# 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/T0314/ # command:# Making conformation for sequence T0314 numbered 1 through 106 Created new target T0314 from T0314.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0314/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b89A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b89A expands to /projects/compbio/data/pdb/1b89.pdb.gz 1b89A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1b89A/merged-good-all-a2m # 1b89A read from 1b89A/merged-good-all-a2m # adding 1b89A to template set # found chain 1b89A in template set T0314 4 :TSTDICQAADAL 1b89A 1344 :NIPKVLRAAEQA # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 # 1b89A read from 1b89A/merged-good-all-a2m # found chain 1b89A in template set T0314 6 :TDICQAADAL 1b89A 1346 :PKVLRAAEQA Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 # 1b89A read from 1b89A/merged-good-all-a2m # found chain 1b89A in template set T0314 4 :TSTDICQAADAL 1b89A 1344 :NIPKVLRAAEQA Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypJ/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rypJ expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1rypJ:# T0314 read from 1rypJ/merged-good-all-a2m # 1rypJ read from 1rypJ/merged-good-all-a2m # adding 1rypJ to template set # found chain 1rypJ in template set T0314 2 :SITSTDICQAADA 1rypJ 72 :AIEPETFTQLVSS T0314 15 :LKG 1rypJ 86 :LYE T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSSV 1rypJ 117 :LIGCIDEAKDFIVSGT T0314 64 :LGREQLQILLEQNI 1rypJ 149 :LEPEDLFETISQAL T0314 78 :NERLNIGEPLLVYLRRQD 1rypJ 167 :DRDALSGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=10 Number of alignments=1 # 1rypJ read from 1rypJ/merged-good-all-a2m # found chain 1rypJ in template set T0314 8 :ICQAADALK 1rypJ 82 :VSSSLYERR T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSS 1rypJ 117 :LIGCIDEAKDFIVSG T0314 58 :RD 1rypJ 146 :EP T0314 64 :LGREQLQILLEQNINERLN 1rypJ 149 :LEPEDLFETISQALLNAAD T0314 83 :IGEPLLVYLRRQD 1rypJ 172 :SGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=17 Number of alignments=2 # 1rypJ read from 1rypJ/merged-good-all-a2m # found chain 1rypJ in template set T0314 2 :SITSTDICQAADA 1rypJ 72 :AIEPETFTQLVSS T0314 15 :LKG 1rypJ 86 :LYE T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSSVRDDVM 1rypJ 117 :LIGCIDEAKDFIVSGTASDQL T0314 63 :RLGREQLQILLEQNI 1rypJ 148 :NLEPEDLFETISQAL T0314 78 :NERLNIGEPLLVYLRRQD 1rypJ 167 :DRDALSGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=24 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wjxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1wjxA/merged-good-all-a2m # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 17 :GFVGF 1wjxA 43 :SFARF T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDLPEITAQ 1wjxA 100 :VPLKIYFNERGYAKVLLG Number of specific fragments extracted= 6 number of extra gaps= 0 total=30 Number of alignments=4 # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 16 :KGFVGFNR 1wjxA 35 :AGKVDFTG T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDL 1wjxA 100 :VPLKIYFNERGY Number of specific fragments extracted= 6 number of extra gaps= 0 total=36 Number of alignments=5 # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 18 :FVGF 1wjxA 44 :FARF T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDLPEIT 1wjxA 100 :VPLKIYFNERGYAKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=42 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f1kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f1kA expands to /projects/compbio/data/pdb/2f1k.pdb.gz 2f1kA:Skipped atom 152, because occupancy 0.4 <= existing 0.600 in 2f1kA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2f1kA Bad short name: OD3 for alphabet: pdb_atoms Skipped atom 1215, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1217, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1219, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1221, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1870, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 2f1kA # T0314 read from 2f1kA/merged-good-all-a2m # 2f1kA read from 2f1kA/merged-good-all-a2m # adding 2f1kA to template set # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 3 :ITSTDICQAADALKGFVGFN 2f1kA 93 :VKTAIAEPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :L 2f1kA 152 :R Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=7 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 9 :CQAADALKGFVGFN 2f1kA 99 :EPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :LE 2f1kA 152 :RS Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 Number of alignments=8 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 3 :ITSTDICQAADALKGFVGFN 2f1kA 93 :VKTAIAEPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :L 2f1kA 152 :R Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mw7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mw7A expands to /projects/compbio/data/pdb/1mw7.pdb.gz 1mw7A:# T0314 read from 1mw7A/merged-good-all-a2m # 1mw7A read from 1mw7A/merged-good-all-a2m # adding 1mw7A to template set # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQI 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMEL T0314 73 :LEQNINERLNIGEPLLVYLR 1mw7A 219 :TEKLLDRIEDDDDVVALYTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=58 Number of alignments=10 # 1mw7A read from 1mw7A/merged-good-all-a2m # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQIL 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMELT T0314 74 :EQNINERLNIGEPLLVYL 1mw7A 220 :EKLLDRIEDDDDVVALYT Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 Number of alignments=11 # 1mw7A read from 1mw7A/merged-good-all-a2m # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQI 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMEL T0314 73 :LEQNINERLNIGEPLLVYLR 1mw7A 219 :TEKLLDRIEDDDDVVALYTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kshA expands to /projects/compbio/data/pdb/1ksh.pdb.gz 1kshA:Skipped atom 280, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 282, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 284, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 286, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 288, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 290, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 292, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1099, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1101, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1150, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1152, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1154, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1156, because occupancy 0.300 <= existing 0.700 in 1kshA # T0314 read from 1kshA/merged-good-all-a2m # 1kshA read from 1kshA/merged-good-all-a2m # adding 1kshA to template set # found chain 1kshA in template set T0314 44 :DSITPTSEFVW 1kshA 42 :DTISPTLGFNI T0314 55 :SSVRDDVMR 1kshA 55 :LEHRGFKLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Number of alignments=13 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=68 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set T0314 21 :FNRKTGRYIVRFSED 1kshA 56 :EHRGFKLNIWDVGGQ T0314 36 :SFGMDV 1kshA 75 :SYWRNY T0314 43 :DDSIT 1kshA 81 :FESTD T0314 52 :FVWSSVRDDVMRLGREQLQILLEQ 1kshA 89 :WVVDSADRQRMQDCQRELQSLLVE T0314 79 :ERLN 1kshA 113 :ERLA T0314 84 :GEPLLVYLRRQDLP 1kshA 117 :GATLLIFANKQDLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=74 Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zicA/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/T0314/1zicA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1zicA/merged-good-all-a2m.gz for input Trying 1zicA/merged-good-all-a2m Error: Couldn't open file 1zicA/merged-good-all-a2m or 1zicA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vemA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vemA expands to /projects/compbio/data/pdb/1vem.pdb.gz 1vemA:Skipped atom 2616, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2618, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2620, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2622, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2624, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2626, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2628, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2630, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2632, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2634, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2636, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2638, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2640, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2642, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2644, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2646, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2648, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2650, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2652, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2654, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2656, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2666, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2668, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2670, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2672, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2674, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2676, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2678, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2680, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2682, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2684, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2686, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2688, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2690, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2692, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2694, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2696, because occupancy 0.500 <= existing 0.500 in 1vemA # T0314 read from 1vemA/merged-good-all-a2m # 1vemA read from 1vemA/merged-good-all-a2m # adding 1vemA to template set # found chain 1vemA in template set T0314 6 :TDICQAADALKGFVGF 1vemA 405 :NSLMGKFKDLLGVTPV T0314 23 :RKTGRYIVRFSEDSFGMDVADDSITPT 1vemA 432 :TIGDTVYITGNRAELGSWDTKQYPIQL T0314 53 :VWSSVRDD 1vemA 459 :YYDSHSND T0314 61 :VMRLGR 1vemA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1vemA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 Number of alignments=15 # 1vemA read from 1vemA/merged-good-all-a2m # found chain 1vemA in template set T0314 23 :RKTGRYIVRFSEDSFGMDVADDSIT 1vemA 432 :TIGDTVYITGNRAELGSWDTKQYPI T0314 51 :EFVWSSVRDD 1vemA 457 :QLYYDSHSND T0314 61 :VMRLGR 1vemA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1vemA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 4 number of extra gaps= 0 total=83 Number of alignments=16 # 1vemA read from 1vemA/merged-good-all-a2m # found chain 1vemA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o17A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o17A expands to /projects/compbio/data/pdb/1o17.pdb.gz 1o17A:# T0314 read from 1o17A/merged-good-all-a2m # 1o17A read from 1o17A/merged-good-all-a2m # adding 1o17A to template set # found chain 1o17A in template set T0314 6 :TDICQAADALK 1o17A 199 :DLLSKSAYELD T0314 25 :TGRYIVRFSEDSF 1o17A 210 :FNKIILVYGEPGI T0314 44 :DSITPTSEF 1o17A 223 :DEVSPIGNT T0314 53 :VWSSVRDDVMRLG 1o17A 235 :IVSKRGIEEVKLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=87 Number of alignments=17 # 1o17A read from 1o17A/merged-good-all-a2m # found chain 1o17A in template set T0314 8 :ICQAADALK 1o17A 201 :LSKSAYELD T0314 21 :F 1o17A 210 :F T0314 26 :GRYIVRFSEDSF 1o17A 211 :NKIILVYGEPGI T0314 44 :DSITPTSEFVWSS 1o17A 223 :DEVSPIGNTFMKI T0314 57 :VRDDVMRLG 1o17A 237 :SKRGIEEVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=92 Number of alignments=18 # 1o17A read from 1o17A/merged-good-all-a2m # found chain 1o17A in template set T0314 6 :TDICQAADALK 1o17A 199 :DLLSKSAYELD T0314 25 :TGRYIVRFSEDSF 1o17A 210 :FNKIILVYGEPGI T0314 44 :DSITPTSEF 1o17A 223 :DEVSPIGNT T0314 53 :VWSSVRDDVMRLG 1o17A 235 :IVSKRGIEEVKLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cb2A expands to /projects/compbio/data/pdb/2cb2.pdb.gz 2cb2A:Skipped atom 164, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 166, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 168, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 170, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 172, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 174, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 176, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 178, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 262, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 264, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 266, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 369, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 371, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 373, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 375, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 542, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 544, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 847, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 849, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 851, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 853, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 855, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 857, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 859, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 861, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 1372, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1374, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1462, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1464, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1466, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1468, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1495, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1497, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1499, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1501, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1503, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1505, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1702, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1704, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1706, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1958, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1960, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1962, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1964, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 2015, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2018, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2405, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 2cb2A # T0314 read from 2cb2A/merged-good-all-a2m # 2cb2A read from 2cb2A/merged-good-all-a2m # adding 2cb2A to template set # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 5 :STD 2cb2A 27 :GPK T0314 11 :AADALKGFVGF 2cb2A 33 :VTARHPGFVGF T0314 27 :RYIVRFSEDSFGMDVADDSITPTSE 2cb2A 44 :QNHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNINE 2cb2A 82 :DWKDHEEMHRQNWSY Number of specific fragments extracted= 5 number of extra gaps= 0 total=101 Number of alignments=20 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 6 :TD 2cb2A 28 :PK T0314 11 :AADALKGFVGFN 2cb2A 33 :VTARHPGFVGFQ T0314 28 :YIVRFSEDSFGMDVADDSITPTSE 2cb2A 45 :NHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNIN 2cb2A 82 :DWKDHEEMHRQNWS Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 Number of alignments=21 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 5 :STD 2cb2A 27 :GPK T0314 11 :AADALKGFVGF 2cb2A 33 :VTARHPGFVGF T0314 27 :RYIVRFSEDSFGMDVADDSITPTSE 2cb2A 44 :QNHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNINE 2cb2A 82 :DWKDHEEMHRQNWSY Number of specific fragments extracted= 5 number of extra gaps= 0 total=111 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1din/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1din/merged-good-all-a2m # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1din 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 66 :REQLQILLEQNI 1din 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=113 Number of alignments=23 # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1din 19 :LVGSPAKAPAPVIVIAQEIFGVNA T0314 66 :REQLQILLEQNI 1din 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=115 Number of alignments=24 # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1din 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 64 :LGREQLQILLEQNI 1din 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1veoA/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/T0314/1veoA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1veoA/merged-good-all-a2m.gz for input Trying 1veoA/merged-good-all-a2m Error: Couldn't open file 1veoA/merged-good-all-a2m or 1veoA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 4icb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 4icb expands to /projects/compbio/data/pdb/4icb.pdb.gz 4icb:Warning: there is no chain 4icb will retry with 4icbA Skipped atom 243, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 245, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 247, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 249, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 562, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 564, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 566, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 568, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 570, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 4icb # T0314 read from 4icb/merged-good-all-a2m # 4icb read from 4icb/merged-good-all-a2m # adding 4icb to template set # found chain 4icb in template set T0314 64 :LGREQLQILLEQNINERLNIGEPL 4icb 23 :LSKEELKLLLQTEFPSLLKGPSTL Number of specific fragments extracted= 1 number of extra gaps= 0 total=118 Number of alignments=26 # 4icb read from 4icb/merged-good-all-a2m # found chain 4icb in template set T0314 3 :ITSTDICQAADALKG 4icb 1 :KSPEELKGIFEKYAA T0314 24 :KTG 4icb 16 :KEG T0314 43 :DDS 4icb 19 :DPN T0314 60 :D 4icb 22 :Q T0314 64 :LGREQLQILLEQNINERLNIGEP 4icb 23 :LSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 5 number of extra gaps= 0 total=123 Number of alignments=27 # 4icb read from 4icb/merged-good-all-a2m # found chain 4icb in template set T0314 64 :LGREQLQILLEQNINERLNIGEPL 4icb 23 :LSKEELKLLLQTEFPSLLKGPSTL Number of specific fragments extracted= 1 number of extra gaps= 0 total=124 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1itcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1itcA expands to /projects/compbio/data/pdb/1itc.pdb.gz 1itcA:# T0314 read from 1itcA/merged-good-all-a2m # 1itcA read from 1itcA/merged-good-all-a2m # adding 1itcA to template set # found chain 1itcA in template set T0314 6 :TDICQAADALKGFVGF 1itcA 405 :NSLMGKFKDLLGVTPV T0314 22 :NRKTGRYIVRFSEDSFGMDVADDSI 1itcA 431 :TTIGDTVYITGNRAELGSWDTKQYP T0314 50 :SEFVWSSVRDD 1itcA 456 :IQLYYDSHSND T0314 61 :VMRLGR 1itcA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1itcA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 5 number of extra gaps= 0 total=129 Number of alignments=29 # 1itcA read from 1itcA/merged-good-all-a2m # found chain 1itcA in template set T0314 22 :NRKTGRYIVRFSEDSFGMDVADDSI 1itcA 431 :TTIGDTVYITGNRAELGSWDTKQYP T0314 50 :SEFVWSSVRDD 1itcA 456 :IQLYYDSHSND T0314 61 :VMRLGR 1itcA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1itcA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 4 number of extra gaps= 0 total=133 Number of alignments=30 # 1itcA read from 1itcA/merged-good-all-a2m # found chain 1itcA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i6uA expands to /projects/compbio/data/pdb/1i6u.pdb.gz 1i6uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1i6uA/merged-good-all-a2m # 1i6uA read from 1i6uA/merged-good-all-a2m # adding 1i6uA to template set # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 55 :SSVRDDVMRLGR 1i6uA 79 :FPVKKFGYEKFE T0314 74 :EQNINE 1i6uA 91 :KRYLPA T0314 84 :GEPLLVYLR 1i6uA 97 :RDFGILIVS Number of specific fragments extracted= 6 number of extra gaps= 0 total=139 Number of alignments=31 # 1i6uA read from 1i6uA/merged-good-all-a2m # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 55 :SSVRDDVMRLGR 1i6uA 79 :FPVKKFGYEKFE T0314 74 :EQNINE 1i6uA 91 :KRYLPA T0314 84 :GEPLLVYLR 1i6uA 97 :RDFGILIVS Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=32 # 1i6uA read from 1i6uA/merged-good-all-a2m # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 47 :T 1i6uA 79 :F T0314 56 :SVRDDVMRLG 1i6uA 80 :PVKKFGYEKF T0314 73 :LEQNINER 1i6uA 90 :EKRYLPAR T0314 84 :GEPL 1i6uA 98 :DFGI T0314 89 :VYL 1i6uA 102 :LIV Number of specific fragments extracted= 8 number of extra gaps= 0 total=153 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sak/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 2sak/merged-good-all-a2m # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 25 :TGRYI 2sak 21 :TGPYL T0314 30 :VRFS 2sak 27 :VNVT T0314 34 :EDSFGMDV 2sak 32 :VDSKGNEL T0314 48 :PTSEFVWSSVRDDV 2sak 40 :LSPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYL 2sak 81 :LDPSAKIEVTY T0314 92 :RRQDLPEITAQRQL 2sak 93 :DKNKKKEETKSFPI Number of specific fragments extracted= 7 number of extra gaps= 0 total=160 Number of alignments=34 # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 22 :NRKTGRYIVRFS 2sak 19 :EPTGPYLMVNVT T0314 35 :DSFGMDVA 2sak 33 :DSKGNELL T0314 49 :TSEFVWSSVRDDV 2sak 41 :SPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYLRRQD 2sak 81 :LDPSAKIEVTYYDKN T0314 96 :LPEITAQRQ 2sak 97 :KKEETKSFP Number of specific fragments extracted= 6 number of extra gaps= 0 total=166 Number of alignments=35 # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 25 :TGRYI 2sak 21 :TGPYL T0314 30 :VRFS 2sak 27 :VNVT T0314 35 :DSFGMDV 2sak 33 :DSKGNEL T0314 48 :PTSEFVWSSVRDDV 2sak 40 :LSPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYL 2sak 81 :LDPSAKIEVTY T0314 92 :RRQDLPEITAQRQLR 2sak 93 :DKNKKKEETKSFPIT Number of specific fragments extracted= 7 number of extra gaps= 0 total=173 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1go4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1go4A expands to /projects/compbio/data/pdb/1go4.pdb.gz 1go4A:# T0314 read from 1go4A/merged-good-all-a2m # 1go4A read from 1go4A/merged-good-all-a2m # adding 1go4A to template set # found chain 1go4A in template set Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADALKGF 1go4A 11 :ITLRGSAEIVAEFFSF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQNINERLNIG 1go4A 62 :IKYLNNVVEQLKDWLYKCS T0314 85 :EPLLVYLRRQDLPEITAQRQ 1go4A 82 :QKLVVVISNIESGEVLERWQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=177 Number of alignments=37 # 1go4A read from 1go4A/merged-good-all-a2m # found chain 1go4A in template set Warning: unaligning (T0314)M1 because of BadResidue code BAD_PEPTIDE in next template residue (1go4A)G10 Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADAL 1go4A 11 :ITLRGSAEIVAEF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQ 1go4A 62 :IKYLNNVVEQ T0314 77 :INERLNIG 1go4A 72 :LKDWLYKC T0314 85 :EPLLVYLRRQDLPEITAQ 1go4A 82 :QKLVVVISNIESGEVLER Number of specific fragments extracted= 5 number of extra gaps= 1 total=182 Number of alignments=38 # 1go4A read from 1go4A/merged-good-all-a2m # found chain 1go4A in template set Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADALKGF 1go4A 11 :ITLRGSAEIVAEFFSF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQNINERLNIG 1go4A 62 :IKYLNNVVEQLKDWLYKCS T0314 85 :EPLLVYLRRQDLPEITAQRQ 1go4A 82 :QKLVVVISNIESGEVLERWQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=186 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zi6A/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/T0314/1zi6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1zi6A/merged-good-all-a2m.gz for input Trying 1zi6A/merged-good-all-a2m Error: Couldn't open file 1zi6A/merged-good-all-a2m or 1zi6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1yyaA/merged-good-all-a2m # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=187 # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=188 # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=189 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ggvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ggvA expands to /projects/compbio/data/pdb/1ggv.pdb.gz 1ggvA:Bad short name: CI2 for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: CI1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms # T0314 read from 1ggvA/merged-good-all-a2m # 1ggvA read from 1ggvA/merged-good-all-a2m # adding 1ggvA to template set # found chain 1ggvA in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1ggvA 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 66 :REQLQILLEQNI 1ggvA 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=191 Number of alignments=40 # 1ggvA read from 1ggvA/merged-good-all-a2m # found chain 1ggvA in template set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1ggvA 19 :LVGSPAKAPAPVIVIAQEIFGVNA T0314 66 :REQLQILLEQNI 1ggvA 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=193 Number of alignments=41 # 1ggvA read from 1ggvA/merged-good-all-a2m # found chain 1ggvA in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1ggvA 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 64 :LGREQLQILLEQNI 1ggvA 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=195 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b5iC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b5iC expands to /projects/compbio/data/pdb/2b5i.pdb.gz 2b5iC:# T0314 read from 2b5iC/merged-good-all-a2m # 2b5iC read from 2b5iC/merged-good-all-a2m # adding 2b5iC to template set # found chain 2b5iC in template set T0314 28 :YIVRFSED 2b5iC 65 :LHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=198 Number of alignments=43 # 2b5iC read from 2b5iC/merged-good-all-a2m # found chain 2b5iC in template set T0314 27 :RYIVRFSED 2b5iC 64 :TLHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=201 Number of alignments=44 # 2b5iC read from 2b5iC/merged-good-all-a2m # found chain 2b5iC in template set T0314 28 :YIVRFSED 2b5iC 65 :LHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=204 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zi8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zi8A expands to /projects/compbio/data/pdb/1zi8.pdb.gz 1zi8A:# T0314 read from 1zi8A/merged-good-all-a2m # 1zi8A read from 1zi8A/merged-good-all-a2m # adding 1zi8A to template set # found chain 1zi8A in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1zi8A 18 :ALVGSPAKAPAPVIVIAQDIFGVN T0314 66 :REQLQILLEQNI 1zi8A 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=206 Number of alignments=46 # 1zi8A read from 1zi8A/merged-good-all-a2m # found chain 1zi8A in template set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1zi8A 19 :LVGSPAKAPAPVIVIAQDIFGVNA T0314 66 :REQLQILLEQNI 1zi8A 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=208 Number of alignments=47 # 1zi8A read from 1zi8A/merged-good-all-a2m # found chain 1zi8A in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1zi8A 18 :ALVGSPAKAPAPVIVIAQDIFGVN T0314 64 :LGREQLQILLEQNI 1zi8A 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=210 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fsrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fsrA expands to /projects/compbio/data/pdb/2fsr.pdb.gz 2fsrA:Skipped atom 26, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 28, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 138, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 140, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 142, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 144, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 146, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 148, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 150, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 154, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 444, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1061, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1063, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1065, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1067, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1069, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1071, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1284, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1286, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1288, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1290, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1292, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1294, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1296, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1379, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1381, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1383, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1385, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1387, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1389, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1391, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1393, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1395, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1457, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 2fsrA # T0314 read from 2fsrA/merged-good-all-a2m # 2fsrA read from 2fsrA/merged-good-all-a2m # adding 2fsrA to template set # found chain 2fsrA in template set T0314 7 :DICQAADALKGFVGF 2fsrA 53 :HDLANWHFFGHGALM T0314 22 :NRKTGRYIVRFS 2fsrA 70 :LGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 64 :LGREQLQILLEQNIN 2fsrA 106 :YAAEAAVALRDWAFE T0314 80 :RLNIG 2fsrA 121 :TLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=216 Number of alignments=49 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0314 3 :ITSTDICQAADALKG 2fsrA 42 :YDLPSTWGVFCHDLA T0314 18 :FVGFNRKTGRYIVRFS 2fsrA 66 :LMIDLGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 64 :LGREQLQILLEQNI 2fsrA 106 :YAAEAAVALRDWAF T0314 79 :ERLNIG 2fsrA 120 :ETLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=222 Number of alignments=50 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0314 7 :DICQAADALKGFVGF 2fsrA 53 :HDLANWHFFGHGALM T0314 22 :NRKTGRYIVRFS 2fsrA 70 :LGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 63 :RLGREQLQILLEQNIN 2fsrA 105 :GYAAEAAVALRDWAFE T0314 80 :RLNIG 2fsrA 121 :TLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g5bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g5bA expands to /projects/compbio/data/pdb/1g5b.pdb.gz 1g5bA:# T0314 read from 1g5bA/merged-good-all-a2m # 1g5bA read from 1g5bA/merged-good-all-a2m # adding 1g5bA to template set # found chain 1g5bA in template set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDSFG 1g5bA 112 :AKALAHKADELPLIIELVSKDKKYVICHADYPFD T0314 45 :SI 1g5bA 146 :EY Number of specific fragments extracted= 2 number of extra gaps= 0 total=230 Number of alignments=52 # 1g5bA read from 1g5bA/merged-good-all-a2m # found chain 1g5bA in template set T0314 6 :TDICQAADALKGFVGFNRKTGRYIVRFSEDSFGMDVADDSIT 1g5bA 113 :KALAHKADELPLIIELVSKDKKYVICHADYPFDEYEFGKPVD T0314 59 :DDV 1g5bA 155 :HQQ T0314 65 :GREQLQILLEQNINER 1g5bA 161 :NRERISNSQNGIVKEI Number of specific fragments extracted= 3 number of extra gaps= 0 total=233 Number of alignments=53 # 1g5bA read from 1g5bA/merged-good-all-a2m # found chain 1g5bA in template set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDSFG 1g5bA 112 :AKALAHKADELPLIIELVSKDKKYVICHADYPFD T0314 45 :SIT 1g5bA 146 :EYE Number of specific fragments extracted= 2 number of extra gaps= 0 total=235 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ig5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1ig5A/merged-good-all-a2m # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 63 :RLGREQLQILLEQNINERLNIGEP 1ig5A 22 :QLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=236 Number of alignments=55 # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 4 :TSTDICQAADALKGF 1ig5A 2 :SPEELKGIFEKYAAK T0314 25 :TG 1ig5A 17 :EG T0314 60 :DVMRLGREQLQILLEQNINERLNIGEP 1ig5A 19 :DPNQLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 3 number of extra gaps= 0 total=239 Number of alignments=56 # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 61 :VMRLGREQLQILLEQNINERLNIGEP 1ig5A 20 :PNQLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=240 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1exnA expands to /projects/compbio/data/pdb/1exn.pdb.gz 1exnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1exnA/merged-good-all-a2m # 1exnA read from 1exnA/merged-good-all-a2m # adding 1exnA to template set # found chain 1exnA in template set T0314 25 :TGRYIVRFSEDSFGMDVADDSI 1exnA 143 :LYDHVWLISTDGDWDTLLTDKV T0314 52 :FVWSSVRDDVMRL 1exnA 165 :SRFSFTTRREYHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=242 Number of alignments=58 # 1exnA read from 1exnA/merged-good-all-a2m # found chain 1exnA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=242 # 1exnA read from 1exnA/merged-good-all-a2m # found chain 1exnA in template set T0314 25 :TGRYIVRFSEDSFGMDVADDSI 1exnA 143 :LYDHVWLISTDGDWDTLLTDKV T0314 52 :FVWSSVRDDVMRL 1exnA 165 :SRFSFTTRREYHL T0314 65 :GREQL 1exnA 188 :DVEQF Number of specific fragments extracted= 3 number of extra gaps= 0 total=245 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1khxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1khxA/merged-good-all-a2m # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FG 1khxA 366 :YG T0314 47 :TPTSEFVWSS 1khxA 368 :WHPATVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYLRR 1khxA 407 :QLTRMCTIRMSFVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=251 Number of alignments=60 # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FGMDVA 1khxA 366 :YGWHPA T0314 51 :EFVWSS 1khxA 372 :TVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYL 1khxA 407 :QLTRMCTIRMSF Number of specific fragments extracted= 6 number of extra gaps= 0 total=257 Number of alignments=61 # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FG 1khxA 366 :YG T0314 47 :TPTSEFVWSS 1khxA 368 :WHPATVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYLRR 1khxA 407 :QLTRMCTIRMSFVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=263 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1venA/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/T0314/1venA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1venA/merged-good-all-a2m.gz for input Trying 1venA/merged-good-all-a2m Error: Couldn't open file 1venA/merged-good-all-a2m or 1venA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ziyA/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/T0314/1ziyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1ziyA/merged-good-all-a2m.gz for input Trying 1ziyA/merged-good-all-a2m Error: Couldn't open file 1ziyA/merged-good-all-a2m or 1ziyA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vepA/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/T0314/1vepA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1vepA/merged-good-all-a2m.gz for input Trying 1vepA/merged-good-all-a2m Error: Couldn't open file 1vepA/merged-good-all-a2m or 1vepA/merged-good-all-a2m.gz for input # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 62 Adding 934 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -206.1643, CN propb: -206.1643 weights: 0.2989 constraints: 263 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 263 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 263 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 671 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 671 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 934 # command: