parameters: 0.6 1.3 0.5 200 50 # 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/T0354/ # command:# Making conformation for sequence T0354 numbered 1 through 130 Created new target T0354 from T0354.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0354/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0354//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0354/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0354//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0354/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0354/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0354/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gfgA expands to /projects/compbio/data/pdb/2gfg.pdb.gz 2gfgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 764, because occupancy 0.5 <= existing 0.500 in 2gfgA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 2gfgA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 2gfgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 2gfgA/merged-good-all-a2m # 2gfgA read from 2gfgA/merged-good-all-a2m # adding 2gfgA to template set # found chain 2gfgA in template set T0354 10 :AIEALEDIKG 2gfgA 101 :VMDALRDLSI # choosing archetypes in rotamer library T0354 26 :DTSKL 2gfgA 111 :PISQL T0354 32 :SLFQRMIVATGDSNRQVKALANSVQV 2gfgA 144 :GIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGSE 2gfgA 170 :TFSISQVPTE Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 2gfgA read from 2gfgA/merged-good-all-a2m # found chain 2gfgA in template set T0354 9 :LAIEALEDIKG 2gfgA 100 :EVMDALRDLSI T0354 26 :DTSK 2gfgA 111 :PISQ T0354 30 :LTSLFQRMIVATGDSNRQVKALANSVQV 2gfgA 142 :YLGIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGS 2gfgA 170 :TFSISQVPT Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 2gfgA read from 2gfgA/merged-good-all-a2m # found chain 2gfgA in template set T0354 10 :AIEALEDI 2gfgA 101 :VMDALRDL T0354 18 :KGKDI 2gfgA 114 :QLKHI T0354 23 :IELDTSKL 2gfgA 126 :AEISYEQG T0354 31 :TSLFQRMIVATGDSNRQVKALANSVQV 2gfgA 143 :LGIEDYEIEFEGTSEEHATVTFQEILK T0354 61 :EAGVDIVGSEG 2gfgA 170 :TFSISQVPTEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=13 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vljA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0354 read from 1vljA/merged-good-all-a2m # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0354 10 :AIEALEDIKGKDI 1vljA 22 :IGEEIKNAGIRKV T0354 37 :MIVATGDS 1vljA 35 :LFLYGGGS T0354 48 :VKA 1vljA 43 :IKK T0354 51 :LANSVQVKLKEAGVDIVGSEGH 1vljA 48 :VYDQVVDSLKKHGIEWVEVSGV T0354 73 :ESGEWVLVDA 1vljA 157 :KTKEKYGVSS Number of specific fragments extracted= 5 number of extra gaps= 0 total=18 Number of alignments=4 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0354 10 :AIEALEDIKGKDIIELDTSKL 1vljA 22 :IGEEIKNAGIRKVLFLYGGGS T0354 48 :VKA 1vljA 43 :IKK T0354 51 :LANSVQVKLKEAGVDIVGSEG 1vljA 48 :VYDQVVDSLKKHGIEWVEVSG Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 Number of alignments=5 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0354 10 :AIEALEDIKGKDI 1vljA 22 :IGEEIKNAGIRKV T0354 37 :MIVATGD 1vljA 35 :LFLYGGG T0354 47 :QVKA 1vljA 42 :SIKK T0354 51 :LANSVQVKLKEAGVDIVGSEGHESG 1vljA 48 :VYDQVVDSLKKHGIEWVEVSGVKPN Number of specific fragments extracted= 4 number of extra gaps= 0 total=25 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jdqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jdqA expands to /projects/compbio/data/pdb/1jdq.pdb.gz 1jdqA:# T0354 read from 1jdqA/merged-good-all-a2m # 1jdqA read from 1jdqA/merged-good-all-a2m # adding 1jdqA to template set # found chain 1jdqA in template set T0354 6 :ISKLAIE 1jdqA 42 :ETKRALQ T0354 16 :DIKGKDIIELDTSKLT 1jdqA 49 :NMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 Number of alignments=7 # 1jdqA read from 1jdqA/merged-good-all-a2m # found chain 1jdqA in template set T0354 5 :EISKLAIEALEDIKGKDIIELDTSKLT 1jdqA 38 :VPDVETKRALQNMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=8 # 1jdqA read from 1jdqA/merged-good-all-a2m # found chain 1jdqA in template set T0354 4 :QEISKL 1jdqA 40 :DVETKR T0354 13 :ALEDIKGKDIIELDTSKLT 1jdqA 46 :ALQNMKPGEILEVWIDYPM T0354 52 :ANSVQVKL 1jdqA 65 :SKERIPET T0354 60 :KEAGVDIVGSEGHESGEWVLV 1jdqA 74 :KKLGHEVLEIEEVGPSEWKIY Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wy7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wy7A expands to /projects/compbio/data/pdb/1wy7.pdb.gz 1wy7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1wy7A/merged-good-all-a2m # 1wy7A read from 1wy7A/merged-good-all-a2m # adding 1wy7A to template set # found chain 1wy7A in template set T0354 4 :QEISKLAIEALEDIKGK 1wy7A 82 :KEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDS 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFG T0354 45 :NRQVKALA 1wy7A 131 :RPFLLKAF T0354 53 :NSVQVKLKEAGVDIVGSEGH 1wy7A 156 :RFIEKFSWEHGFVVTHRLTT T0354 73 :ESGEWVLVDA 1wy7A 191 :ERITVDIYRF Number of specific fragments extracted= 5 number of extra gaps= 0 total=41 Number of alignments=10 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set T0354 3 :IQEISKLAIEALEDIKGK 1wy7A 81 :DKEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDSN 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFGS T0354 46 :RQVKALA 1wy7A 132 :PFLLKAF T0354 53 :NSVQVKLKEAGVDIVGSEG 1wy7A 156 :RFIEKFSWEHGFVVTHRLT T0354 72 :HESGEWVLVDA 1wy7A 190 :LERITVDIYRF Number of specific fragments extracted= 5 number of extra gaps= 0 total=46 Number of alignments=11 # 1wy7A read from 1wy7A/merged-good-all-a2m # found chain 1wy7A in template set T0354 4 :QEISKLAIEALEDIKGK 1wy7A 82 :KEAVDVLIENLGEFKGK T0354 21 :DIIELDTSKLTSLFQRMIVATGDSN 1wy7A 100 :KVFIGDVSEFNSRVDIVIMNPPFGS T0354 53 :NSVQVKLKEA 1wy7A 131 :RPFLLKAFEI T0354 76 :E 1wy7A 142 :D T0354 78 :VL 1wy7A 143 :VV T0354 85 :VVVHVMLPAVRDYYD 1wy7A 145 :YSIHLAKPEVRRFIE T0354 102 :A 1wy7A 160 :K Number of specific fragments extracted= 7 number of extra gaps= 0 total=53 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1usgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0354 read from 1usgA/merged-good-all-a2m # 1usgA read from 1usgA/merged-good-all-a2m # found chain 1usgA in training set T0354 6 :ISKLAIEALEDI 1usgA 124 :QGPTAAKYILET T0354 18 :KGKDIIELDTSK 1usgA 137 :KPQRIAIIHDKQ T0354 46 :RQVKALANSVQVKLKEAGVDIVGSEGHESGE 1usgA 149 :QYGEGLARSVQDGLKAANANVVFFDGITAGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=56 Number of alignments=13 # 1usgA read from 1usgA/merged-good-all-a2m # found chain 1usgA in training set T0354 6 :ISKLAIEAL 1usgA 124 :QGPTAAKYI T0354 15 :EDIKGKDIIELDTSK 1usgA 134 :ETVKPQRIAIIHDKQ T0354 46 :RQVKALANSVQVKLKEAGVDIVGSEGHESG 1usgA 149 :QYGEGLARSVQDGLKAANANVVFFDGITAG Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Number of alignments=14 # 1usgA read from 1usgA/merged-good-all-a2m # found chain 1usgA in training set T0354 6 :ISKLAIEAL 1usgA 124 :QGPTAAKYI T0354 15 :EDIKGKDI 1usgA 134 :ETVKPQRI T0354 38 :IVATGDSNRQ 1usgA 142 :AIIHDKQQYG T0354 49 :KALANSVQVKLKEAGVDIVGSEGHESGE 1usgA 152 :EGLARSVQDGLKAANANVVFFDGITAGE Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tqjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0354 read from 1tqjA/merged-good-all-a2m # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0354)G42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0354)D43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0354)S44 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 T0354 8 :KLAIEALEDIKGKDIIELD 1tqjA 102 :HRTLCQIRELGKKAGAVLN T0354 27 :TSKLTSLFQRMIVAT 1tqjA 128 :LEYVLPVCDLILIMS T0354 48 :VKALANSVQVKLKEAGVDIV 1tqjA 156 :VLPKIRALRQMCDERGLDPW T0354 85 :VVV 1tqjA 176 :IEV Number of specific fragments extracted= 4 number of extra gaps= 1 total=67 Number of alignments=16 # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0354)G42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0354)D43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0354)S44 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 T0354 8 :KLAIEALEDIKGKDIIELD 1tqjA 102 :HRTLCQIRELGKKAGAVLN T0354 27 :TSKLTSLFQRMIVAT 1tqjA 128 :LEYVLPVCDLILIMS T0354 48 :VKALANSVQVKLKEAGVDIVG 1tqjA 156 :VLPKIRALRQMCDERGLDPWI Number of specific fragments extracted= 3 number of extra gaps= 1 total=70 Number of alignments=17 # 1tqjA read from 1tqjA/merged-good-all-a2m # found chain 1tqjA in training set Warning: unaligning (T0354)G42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tqjA)N144 Warning: unaligning (T0354)D43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tqjA)N144 Warning: unaligning (T0354)S44 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tqjA)Q150 T0354 5 :E 1tqjA 103 :R T0354 10 :AIEALEDIKGKDIIELD 1tqjA 104 :TLCQIRELGKKAGAVLN T0354 27 :TSKLTSLFQRMIVAT 1tqjA 128 :LEYVLPVCDLILIMS T0354 46 :RQV 1tqjA 158 :PKI T0354 53 :NSVQVKLKEAGVDIV 1tqjA 161 :RALRQMCDERGLDPW T0354 78 :VLVD 1tqjA 176 :IEVD Number of specific fragments extracted= 6 number of extra gaps= 1 total=76 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dgjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dgjA expands to /projects/compbio/data/pdb/1dgj.pdb.gz 1dgjA:# T0354 read from 1dgjA/merged-good-all-a2m # 1dgjA read from 1dgjA/merged-good-all-a2m # adding 1dgjA to template set # found chain 1dgjA in template set T0354 48 :VKALANSVQV 1dgjA 710 :IRVACEMLIE T0354 58 :KLKEAGVDIVGSEGH 1dgjA 733 :EMKAEGRPMRYDGKW T0354 73 :ESGEWVL 1dgjA 780 :ATGKATV T0354 83 :GDVVVHV 1dgjA 787 :EKMVCVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=80 Number of alignments=19 # 1dgjA read from 1dgjA/merged-good-all-a2m # found chain 1dgjA in template set T0354 47 :QVKALANSVQV 1dgjA 709 :AIRVACEMLIE T0354 58 :KLKEAGVDIVGSEG 1dgjA 733 :EMKAEGRPMRYDGK T0354 72 :HESGEWV 1dgjA 779 :VATGKAT T0354 82 :AGDVVVHV 1dgjA 786 :VEKMVCVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=84 Number of alignments=20 # 1dgjA read from 1dgjA/merged-good-all-a2m # found chain 1dgjA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y2qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y2qA expands to /projects/compbio/data/pdb/1y2q.pdb.gz 1y2qA:# T0354 read from 1y2qA/merged-good-all-a2m # 1y2qA read from 1y2qA/merged-good-all-a2m # adding 1y2qA to template set # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSLF 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSEL T0354 42 :GDSNRQV 1y2qA 89 :AKPSVAM T0354 50 :ALANSVQVKLKEAGVDIVGS 1y2qA 96 :DILNRVYQGLKERGFNVGKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=87 Number of alignments=21 # 1y2qA read from 1y2qA/merged-good-all-a2m # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSLF 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSEL T0354 42 :GD 1y2qA 89 :AK T0354 45 :NRQVKALANSVQVKLKEAGVDIVGS 1y2qA 91 :PSVAMDILNRVYQGLKERGFNVGKA Number of specific fragments extracted= 3 number of extra gaps= 0 total=90 Number of alignments=22 # 1y2qA read from 1y2qA/merged-good-all-a2m # found chain 1y2qA in template set T0354 3 :IQEISKLAIEALEDIKGKDIIELDTSKLTSL 1y2qA 57 :SLKAIEEISKVAEQVKAENVFVYPFAHLSSE T0354 41 :TGDSNRQVK 1y2qA 88 :LAKPSVAMD T0354 51 :LANSVQVKLKEAGVDIVGSE 1y2qA 97 :ILNRVYQGLKERGFNVGKAP Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qysA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qysA expands to /projects/compbio/data/pdb/1qys.pdb.gz 1qysA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1qysA/merged-good-all-a2m # 1qysA read from 1qysA/merged-good-all-a2m # adding 1qysA to template set # found chain 1qysA in template set T0354 3 :IQEISKLAIEALEDIKGK 1qysA 29 :LQKVLNELMDYIKKQGAK T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSE 1qysA 47 :RVRISITARTKKEAEKFAAILIKVFAELGYNDINVT T0354 72 :HESGEWVL 1qysA 83 :FDGDTVTV Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 Number of alignments=24 # 1qysA read from 1qysA/merged-good-all-a2m # found chain 1qysA in template set T0354 3 :IQEISKLAIEALEDIKGKD 1qysA 29 :LQKVLNELMDYIKKQGAKR T0354 36 :RMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSE 1qysA 48 :VRISITARTKKEAEKFAAILIKVFAELGYNDINVT T0354 72 :HESGEWVL 1qysA 83 :FDGDTVTV Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 Number of alignments=25 # 1qysA read from 1qysA/merged-good-all-a2m # found chain 1qysA in template set T0354 2 :EIQEISKLAIEALEDIKGKDII 1qysA 28 :ELQKVLNELMDYIKKQGAKRVR T0354 38 :IVATGDSNRQVKALANSVQVKLKEAGVDIVGSEG 1qysA 50 :ISITARTKKEAEKFAAILIKVFAELGYNDINVTF T0354 73 :ESGE 1qysA 84 :DGDT Number of specific fragments extracted= 3 number of extra gaps= 0 total=102 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rtxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rtxA expands to /projects/compbio/data/pdb/1rtx.pdb.gz 1rtxA:# T0354 read from 1rtxA/merged-good-all-a2m # 1rtxA read from 1rtxA/merged-good-all-a2m # adding 1rtxA to template set # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALED 1rtxA 62 :DGRYMREAHKELVEN T0354 41 :TGDSNRQVKALANSVQVKLKEAGVD 1rtxA 77 :HGLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=104 Number of alignments=27 # 1rtxA read from 1rtxA/merged-good-all-a2m # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALED 1rtxA 62 :DGRYMREAHKELVEN T0354 41 :TGDSNRQVKALANSVQVKLKEAGVD 1rtxA 77 :HGLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=106 Number of alignments=28 # 1rtxA read from 1rtxA/merged-good-all-a2m # found chain 1rtxA in template set T0354 2 :EIQEISKLAIEALEDIK 1rtxA 62 :DGRYMREAHKELVENHG T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1rtxA 79 :LNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 2 number of extra gaps= 0 total=108 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vdxA expands to /projects/compbio/data/pdb/1vdx.pdb.gz 1vdxA:# T0354 read from 1vdxA/merged-good-all-a2m # 1vdxA read from 1vdxA/merged-good-all-a2m # adding 1vdxA to template set # found chain 1vdxA in template set T0354 4 :QEISKLAIEALEDI 1vdxA 51 :EEQAEEIKNILKKI T0354 18 :KGK 1vdxA 67 :KYK T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vdxA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=112 Number of alignments=30 # 1vdxA read from 1vdxA/merged-good-all-a2m # found chain 1vdxA in template set T0354 4 :QEISKLAIEALEDI 1vdxA 51 :EEQAEEIKNILKKI T0354 18 :KGKD 1vdxA 69 :KKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vdxA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=116 Number of alignments=31 # 1vdxA read from 1vdxA/merged-good-all-a2m # found chain 1vdxA in template set T0354 2 :EIQEISKLAIEALEDIKGKD 1vdxA 53 :QAEEIKNILKKIAEKYKKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vdxA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIVGS 1vdxA 100 :IREMAREIEDELAKLGFKKEGN Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufkA expands to /projects/compbio/data/pdb/1ufk.pdb.gz 1ufkA:# T0354 read from 1ufkA/merged-good-all-a2m # 1ufkA read from 1ufkA/merged-good-all-a2m # adding 1ufkA to template set # found chain 1ufkA in template set T0354 9 :LAIEALEDIKGK 1ufkA 157 :QAEANAKRNGVR T0354 21 :DIIELDTSKLTSLFQ 1ufkA 170 :RFLEGSLEAALPFGP T0354 36 :RMIVATGDSNRQ 1ufkA 186 :DLLVANLYAELH T0354 50 :ALAN 1ufkA 203 :RYRE T0354 54 :SVQVKLKEAGVDIVGSEGHES 1ufkA 226 :LVREAMAGAGFRPLEEAAEGE T0354 77 :WVLVDAG 1ufkA 247 :WVLLAYG Number of specific fragments extracted= 6 number of extra gaps= 0 total=125 Number of alignments=33 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set T0354 7 :SKLAIEALEDIKGK 1ufkA 155 :LPQAEANAKRNGVR T0354 21 :DIIELDTSKLTSLFQ 1ufkA 170 :RFLEGSLEAALPFGP T0354 36 :RMIVATGDSNRQ 1ufkA 186 :DLLVANLYAELH T0354 50 :ALAN 1ufkA 203 :RYRE T0354 54 :SVQVKLKEAGVDIVGSEGHES 1ufkA 226 :LVREAMAGAGFRPLEEAAEGE T0354 77 :WVLVDAG 1ufkA 247 :WVLLAYG Number of specific fragments extracted= 6 number of extra gaps= 0 total=131 Number of alignments=34 # 1ufkA read from 1ufkA/merged-good-all-a2m # found chain 1ufkA in template set T0354 4 :QEISKLAIEAL 1ufkA 198 :AALAPRYREAL T0354 32 :SLFQRMIVATGDSNR 1ufkA 209 :VPGGRALLTGILKDR T0354 52 :ANSVQVKLKEAGVDIVGSE 1ufkA 224 :APLVREAMAGAGFRPLEEA T0354 73 :ESGEWVLVDAG 1ufkA 243 :AEGEWVLLAYG Number of specific fragments extracted= 4 number of extra gaps= 0 total=135 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rz3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rz3A expands to /projects/compbio/data/pdb/1rz3.pdb.gz 1rz3A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1rz3A/merged-good-all-a2m # 1rz3A read from 1rz3A/merged-good-all-a2m # adding 1rz3A to template set # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 37 :MIVATGDSN 1rz3A 26 :GIDGLSRSG T0354 48 :VKALANSVQVKLKEAGVDIVGS 1rz3A 35 :KTTLANQLSQTLREQGISVCVF Number of specific fragments extracted= 3 number of extra gaps= 0 total=138 Number of alignments=36 # 1rz3A read from 1rz3A/merged-good-all-a2m # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 37 :MIVATGDSN 1rz3A 26 :GIDGLSRSG T0354 48 :VKALANSVQVKLKEAGVDIVGS 1rz3A 35 :KTTLANQLSQTLREQGISVCVF Number of specific fragments extracted= 3 number of extra gaps= 0 total=141 Number of alignments=37 # 1rz3A read from 1rz3A/merged-good-all-a2m # found chain 1rz3A in template set T0354 1 :MEIQEISKLAIEALEDIKGKDIIEL 1rz3A 1 :MELRDRIDFLCKTILAIKTAGRLVL T0354 39 :VATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHE 1rz3A 26 :GIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDD T0354 88 :HVMLPAVR 1rz3A 61 :HIVERAKR Number of specific fragments extracted= 3 number of extra gaps= 0 total=144 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vgjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vgjA expands to /projects/compbio/data/pdb/1vgj.pdb.gz 1vgjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0354 read from 1vgjA/merged-good-all-a2m # 1vgjA read from 1vgjA/merged-good-all-a2m # adding 1vgjA to template set # found chain 1vgjA in template set T0354 4 :QEISKLAIEALEDI 1vgjA 51 :EEQAEEIKNILKKI T0354 18 :KGK 1vgjA 67 :KYK T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vgjA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=148 Number of alignments=39 # 1vgjA read from 1vgjA/merged-good-all-a2m # found chain 1vgjA in template set T0354 3 :IQEISKLAIEALEDI 1vgjA 50 :TEEQAEEIKNILKKI T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIV 1vgjA 100 :IREMAREIEDELAKLGFKKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=151 Number of alignments=40 # 1vgjA read from 1vgjA/merged-good-all-a2m # found chain 1vgjA in template set T0354 2 :EIQEISKLAIEALEDIKGKD 1vgjA 53 :QAEEIKNILKKIAEKYKKHE T0354 22 :IIELDTSKLTSLFQRMIVATGDSNR 1vgjA 75 :VKGIGVFPNPNYIRVIWAGIENDEI T0354 48 :VKALANSVQVKLKEAGVDIVGSEG 1vgjA 100 :IREMAREIEDELAKLGFKKEGNFV T0354 78 :VLVDAGDV 1vgjA 124 :AHITLGRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=155 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v6tA expands to /projects/compbio/data/pdb/1v6t.pdb.gz 1v6tA:# T0354 read from 1v6tA/merged-good-all-a2m # 1v6tA read from 1v6tA/merged-good-all-a2m # adding 1v6tA to template set # found chain 1v6tA in template set T0354 2 :EIQEISKLAIEALED 1v6tA 188 :DKEEIAERVISMVKD T0354 17 :IKG 1v6tA 208 :ING T0354 29 :KLTSLFQRMIVATGDSNRQVK 1v6tA 211 :EWVDLKVDTICVHGDNPKAVE T0354 51 :LANSVQVKLKEAGVDIVG 1v6tA 232 :ITSYIRKVLEEEGVKIVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=159 Number of alignments=42 # 1v6tA read from 1v6tA/merged-good-all-a2m # found chain 1v6tA in template set T0354 1 :MEIQEISKLAIEALED 1v6tA 187 :EDKEEIAERVISMVKD T0354 26 :DTSK 1v6tA 206 :RAIN T0354 30 :LTSLFQRMIVATGDSNRQVK 1v6tA 212 :WVDLKVDTICVHGDNPKAVE T0354 51 :LANSVQVKLKEAGVDIVG 1v6tA 232 :ITSYIRKVLEEEGVKIVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=163 Number of alignments=43 # 1v6tA read from 1v6tA/merged-good-all-a2m # found chain 1v6tA in template set T0354 1 :MEIQEISKLAIEALEDI 1v6tA 187 :EDKEEIAERVISMVKDG T0354 18 :KGKDIIELDT 1v6tA 206 :RAINGEWVDL T0354 34 :FQRMIVATGDSNRQVKA 1v6tA 216 :KVDTICVHGDNPKAVEI T0354 52 :ANSVQVKLKEAGVDIVGSE 1v6tA 233 :TSYIRKVLEEEGVKIVPMK Number of specific fragments extracted= 4 number of extra gaps= 0 total=167 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0354/1g7uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0354/1g7uA/merged-good-all-a2m.gz for input Trying 1g7uA/merged-good-all-a2m Error: Couldn't open file 1g7uA/merged-good-all-a2m or 1g7uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e1dA expands to /projects/compbio/data/pdb/1e1d.pdb.gz 1e1dA:# T0354 read from 1e1dA/merged-good-all-a2m # 1e1dA read from 1e1dA/merged-good-all-a2m # adding 1e1dA to template set # found chain 1e1dA in template set T0354 2 :EIQEISKLA 1e1dA 350 :DFSALIAQA T0354 17 :IKGKDIIELDTSK 1e1dA 359 :KKCPPPVEIETGS T0354 39 :VATGDSNRQVKALANSVQVKLKEAGV 1e1dA 372 :IVGGFAHHQVLALADKVVEAVKSGAI T0354 83 :GDVVVHVM 1e1dA 398 :KRFVVMAG T0354 91 :LPAVRDYYD 1e1dA 409 :RQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=172 Number of alignments=45 # 1e1dA read from 1e1dA/merged-good-all-a2m # found chain 1e1dA in template set T0354 1 :MEIQEISKLA 1e1dA 349 :KDFSALIAQA T0354 17 :IKGKDIIELDTSK 1e1dA 359 :KKCPPPVEIETGS T0354 39 :VATGDSNRQVKALANSVQVKLKEAGVD 1e1dA 372 :IVGGFAHHQVLALADKVVEAVKSGAIK T0354 84 :DVVVHVM 1e1dA 399 :RFVVMAG T0354 91 :LPAVRDYYD 1e1dA 409 :RQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=177 Number of alignments=46 # 1e1dA read from 1e1dA/merged-good-all-a2m # found chain 1e1dA in template set T0354 2 :EIQEISKLA 1e1dA 350 :DFSALIAQA T0354 17 :IKGKDIIELDTSKL 1e1dA 359 :KKCPPPVEIETGSI T0354 40 :ATGDSNRQVKALANSVQVKLKEAGVD 1e1dA 373 :VGGFAHHQVLALADKVVEAVKSGAIK T0354 84 :DVVVHV 1e1dA 399 :RFVVMA T0354 90 :MLPAVRDYYD 1e1dA 408 :GRQKSRSYYT Number of specific fragments extracted= 5 number of extra gaps= 0 total=182 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wqaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wqaA expands to /projects/compbio/data/pdb/1wqa.pdb.gz 1wqaA:# T0354 read from 1wqaA/merged-good-all-a2m # 1wqaA read from 1wqaA/merged-good-all-a2m # adding 1wqaA to template set # found chain 1wqaA in template set T0354 48 :VKALANSVQVKLKEAGVDIVGSEGH 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDGA T0354 73 :ESGEWVLVDAGD 1wqaA 411 :FEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=185 Number of alignments=48 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0354 48 :VKALANSVQVKLKEAGVDIVGSEG 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDG T0354 72 :HESGEWVLVDAGD 1wqaA 410 :IFEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=188 Number of alignments=49 # 1wqaA read from 1wqaA/merged-good-all-a2m # found chain 1wqaA in template set T0354 12 :EALEDIKGK 1wqaA 362 :ELIDELPKY T0354 23 :IELDTSKL 1wqaA 371 :YQIKTKRH T0354 42 :GDSN 1wqaA 379 :VEGD T0354 48 :VKALANSVQVKLKEAGVDIVGSEGH 1wqaA 383 :RHAIVNKVAEMARERGYTVDTTDGA T0354 73 :ESGEWVLVDAGD 1wqaA 411 :FEDGWVLVRASG T0354 85 :VVVHVMLPAVRDYY 1wqaA 429 :IFSEAKSKEKAQEY Number of specific fragments extracted= 6 number of extra gaps= 0 total=194 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dlyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dlyA expands to /projects/compbio/data/pdb/1dly.pdb.gz 1dlyA:# T0354 read from 1dlyA/merged-good-all-a2m # 1dlyA read from 1dlyA/merged-good-all-a2m # adding 1dlyA to template set # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALEDIKG 1dlyA 37 :DMKVQRSKQFAFLAYALG T0354 28 :SKLTSLF 1dlyA 69 :KDLVPHL T0354 44 :SNRQVKALANSVQVKLKEAGVD 1dlyA 76 :SDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 3 number of extra gaps= 0 total=197 Number of alignments=51 # 1dlyA read from 1dlyA/merged-good-all-a2m # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALEDIKG 1dlyA 37 :DMKVQRSKQFAFLAYALG T0354 27 :TSK 1dlyA 59 :WKG T0354 30 :LTSLFQ 1dlyA 64 :MRTAHK T0354 44 :SNRQVKALANSVQVKLKEAGVD 1dlyA 76 :SDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=201 Number of alignments=52 # 1dlyA read from 1dlyA/merged-good-all-a2m # found chain 1dlyA in template set T0354 2 :EIQEISKLAIEALE 1dlyA 37 :DMKVQRSKQFAFLA T0354 16 :DIKGKD 1dlyA 58 :EWKGKD T0354 28 :SKLTSL 1dlyA 69 :KDLVPH T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1dlyA 75 :LSDVHFQAVARHLSDTLTELGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=205 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s69A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0354 read from 1s69A/merged-good-all-a2m # 1s69A read from 1s69A/merged-good-all-a2m # found chain 1s69A in training set T0354 1 :MEIQEISKLAIEALEDIKG 1s69A 38 :VDMAKQRAHQKAFLTYAFG T0354 20 :KD 1s69A 58 :TD T0354 26 :DTSKL 1s69A 60 :KYDGR T0354 43 :DSNRQVKALANSVQVKLKEAGVD 1s69A 79 :LNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=209 Number of alignments=54 # 1s69A read from 1s69A/merged-good-all-a2m # found chain 1s69A in training set T0354 1 :MEIQEISKLAIEALEDIKG 1s69A 38 :VDMAKQRAHQKAFLTYAFG T0354 20 :KD 1s69A 58 :TD T0354 26 :DTSK 1s69A 60 :KYDG T0354 42 :GDSNRQVKALANSVQVKLKEAGVD 1s69A 78 :GLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=213 Number of alignments=55 # 1s69A read from 1s69A/merged-good-all-a2m # found chain 1s69A in training set T0354 1 :MEIQEISKLAIEALED 1s69A 38 :VDMAKQRAHQKAFLTY T0354 17 :IKGKD 1s69A 55 :FGGTD T0354 26 :DTSKLTS 1s69A 60 :KYDGRYM T0354 42 :GDSNRQVKALANSVQVKLKEAGVD 1s69A 78 :GLNGEHFDAVAEDLLATLKEMGVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=217 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mp9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mp9A expands to /projects/compbio/data/pdb/1mp9.pdb.gz 1mp9A:# T0354 read from 1mp9A/merged-good-all-a2m # 1mp9A read from 1mp9A/merged-good-all-a2m # adding 1mp9A to template set # found chain 1mp9A in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVL 1mp9A 67 :GKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVA Number of specific fragments extracted= 1 number of extra gaps= 0 total=218 Number of alignments=57 # 1mp9A read from 1mp9A/merged-good-all-a2m # found chain 1mp9A in template set T0354 23 :IELDTSKLTSLF 1mp9A 50 :LIFRLESPKITS T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVD 1mp9A 67 :GKMVVTGAKSTDELIKAVKRIIKTLKKYGMQ T0354 66 :IVGSEG 1mp9A 103 :KIQIQN T0354 72 :HESGEWVL 1mp9A 155 :FSSGKMVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=222 Number of alignments=58 # 1mp9A read from 1mp9A/merged-good-all-a2m # found chain 1mp9A in template set T0354 20 :KDIIELDTSKL 1mp9A 47 :FPGLIFRLESP T0354 31 :TSLFQRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVL 1mp9A 63 :IFKSGKMVVTGAKSTDELIKAVKRIIKTLKKYGMQLTGKPKIQIQNIVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=224 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aisA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aisA expands to /projects/compbio/data/pdb/1ais.pdb.gz 1aisA:# T0354 read from 1aisA/merged-good-all-a2m # 1aisA read from 1aisA/merged-good-all-a2m # adding 1aisA to template set # found chain 1aisA in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGH 1aisA 63 :GKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQI T0354 73 :ESGEWVL 1aisA 152 :SSGKIVC Number of specific fragments extracted= 2 number of extra gaps= 0 total=226 Number of alignments=60 # 1aisA read from 1aisA/merged-good-all-a2m # found chain 1aisA in template set T0354 35 :QRMIVATGDSNRQVKALANSVQVKLKEAGVDI 1aisA 63 :GKLVVTGAKSVQDIERAVAKLAQKLKSIGVKF T0354 67 :VGSEG 1aisA 98 :PQIDV T0354 72 :HESGEWVL 1aisA 151 :FSSGKIVC Number of specific fragments extracted= 3 number of extra gaps= 0 total=229 Number of alignments=61 # 1aisA read from 1aisA/merged-good-all-a2m # found chain 1aisA in template set Warning: unaligning (T0354)K29 because of BadResidue code BAD_PEPTIDE in next template residue (1aisA)P53 Warning: unaligning (T0354)L30 because of BadResidue code BAD_PEPTIDE at template residue (1aisA)P53 T0354 21 :DIIELDTS 1aisA 44 :PGIICHLD T0354 31 :TSLFQR 1aisA 54 :KVALLI T0354 37 :MIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEW 1aisA 65 :LVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNM Number of specific fragments extracted= 3 number of extra gaps= 1 total=232 Number of alignments=62 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 62 Done printing distance constraints # command: