2essA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 7, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 13, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1165, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2essA/T0364-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0364-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2essA to template set # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0364)Q139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 Warning: unaligning (T0364)E140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)H130 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2essA 6 :KIGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0364 99 :GFDEVLAASEQMLLHVDLA 2essA 101 :KDGKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K T0364 141 :GAQAPQYM 2essA 131 :GGSIVDYI T0364 149 :GRTIKLPA 2essA 140 :DEPCPIEK Number of specific fragments extracted= 5 number of extra gaps= 2 total=80 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 2essA/T0364-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2essA/T0364-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0364-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0364)Q139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 Warning: unaligning (T0364)E140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)H130 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2essA 6 :KIGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVIDKD T0364 101 :DEVLAASEQMLLHVDLA 2essA 103 :GKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K T0364 141 :GAQAPQ 2essA 131 :GGSIVD Number of specific fragments extracted= 4 number of extra gaps= 2 total=84 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 2essA/T0364-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2essA/T0364-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0364-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2essA in template set Warning: unaligning (T0364)G118 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0364)P119 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0364)S121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0364)A122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2essA 7 :IGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0364 99 :GFDEVLAASEQMLLHVDLA 2essA 101 :KDGKKIGYARSVWAMINLN T0364 120 :Q 2essA 122 :K Number of specific fragments extracted= 3 number of extra gaps= 2 total=87 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 1njkA/T0364-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1njkA expands to /projects/compbio/data/pdb/1njk.pdb.gz 1njkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1njkA/T0364-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0364-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1njkA to template set # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=89 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 1njkA/T0364-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1njkA/T0364-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0364-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=91 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 1njkA/T0364-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1njkA/T0364-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0364-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1njkA in template set Warning: unaligning (T0364)L4 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0364)E137 because last residue in template chain is (1njkA)K132 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMD 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNHLV 1njkA 41 :FQWMTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLEPEGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 2 number of extra gaps= 0 total=93 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 2av9A/T0364-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2av9A expands to /projects/compbio/data/pdb/2av9.pdb.gz 2av9A:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2av9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2av9A/T0364-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0364-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2av9A to template set # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIE T0364 42 :IGLDAD 2av9A 52 :GGLDIQ T0364 51 :QSGNSLFTLEAHINYLHEV 2av9A 58 :GGEVIGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 4 number of extra gaps= 1 total=97 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 2av9A/T0364-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2av9A/T0364-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0364-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYL T0364 40 :DRIGLDAD 2av9A 50 :ERGGLDIQ T0364 51 :QSGNSLFTLEAHINYLHEV 2av9A 58 :GGEVIGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 4 number of extra gaps= 1 total=101 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 2av9A/T0364-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2av9A/T0364-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0364-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2av9A in template set Warning: unaligning (T0364)K70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0364)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2av9A 13 :LHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYL T0364 40 :DRIGLD 2av9A 50 :ERGGLD T0364 51 :QSGN 2av9A 56 :IQGG T0364 55 :SLFTLEAHINYLHEV 2av9A 62 :IGLVVSSSCDYFAPV T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLLHVDLAGPQSAPFGHTTVCRLNH 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQREACAAGRFVHVFVERRSSRPVAIPQELRDALAA Number of specific fragments extracted= 5 number of extra gaps= 1 total=106 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 1yliA/T0364-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yliA expands to /projects/compbio/data/pdb/1yli.pdb.gz 1yliA:Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1yliA # T0364 read from 1yliA/T0364-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0364-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yliA to template set # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 4 :LITY 1yliA 16 :VLLL T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEI T0364 46 :A 1yliA 55 :A T0364 53 :GNSLFTLEAH 1yliA 56 :HGRVVTVAVE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0364 98 :AGFDEVLAASEQMLLHVD 1yliA 109 :IGERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 7 number of extra gaps= 1 total=113 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 1yliA/T0364-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1yliA/T0364-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0364-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 7 :Y 1yliA 19 :L T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDAL 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAIL T0364 46 :ADSRGQSGNSLFTLE 1yliA 51 :AKEIAHGRVVTVAVE T0364 62 :HINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1yliA 66 :SMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0364 100 :FDEVLAASEQMLLHVD 1yliA 111 :ERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 6 number of extra gaps= 1 total=119 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 1yliA/T0364-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1yliA/T0364-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0364-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yliA in template set Warning: unaligning (T0364)R8 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0364)A142 because last residue in template chain is (1yliA)Q152 T0364 7 :Y 1yliA 19 :L T0364 10 :TVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEI T0364 51 :QSG 1yliA 55 :AHG T0364 55 :SLFTLEAH 1yliA 58 :RVVTVAVE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVW T0364 98 :AGFDEVLAASEQMLLHVD 1yliA 109 :IGERYCVTDAVFTFVAVD T0364 117 :AGPQSAPFGHTTVCRLNHLVEQQEG 1yliA 127 :NNGRSRTIPRENNQELEKALALISE Number of specific fragments extracted= 7 number of extra gaps= 1 total=126 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 1vpmA/T0364-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpmA expands to /projects/compbio/data/pdb/1vpm.pdb.gz 1vpmA:Skipped atom 82, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 84, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 86, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 88, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 90, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 92, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 313, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 315, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 317, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 319, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 321, because occupancy 0.350 <= existing 0.650 in 1vpmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 405, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 407, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 466, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 468, because occupancy 0.350 <= existing 0.650 in 1vpmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1002, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1004, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1006, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1008, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1010, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1165, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1167, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1169, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1171, because occupancy 0.350 <= existing 0.650 in 1vpmA # T0364 read from 1vpmA/T0364-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0364-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpmA to template set # found chain 1vpmA in template set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAA T0364 46 :ADSRGQSG 1vpmA 44 :LTAMKHAN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHSNN T0364 100 :FDEVLAASEQMLLHVD 1vpmA 103 :ERTLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQE 1vpmA 134 :EEEKRLYETAPARKE Number of specific fragments extracted= 7 number of extra gaps= 1 total=133 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 1vpmA/T0364-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1vpmA/T0364-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0364-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpmA in template set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKH T0364 52 :SG 1vpmA 50 :AN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHSNN T0364 100 :FDEVLAASEQMLLHVD 1vpmA 103 :ERTLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQEG 1vpmA 134 :EEEKRLYETAPARKEN Number of specific fragments extracted= 7 number of extra gaps= 1 total=140 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 1vpmA/T0364-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1vpmA/T0364-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0364-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpmA in template set Warning: unaligning (T0364)N54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0364)S55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKH T0364 52 :SG 1vpmA 50 :AN T0364 56 :LFTLEAH 1vpmA 54 :VVTASID T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVH T0364 97 :RAGFD 1vpmA 98 :NLLTG T0364 102 :EVLAASEQMLLHVD 1vpmA 105 :TLTTESFLTMVAVD T0364 117 :AGPQSAPFG 1vpmA 119 :ESGKPKPVP T0364 126 :HTTVCRLNHLVEQQEG 1vpmA 134 :EEEKRLYETAPARKEN Number of specific fragments extracted= 8 number of extra gaps= 1 total=148 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 2h4uA/T0364-2h4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h4uA expands to /projects/compbio/data/pdb/2h4u.pdb.gz 2h4uA:# T0364 read from 2h4uA/T0364-2h4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h4uA read from 2h4uA/T0364-2h4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h4uA to template set # found chain 2h4uA in template set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 37 :KVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLL 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=150 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 2h4uA/T0364-2h4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2h4uA/T0364-2h4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h4uA read from 2h4uA/T0364-2h4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h4uA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 36 :GKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQMLL 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=152 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 2h4uA/T0364-2h4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2h4uA/T0364-2h4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h4uA read from 2h4uA/T0364-2h4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h4uA in template set T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2h4uA 39 :ICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCT T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFDEVLAASEQML 2h4uA 76 :ERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTNKATGKLIAQGRHTK Number of specific fragments extracted= 2 number of extra gaps= 0 total=154 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 1bvqA/T0364-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bvqA expands to /projects/compbio/data/pdb/1bvq.pdb.gz 1bvqA:# T0364 read from 1bvqA/T0364-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0364-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bvqA to template set # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGN 1bvqA 46 :PWRQTVVERG T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 99 :GFD 1bvqA 103 :PGG T0364 102 :EVLAASEQMLLHV 1bvqA 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFG 1bvqA 123 :DGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=161 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 1bvqA/T0364-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1bvqA/T0364-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0364-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 Warning: unaligning (T0364)L132 because last residue in template chain is (1bvqA)C140 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLD 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP T0364 46 :ADSRG 1bvqA 47 :WRQTV T0364 51 :QSGN 1bvqA 53 :ERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0364 98 :A 1bvqA 103 :P T0364 100 :FD 1bvqA 104 :GG T0364 102 :EVLAASEQMLLHV 1bvqA 108 :QLVMRADEIRVFA T0364 115 :DLAGPQSAPFG 1bvqA 123 :DGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 9 number of extra gaps= 1 total=170 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 1bvqA/T0364-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1bvqA/T0364-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0364-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bvqA in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1bvqA)A2 Warning: unaligning (T0364)H126 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0364)T127 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0364 45 :DADSRGQSGNS 1bvqA 46 :PWRQTVVERGI T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAGFD 1bvqA 59 :TPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG T0364 102 :EVLAASEQML 1bvqA 108 :QLVMRADEIR T0364 112 :LHVDLAGPQSAPFG 1bvqA 120 :AMNDGERLRAIEVP T0364 128 :TVCR 1bvqA 136 :YIEL Number of specific fragments extracted= 6 number of extra gaps= 1 total=176 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 2gvhA/T0364-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gvhA expands to /projects/compbio/data/pdb/2gvh.pdb.gz 2gvhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2gvhA/T0364-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0364-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gvhA to template set # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAF T0364 46 :ADSRGQSGNSLFTLEAH 2gvhA 180 :VAASRYCGKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWSEN T0364 100 :FDEVLAASEQMLLHV 2gvhA 239 :ERHITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 5 number of extra gaps= 0 total=181 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 2gvhA/T0364-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2gvhA/T0364-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0364-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAA T0364 47 :DSRG 2gvhA 183 :SRYC T0364 53 :GNSLFTLEAH 2gvhA 187 :GKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWSEN T0364 100 :FDEVLAASEQMLLHV 2gvhA 239 :ERHITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=187 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 2gvhA/T0364-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2gvhA/T0364-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0364-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gvhA in template set Warning: unaligning (T0364)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0364)D115 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0364)Q120 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0364)F124 because last residue in template chain is (2gvhA)I262 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAA T0364 49 :RGQSGNSLFTLEAH 2gvhA 183 :SRYCGKLVVLASSE T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLH 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLW T0364 97 :RAGFD 2gvhA 234 :NLLTG T0364 102 :EVLAASEQMLLHV 2gvhA 241 :HITATGHFTMVAV T0364 121 :SAP 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=193 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 2fs2A/T0364-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fs2A expands to /projects/compbio/data/pdb/2fs2.pdb.gz 2fs2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2fs2A/T0364-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0364-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fs2A to template set # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0364)L112 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0364 5 :ITYR 2fs2A 34 :AVVT T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATD 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFA T0364 47 :DSRGQSGNSLFTLEAH 2fs2A 66 :YACNSQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAA 2fs2A 117 :QQQKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=199 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 2fs2A/T0364-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2fs2A/T0364-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0364-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0364)L112 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0364 3 :ALITYR 2fs2A 32 :GFAVVT T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATDAL 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYA T0364 49 :RGQSGNSLFTLEAH 2fs2A 68 :CNSQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQ T0364 101 :DEVLAA 2fs2A 119 :QKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=205 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 2fs2A/T0364-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2fs2A/T0364-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0364-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fs2A in template set Warning: unaligning (T0364)T9 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0364)T10 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0364)I63 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0364)N64 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0364)S107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0364)E108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 T0364 11 :VQEDWVDYNGHLRDAFYLLIFSYATDALMD 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACN T0364 51 :QSGNSLFTLEAH 2fs2A 70 :SQGLAAVASACT T0364 65 :YLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAA 2fs2A 117 :QQQKTVAL T0364 109 :QML 2fs2A 127 :GKS Number of specific fragments extracted= 5 number of extra gaps= 3 total=210 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 1wluA/T0364-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wluA expands to /projects/compbio/data/pdb/1wlu.pdb.gz 1wluA:# T0364 read from 1wluA/T0364-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0364-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wluA to template set # found chain 1wluA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1wluA)L117 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1wluA 19 :GEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRG T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1wluA 60 :PAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1wluA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=213 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 1wluA/T0364-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1wluA/T0364-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0364-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wluA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1wluA)L117 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1wluA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1wluA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1wluA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=216 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 1wluA/T0364-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1wluA/T0364-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0364-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wluA in template set T0364 9 :TTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1wluA 25 :GEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVS T0364 100 :FDEVLAASEQMLLH 1wluA 103 :EGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=219 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 1j1yA/T0364-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j1yA expands to /projects/compbio/data/pdb/1j1y.pdb.gz 1j1yA:# T0364 read from 1j1yA/T0364-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0364-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j1yA to template set # found chain 1j1yA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1j1yA)L117 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1j1yA 21 :AVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1j1yA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=222 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 1j1yA/T0364-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1j1yA/T0364-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0364-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1yA in template set Warning: unaligning (T0364)V114 because last residue in template chain is (1j1yA)L117 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGL 1j1yA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0364 56 :LFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSE T0364 101 :DEVLAASEQMLLH 1j1yA 104 :GKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=225 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 1j1yA/T0364-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1j1yA/T0364-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0364-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1yA in template set T0364 7 :YRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1j1yA 23 :VAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVS T0364 100 :FDEVLAASEQMLLH 1j1yA 103 :EGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=228 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 1ixlA/T0364-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ixlA expands to /projects/compbio/data/pdb/1ixl.pdb.gz 1ixlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1ixlA/T0364-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0364-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ixlA to template set # found chain 1ixlA in template set T0364 5 :ITYRTTVQEDWV 1ixlA 28 :AEVELETIDEMK T0364 17 :DYNGHLRDAFYLLIFSYATD 1ixlA 41 :DEKGLVHGGFTFGLADYAAM T0364 46 :ADS 1ixlA 61 :LAV T0364 50 :GQS 1ixlA 64 :NEP T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1ixlA 67 :TVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYRE T0364 101 :DEVLAASEQMLLHV 1ixlA 111 :EEVVLEGKFYCYVL T0364 117 :AG 1ixlA 125 :EK 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=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixlA/T0364-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1ixlA/T0364-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0364-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ixlA in template set T0364 3 :ALITYRTTVQEDWV 1ixlA 26 :GYAEVELETIDEMK T0364 17 :DYNGHLRDAFYLLIFSYATDALM 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0364 50 :GQSGN 1ixlA 64 :NEPTV T0364 57 :FTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1ixlA 69 :VLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYRE T0364 101 :DEVLAASEQMLLHV 1ixlA 111 :EEVVLEGKFYCYVL T0364 117 :AG 1ixlA 125 :EK 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=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixlA/T0364-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1ixlA/T0364-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0364-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ixlA in template set T0364 7 :YRTTVQEDW 1ixlA 30 :VELETIDEM T0364 17 :DYNGHLRDAFYLLIFSYATDALM 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0364 54 :NSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1ixlA 66 :PTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYR T0364 100 :FDEVLAASEQMLL 1ixlA 110 :EEEVVLEGKFYCY Number of specific fragments extracted= 4 number of extra gaps= 0 total=245 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 1zkiA/T0364-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zkiA expands to /projects/compbio/data/pdb/1zki.pdb.gz 1zkiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 33, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 299, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 528, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1zkiA # T0364 read from 1zkiA/T0364-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0364-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zkiA to template set # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDR 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSS T0364 49 :RGQSGNSLFTLEAHINYLHEVK 1zkiA 67 :SHGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQG T0364 101 :DEVLAASEQMLL 1zkiA 116 :DKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=249 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 1zkiA/T0364-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1zkiA/T0364-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0364-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDAL 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLA T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVK 1zkiA 64 :CSSSHGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHRA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQG T0364 101 :DEVLAASEQMLL 1zkiA 116 :DKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=253 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 1zkiA/T0364-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1zkiA/T0364-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0364-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkiA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSS T0364 50 :GQSGNSLFTLEAHINYLHEVK 1zkiA 68 :HGFDRQSVTLECKINYIRAVA T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQ T0364 100 :FDEVLAASEQMLL 1zkiA 115 :GDKLVAKGQGTFA 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=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/T0364-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cwzA expands to /projects/compbio/data/pdb/2cwz.pdb.gz 2cwzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2cwzA/T0364-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0364-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cwzA to template set # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 1 :M 2cwzA 5 :P T0364 2 :PALITYRTTVQEDWV 2cwzA 7 :GYEAVFETVVTPEMT T0364 24 :DAFYLLIFSYATDAL 2cwzA 36 :TYWMVKHMELAGRKI T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cwzA 51 :ILPFLEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0364 99 :GFDEVLAASEQMLLHVD 2cwzA 103 :ELGDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=263 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 2cwzA/T0364-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2cwzA/T0364-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0364-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 2 :PALITYRTTVQEDWV 2cwzA 7 :GYEAVFETVVTPEMT T0364 22 :LRDAFYLLIFSYATDAL 2cwzA 34 :YATYWMVKHMELAGRKI T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 2cwzA 51 :ILPFLEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNEL T0364 101 :DEVLAASEQMLLHVD 2cwzA 105 :GDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 5 number of extra gaps= 0 total=268 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 2cwzA/T0364-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2cwzA/T0364-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0364-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cwzA in template set Warning: unaligning (T0364)Q143 because last residue in template chain is (2cwzA)R138 T0364 3 :ALITYRTTVQEDWV 2cwzA 8 :YEAVFETVVTPEMT T0364 22 :LRDAFYLLIFSYATDALMDRI 2cwzA 34 :YATYWMVKHMELAGRKIILPF T0364 44 :L 2cwzA 55 :L T0364 51 :QSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 2cwzA 56 :EEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0364 99 :GFDEVLAASEQMLLHVD 2cwzA 103 :ELGDLIGVGRTEQVILP T0364 125 :GHTTVCRLNHLVEQQEGA 2cwzA 120 :KAKVEALFRRLKERWEAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=274 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 1q4uA/T0364-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q4uA expands to /projects/compbio/data/pdb/1q4u.pdb.gz 1q4uA:Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1q4uA # T0364 read from 1q4uA/T0364-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0364-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q4uA to template set # found chain 1q4uA in template set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 46 :ATASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0364 99 :GFDEVLAASEQMLLH 1q4uA 132 :DAGRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=279 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 1q4uA/T0364-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1q4uA/T0364-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0364-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q4uA in template set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 46 :ATASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHRAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDDA T0364 101 :DEVLAASEQMLLH 1q4uA 134 :GRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=284 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 1q4uA/T0364-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1q4uA/T0364-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0364-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q4uA in template set Warning: unaligning (T0364)P123 because last residue in template chain is (1q4uA)R150 T0364 6 :TYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1q4uA 47 :TASVEVTDTLRQRWGLVHGGAYCALAEMLATEAT T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLG 1q4uA 81 :VAVVHEKGMMAVGQSNHTSFFRPVKEG T0364 74 :EVWVQTQILGFDRKRLHVYHSLHR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0364 99 :GFDEVLAASEQMLLH 1q4uA 132 :DAGRLCAVSSMSIAV T0364 120 :QSA 1q4uA 147 :RPR Number of specific fragments extracted= 5 number of extra gaps= 0 total=289 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 2b3nA/T0364-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b3nA expands to /projects/compbio/data/pdb/2b3n.pdb.gz 2b3nA:Skipped atom 125, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 126, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 130, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 131, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 133, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 134, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2b3nA # T0364 read from 2b3nA/T0364-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0364-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b3nA to template set # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 2 :PALITYRTTVQE 2b3nA 39 :GYRFEYEKKLCE T0364 33 :YATDALMDRIGLDAD 2b3nA 51 :IDVAMFGLISGDLNP T0364 48 :SRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 95 :AVARLPGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 98 :A 2b3nA 145 :G T0364 101 :DEVLAASEQMLLH 2b3nA 146 :DKVVAEGVVKVLI Number of specific fragments extracted= 5 number of extra gaps= 1 total=294 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 2b3nA/T0364-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2b3nA/T0364-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0364-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 2 :PALITYRTTVQE 2b3nA 39 :GYRFEYEKKLCE T0364 33 :YATDALMDRIGL 2b3nA 51 :IDVAMFGLISGD T0364 45 :DADSRGQS 2b3nA 69 :DEDFASKT T0364 53 :GNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 98 :A 2b3nA 145 :G T0364 101 :DEVLAASEQMLLH 2b3nA 146 :DKVVAEGVVKVLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=300 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 2b3nA/T0364-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2b3nA/T0364-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0364-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3nA in template set Warning: unaligning (T0364)H96 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0364)R97 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0364 3 :ALITYRTTVQEDWVDYNG 2b3nA 40 :YRFEYEKKLCEIDVAMFG T0364 21 :HLRDAFYLLIFSYA 2b3nA 82 :VVHGMLTTSLVSAA T0364 49 :RGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSL 2b3nA 96 :VARLPGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0364 100 :FDEVLAASEQMLLH 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 4 number of extra gaps= 1 total=304 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 1o0iA/T0364-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o0iA expands to /projects/compbio/data/pdb/1o0i.pdb.gz 1o0iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1o0iA/T0364-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0364-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o0iA to template set # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 1o0iA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 1o0iA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=309 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 1o0iA/T0364-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1o0iA/T0364-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0364-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVKL 1o0iA 75 :EEGKTVVGLDINANHLRPVRS T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 1o0iA 96 :GKVTARATPINLGRNIQVWQIDIRTEE T0364 101 :DEVLAASEQMLLHV 1o0iA 123 :NKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=314 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 1o0iA/T0364-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1o0iA/T0364-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0364-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0iA in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 1o0iA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 1o0iA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 1o0iA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLH 1o0iA 121 :EENKLCCVSRLTLSV Number of specific fragments extracted= 5 number of extra gaps= 0 total=319 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 1psuA/T0364-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1psuA expands to /projects/compbio/data/pdb/1psu.pdb.gz 1psuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1psuA/T0364-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0364-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1psuA to template set # found chain 1psuA in template set T0364 5 :ITYRTTVQEDWVDYNGHLRDAFYLLIFSYATD 1psuA 34 :AVVTMTVTAQMLNGHQSCHGGQLFSLADTAFA T0364 47 :DSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1psuA 66 :YACNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAASEQMLL 1psuA 117 :QQQKTVALFRGKSH Number of specific fragments extracted= 3 number of extra gaps= 0 total=322 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 1psuA/T0364-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1psuA/T0364-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0364-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1psuA in template set T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDAL 1psuA 32 :GFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYA T0364 49 :RGQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1psuA 68 :CNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQ T0364 101 :DEVLAASEQMLL 1psuA 119 :QKTVALFRGKSH Number of specific fragments extracted= 3 number of extra gaps= 0 total=325 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 1psuA/T0364-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1psuA/T0364-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0364-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1psuA in template set T0364 8 :RTTVQEDWVDYNGHLRDAFYLLIFSYATDALM 1psuA 37 :TMTVTAQMLNGHQSCHGGQLFSLADTAFAYAC T0364 50 :GQSGNSLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1psuA 69 :NSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0364 99 :GFDEVLAASEQML 1psuA 117 :QQQKTVALFRGKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=328 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 1vh5A/T0364-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vh5A expands to /projects/compbio/data/pdb/1vh5.pdb.gz 1vh5A:Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 521, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 523, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 529, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 531, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 533, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 628, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 630, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 632, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 1012, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 1014, because occupancy 0.350 <= existing 0.650 in 1vh5A # T0364 read from 1vh5A/T0364-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0364-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vh5A to template set # found chain 1vh5A in template set T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVK 1vh5A 75 :EGEQKVVGLEINANHVRSAR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFD T0364 99 :GFDEVLAASEQMLLHV 1vh5A 121 :EKGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=332 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 1vh5A/T0364-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1vh5A/T0364-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0364-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vh5A in template set Warning: unaligning (T0364)D115 because last residue in template chain is (1vh5A)E137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVKL 1vh5A 75 :EGEQKVVGLEINANHVRSARE T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 1vh5A 96 :GRVRGVCKPLHLGSRHQVWQIEIFDEK T0364 101 :DEVLAASEQMLLHV 1vh5A 123 :GRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=336 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 1vh5A/T0364-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1vh5A/T0364-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0364-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vh5A in template set T0364 4 :LITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIG 1vh5A 35 :TLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0364 51 :QSGNSLFTLEAHINYLHEVK 1vh5A 75 :EGEQKVVGLEINANHVRSAR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFD T0364 99 :GFDEVLAASEQMLLHV 1vh5A 121 :EKGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=340 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 1t82A/T0364-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t82A expands to /projects/compbio/data/pdb/1t82.pdb.gz 1t82A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1t82A/T0364-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0364-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t82A to template set # found chain 1t82A in template set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDR 1t82A 41 :APNINLHHTMFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 82 :LGFDRKRLHVYHSLHRA 1t82A 112 :QRGRKAKVKLEVQLFCD T0364 101 :DEVLAASEQMLLHV 1t82A 129 :GKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=344 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 1t82A/T0364-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1t82A/T0364-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0364-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t82A in template set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDR 1t82A 41 :APNINLHHTMFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 83 :GFDRKRLHVYHSLHRA 1t82A 113 :RGRKAKVKLEVQLFCD T0364 101 :DEVLAASEQMLLHV 1t82A 129 :GKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=348 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 1t82A/T0364-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1t82A/T0364-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0364-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t82A in template set Warning: unaligning (T0364)D115 because last residue in template chain is (1t82A)P143 T0364 22 :LRDAFYLLIFSYATDALMDR 1t82A 50 :MFAGSIYTIMTLTGWGMVWL T0364 46 :ADSRGQSGNSLFTLEAHINYLHEVKLGTEVWVQ 1t82A 70 :QQQLLNVDGDIVLADAHIRYLAPVTSAPEVKVR T0364 82 :LGFDRKRLHVYHSLHR 1t82A 112 :QRGRKAKVKLEVQLFC T0364 100 :FDEVLAASEQMLLHV 1t82A 128 :DGKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=352 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 2b6eA/T0364-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b6eA expands to /projects/compbio/data/pdb/2b6e.pdb.gz 2b6eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 2b6eA/T0364-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0364-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b6eA to template set # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 2b6eA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVK 2b6eA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 2b6eA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=357 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 2b6eA/T0364-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2b6eA/T0364-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0364-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRI 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0364 44 :L 2b6eA 74 :L T0364 51 :QSGNSLFTLEAHINYLHEVKL 2b6eA 75 :EEGKTVVGLDINANHLRPVRS T0364 73 :TEVWVQTQILGFDRKRLHVYHSLHRAG 2b6eA 96 :GKVTARATPINLGRNIQVWQIDIRTEE T0364 101 :DEVLAASEQMLLHV 2b6eA 123 :NKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=362 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 2b6eA/T0364-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 2b6eA/T0364-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0364-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6eA in template set Warning: unaligning (T0364)D115 because last residue in template chain is (2b6eA)N137 T0364 2 :PALITYRTTVQEDWVDYNGHLRDAFYLLIFS 2b6eA 33 :EDWIEATMPVDHRTMQPFGVLHGGVSVALAE T0364 34 :ATDALMDRIGL 2b6eA 64 :TIGSLAGSLCL T0364 51 :QSGNSLFTLEAHINYLHEVK 2b6eA 75 :EEGKTVVGLDINANHLRPVR T0364 72 :GTEVWVQTQILGFDRKRLHVYHSLHR 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0364 99 :GFDEVLAASEQMLLHV 2b6eA 121 :EENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=367 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 1sh8A/T0364-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sh8A expands to /projects/compbio/data/pdb/1sh8.pdb.gz 1sh8A:# T0364 read from 1sh8A/T0364-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0364-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sh8A to template set # found chain 1sh8A in template set T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDRI 1sh8A 41 :AGNENHIGSMYAGALFTLAELPGGALFLTS T0364 44 :LDAD 1sh8A 71 :FDSA T0364 53 :GNSLFTLEAHINYLHEVKL 1sh8A 75 :RFYPIVKEMTLRFRRPAKG T0364 74 :EVWVQTQIL 1sh8A 94 :DIRVEARLD T0364 85 :DRKRLHVYHSLHR 1sh8A 117 :GKAEYSLELQLTD T0364 99 :GFDEVLAASEQMLLHVDLAG 1sh8A 130 :EQGEVVAESAALYQLRSHAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=373 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 1sh8A/T0364-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1sh8A/T0364-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0364-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sh8A in template set T0364 13 :EDWVDYNGHLRDAFYLLIFSYATDALMDRI 1sh8A 41 :AGNENHIGSMYAGALFTLAELPGGALFLTS T0364 44 :LDA 1sh8A 71 :FDS T0364 52 :SGNSLFTLEAHINYLHEVK 1sh8A 74 :ARFYPIVKEMTLRFRRPAK T0364 73 :TEVWVQTQIL 1sh8A 93 :GDIRVEARLD T0364 85 :DRKRLHVYHSLHRAG 1sh8A 117 :GKAEYSLELQLTDEQ T0364 101 :DEVLAASEQMLLHVDLAG 1sh8A 132 :GEVVAESAALYQLRSHAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=379 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 1sh8A/T0364-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1sh8A/T0364-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0364-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sh8A in template set T0364 19 :NGHLRDAFYLLIFSYATDALMDRI 1sh8A 47 :IGSMYAGALFTLAELPGGALFLTS T0364 44 :LD 1sh8A 71 :FD T0364 51 :QSGNSLFTLEAHINYLHEVK 1sh8A 73 :SARFYPIVKEMTLRFRRPAK T0364 73 :TEVWVQTQI 1sh8A 93 :GDIRVEARL T0364 85 :DRKRLHVYHSLHR 1sh8A 117 :GKAEYSLELQLTD T0364 99 :GFDEVLAASEQMLLHVD 1sh8A 130 :EQGEVVAESAALYQLRS Number of specific fragments extracted= 6 number of extra gaps= 0 total=385 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 1u1zA/T0364-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u1zA expands to /projects/compbio/data/pdb/1u1z.pdb.gz 1u1zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0364 read from 1u1zA/T0364-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0364-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u1zA to template set # found chain 1u1zA in template set Warning: unaligning (T0364)H21 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 6 :TYRTTVQEDWVDYNG 1u1zA 34 :RAYKNVSINEPFFNG T0364 22 :LRDAFYLLIFSYATDALMDR 1u1zA 56 :MPGVLIIEAMAQAAGILGFK T0364 42 :IGLD 1u1zA 77 :LDVK T0364 55 :SLFTLEAH 1u1zA 86 :LYYFVGSD T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVD T0364 101 :DEVLAASEQMLL 1u1zA 131 :DKPVCSAEIICA Number of specific fragments extracted= 6 number of extra gaps= 1 total=391 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 1u1zA/T0364-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1u1zA/T0364-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0364-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1zA in template set Warning: unaligning (T0364)H21 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 3 :ALITYRTTVQEDWVDYNG 1u1zA 31 :KRIRAYKNVSINEPFFNG T0364 22 :LRDAFYLLIFSYATDALMDRI 1u1zA 56 :MPGVLIIEAMAQAAGILGFKM T0364 43 :GLD 1u1zA 78 :DVK T0364 55 :SLFTLEAH 1u1zA 86 :LYYFVGSD T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRA 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVD T0364 101 :DEVLAASEQMLL 1u1zA 131 :DKPVCSAEIICA Number of specific fragments extracted= 6 number of extra gaps= 1 total=397 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 1u1zA/T0364-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0364 read from 1u1zA/T0364-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0364-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1zA in template set Warning: unaligning (T0364)A46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0364)N54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0364 24 :DAFYLLIFSYATDALMDRI 1u1zA 58 :GVLIIEAMAQAAGILGFKM T0364 43 :GLD 1u1zA 78 :DVK T0364 55 :SLFTLEA 1u1zA 86 :LYYFVGS T0364 63 :INYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHR 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATV T0364 100 :FDEVLAASEQMLLH 1u1zA 130 :DDKPVCSAEIICAE Number of specific fragments extracted= 5 number of extra gaps= 0 total=402 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 1lo9A/T0364-1lo9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lo9A expands to /projects/compbio/data/pdb/1lo9.pdb.gz 1lo9A:# T0364 read from 1lo9A/T0364-1lo9A-t06-local-adpstyle5.a2m # 1lo9A read from 1lo9A/T0364-1lo9A-t06-local-adpstyle5.a2m # adding 1lo9A to template set # found chain 1lo9A in template set Warning: unaligning (T0364)P2 because first residue in template chain is (1lo9A)A2 T0364 3 :ALITYRTTVQEDWVDYNGHLRDAFYLLIFSYATDALMDRIGLDAD 1lo9A 3 :RSITMQQRIEFGDCNPAGIVWYPNYHRWLDAASRNYFIKCGLPPW T0364 48 :SRGQSGN 1lo9A 50 :TVVERGI T0364 55 :SLFTLEAHINYLHEVKLGTEVWVQTQILGFDRKRLHVYHSLHRAG 1lo9A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTT T0364 100 :FDEVLAASEQMLLHV 1lo9A 106 :DVQLVMRADEIRVFA T0364 115 :DLAGPQSAPFGHTTVCR 1lo9A 123 :DGERLRAIEVPADYIEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=407 Will force an alignment to be made, even if fragment is small Number of alignments=88 # command:CPU_time= 21.317 sec, elapsed time= 22.898 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 88 Adding 12090 constraints to all_contacts Done adding distance constraints # command:CPU_time= 21.388 sec, elapsed time= 22.970 sec. # command:Reading probabilities from T0364.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 46.270 Optimizing... Probability sum: -290.699, CN propb: -290.699 weights: 0.516 constraints: 363 # command:CPU_time= 26.223 sec, elapsed time= 27.839 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 363 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 363 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 501 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 501 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 10014 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 10014 # command:CPU_time= 26.417 sec, elapsed time= 28.197 sec. # command: