# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0311//projects/compbio/experiments/protein-predict/casp7/T0311/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0311//projects/compbio/experiments/protein-predict/casp7/T0311/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0311/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0311/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0311)F27.CB, (T0311)A38.CB) [> 3.3384 = 5.5640 < 7.2332] w=1.0000 to align # Constraint # added constraint: constraint((T0311)L24.CB, (T0311)A38.CB) [> 3.0971 = 5.1618 < 6.7103] w=1.0000 to align # Constraint # added constraint: constraint((T0311)L24.CB, (T0311)S39.CB) [> 3.5542 = 5.9237 < 7.7008] w=0.9769 to align # Constraint # added constraint: constraint((T0311)L24.CB, (T0311)P35.CB) [> 3.2458 = 5.4097 < 7.0326] w=0.9692 to align # Constraint # added constraint: constraint((T0311)A28.CB, (T0311)A38.CB) [> 2.8086 = 4.6810 < 6.0853] w=0.9669 to align # Constraint # added constraint: constraint((T0311)R25.CB, (T0311)P35.CB) [> 3.2009 = 5.3348 < 6.9352] w=0.9398 to align # Constraint # added constraint: constraint((T0311)A28.CB, (T0311)T37.CB) [> 4.1431 = 6.9052 < 8.9768] w=0.8675 to align # Constraint # added constraint: constraint((T0311)L24.CB, (T0311)L42.CB) [> 4.3952 = 7.3253 < 9.5229] w=0.8198 to align # Constraint # added constraint: constraint((T0311)M31.CB, (T0311)K55.CB) [> 3.1264 = 5.2107 < 6.7739] w=0.8119 to align # Constraint # added constraint: constraint((T0311)M31.CB, (T0311)L56.CB) [> 3.4604 = 5.7673 < 7.4974] w=0.7835 to align # Constraint # added constraint: constraint((T0311)L17.CB, (T0311)F27.CB) [> 3.4272 = 5.7120 < 7.4256] w=0.7408 to align # Constraint # added constraint: constraint((T0311)F27.CB, (T0311)V59.CB) [> 3.5530 = 5.9217 < 7.6982] w=0.6800 to align # Constraint # added constraint: constraint((T0311)Q14.CB, (T0311)L42.CB) [> 3.2294 = 5.3823 < 6.9970] w=0.6394 to align # Constraint # added constraint: constraint((T0311)M31.CB, (T0311)V59.CB) [> 3.0156 = 5.0260 < 6.5338] w=0.6314 to align # Constraint # added constraint: constraint((T0311)A30.CB, (T0311)V59.CB) [> 2.6603 = 4.4339 < 5.7640] w=0.6277 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)L56.CB) [> 4.0541 = 6.7568 < 8.7839] w=0.5814 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)L41.CB) [> 3.5845 = 5.9742 < 7.7665] w=0.5808 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)I60.CB) [> 3.3075 = 5.5124 < 7.1661] w=0.5765 to align # Constraint # added constraint: constraint((T0311)L20.CB, (T0311)I60.CB) [> 4.1946 = 6.9909 < 9.0882] w=0.5443 to align # Constraint # added constraint: constraint((T0311)I33.CB, (T0311)M52.CB) [> 4.0813 = 6.8021 < 8.8428] w=0.5400 to align # Constraint # added constraint: constraint((T0311)F27.CB, (T0311)L56.CB) [> 3.9901 = 6.6502 < 8.6453] w=0.5392 to align # Constraint # added constraint: constraint((T0311)L17.CB, (T0311)I60.CB) [> 4.1239 = 6.8731 < 8.9350] w=0.5359 to align # Constraint # added constraint: constraint((T0311)M31.CB, (T0311)M52.CB) [> 4.0321 = 6.7202 < 8.7363] w=0.5234 to align # Constraint # added constraint: constraint((T0311)L17.CB, (T0311)L42.CB) [> 4.5206 = 7.5343 < 9.7945] w=0.5233 to align # Constraint # added constraint: constraint((T0311)I54.CB, (T0311)P64.CB) [> 3.6652 = 6.1087 < 7.9412] w=0.4853 to align # Constraint # added constraint: constraint((T0311)A53.CB, (T0311)P64.CB) [> 3.3626 = 5.6043 < 7.2856] w=0.4853 to align # Constraint # added constraint: constraint((T0311)E32.CB, (T0311)K55.CB) [> 3.7974 = 6.3291 < 8.2278] w=0.4804 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)S62.CB) [> 3.7766 = 6.2943 < 8.1826] w=0.4782 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)I60.CB) [> 4.2139 = 7.0232 < 9.1302] w=0.4743 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)L56.CB) [> 3.9625 = 6.6042 < 8.5855] w=0.4570 to align # Constraint # added constraint: constraint((T0311)A38.CB, (T0311)L56.CB) [> 4.0032 = 6.6720 < 8.6736] w=0.4327 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)M52.CB) [> 4.2381 = 7.0636 < 9.1826] w=0.4106 to align # Constraint # added constraint: constraint((T0311)I33.CB, (T0311)L56.CB) [> 4.0091 = 6.6819 < 8.6864] w=0.3821 to align # Constraint # added constraint: constraint((T0311)L20.CB, (T0311)G61.CA) [> 4.6061 = 7.6768 < 9.9798] w=0.3503 to align # Constraint # added constraint: constraint((T0311)T37.CB, (T0311)M52.CB) [> 4.1673 = 6.9455 < 9.0291] w=0.3478 to align # Constraint # added constraint: constraint((T0311)A53.CB, (T0311)W67.CB) [> 3.9191 = 6.5318 < 8.4914] w=0.3354 to align # Constraint # added constraint: constraint((T0311)S57.CB, (T0311)W67.CB) [> 3.3449 = 5.5748 < 7.2472] w=0.3342 to align # Constraint # added constraint: constraint((T0311)M31.CB, (T0311)V58.CB) [> 4.3430 = 7.2383 < 9.4097] w=0.3308 to align # Constraint # added constraint: constraint((T0311)I33.CB, (T0311)K55.CB) [> 3.9690 = 6.6151 < 8.5996] w=0.3196 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)A38.CB) [> 4.4855 = 7.4759 < 9.7186] w=0.3180 to align # Constraint # added constraint: constraint((T0311)S57.CB, (T0311)M66.CB) [> 4.3484 = 7.2473 < 9.4215] w=0.2948 to align # Constraint # added constraint: constraint((T0311)G10.CA, (T0311)L41.CB) [> 3.4170 = 5.6950 < 7.4035] w=0.2836 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)F27.CB) [> 4.2133 = 7.0221 < 9.1288] w=0.2745 to align # Constraint # added constraint: constraint((T0311)G10.CA, (T0311)G44.CA) [> 3.2636 = 5.4394 < 7.0712] w=0.2724 to align # Constraint # added constraint: constraint((T0311)I12.CB, (T0311)W67.CB) [> 3.4559 = 5.7599 < 7.4879] w=0.2694 to align # Constraint # added constraint: constraint((T0311)L17.CB, (T0311)A38.CB) [> 4.7024 = 7.8373 < 10.1885] w=0.2610 to align # Constraint # added constraint: constraint((T0311)V22.CB, (T0311)V59.CB) [> 4.3493 = 7.2489 < 9.4236] w=0.2537 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)G61.CA) [> 4.3584 = 7.2640 < 9.4432] w=0.2481 to align # Constraint # added constraint: constraint((T0311)V22.CB, (T0311)I60.CB) [> 4.4709 = 7.4515 < 9.6870] w=0.2464 to align # Constraint # added constraint: constraint((T0311)I12.CB, (T0311)M66.CB) [> 4.2614 = 7.1024 < 9.2331] w=0.2333 to align # Constraint # added constraint: constraint((T0311)T37.CB, (T0311)L48.CB) [> 4.0693 = 6.7821 < 8.8168] w=0.2210 to align # Constraint # added constraint: constraint((T0311)A30.CB, (T0311)K55.CB) [> 4.1431 = 6.9052 < 8.9767] w=0.1930 to align # Constraint # added constraint: constraint((T0311)A53.CB, (T0311)L68.CB) [> 4.5233 = 7.5389 < 9.8006] w=0.1930 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)W67.CB) [> 4.3636 = 7.2726 < 9.4544] w=0.1848 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)A53.CB) [> 3.4491 = 5.7484 < 7.4730] w=0.1833 to align # Constraint # added constraint: constraint((T0311)L20.CB, (T0311)V59.CB) [> 4.6604 = 7.7673 < 10.0975] w=0.1682 to align # Constraint # added constraint: constraint((T0311)A30.CB, (T0311)I60.CB) [> 4.4186 = 7.3643 < 9.5736] w=0.1525 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)F27.CB) [> 3.3354 = 5.5590 < 7.2267] w=0.1425 to align # Constraint # added constraint: constraint((T0311)P50.CB, (T0311)P64.CB) [> 4.4727 = 7.4545 < 9.6908] w=0.1366 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)A30.CB) [> 3.9246 = 6.5409 < 8.5032] w=0.1326 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)S57.CB) [> 3.8820 = 6.4700 < 8.4110] w=0.1305 to align # Constraint # added constraint: constraint((T0311)E26.CB, (T0311)V59.CB) [> 4.3709 = 7.2848 < 9.4702] w=0.1256 to align # Constraint # added constraint: constraint((T0311)P9.CB, (T0311)L41.CB) [> 4.4409 = 7.4015 < 9.6219] w=0.1199 to align # Constraint # added constraint: constraint((T0311)P9.CB, (T0311)W67.CB) [> 3.8497 = 6.4162 < 8.3410] w=0.1086 to align # Constraint # added constraint: constraint((T0311)I12.CB, (T0311)M31.CB) [> 3.7852 = 6.3088 < 8.2014] w=0.1081 to align # Constraint # added constraint: constraint((T0311)S23.CB, (T0311)P35.CB) [> 4.6545 = 7.7575 < 10.0848] w=0.0918 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)L48.CB) [> 3.5370 = 5.8949 < 7.6634] w=0.0873 to align # Constraint # added constraint: constraint((T0311)P9.CB, (T0311)L48.CB) [> 4.0647 = 6.7745 < 8.8069] w=0.0866 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)S62.CB) [> 4.3623 = 7.2705 < 9.4517] w=0.0825 to align # Constraint # added constraint: constraint((T0311)A28.CB, (T0311)V59.CB) [> 4.4722 = 7.4536 < 9.6897] w=0.0802 to align # Constraint # added constraint: constraint((T0311)S57.CB, (T0311)L70.CB) [> 4.1594 = 6.9323 < 9.0120] w=0.0763 to align # Constraint # added constraint: constraint((T0311)P64.CB, (T0311)A79.CB) [> 3.7990 = 6.3317 < 8.2312] w=0.0749 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)A53.CB) [> 4.1428 = 6.9046 < 8.9760] w=0.0695 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)V22.CB) [> 3.9562 = 6.5937 < 8.5718] w=0.0662 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)A46.CB) [> 4.1838 = 6.9730 < 9.0649] w=0.0661 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)L70.CB) [> 4.3757 = 7.2929 < 9.4808] w=0.0645 to align # Constraint # added constraint: constraint((T0311)I12.CB, (T0311)L70.CB) [> 3.0855 = 5.1426 < 6.6853] w=0.0645 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)M66.CB) [> 4.6707 = 7.7845 < 10.1199] w=0.0616 to align # Constraint # added constraint: constraint((T0311)A47.CB, (T0311)Q71.CB) [> 3.5839 = 5.9731 < 7.7651] w=0.0616 to align # Constraint # added constraint: constraint((T0311)L48.CB, (T0311)L70.CB) [> 2.8611 = 4.7685 < 6.1990] w=0.0616 to align # Constraint # added constraint: constraint((T0311)L48.CB, (T0311)Q71.CB) [> 3.5243 = 5.8739 < 7.6360] w=0.0616 to align # Constraint # added constraint: constraint((T0311)T49.CB, (T0311)Q71.CB) [> 4.3815 = 7.3026 < 9.4934] w=0.0616 to align # Constraint # added constraint: constraint((T0311)F27.CB, (T0311)A79.CB) [> 2.9858 = 4.9763 < 6.4692] w=0.0571 to align # Constraint # added constraint: constraint((T0311)P9.CB, (T0311)A47.CB) [> 3.8485 = 6.4142 < 8.3384] w=0.0552 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)L56.CB) [> 3.0503 = 5.0838 < 6.6089] w=0.0551 to align # Constraint # added constraint: constraint((T0311)P50.CB, (T0311)A79.CB) [> 3.2510 = 5.4184 < 7.0439] w=0.0551 to align # Constraint # added constraint: constraint((T0311)P50.CB, (T0311)V83.CB) [> 3.2293 = 5.3821 < 6.9968] w=0.0551 to align # Constraint # added constraint: constraint((T0311)A53.CB, (T0311)A79.CB) [> 3.2071 = 5.3452 < 6.9487] w=0.0551 to align # Constraint # added constraint: constraint((T0311)P9.CB, (T0311)L68.CB) [> 4.2006 = 7.0009 < 9.1012] w=0.0534 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)K55.CB) [> 4.1285 = 6.8808 < 8.9450] w=0.0481 to align # Constraint # added constraint: constraint((T0311)T49.CB, (T0311)A79.CB) [> 4.5292 = 7.5487 < 9.8133] w=0.0441 to align # Constraint # added constraint: constraint((T0311)S63.CB, (T0311)E80.CB) [> 4.3087 = 7.1812 < 9.3356] w=0.0441 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)L76.CB) [> 3.4190 = 5.6983 < 7.4078] w=0.0438 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)M52.CB) [> 4.5337 = 7.5562 < 9.8230] w=0.0364 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)M66.CB) [> 4.4717 = 7.4528 < 9.6887] w=0.0331 to align # Constraint # added constraint: constraint((T0311)M52.CB, (T0311)L76.CB) [> 3.6528 = 6.0880 < 7.9145] w=0.0330 to align # Constraint # added constraint: constraint((T0311)I54.CB, (T0311)E78.CB) [> 3.9641 = 6.6069 < 8.5889] w=0.0328 to align # Constraint # added constraint: constraint((T0311)L20.CB, (T0311)S62.CB) [> 4.7973 = 7.9955 < 10.3941] w=0.0313 to align # Constraint # added constraint: constraint((T0311)S39.CB, (T0311)I54.CB) [> 4.1671 = 6.9452 < 9.0288] w=0.0310 to align # Constraint # added constraint: constraint((T0311)P64.CB, (T0311)L76.CB) [> 2.9645 = 4.9408 < 6.4231] w=0.0308 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)V58.CB) [> 3.2030 = 5.3384 < 6.9399] w=0.0231 to align # Constraint # added constraint: constraint((T0311)E51.CB, (T0311)A73.CB) [> 4.2503 = 7.0839 < 9.2091] w=0.0221 to align # Constraint # added constraint: constraint((T0311)T49.CB, (T0311)A73.CB) [> 4.0712 = 6.7854 < 8.8210] w=0.0221 to align # Constraint # added constraint: constraint((T0311)A53.CB, (T0311)L76.CB) [> 4.1573 = 6.9289 < 9.0075] w=0.0219 to align # Constraint # added constraint: constraint((T0311)E51.CB, (T0311)S75.CB) [> 3.9380 = 6.5633 < 8.5323] w=0.0217 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)I54.CB) [> 4.3478 = 7.2463 < 9.4202] w=0.0197 to align # Constraint # added constraint: constraint((T0311)L42.CB, (T0311)I54.CB) [> 3.2140 = 5.3566 < 6.9636] w=0.0197 to align # Constraint # added constraint: constraint((T0311)V58.CB, (T0311)L68.CB) [> 3.3155 = 5.5258 < 7.1835] w=0.0180 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)L76.CB) [> 3.9550 = 6.5918 < 8.5693] w=0.0155 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)L68.CB) [> 4.4745 = 7.4574 < 9.6946] w=0.0147 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)N69.CB) [> 4.2705 = 7.1175 < 9.2528] w=0.0147 to align # Constraint # added constraint: constraint((T0311)K55.CB, (T0311)L68.CB) [> 4.0332 = 6.7220 < 8.7386] w=0.0147 to align # Constraint # added constraint: constraint((T0311)R40.CB, (T0311)E51.CB) [> 4.0755 = 6.7925 < 8.8303] w=0.0145 to align # Constraint # added constraint: constraint((T0311)A28.CB, (T0311)L41.CB) [> 4.6088 = 7.6814 < 9.9858] w=0.0134 to align # Constraint # added constraint: constraint((T0311)P50.CB, (T0311)Q65.CB) [> 4.0214 = 6.7023 < 8.7130] w=0.0134 to align # Constraint # added constraint: constraint((T0311)L41.CB, (T0311)P50.CB) [> 4.4770 = 7.4616 < 9.7001] w=0.0112 to align # Constraint # added constraint: constraint((T0311)T49.CB, (T0311)V83.CB) [> 4.5464 = 7.5773 < 9.8504] w=0.0110 to align # Constraint # added constraint: constraint((T0311)M66.CB, (T0311)L91.CB) [> 3.7954 = 6.3257 < 8.2234] w=0.0110 to align # Constraint # added constraint: constraint((T0311)K45.CB, (T0311)I54.CB) [> 3.8407 = 6.4012 < 8.3215] w=0.0110 to align # Constraint # added constraint: constraint((T0311)W74.CB, (T0311)R87.CB) [> 4.7002 = 7.8336 < 10.1837] w=0.0110 to align # Constraint # added constraint: constraint((T0311)L70.CB, (T0311)L91.CB) [> 4.7582 = 7.9303 < 10.3094] w=0.0110 to align # Constraint # added constraint: constraint((T0311)W67.CB, (T0311)L91.CB) [> 3.5414 = 5.9023 < 7.6730] w=0.0110 to align # Constraint # added constraint: constraint((T0311)L24.CB, (T0311)R87.CB) [> 4.6218 = 7.7030 < 10.0139] w=0.0109 to align # Constraint # added constraint: constraint((T0311)P50.CB, (T0311)W74.CB) [> 3.7683 = 6.2805 < 8.1646] w=0.0109 to align # Constraint # added constraint: constraint((T0311)I13.CB, (T0311)W74.CB) [> 3.8897 = 6.4829 < 8.4278] w=0.0089 to align # Constraint # added constraint: constraint((T0311)S16.CB, (T0311)W74.CB) [> 4.1224 = 6.8707 < 8.9319] w=0.0089 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0311/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0311/decoys/ # ReadConformPDB reading from PDB file fromTry1cTermRotAndCap.renum.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file fromTry4breakatS75.renum.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file helixDownFromTry6.renum.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-1utxA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-1utxA # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-2b5aA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-2b5aA # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 26 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 43, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0311)D84.O and (T0311)V85.N only 0.000 apart, marking (T0311)V85.N as missing # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0311)V22.O and (T0311)S23.N only 0.000 apart, marking (T0311)S23.N as missing # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0311 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.5331 model score -0.5413 model score -0.5315 model score -0.2293 model score -0.2292 model score -0.0191 model score 0.4400 model score -0.3919 model score -0.2012 model score -0.0114 model score -0.3752 model score -0.2119 model score -0.2783 model score -0.2214 model score -0.2494 model score -0.2248 model score -0.2071 model score -0.4864 model score -0.2169 model score -0.4069 model score -0.5659 model score 0.4268 model score -0.4807 model score -0.3155 model score -0.5119 model score 1.1100 model score 0.9551 model score 0.8613 model score 0.4546 model score 0.3955 model score -0.0348 model score -0.3661 model score -0.3695 model score -0.3661 model score -0.3748 model score -0.3750 model score -0.4938 model score -0.5445 model score -0.5559 model score -0.4857 model score -0.5091 model score 0.3537 model score -0.4239 model score -0.0874 model score 0.0156 model score -0.0630 model score 1.5453 model score 1.2687 model score 1.2787 model score 1.2691 model score 1.2719 model score 1.2719 model score -0.4102 model score -0.4788 model score -0.4738 model score -0.4233 model score -0.4061 model score -0.3211 model score -0.4938 model score -0.5445 model score -0.5559 model score -0.5091 model score -0.5580 model score -0.4966 model score -0.5376 model score -0.4957 model score -0.4454 model score 1.2607 model score 1.2623 model score 1.2734 model score 1.2584 model score 1.2572 model score 1.2607 model score 1.2734 model score 1.2623 model score 1.2623 model score 1.2584 model score 2.0240 model score 2.1730 model score 1.6386 model score 2.0751 model score 1.4324 model score -0.3482 model score -0.1442 model score -0.3297 model score -0.0484 model score -0.3476 model score 1.2707 model score 1.2590 model score 1.2734 model score 1.2623 model score 1.2607 model score -0.5519 model score -0.4121 model score -0.4553 model score -0.5247 model score -0.4319 model score -0.5285 model score -0.5207 model score -0.4781 model score -0.5260 model score -0.3156 model score -0.5646 model score -0.5702 model score -0.5702 model score -0.5342 model score 0.0143 model score -0.4252 model score -0.1189 model score 1.4967 model score -0.4960 model score -0.4361 model score -0.1801 model score 0.0294 model score -0.5235 model score 1.2784 model score 1.6315 model score -0.4598 model score -0.4458 model score -0.4168 model score -0.3702 model score -0.2925 model score -0.3881 model score -0.3171 model score -0.3432 model score -0.3130 model score -0.4960 model score 1.4112 model score 1.2092 model score 1.0912 model score 1.3194 model score 1.2883 model score 0.2731 model score 1.4779 model score 0.2198 model score 1.4687 model score -0.4993 model score -0.4993 model score -0.1449 model score -0.4362 model score 0.0529 model score -0.5448 model score -0.5556 model score -0.6001 model score -0.5420 model score -0.5849 model score -0.5564 model score -0.3650 model score -0.4799 model score -0.4887 model score -0.4887 model score -0.4781 model score -0.4887 model score -0.5408 model score -0.4873 model score -0.4713 model score -0.5215 model score -0.4814 model score -0.4709 model score -0.4617 model score -0.4682 model score -0.5103 model score -0.4746 model score -0.3464 model score 0.0143 model score -0.3742 model score -0.3044 model score 0.3871 model score -0.4614 model score -0.4806 model score -0.4575 model score -0.3877 model score -0.1042 model score -0.5294 model score -0.4636 model score -0.4512 model score -0.4795 model score -0.5215 model score -0.4019 model score -0.5189 model score -0.4478 model score -0.5232 model score -0.4795 model score 1.2771 model score 1.2572 model score 1.2771 model score 1.2578 model score 1.2584 model score 1.2771 model score 1.2574 model score 1.2573 model score 1.2574 model score 1.2581 model score -0.5281 model score -0.5277 model score -0.2474 model score -0.0714 model score -0.2361 model score -0.4802 model score -0.4746 model score -0.4371 model score -0.2633 model score -0.4501 model score -0.4534 model score -0.4802 model score -0.4694 model score -0.4371 model score -0.2633 model score -0.2633 model score -0.4695 model score -0.4371 model score -0.3994 model score -0.4206 model score 1.2579 model score 1.2584 model score 1.2707 model score 1.2607 model score 1.2586 model score -0.5579 model score 1.2579 model score 1.2584 model score 1.2707 model score 1.2586 model score 1.2582 model score -0.4941 model score -0.4261 model score -0.4339 model score -0.5215 model score -0.4633 model score -0.5216 model score -0.5306 model score 1.2582 model score 1.2734 model score 1.2584 model score 1.2584 model score 1.2771 model score 1.2579 model score 1.2586 model score 1.2584 model score 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cost: -0.2707 min: -0.6001 max: 2.1730 USE_META, weight: 0.9442 cost: -0.4280 min: -0.6001 max: 2.1730 USE_META, weight: 0.8681 cost: -0.1937 min: -0.6001 max: 2.1730 USE_META, weight: 0.9744 cost: -0.5213 min: -0.6001 max: 2.1730 USE_META, weight: 0.9490 cost: -0.4431 min: -0.6001 max: 2.1730 USE_META, weight: 0.8802 cost: -0.2309 min: -0.6001 max: 2.1730 USE_META, weight: 0.8317 cost: -0.0815 min: -0.6001 max: 2.1730 USE_META, weight: 0.9494 cost: -0.4441 min: -0.6001 max: 2.1730 USE_META, weight: 0.9281 cost: -0.3785 min: -0.6001 max: 2.1730 USE_META, weight: 0.9793 cost: -0.5364 min: -0.6001 max: 2.1730 USE_META, weight: 0.7572 cost: 0.1479 min: -0.6001 max: 2.1730 USE_META, weight: 0.9519 cost: -0.4518 min: -0.6001 max: 2.1730 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9964 eval: 0.0038 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9964 eval: 0.0038 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9964 eval: 0.0038 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9456 eval: 0.0581 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9456 eval: 0.0581 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9456 eval: 0.0581 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.7741 eval: 0.2410 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.7741 eval: 0.2410 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.7741 eval: 0.2410 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6327 eval: 0.3920 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6327 eval: 0.3920 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6327 eval: 0.3920 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6977 eval: 0.3225 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6977 eval: 0.3225 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6977 eval: 0.3225 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8577 eval: 0.1518 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8577 eval: 0.1518 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8577 eval: 0.1518 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9310 eval: 0.0737 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9310 eval: 0.0737 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9310 eval: 0.0737 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9968 eval: 0.0034 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9968 eval: 0.0034 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9968 eval: 0.0034 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9981 eval: 0.0021 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9981 eval: 0.0021 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9981 eval: 0.0021 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.4048 eval: 0.6351 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.4048 eval: 0.6351 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.4048 eval: 0.6351 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6667 eval: 0.3556 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6667 eval: 0.3556 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.6667 eval: 0.3556 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5730 eval: 0.4557 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5730 eval: 0.4557 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5730 eval: 0.4557 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8570 eval: 0.1526 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8570 eval: 0.1526 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8570 eval: 0.1526 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9878 eval: 0.0130 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9878 eval: 0.0130 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9878 eval: 0.0130 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.1000 eval: 0.9604 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.1000 eval: 0.9604 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.1000 eval: 0.9604 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9846 eval: 0.0164 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9846 eval: 0.0164 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9846 eval: 0.0164 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9923 eval: 0.0082 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9923 eval: 0.0082 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9923 eval: 0.0082 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.3388 eval: 0.7056 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.3388 eval: 0.7056 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.3388 eval: 0.7056 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9973 eval: 0.0029 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9973 eval: 0.0029 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9973 eval: 0.0029 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9706 eval: 0.0314 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9706 eval: 0.0314 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9706 eval: 0.0314 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9993 eval: 0.0007 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9993 eval: 0.0007 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9993 eval: 0.0007 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9962 eval: 0.0041 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9962 eval: 0.0041 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.9962 eval: 0.0041 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8861 eval: 0.1216 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8861 eval: 0.1216 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.8861 eval: 0.1216 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5957 eval: 0.4314 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5957 eval: 0.4314 min: 0.0000 max: 0.9604 USE_EVALUE, weight: 0.5957 eval: 0.4314 min: 0.0000 max: 0.9604 Number of contacts in models: 269 Number of contacts in alignments: 105 NUMB_ALIGNS: 105 Adding 2673 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -168.8501, CN propb: -168.8501 weights: 0.2871 constraints: 153 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 153 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 153 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2520 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2520 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2673 # command: