# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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 /projects/compbio/experiments/protein-predict/casp7/T0311/ # command:# Making conformation for sequence T0311 numbered 1 through 97 Created new target T0311 from T0311.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0311/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0311//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0311/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0311//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0311/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0311/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0311/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lmb3/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0311 read from 1lmb3/merged-good-all-a2m # 1lmb3 read from 1lmb3/merged-good-all-a2m # found chain 1lmb3 in training set Warning: unaligning (T0311)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1lmb3)D38 Warning: unaligning (T0311)R29 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1lmb3)D38 T0311 11 :DIIQESLDELNVSLREF 1lmb3 20 :AIYEKKKNELGLSQESV # choosing archetypes in rotamer library T0311 30 :AMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1lmb3 39 :KMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE T0311 73 :AWSLAEAEKTVD 1lmb3 78 :PSIAREIYEMYE Number of specific fragments extracted= 3 number of extra gaps= 1 total=3 Number of alignments=1 # 1lmb3 read from 1lmb3/merged-good-all-a2m # found chain 1lmb3 in training set Warning: unaligning (T0311)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1lmb3)D38 Warning: unaligning (T0311)R29 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1lmb3)D38 T0311 11 :DIIQESLDELNVSLREF 1lmb3 20 :AIYEKKKNELGLSQESV T0311 30 :AMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1lmb3 39 :KMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE T0311 77 :AEAEKTVDVSR 1lmb3 78 :PSIAREIYEMY Number of specific fragments extracted= 3 number of extra gaps= 1 total=6 Number of alignments=2 # 1lmb3 read from 1lmb3/merged-good-all-a2m # found chain 1lmb3 in training set Warning: unaligning (T0311)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1lmb3)D38 Warning: unaligning (T0311)R29 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1lmb3)D38 T0311 11 :DIIQESLDELNVSLREF 1lmb3 20 :AIYEKKKNELGLSQESV T0311 30 :AMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMW 1lmb3 39 :KMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEF T0311 81 :KTVDVSRLRRLV 1lmb3 78 :PSIAREIYEMYE Number of specific fragments extracted= 3 number of extra gaps= 1 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1utxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1utxA expands to /projects/compbio/data/pdb/1utx.pdb.gz 1utxA:Skipped atom 6, because occupancy 0.5 <= existing 0.500 in 1utxA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1utxA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1utxA # T0311 read from 1utxA/merged-good-all-a2m # 1utxA read from 1utxA/merged-good-all-a2m # adding 1utxA to template set # found chain 1utxA in template set T0311 13 :IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1utxA 6 :LKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE Number of specific fragments extracted= 1 number of extra gaps= 0 total=10 Number of alignments=4 # 1utxA read from 1utxA/merged-good-all-a2m # found chain 1utxA in template set T0311 13 :IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1utxA 6 :LKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE Number of specific fragments extracted= 1 number of extra gaps= 0 total=11 Number of alignments=5 # 1utxA read from 1utxA/merged-good-all-a2m # found chain 1utxA in template set T0311 13 :IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1utxA 6 :LKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE Number of specific fragments extracted= 1 number of extra gaps= 0 total=12 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zzcA expands to /projects/compbio/data/pdb/1zzc.pdb.gz 1zzcA:# T0311 read from 1zzcA/merged-good-all-a2m # 1zzcA read from 1zzcA/merged-good-all-a2m # adding 1zzcA to template set # found chain 1zzcA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zzcA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 1zzcA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=14 Number of alignments=7 # 1zzcA read from 1zzcA/merged-good-all-a2m # found chain 1zzcA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zzcA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 1zzcA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 Number of alignments=8 # 1zzcA read from 1zzcA/merged-good-all-a2m # found chain 1zzcA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zzcA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 1zzcA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=18 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2awiA expands to /projects/compbio/data/pdb/2awi.pdb.gz 2awiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 2awiA/merged-good-all-a2m # 2awiA read from 2awiA/merged-good-all-a2m # adding 2awiA to template set # found chain 2awiA in template set Warning: unaligning (T0311)P7 because first residue in template chain is (2awiA)F2 T0311 8 :RPGDIIQESLDELNVSLREFARAM 2awiA 3 :KIGSVLKQIRQELNYHQIDLYSGI T0311 33 :IAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNL 2awiA 27 :MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEILNR T0311 71 :QNAWSLAEAEKTVD 2awiA 74 :ETGKEKLLISKIFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 Number of alignments=10 # 2awiA read from 2awiA/merged-good-all-a2m # found chain 2awiA in template set Warning: unaligning (T0311)P7 because first residue in template chain is (2awiA)F2 T0311 8 :RPGDIIQESLDELNVSLREFARAM 2awiA 3 :KIGSVLKQIRQELNYHQIDLYSGI T0311 33 :IAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNL 2awiA 27 :MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEILNR T0311 71 :QNAWSLAEAEKTVD 2awiA 74 :ETGKEKLLISKIFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 Number of alignments=11 # 2awiA read from 2awiA/merged-good-all-a2m # found chain 2awiA in template set T0311 8 :RPGDIIQESLDELNVSLREFARA 2awiA 3 :KIGSVLKQIRQELNYHQIDLYSG T0311 33 :IAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNL 2awiA 27 :MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEILNR T0311 71 :QNAWSLAEAEKTV 2awiA 74 :ETGKEKLLISKIF Number of specific fragments extracted= 3 number of extra gaps= 0 total=27 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lccA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lccA expands to /projects/compbio/data/pdb/1lcc.pdb.gz 1lccA:# T0311 read from 1lccA/merged-good-all-a2m # 1lccA read from 1lccA/merged-good-all-a2m # adding 1lccA to template set # found chain 1lccA in template set Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lccA)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)S28 T0311 21 :NVSLREFARAMEIAPSTASRLLT 1lccA 3 :PVTLYDVAEYAGVSYQTVSRVVN T0311 47 :ALTPEMAIKLSVV 1lccA 29 :HVSAKTREKVEAA Number of specific fragments extracted= 2 number of extra gaps= 1 total=29 Number of alignments=13 # 1lccA read from 1lccA/merged-good-all-a2m # found chain 1lccA in template set Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lccA)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)S28 T0311 21 :NVSLREFARAMEIAPSTASRLLT 1lccA 3 :PVTLYDVAEYAGVSYQTVSRVVN T0311 47 :ALTPEMAIKLSVV 1lccA 29 :HVSAKTREKVEAA Number of specific fragments extracted= 2 number of extra gaps= 1 total=31 Number of alignments=14 # 1lccA read from 1lccA/merged-good-all-a2m # found chain 1lccA in template set Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lccA)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lccA)S28 T0311 21 :NVSLREFARAMEIAPSTASRLLT 1lccA 3 :PVTLYDVAEYAGVSYQTVSRVVN T0311 47 :ALTPEMAIKLSVV 1lccA 29 :HVSAKTREKVEAA Number of specific fragments extracted= 2 number of extra gaps= 1 total=33 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b0nA expands to /projects/compbio/data/pdb/1b0n.pdb.gz 1b0nA:Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 1b0nA Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 1b0nA Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1b0nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 1b0nA # T0311 read from 1b0nA/merged-good-all-a2m # 1b0nA read from 1b0nA/merged-good-all-a2m # adding 1b0nA to template set # found chain 1b0nA in template set T0311 9 :PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTG 1b0nA 2 :IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERN T0311 45 :KAALTPEMAIKLSVVIGSSPQMWL 1b0nA 39 :QTNPSIQFLEKVSAVLDVSVHTLL T0311 69 :NLQNAWS 1b0nA 80 :KLVRDAM T0311 76 :LAEAEKTVDVSRLR 1b0nA 92 :KKQFREFLDYQKWR Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 Number of alignments=16 # 1b0nA read from 1b0nA/merged-good-all-a2m # found chain 1b0nA in template set T0311 9 :PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTG 1b0nA 2 :IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERN T0311 45 :KAALTPEMAIKLSVVIGSSPQMWL 1b0nA 39 :QTNPSIQFLEKVSAVLDVSVHTLL T0311 75 :SLAEAE 1b0nA 78 :WEKLVR Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 Number of alignments=17 # 1b0nA read from 1b0nA/merged-good-all-a2m # found chain 1b0nA in template set Warning: unaligning (T0311)V92 because last residue in template chain is (1b0nA)Q108 T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTG 1b0nA 3 :GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERN T0311 45 :KAALTPEMAIKLSVVIGSSPQMWL 1b0nA 39 :QTNPSIQFLEKVSAVLDVSVHTLL T0311 69 :NLQNAWSL 1b0nA 78 :WEKLVRDA T0311 77 :AEAEKTVDVSRLRRL 1b0nA 93 :KQFREFLDYQKWRKS Number of specific fragments extracted= 4 number of extra gaps= 0 total=44 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zug/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zug expands to /projects/compbio/data/pdb/1zug.pdb.gz 1zug:Warning: there is no chain 1zug will retry with 1zugA # T0311 read from 1zug/merged-good-all-a2m # 1zug read from 1zug/merged-good-all-a2m # adding 1zug to template set # found chain 1zug in template set Warning: unaligning (T0311)G10 because of BadResidue code BAD_PEPTIDE in next template residue (1zug)E6 Warning: unaligning (T0311)D11 because of BadResidue code BAD_PEPTIDE at template residue (1zug)E6 T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zug 7 :RLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 1zug 47 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 1 total=46 Number of alignments=19 # 1zug read from 1zug/merged-good-all-a2m # found chain 1zug in template set Warning: unaligning (T0311)G10 because of BadResidue code BAD_PEPTIDE in next template residue (1zug)E6 Warning: unaligning (T0311)D11 because of BadResidue code BAD_PEPTIDE at template residue (1zug)E6 T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zug 7 :RLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 1zug 47 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 1 total=48 Number of alignments=20 # 1zug read from 1zug/merged-good-all-a2m # found chain 1zug in template set Warning: unaligning (T0311)D11 because of BadResidue code BAD_PEPTIDE at template residue (1zug)E6 T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1zug 7 :RLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 1zug 47 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 1 total=50 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lqc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lqc expands to /projects/compbio/data/pdb/1lqc.pdb.gz 1lqc:Warning: there is no chain 1lqc will retry with 1lqcA # T0311 read from 1lqc/merged-good-all-a2m # 1lqc read from 1lqc/merged-good-all-a2m # adding 1lqc to template set # found chain 1lqc in template set Warning: unaligning (T0311)M31 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)G14 Warning: unaligning (T0311)E32 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)G14 Warning: unaligning (T0311)I33 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)S16 Warning: unaligning (T0311)A34 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S16 Warning: unaligning (T0311)T37 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)V20 Warning: unaligning (T0311)A38 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)V20 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S28 T0311 23 :SLREFARA 1lqc 5 :TLYDVAEY T0311 35 :PS 1lqc 17 :YQ T0311 39 :SRLLT 1lqc 21 :SRVVN T0311 47 :ALTPEMAIKLSVVI 1lqc 29 :HVSAKTREKVEAAM Number of specific fragments extracted= 4 number of extra gaps= 3 total=54 # 1lqc read from 1lqc/merged-good-all-a2m # found chain 1lqc in template set Warning: unaligning (T0311)M31 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)G14 Warning: unaligning (T0311)E32 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)G14 Warning: unaligning (T0311)I33 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)S16 Warning: unaligning (T0311)A34 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S16 Warning: unaligning (T0311)T37 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)V20 Warning: unaligning (T0311)A38 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)V20 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S28 T0311 23 :SLREFARA 1lqc 5 :TLYDVAEY T0311 35 :PS 1lqc 17 :YQ T0311 39 :SRLLT 1lqc 21 :SRVVN T0311 47 :ALTPEMAIKLSVVI 1lqc 29 :HVSAKTREKVEAAM Number of specific fragments extracted= 4 number of extra gaps= 3 total=58 # 1lqc read from 1lqc/merged-good-all-a2m # found chain 1lqc in template set Warning: unaligning (T0311)M31 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)G14 Warning: unaligning (T0311)E32 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)G14 Warning: unaligning (T0311)I33 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)S16 Warning: unaligning (T0311)A34 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S16 Warning: unaligning (T0311)T37 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)V20 Warning: unaligning (T0311)A38 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)V20 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1lqc)A27 Warning: unaligning (T0311)K45 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)A27 Warning: unaligning (T0311)A46 because of BadResidue code BAD_PEPTIDE at template residue (1lqc)S28 T0311 23 :SLREFARA 1lqc 5 :TLYDVAEY T0311 35 :PS 1lqc 17 :YQ T0311 39 :SRLLT 1lqc 21 :SRVVN T0311 47 :ALTPEMAIKLSVVI 1lqc 29 :HVSAKTREKVEAAM Number of specific fragments extracted= 4 number of extra gaps= 3 total=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wpkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wpkA expands to /projects/compbio/data/pdb/1wpk.pdb.gz 1wpkA:Bad short name: CS for alphabet: pdb_atoms # T0311 read from 1wpkA/merged-good-all-a2m # 1wpkA read from 1wpkA/merged-good-all-a2m # adding 1wpkA to template set # found chain 1wpkA in template set T0311 14 :QESLD 1wpkA 91 :CRLLE T0311 19 :ELNVSLREFARAMEIAPSTASRL 1wpkA 97 :ETPVTLEALADQVAMSPFHLHRL T0311 56 :LSVVIGSSPQMW 1wpkA 120 :FKATTGMTPKAW T0311 71 :QNAWSLAEAEKTV 1wpkA 132 :QQAWRARRLRESL Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 Number of alignments=22 # 1wpkA read from 1wpkA/merged-good-all-a2m # found chain 1wpkA in template set T0311 14 :QESLD 1wpkA 91 :CRLLE T0311 19 :ELNVSLREFARAMEIAPSTASRL 1wpkA 97 :ETPVTLEALADQVAMSPFHLHRL T0311 56 :LSVVIGSSPQMW 1wpkA 120 :FKATTGMTPKAW T0311 71 :QNAWSLAEAEKTV 1wpkA 132 :QQAWRARRLRESL Number of specific fragments extracted= 4 number of extra gaps= 0 total=70 Number of alignments=23 # 1wpkA read from 1wpkA/merged-good-all-a2m # found chain 1wpkA in template set T0311 14 :QESLD 1wpkA 91 :CRLLE T0311 19 :ELNVSLREFARAMEIAPSTASRL 1wpkA 97 :ETPVTLEALADQVAMSPFHLHRL T0311 56 :LSVVIGSSPQMW 1wpkA 120 :FKATTGMTPKAW T0311 71 :QNAWSLAEAEKTV 1wpkA 132 :QQAWRARRLRESL Number of specific fragments extracted= 4 number of extra gaps= 0 total=74 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dw9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dw9A expands to /projects/compbio/data/pdb/1dw9.pdb.gz 1dw9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 196, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 198, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 200, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 202, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 217, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 219, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 221, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 249, because occupancy 0.250 <= existing 0.750 in 1dw9A Skipped atom 251, because occupancy 0.250 <= existing 0.750 in 1dw9A Skipped atom 253, because occupancy 0.250 <= existing 0.750 in 1dw9A Skipped atom 255, because occupancy 0.250 <= existing 0.750 in 1dw9A Skipped atom 257, because occupancy 0.250 <= existing 0.750 in 1dw9A Skipped atom 277, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 279, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 281, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 498, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 500, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 502, because occupancy 0.400 <= existing 0.600 in 1dw9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 597, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1dw9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 794, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 796, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 798, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 1005, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1006, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1008, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1009, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1011, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1012, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1014, because occupancy 0.300 <= existing 0.400 in 1dw9A Skipped atom 1045, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 1047, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 1049, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 1051, because occupancy 0.300 <= existing 0.700 in 1dw9A Skipped atom 1058, because occupancy 0.400 <= existing 0.600 in 1dw9A Skipped atom 1060, because occupancy 0.400 <= existing 0.600 in 1dw9A # T0311 read from 1dw9A/merged-good-all-a2m # 1dw9A read from 1dw9A/merged-good-all-a2m # adding 1dw9A to template set # found chain 1dw9A in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dw9A 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQST 1dw9A 93 :TMYRFYEMLQVYGTTLKALVHEKFG Number of specific fragments extracted= 2 number of extra gaps= 0 total=76 Number of alignments=25 # 1dw9A read from 1dw9A/merged-good-all-a2m # found chain 1dw9A in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dw9A 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQSTP 1dw9A 93 :TMYRFYEMLQVYGTTLKALVHEKFGD Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 Number of alignments=26 # 1dw9A read from 1dw9A/merged-good-all-a2m # found chain 1dw9A in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dw9A 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQST 1dw9A 93 :TMYRFYEMLQVYGTTLKALVHEKFG Number of specific fragments extracted= 2 number of extra gaps= 0 total=80 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b5aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b5aA expands to /projects/compbio/data/pdb/2b5a.pdb.gz 2b5aA:Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 2b5aA # T0311 read from 2b5aA/merged-good-all-a2m # 2b5aA read from 2b5aA/merged-good-all-a2m # adding 2b5aA to template set # found chain 2b5aA in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQNA 2b5aA 12 :GRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFRKMEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 Number of alignments=28 # 2b5aA read from 2b5aA/merged-good-all-a2m # found chain 2b5aA in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQNA 2b5aA 12 :GRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFRKMEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=82 Number of alignments=29 # 2b5aA read from 2b5aA/merged-good-all-a2m # found chain 2b5aA in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQNA 2b5aA 12 :GRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFRKMEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=83 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y7yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0311 read from 1y7yA/merged-good-all-a2m # 1y7yA read from 1y7yA/merged-good-all-a2m # found chain 1y7yA in training set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1y7yA 15 :GQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPR Number of specific fragments extracted= 1 number of extra gaps= 0 total=84 Number of alignments=31 # 1y7yA read from 1y7yA/merged-good-all-a2m # found chain 1y7yA in training set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1y7yA 15 :GQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPR Number of specific fragments extracted= 1 number of extra gaps= 0 total=85 Number of alignments=32 # 1y7yA read from 1y7yA/merged-good-all-a2m # found chain 1y7yA in training set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1y7yA 15 :GQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPR Number of specific fragments extracted= 1 number of extra gaps= 0 total=86 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rzrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rzrA expands to /projects/compbio/data/pdb/1rzr.pdb.gz 1rzrA:# T0311 read from 1rzrA/merged-good-all-a2m # 1rzrA read from 1rzrA/merged-good-all-a2m # adding 1rzrA to template set # found chain 1rzrA in template set Warning: unaligning (T0311)N21 because first residue in template chain is (1rzrA)N2 Warning: unaligning (T0311)A34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rzrA)A17 Warning: unaligning (T0311)S36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rzrA)A17 T0311 22 :VSLREFARAMEI 1rzrA 3 :VTIYDVAREASV T0311 37 :TASRLLTGKAALTPEMAIKLSVVI 1rzrA 18 :TVSRVVNGNPNVKPSTRKKVLETI Number of specific fragments extracted= 2 number of extra gaps= 0 total=88 Number of alignments=34 # 1rzrA read from 1rzrA/merged-good-all-a2m # found chain 1rzrA in template set Warning: unaligning (T0311)N21 because first residue in template chain is (1rzrA)N2 Warning: unaligning (T0311)A34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rzrA)A17 Warning: unaligning (T0311)S36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rzrA)A17 T0311 22 :VSLREFARAMEI 1rzrA 3 :VTIYDVAREASV T0311 37 :TASRLLTGKAALTPEMAIKLSVVI 1rzrA 18 :TVSRVVNGNPNVKPSTRKKVLETI Number of specific fragments extracted= 2 number of extra gaps= 0 total=90 Number of alignments=35 # 1rzrA read from 1rzrA/merged-good-all-a2m # found chain 1rzrA in template set Warning: unaligning (T0311)N21 because first residue in template chain is (1rzrA)N2 Warning: unaligning (T0311)A34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rzrA)A17 Warning: unaligning (T0311)S36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rzrA)A17 T0311 22 :VSLREFARAMEI 1rzrA 3 :VTIYDVAREASV T0311 37 :TASRLLTGKAALTPEMAIKLSVVI 1rzrA 18 :TVSRVVNGNPNVKPSTRKKVLETI Number of specific fragments extracted= 2 number of extra gaps= 0 total=92 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bnmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bnmA expands to /projects/compbio/data/pdb/2bnm.pdb.gz 2bnmA:Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 138, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 140, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 142, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 144, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 146, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 268, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 270, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 272, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 274, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 276, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 329, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 331, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 333, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 335, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 422, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 425, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 428, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 431, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 434, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 437, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 440, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 619, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 621, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 623, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 625, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 769, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 770, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 772, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 773, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 775, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 776, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 778, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 779, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 907, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 909, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1061, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1063, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1146, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1148, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1150, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1152, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1158, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1160, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1162, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1164, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1166, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1306, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1308, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1310, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1312, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1524, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1526, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1528, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1530, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 2bnmA # T0311 read from 2bnmA/merged-good-all-a2m # 2bnmA read from 2bnmA/merged-good-all-a2m # adding 2bnmA to template set # found chain 2bnmA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2bnmA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 2bnmA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=94 Number of alignments=37 # 2bnmA read from 2bnmA/merged-good-all-a2m # found chain 2bnmA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2bnmA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 2bnmA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=96 Number of alignments=38 # 2bnmA read from 2bnmA/merged-good-all-a2m # found chain 2bnmA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2bnmA 13 :ELLKDRREQVKMDHAALASLLGETPETVAAWENGEGG T0311 48 :LTPEMAIKLSVVIGSSPQ 2bnmA 51 :LTLTQLGRIAHVLGTSIG Number of specific fragments extracted= 2 number of extra gaps= 0 total=98 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lliA expands to /projects/compbio/data/pdb/1lli.pdb.gz 1lliA:# T0311 read from 1lliA/merged-good-all-a2m # 1lliA read from 1lliA/merged-good-all-a2m # adding 1lliA to template set # found chain 1lliA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1lliA 20 :AIYEKKKNELGLSQESLADKLGMGQSGIGALFNGINALNAYNAALLAKILKVSVE T0311 77 :AEAEKTVDVSRL 1lliA 78 :PSIAREIYEMYE Number of specific fragments extracted= 2 number of extra gaps= 0 total=100 Number of alignments=40 # 1lliA read from 1lliA/merged-good-all-a2m # found chain 1lliA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1lliA 20 :AIYEKKKNELGLSQESLADKLGMGQSGIGALFNGINALNAYNAALLAKILKVSVE T0311 77 :AEAEKTVDVSRL 1lliA 78 :PSIAREIYEMYE Number of specific fragments extracted= 2 number of extra gaps= 0 total=102 Number of alignments=41 # 1lliA read from 1lliA/merged-good-all-a2m # found chain 1lliA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMW 1lliA 20 :AIYEKKKNELGLSQESLADKLGMGQSGIGALFNGINALNAYNAALLAKILKVSVEEF T0311 77 :AEAEKTVDVSRL 1lliA 78 :PSIAREIYEMYE Number of specific fragments extracted= 2 number of extra gaps= 0 total=104 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hlvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hlvA expands to /projects/compbio/data/pdb/1hlv.pdb.gz 1hlvA:# T0311 read from 1hlvA/merged-good-all-a2m # 1hlvA read from 1hlvA/merged-good-all-a2m # adding 1hlvA to template set # found chain 1hlvA in template set T0311 12 :I 1hlvA 16 :I T0311 14 :QESLDE 1hlvA 17 :IQEVEE T0311 20 :LNVSLREFARAMEIAPSTASRLLTGK 1hlvA 24 :PDLRKGEIARRFNIPPSTLSTILKNK T0311 65 :Q 1hlvA 50 :R T0311 75 :SLAEAEKTVDVS 1hlvA 51 :AILASERKYGVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=109 Number of alignments=43 # 1hlvA read from 1hlvA/merged-good-all-a2m # found chain 1hlvA in template set T0311 12 :I 1hlvA 16 :I T0311 14 :QESLDE 1hlvA 17 :IQEVEE T0311 20 :LNVSLREFARAMEIAPSTASRLLTGK 1hlvA 24 :PDLRKGEIARRFNIPPSTLSTILKNK T0311 74 :WSLAEAEKTVDVSRLRRLVTQS 1hlvA 50 :RAILASERKYGVASTCRKTNKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=113 Number of alignments=44 # 1hlvA read from 1hlvA/merged-good-all-a2m # found chain 1hlvA in template set T0311 12 :I 1hlvA 16 :I T0311 14 :QESLDE 1hlvA 17 :IQEVEE T0311 20 :LNVSLREFARAMEIAPSTASRLLTGK 1hlvA 24 :PDLRKGEIARRFNIPPSTLSTILKNK T0311 51 :EMAIKLSVVIG 1hlvA 50 :RAILASERKYG T0311 64 :PQMWLNLQNAWSL 1hlvA 74 :YDKLEGLLIAWFQ T0311 77 :AEAEKTV 1hlvA 98 :IILKEKA T0311 85 :VSRLRRLVTQSTP 1hlvA 105 :LRIAEELGMDDFT Number of specific fragments extracted= 7 number of extra gaps= 0 total=120 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a6cA expands to /projects/compbio/data/pdb/2a6c.pdb.gz 2a6cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 94, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 2a6cA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 2a6cA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 2a6cA/merged-good-all-a2m # 2a6cA read from 2a6cA/merged-good-all-a2m # adding 2a6cA to template set # found chain 2a6cA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2a6cA 9 :IVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKID T0311 48 :LTPEMAIKLSVVIGSS 2a6cA 47 :FSLESLIDMITSIGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=122 Number of alignments=46 # 2a6cA read from 2a6cA/merged-good-all-a2m # found chain 2a6cA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2a6cA 9 :IVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKID T0311 48 :LTPEMAIKLSVVIGSS 2a6cA 47 :FSLESLIDMITSIGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=124 Number of alignments=47 # 2a6cA read from 2a6cA/merged-good-all-a2m # found chain 2a6cA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2a6cA 9 :IVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKID T0311 48 :LTPEMAIKLSVVIGSS 2a6cA 47 :FSLESLIDMITSIGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=126 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wh8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wh8A expands to /projects/compbio/data/pdb/1wh8.pdb.gz 1wh8A:# T0311 read from 1wh8A/merged-good-all-a2m # 1wh8A read from 1wh8A/merged-good-all-a2m # adding 1wh8A to template set # found chain 1wh8A in template set Warning: unaligning (T0311)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1wh8A)K104 Warning: unaligning (T0311)D84 because of BadResidue code BAD_PEPTIDE at template residue (1wh8A)K104 T0311 12 :IIQESLDELNVSLREFARA 1wh8A 35 :RVKEVLTDNNLGQRLFGES T0311 31 :MEIAPSTASRLLTGKAA 1wh8A 55 :LGLTQGSVSDLLSRPKP T0311 48 :LTPEM 1wh8A 75 :LSLKG T0311 64 :PQMWLNLQNAWS 1wh8A 80 :REPFVRMQLWLN T0311 76 :LAEAEKT 1wh8A 96 :VEKLRDM T0311 85 :VS 1wh8A 105 :LS Number of specific fragments extracted= 6 number of extra gaps= 1 total=132 Number of alignments=49 # 1wh8A read from 1wh8A/merged-good-all-a2m # found chain 1wh8A in template set Warning: unaligning (T0311)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1wh8A)K104 Warning: unaligning (T0311)D84 because of BadResidue code BAD_PEPTIDE at template residue (1wh8A)K104 T0311 11 :DIIQESLDELNVSLREFARA 1wh8A 34 :KRVKEVLTDNNLGQRLFGES T0311 31 :MEIAPSTASRLLTGKAA 1wh8A 55 :LGLTQGSVSDLLSRPKP T0311 48 :LTPEM 1wh8A 75 :LSLKG T0311 64 :PQMWLNLQNAWS 1wh8A 80 :REPFVRMQLWLN T0311 76 :LAEAEKT 1wh8A 96 :VEKLRDM T0311 85 :V 1wh8A 105 :L Number of specific fragments extracted= 6 number of extra gaps= 1 total=138 Number of alignments=50 # 1wh8A read from 1wh8A/merged-good-all-a2m # found chain 1wh8A in template set Warning: unaligning (T0311)V92 because of BadResidue code BAD_PEPTIDE in next template residue (1wh8A)K104 Warning: unaligning (T0311)T93 because of BadResidue code BAD_PEPTIDE at template residue (1wh8A)K104 T0311 12 :IIQESLDELNVSLREFARA 1wh8A 35 :RVKEVLTDNNLGQRLFGES T0311 31 :MEIAPSTASRLLTGKAA 1wh8A 55 :LGLTQGSVSDLLSRPKP T0311 48 :LTPEMA 1wh8A 75 :LSLKGR T0311 65 :QMWLNLQ 1wh8A 81 :EPFVRMQ T0311 78 :EAEKTVD 1wh8A 88 :LWLNDPH T0311 85 :VSRLRRL 1wh8A 96 :VEKLRDM T0311 94 :QSTP 1wh8A 105 :LSGP Number of specific fragments extracted= 7 number of extra gaps= 1 total=145 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s4kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s4kA expands to /projects/compbio/data/pdb/1s4k.pdb.gz 1s4kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 1s4kA/merged-good-all-a2m # 1s4kA read from 1s4kA/merged-good-all-a2m # adding 1s4kA to template set # found chain 1s4kA in template set T0311 10 :GDIIQESLDELNVSLREFARAM 1s4kA 4 :ALELQALRRIFDMTIEECTIYI T0311 32 :EIAPSTASRLLTGKAALTPEMAIKLSV 1s4kA 28 :DNNSATWQRWEAGDIPISPEIIARLKE T0311 68 :LNLQNAWSLAEAEKTVDVSRLRRLV 1s4kA 55 :MKARRQRRINAIVDKINNRIGNNTM Number of specific fragments extracted= 3 number of extra gaps= 0 total=148 Number of alignments=52 # 1s4kA read from 1s4kA/merged-good-all-a2m # found chain 1s4kA in template set T0311 10 :GDIIQESLDELNVSLREFARAM 1s4kA 4 :ALELQALRRIFDMTIEECTIYI T0311 32 :EIAPSTASRLLTGKAALTPEMAIKLSV 1s4kA 28 :DNNSATWQRWEAGDIPISPEIIARLKE T0311 68 :LNLQNAWSLAEAEKTVDVSRLRRLVTQSTP 1s4kA 55 :MKARRQRRINAIVDKINNRIGNNTMRYFPD Number of specific fragments extracted= 3 number of extra gaps= 0 total=151 Number of alignments=53 # 1s4kA read from 1s4kA/merged-good-all-a2m # found chain 1s4kA in template set T0311 11 :DIIQESLDELNVSLREFARAM 1s4kA 5 :LELQALRRIFDMTIEECTIYI T0311 32 :EIAPSTASRLLTGKAALTPEMAIKLSVV 1s4kA 28 :DNNSATWQRWEAGDIPISPEIIARLKEM T0311 77 :AEAEKTVDVSRLRRLVTQSTP 1s4kA 56 :KARRQRRINAIVDKINNRIGN Number of specific fragments extracted= 3 number of extra gaps= 0 total=154 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dwkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0311 read from 1dwkA/merged-good-all-a2m # 1dwkA read from 1dwkA/merged-good-all-a2m # found chain 1dwkA in training set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dwkA 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQST 1dwkA 93 :TMYRFYEMLQVYGTTLKALVHEKFG Number of specific fragments extracted= 2 number of extra gaps= 0 total=156 Number of alignments=55 # 1dwkA read from 1dwkA/merged-good-all-a2m # found chain 1dwkA in training set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dwkA 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQSTP 1dwkA 93 :TMYRFYEMLQVYGTTLKALVHEKFGD Number of specific fragments extracted= 2 number of extra gaps= 0 total=158 Number of alignments=56 # 1dwkA read from 1dwkA/merged-good-all-a2m # found chain 1dwkA in training set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQ 1dwkA 16 :DAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQ T0311 72 :NAWSLAEAEKTVDVSRLRRLVTQSTP 1dwkA 93 :TMYRFYEMLQVYGTTLKALVHEKFGD Number of specific fragments extracted= 2 number of extra gaps= 0 total=160 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zx4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zx4A expands to /projects/compbio/data/pdb/1zx4.pdb.gz 1zx4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 1zx4A/merged-good-all-a2m # 1zx4A read from 1zx4A/merged-good-all-a2m # adding 1zx4A to template set # found chain 1zx4A in template set Warning: unaligning (T0311)T82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zx4A)E246 Warning: unaligning (T0311)D84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zx4A)E246 T0311 10 :GDIIQESLDE 1zx4A 155 :GLRLMRMKND T0311 21 :NVSLREFARAMEIAPSTASRLLTG 1zx4A 165 :GMSQKDIAAKEGLSQAKVTRALQA T0311 45 :KAALTPEMAIKLSVV 1zx4A 202 :QSELTFSDYKTLCAV T0311 60 :IGSSPQMWLNLQNAWS 1zx4A 220 :MGNKNLEFDQLIQNIS T0311 76 :LAEAEK 1zx4A 238 :INDILS T0311 85 :VSRL 1zx4A 247 :MAED Number of specific fragments extracted= 6 number of extra gaps= 0 total=166 Number of alignments=58 # 1zx4A read from 1zx4A/merged-good-all-a2m # found chain 1zx4A in template set Warning: unaligning (T0311)T82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zx4A)E246 Warning: unaligning (T0311)D84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zx4A)E246 T0311 10 :GDIIQESLDE 1zx4A 155 :GLRLMRMKND T0311 21 :NVSLREFARAMEIAPSTASRLLTG 1zx4A 165 :GMSQKDIAAKEGLSQAKVTRALQA T0311 45 :KAALTPEMAIKLSVV 1zx4A 202 :QSELTFSDYKTLCAV T0311 60 :IGSSPQMWLNLQNAWS 1zx4A 220 :MGNKNLEFDQLIQNIS T0311 76 :LAEAEK 1zx4A 238 :INDILS T0311 85 :VS 1zx4A 247 :MA Number of specific fragments extracted= 6 number of extra gaps= 0 total=172 Number of alignments=59 # 1zx4A read from 1zx4A/merged-good-all-a2m # found chain 1zx4A in template set Warning: unaligning (T0311)T93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zx4A)E246 Warning: unaligning (T0311)S95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zx4A)E246 T0311 10 :GDIIQESLDE 1zx4A 155 :GLRLMRMKND T0311 21 :NVSLREFARAMEIAPSTASRLLTG 1zx4A 165 :GMSQKDIAAKEGLSQAKVTRALQA T0311 45 :KAALTPEMAIKLSVV 1zx4A 202 :QSELTFSDYKTLCAV T0311 60 :IGSSPQMWLNL 1zx4A 220 :MGNKNLEFDQL T0311 80 :EKTVDVSRLRRLV 1zx4A 231 :IQNISPEINDILS T0311 96 :TP 1zx4A 247 :MA Number of specific fragments extracted= 6 number of extra gaps= 0 total=178 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1adr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1adr expands to /projects/compbio/data/pdb/1adr.pdb.gz 1adr:Warning: there is no chain 1adr will retry with 1adrA # T0311 read from 1adr/merged-good-all-a2m # 1adr read from 1adr/merged-good-all-a2m # adding 1adr to template set # found chain 1adr in template set Warning: unaligning (T0311)N69 because of BadResidue code BAD_PEPTIDE in next template residue (1adr)G67 T0311 5 :NHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWL 1adr 2 :NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL Number of specific fragments extracted= 1 number of extra gaps= 1 total=179 Number of alignments=61 # 1adr read from 1adr/merged-good-all-a2m # found chain 1adr in template set Warning: unaligning (T0311)N69 because of BadResidue code BAD_PEPTIDE in next template residue (1adr)G67 T0311 5 :NHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWL 1adr 2 :NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL Number of specific fragments extracted= 1 number of extra gaps= 1 total=180 Number of alignments=62 # 1adr read from 1adr/merged-good-all-a2m # found chain 1adr in template set Warning: unaligning (T0311)N69 because of BadResidue code BAD_PEPTIDE in next template residue (1adr)G67 T0311 5 :NHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWL 1adr 2 :NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLL Number of specific fragments extracted= 1 number of extra gaps= 1 total=181 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1neq/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1neq expands to /projects/compbio/data/pdb/1neq.pdb.gz 1neq:Warning: there is no chain 1neq will retry with 1neqA # T0311 read from 1neq/merged-good-all-a2m # 1neq read from 1neq/merged-good-all-a2m # adding 1neq to template set # found chain 1neq in template set T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKA 1neq 13 :DVIAGLKKRKLSLSALSRQFGYAPTTLANALERHW T0311 50 :PEMAIKLSVVIGSSPQM 1neq 48 :PKGEQIIANALETKPEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=183 Number of alignments=64 # 1neq read from 1neq/merged-good-all-a2m # found chain 1neq in template set T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKA 1neq 13 :DVIAGLKKRKLSLSALSRQFGYAPTTLANALERHW T0311 50 :PEMAIKLSVVIGSSPQM 1neq 48 :PKGEQIIANALETKPEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=185 Number of alignments=65 # 1neq read from 1neq/merged-good-all-a2m # found chain 1neq in template set T0311 12 :IIQESLDELNVSLREFARAMEIAPSTASRLLTGKA 1neq 13 :DVIAGLKKRKLSLSALSRQFGYAPTTLANALERHW T0311 50 :PEMAIKLSVVIGSSPQM 1neq 48 :PKGEQIIANALETKPEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=187 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bjcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bjcA expands to /projects/compbio/data/pdb/2bjc.pdb.gz 2bjcA:# T0311 read from 2bjcA/merged-good-all-a2m # 2bjcA read from 2bjcA/merged-good-all-a2m # adding 2bjcA to template set # found chain 2bjcA in template set T0311 21 :NVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVI 2bjcA 3 :PVTLYDVAEYAGVSVATVSRVVNQASHVSAKTREKVEAAM T0311 81 :KT 2bjcA 43 :AE Number of specific fragments extracted= 2 number of extra gaps= 0 total=189 Number of alignments=67 # 2bjcA read from 2bjcA/merged-good-all-a2m # found chain 2bjcA in template set T0311 21 :NVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVI 2bjcA 3 :PVTLYDVAEYAGVSVATVSRVVNQASHVSAKTREKVEAAM T0311 77 :AEAEKTVDVS 2bjcA 51 :RCAQQLAGKQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=191 Number of alignments=68 # 2bjcA read from 2bjcA/merged-good-all-a2m # found chain 2bjcA in template set T0311 21 :NVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVI 2bjcA 3 :PVTLYDVAEYAGVSVATVSRVVNQASHVSAKTREKVEAAM Number of specific fragments extracted= 1 number of extra gaps= 0 total=192 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lcdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lcdA expands to /projects/compbio/data/pdb/1lcd.pdb.gz 1lcdA:# T0311 read from 1lcdA/merged-good-all-a2m # 1lcdA read from 1lcdA/merged-good-all-a2m # adding 1lcdA to template set # found chain 1lcdA in template set Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)D8 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)D8 Warning: unaligning (T0311)R40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)V23 Warning: unaligning (T0311)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)V23 Warning: unaligning (T0311)T43 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)Q26 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)Q26 Warning: unaligning (T0311)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)S31 Warning: unaligning (T0311)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)S31 T0311 21 :NVSL 1lcdA 3 :PVTL T0311 27 :FARAMEIAPSTAS 1lcdA 9 :VAEYAGVSYQTVS T0311 42 :L 1lcdA 24 :V T0311 45 :KAA 1lcdA 27 :ASH T0311 50 :PEMAIKLSVV 1lcdA 32 :AKTREKVEAA Number of specific fragments extracted= 5 number of extra gaps= 4 total=197 # 1lcdA read from 1lcdA/merged-good-all-a2m # found chain 1lcdA in template set Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)D8 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)D8 Warning: unaligning (T0311)R40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)V23 Warning: unaligning (T0311)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)V23 Warning: unaligning (T0311)T43 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)Q26 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)Q26 Warning: unaligning (T0311)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)S31 Warning: unaligning (T0311)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)S31 T0311 21 :NVSL 1lcdA 3 :PVTL T0311 27 :FARAMEIAPSTAS 1lcdA 9 :VAEYAGVSYQTVS T0311 42 :L 1lcdA 24 :V T0311 45 :KAA 1lcdA 27 :ASH T0311 50 :PEMAIKLSVV 1lcdA 32 :AKTREKVEAA Number of specific fragments extracted= 5 number of extra gaps= 4 total=202 # 1lcdA read from 1lcdA/merged-good-all-a2m # found chain 1lcdA in template set Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)D8 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)D8 Warning: unaligning (T0311)R40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)V23 Warning: unaligning (T0311)L41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)V23 Warning: unaligning (T0311)T43 because of BadResidue code BAD_PEPTIDE in next template residue (1lcdA)Q26 Warning: unaligning (T0311)G44 because of BadResidue code BAD_PEPTIDE at template residue (1lcdA)Q26 Warning: unaligning (T0311)L48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lcdA)S31 Warning: unaligning (T0311)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lcdA)S31 T0311 21 :NVSL 1lcdA 3 :PVTL T0311 27 :FARAMEIAPSTAS 1lcdA 9 :VAEYAGVSYQTVS T0311 42 :L 1lcdA 24 :V T0311 45 :KAA 1lcdA 27 :ASH T0311 50 :PEMAIKLSVV 1lcdA 32 :AKTREKVEAA Number of specific fragments extracted= 5 number of extra gaps= 4 total=207 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s7oA expands to /projects/compbio/data/pdb/1s7o.pdb.gz 1s7oA:# T0311 read from 1s7oA/merged-good-all-a2m # 1s7oA read from 1s7oA/merged-good-all-a2m # adding 1s7oA to template set # found chain 1s7oA in template set T0311 12 :IIQESLDE 1s7oA 30 :YIELYYAD T0311 21 :NVSLREFARAMEIAPSTASRLLT 1s7oA 38 :DYSLAEIADEFGVSRQAVYDNIK T0311 51 :EMAIKLSVV 1s7oA 61 :RTEKILETY T0311 67 :WLNLQNAWSLAEAEKTVDVSRLRR 1s7oA 70 :EMKLHMYSDYVVRSEIFDDMIAHY Number of specific fragments extracted= 4 number of extra gaps= 0 total=211 Number of alignments=70 # 1s7oA read from 1s7oA/merged-good-all-a2m # found chain 1s7oA in template set T0311 12 :IIQESLDE 1s7oA 30 :YIELYYAD T0311 21 :NVSLREFARAMEIAPSTASRLLT 1s7oA 38 :DYSLAEIADEFGVSRQAVYDNIK T0311 51 :EMAIKLSVV 1s7oA 61 :RTEKILETY T0311 67 :WLNLQNAWSLAEAEKTVDVSRLRR 1s7oA 70 :EMKLHMYSDYVVRSEIFDDMIAHY Number of specific fragments extracted= 4 number of extra gaps= 0 total=215 Number of alignments=71 # 1s7oA read from 1s7oA/merged-good-all-a2m # found chain 1s7oA in template set T0311 11 :DIIQESLDE 1s7oA 29 :NYIELYYAD T0311 21 :NVSLREFARAMEIAPSTASRLLT 1s7oA 38 :DYSLAEIADEFGVSRQAVYDNIK T0311 51 :EMAIKLSVV 1s7oA 61 :RTEKILETY T0311 67 :WLNLQNAWSLAEAEKTVDVSRLR 1s7oA 70 :EMKLHMYSDYVVRSEIFDDMIAH Number of specific fragments extracted= 4 number of extra gaps= 0 total=219 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jftA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jftA expands to /projects/compbio/data/pdb/1jft.pdb.gz 1jftA:# T0311 read from 1jftA/merged-good-all-a2m # 1jftA read from 1jftA/merged-good-all-a2m # adding 1jftA to template set # found chain 1jftA in template set T0311 23 :SLREFARAMEIAPSTASRLLTGKAALTPEM 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEET T0311 73 :AWSLAEAEKTVDVSRLR 1jftA 33 :RNAVWAAIKELHYSPSA Number of specific fragments extracted= 2 number of extra gaps= 0 total=221 Number of alignments=73 # 1jftA read from 1jftA/merged-good-all-a2m # found chain 1jftA in template set T0311 23 :SLREFARAMEIAPSTASRLLTGKAALTPEMAI 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRN T0311 75 :SLAEAEKTVD 1jftA 35 :AVWAAIKELH Number of specific fragments extracted= 2 number of extra gaps= 0 total=223 Number of alignments=74 # 1jftA read from 1jftA/merged-good-all-a2m # found chain 1jftA in template set T0311 23 :SLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 1jftA 3 :TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAA T0311 80 :EKTV 1jftA 40 :IKEL Number of specific fragments extracted= 2 number of extra gaps= 0 total=225 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y9qA expands to /projects/compbio/data/pdb/1y9q.pdb.gz 1y9qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 1y9qA/merged-good-all-a2m # 1y9qA read from 1y9qA/merged-good-all-a2m # adding 1y9qA to template set # found chain 1y9qA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSS 1y9qA 14 :NQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEAS Number of specific fragments extracted= 1 number of extra gaps= 0 total=226 Number of alignments=76 # 1y9qA read from 1y9qA/merged-good-all-a2m # found chain 1y9qA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSS 1y9qA 14 :NQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEAS Number of specific fragments extracted= 1 number of extra gaps= 0 total=227 Number of alignments=77 # 1y9qA read from 1y9qA/merged-good-all-a2m # found chain 1y9qA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ 1y9qA 14 :NQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFS Number of specific fragments extracted= 1 number of extra gaps= 0 total=228 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cjgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cjgA expands to /projects/compbio/data/pdb/1cjg.pdb.gz 1cjgA:# T0311 read from 1cjgA/merged-good-all-a2m # 1cjgA read from 1cjgA/merged-good-all-a2m # adding 1cjgA to template set # found chain 1cjgA in template set T0311 22 :VSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLS 1cjgA 4 :VTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVE T0311 78 :EAEKTVD 1cjgA 40 :AAMAELN T0311 85 :VSRLRRLVTQST 1cjgA 50 :NRVAQQLAGKQS Number of specific fragments extracted= 3 number of extra gaps= 0 total=231 Number of alignments=79 # 1cjgA read from 1cjgA/merged-good-all-a2m # found chain 1cjgA in template set T0311 22 :VSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLS 1cjgA 4 :VTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVE T0311 78 :EAEKTVD 1cjgA 40 :AAMAELN T0311 85 :VSRLRRLVTQST 1cjgA 50 :NRVAQQLAGKQS Number of specific fragments extracted= 3 number of extra gaps= 0 total=234 Number of alignments=80 # 1cjgA read from 1cjgA/merged-good-all-a2m # found chain 1cjgA in template set T0311 22 :VSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 1cjgA 4 :VTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAA T0311 80 :EKTV 1cjgA 42 :MAEL T0311 84 :DVSRLRRLV 1cjgA 50 :NRVAQQLAG Number of specific fragments extracted= 3 number of extra gaps= 0 total=237 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r71A expands to /projects/compbio/data/pdb/1r71.pdb.gz 1r71A:# T0311 read from 1r71A/merged-good-all-a2m # 1r71A read from 1r71A/merged-good-all-a2m # adding 1r71A to template set # found chain 1r71A in template set Warning: unaligning (T0311)D84 because of BadResidue code BAD_PEPTIDE in next template residue (1r71A)E252 Warning: unaligning (T0311)V85 because of BadResidue code BAD_PEPTIDE at template residue (1r71A)E252 T0311 6 :HPRPGDII 1r71A 151 :ELTPREIA T0311 14 :QESLDE 1r71A 162 :GRELAK T0311 21 :NVSLREFARAMEIAPSTASRLL 1r71A 168 :GKKKGDIAKEIGKSPAFITQHV T0311 43 :TGKAALTPEMAIKLSVVIGSSPQMWLNLQN 1r71A 203 :NTGRVRDVTVVNELVTAFKKRPEEVEAWLD T0311 73 :AWSLAEAEKTV 1r71A 240 :RGTVKLLREFL Number of specific fragments extracted= 5 number of extra gaps= 1 total=242 Number of alignments=82 # 1r71A read from 1r71A/merged-good-all-a2m # found chain 1r71A in template set Warning: unaligning (T0311)D84 because of BadResidue code BAD_PEPTIDE in next template residue (1r71A)E252 Warning: unaligning (T0311)V85 because of BadResidue code BAD_PEPTIDE at template residue (1r71A)E252 T0311 6 :HPRPGDII 1r71A 151 :ELTPREIA T0311 14 :QESLDE 1r71A 162 :GRELAK T0311 21 :NVSLREFARAMEIAPSTASRLL 1r71A 168 :GKKKGDIAKEIGKSPAFITQHV T0311 43 :TGKAALTPEMAIKLSVVIGSSPQMWLNLQN 1r71A 203 :NTGRVRDVTVVNELVTAFKKRPEEVEAWLD T0311 73 :AWSLAEAEKTV 1r71A 240 :RGTVKLLREFL Number of specific fragments extracted= 5 number of extra gaps= 1 total=247 Number of alignments=83 # 1r71A read from 1r71A/merged-good-all-a2m # found chain 1r71A in template set Warning: unaligning (T0311)D84 because of BadResidue code BAD_PEPTIDE in next template residue (1r71A)E252 Warning: unaligning (T0311)V85 because of BadResidue code BAD_PEPTIDE at template residue (1r71A)E252 T0311 5 :NHPRPGDII 1r71A 150 :NELTPREIA T0311 14 :QESLDE 1r71A 162 :GRELAK T0311 21 :NVSLREFARAMEIAPSTASRLL 1r71A 168 :GKKKGDIAKEIGKSPAFITQHV T0311 43 :TGKAALTPEMAIKLSVVIGSSPQMWLNLQN 1r71A 203 :NTGRVRDVTVVNELVTAFKKRPEEVEAWLD T0311 73 :AWSLAEAEKTV 1r71A 240 :RGTVKLLREFL Number of specific fragments extracted= 5 number of extra gaps= 1 total=252 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r69/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r69 expands to /projects/compbio/data/pdb/1r69.pdb.gz 1r69:Warning: there is no chain 1r69 will retry with 1r69A # T0311 read from 1r69/merged-good-all-a2m # 1r69 read from 1r69/merged-good-all-a2m # adding 1r69 to template set # found chain 1r69 in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1r69 3 :SSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWLN 1r69 45 :LPELASALGVSVDWLLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=254 Number of alignments=85 # 1r69 read from 1r69/merged-good-all-a2m # found chain 1r69 in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1r69 3 :SSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWLN 1r69 45 :LPELASALGVSVDWLLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=256 Number of alignments=86 # 1r69 read from 1r69/merged-good-all-a2m # found chain 1r69 in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1r69 4 :SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWLN 1r69 45 :LPELASALGVSVDWLLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=258 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2auwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2auwA expands to /projects/compbio/data/pdb/2auw.pdb.gz 2auwA:Skipped atom 79, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 153, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 155, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 157, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 159, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 161, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 163, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 169, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 171, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 173, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 320, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 516, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 518, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 522, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2auwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 831, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2auwA Skipped atom 924, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 926, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 928, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 930, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 932, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 934, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 936, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 938, because occupancy 0.400 <= existing 0.600 in 2auwA Skipped atom 940, because occupancy 0.400 <= existing 0.600 in 2auwA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 2auwA/merged-good-all-a2m # 2auwA read from 2auwA/merged-good-all-a2m # adding 2auwA to template set # found chain 2auwA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 2auwA 91 :EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGW Number of specific fragments extracted= 1 number of extra gaps= 0 total=259 Number of alignments=88 # 2auwA read from 2auwA/merged-good-all-a2m # found chain 2auwA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 2auwA 91 :EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGW Number of specific fragments extracted= 1 number of extra gaps= 0 total=260 Number of alignments=89 # 2auwA read from 2auwA/merged-good-all-a2m # found chain 2auwA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVV 2auwA 91 :EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACLGW Number of specific fragments extracted= 1 number of extra gaps= 0 total=261 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rzsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rzsA expands to /projects/compbio/data/pdb/1rzs.pdb.gz 1rzsA:# T0311 read from 1rzsA/merged-good-all-a2m # 1rzsA read from 1rzsA/merged-good-all-a2m # adding 1rzsA to template set # found chain 1rzsA in template set T0311 12 :IIQESLD 1rzsA 5 :DVIDHFG T0311 23 :SLREFARAMEIAPSTASR 1rzsA 12 :TQRAVAKALGISDAAVSQ T0311 45 :KAALTPEMAIKLSVVIGSS 1rzsA 31 :KEVIPEKDAYRLEIVTAGA Number of specific fragments extracted= 3 number of extra gaps= 0 total=264 Number of alignments=91 # 1rzsA read from 1rzsA/merged-good-all-a2m # found chain 1rzsA in template set T0311 12 :IIQESLD 1rzsA 5 :DVIDHFG T0311 23 :SLREFARAMEIAPSTASR 1rzsA 12 :TQRAVAKALGISDAAVSQ T0311 45 :KAALTPEMAIKLSVVIGSS 1rzsA 31 :KEVIPEKDAYRLEIVTAGA Number of specific fragments extracted= 3 number of extra gaps= 0 total=267 Number of alignments=92 # 1rzsA read from 1rzsA/merged-good-all-a2m # found chain 1rzsA in template set T0311 12 :IIQESL 1rzsA 5 :DVIDHF T0311 22 :VSLREFARAMEIAPSTASR 1rzsA 11 :GTQRAVAKALGISDAAVSQ T0311 45 :KAALTPEMAIKLSVVIGSS 1rzsA 31 :KEVIPEKDAYRLEIVTAGA Number of specific fragments extracted= 3 number of extra gaps= 0 total=270 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cro/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cro expands to /projects/compbio/data/pdb/2cro.pdb.gz 2cro:Warning: there is no chain 2cro will retry with 2croA # T0311 read from 2cro/merged-good-all-a2m # 2cro read from 2cro/merged-good-all-a2m # adding 2cro to template set # found chain 2cro in template set T0311 9 :PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2cro 2 :LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 2cro 45 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 0 total=272 Number of alignments=94 # 2cro read from 2cro/merged-good-all-a2m # found chain 2cro in template set T0311 9 :PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2cro 2 :LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 2cro 45 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 0 total=274 Number of alignments=95 # 2cro read from 2cro/merged-good-all-a2m # found chain 2cro in template set T0311 10 :GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 2cro 3 :SERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK T0311 53 :AIKLSVVIGSSPQMW 2cro 45 :LFEIAMALNCDPVWL Number of specific fragments extracted= 2 number of extra gaps= 0 total=276 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1umqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1umqA expands to /projects/compbio/data/pdb/1umq.pdb.gz 1umqA:# T0311 read from 1umqA/merged-good-all-a2m # 1umqA read from 1umqA/merged-good-all-a2m # adding 1umqA to template set # found chain 1umqA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1umqA 44 :EHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRSP Number of specific fragments extracted= 1 number of extra gaps= 0 total=277 Number of alignments=97 # 1umqA read from 1umqA/merged-good-all-a2m # found chain 1umqA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1umqA 44 :EHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRSP Number of specific fragments extracted= 1 number of extra gaps= 0 total=278 Number of alignments=98 # 1umqA read from 1umqA/merged-good-all-a2m # found chain 1umqA in template set T0311 11 :DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAA 1umqA 44 :EHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRSP Number of specific fragments extracted= 1 number of extra gaps= 0 total=279 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2or1L/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2or1L expands to /projects/compbio/data/pdb/2or1.pdb.gz 2or1L:# T0311 read from 2or1L/merged-good-all-a2m # 2or1L read from 2or1L/merged-good-all-a2m # adding 2or1L to template set # found chain 2or1L in template set Warning: unaligning (T0311)E15 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K9 Warning: unaligning (T0311)S16 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K9 Warning: unaligning (T0311)E19 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)L13 Warning: unaligning (T0311)L20 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)L13 Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)E19 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)E19 Warning: unaligning (T0311)R29 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K23 Warning: unaligning (T0311)A30 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K23 T0311 10 :GDIIQ 2or1L 3 :SSRVK T0311 17 :LD 2or1L 10 :RI T0311 21 :NVSL 2or1L 14 :GLNQ T0311 27 :FA 2or1L 20 :LA T0311 31 :MEIAPSTASRLLTGKAA 2or1L 24 :VGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWL 2or1L 45 :LPELASALGVSVDWLL Number of specific fragments extracted= 6 number of extra gaps= 4 total=285 Number of alignments=100 # 2or1L read from 2or1L/merged-good-all-a2m # found chain 2or1L in template set Warning: unaligning (T0311)E15 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K9 Warning: unaligning (T0311)S16 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K9 Warning: unaligning (T0311)E19 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)L13 Warning: unaligning (T0311)L20 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)L13 Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)E19 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)E19 Warning: unaligning (T0311)R29 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K23 Warning: unaligning (T0311)A30 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K23 T0311 10 :GDIIQ 2or1L 3 :SSRVK T0311 17 :LD 2or1L 10 :RI T0311 21 :NVSL 2or1L 14 :GLNQ T0311 27 :FA 2or1L 20 :LA T0311 31 :MEIAPSTASRLLTGKAA 2or1L 24 :VGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWL 2or1L 45 :LPELASALGVSVDWLL Number of specific fragments extracted= 6 number of extra gaps= 4 total=291 Number of alignments=101 # 2or1L read from 2or1L/merged-good-all-a2m # found chain 2or1L in template set Warning: unaligning (T0311)E15 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K9 Warning: unaligning (T0311)S16 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K9 Warning: unaligning (T0311)E19 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)L13 Warning: unaligning (T0311)L20 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)L13 Warning: unaligning (T0311)R25 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)E19 Warning: unaligning (T0311)E26 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)E19 Warning: unaligning (T0311)R29 because of BadResidue code BAD_PEPTIDE in next template residue (2or1L)K23 Warning: unaligning (T0311)A30 because of BadResidue code BAD_PEPTIDE at template residue (2or1L)K23 T0311 11 :DIIQ 2or1L 4 :SRVK T0311 17 :LD 2or1L 10 :RI T0311 21 :NVSL 2or1L 14 :GLNQ T0311 27 :FA 2or1L 20 :LA T0311 31 :MEIAPSTASRLLTGKAA 2or1L 24 :VGTTQQSIEQLENGKTK T0311 53 :AIKLSVVIGSSPQMWL 2or1L 45 :LPELASALGVSVDWLL Number of specific fragments extracted= 6 number of extra gaps= 4 total=297 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zljA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zljA expands to /projects/compbio/data/pdb/1zlj.pdb.gz 1zljA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0311 read from 1zljA/merged-good-all-a2m # 1zljA read from 1zljA/merged-good-all-a2m # adding 1zljA to template set # found chain 1zljA in template set T0311 11 :DIIQESLDE 1zljA 155 :RTLLGLLSE T0311 21 :NVSLREFARAMEIAPSTASRLL 1zljA 164 :GLTNKQIADRMFLAEKTVKNYV T0311 54 :IKLSVVIGSSP 1zljA 186 :SRLLAKLGMER T0311 76 :LAEAEKTVDVSRLR 1zljA 197 :RTQAAVFATELKRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=301 Number of alignments=103 # 1zljA read from 1zljA/merged-good-all-a2m # found chain 1zljA in template set T0311 11 :DIIQESLDE 1zljA 155 :RTLLGLLSE T0311 21 :NVSLREFARAMEIAPSTASRLL 1zljA 164 :GLTNKQIADRMFLAEKTVKNYV T0311 54 :IKLSVVIGSSP 1zljA 186 :SRLLAKLGMER T0311 76 :LAEAEKTVDVSRLRR 1zljA 197 :RTQAAVFATELKRSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=305 Number of alignments=104 # 1zljA read from 1zljA/merged-good-all-a2m # found chain 1zljA in template set T0311 12 :IIQESLD 1zljA 157 :LLGLLSE T0311 21 :NVSLREFARAMEIAPSTASRLL 1zljA 164 :GLTNKQIADRMFLAEKTVKNYV T0311 54 :IKLSVVIGSSP 1zljA 186 :SRLLAKLGMER T0311 76 :LAEAEKTVDVSRLR 1zljA 197 :RTQAAVFATELKRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=309 Number of alignments=105 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 105 Adding 517 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -168.6246, CN propb: -168.6246 weights: 0.2473 constraints: 126 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 126 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 126 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 391 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 391 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 517 # command: