# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0304 numbered 1 through 122 Created new target T0304 from T0304.a2m # command:CPU_time= 6.346 sec, elapsed time= 6.389 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rybA/T0304-1rybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rybA expands to /projects/compbio/data/pdb/1ryb.pdb.gz 1rybA:Skipped atom 336, because occupancy 0.5 <= existing 0.500 in 1rybA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1rybA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1rybA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 1rybA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 1rybA # T0304 read from 1rybA/T0304-1rybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rybA read from 1rybA/T0304-1rybA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rybA to template set # found chain 1rybA in template set T0304 53 :LFSDADAYHLDQAFPLLMKQLELML 1rybA 11 :NPGNKYYGTRHNVGFEMVDRIAAEE # choosing archetypes in rotamer library T0304 79 :SGELN 1rybA 36 :GITMN T0304 86 :HQH 1rybA 41 :TIQ T0304 95 :KGLTCKADTLSSCDYVYLAVYPTP 1rybA 44 :SKSLLGIGSIGEVPVLVVKPQSYM Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rybA/T0304-1rybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1rybA/T0304-1rybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rybA read from 1rybA/T0304-1rybA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rybA in template set T0304 53 :LFSDADAYHLDQAFPLLMKQLELML 1rybA 11 :NPGNKYYGTRHNVGFEMVDRIAAEE T0304 79 :SGELN 1rybA 36 :GITMN T0304 86 :HQH 1rybA 41 :TIQ T0304 95 :KGLTCKADTLSSCDYVYLAVYPTP 1rybA 44 :SKSLLGIGSIGEVPVLVVKPQSYM Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rybA/T0304-1rybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1rybA/T0304-1rybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rybA read from 1rybA/T0304-1rybA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rybA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gulA/T0304-1gulA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gulA expands to /projects/compbio/data/pdb/1gul.pdb.gz 1gulA:# T0304 read from 1gulA/T0304-1gulA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gulA read from 1gulA/T0304-1gulA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gulA to template set # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=10 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gulA/T0304-1gulA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1gulA/T0304-1gulA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gulA read from 1gulA/T0304-1gulA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gulA/T0304-1gulA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1gulA/T0304-1gulA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gulA read from 1gulA/T0304-1gulA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gulA in template set Warning: unaligning (T0304)L34 because of BadResidue code BAD_PEPTIDE in next template residue (1gulA)V66 Warning: unaligning (T0304)V35 because of BadResidue code BAD_PEPTIDE at template residue (1gulA)V66 T0304 36 :QEGNRLHYLADRAGIRGL 1gulA 67 :QTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gulA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 1 total=14 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1womA/T0304-1womA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1womA expands to /projects/compbio/data/pdb/1wom.pdb.gz 1womA:Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1womA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 1womA # T0304 read from 1womA/T0304-1womA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1womA read from 1womA/T0304-1womA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1womA to template set # found chain 1womA in template set T0304 27 :TPCFGARLVQEGNRLHYLADRAGIRGLFSDADAYHLDQAFPL 1womA 109 :RPELFSHLVMVGPSPCYLNDPPEYYGGFEEEQLLGLLEMMEK T0304 69 :LMKQLELM 1womA 155 :WATVFAAT Number of specific fragments extracted= 2 number of extra gaps= 0 total=16 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1womA/T0304-1womA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1womA/T0304-1womA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1womA read from 1womA/T0304-1womA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1womA in template set T0304 27 :TPCFGARLVQEGNRLHYLADRAGIRGLFSDADAYHLDQAFPL 1womA 109 :RPELFSHLVMVGPSPCYLNDPPEYYGGFEEEQLLGLLEMMEK T0304 69 :LMKQLELM 1womA 155 :WATVFAAT Number of specific fragments extracted= 2 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1womA/T0304-1womA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1womA/T0304-1womA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1womA read from 1womA/T0304-1womA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1womA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gumA/T0304-1gumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gumA expands to /projects/compbio/data/pdb/1gum.pdb.gz 1gumA:# T0304 read from 1gumA/T0304-1gumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gumA read from 1gumA/T0304-1gumA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gumA to template set # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gumA/T0304-1gumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1gumA/T0304-1gumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gumA read from 1gumA/T0304-1gumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=22 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gumA/T0304-1gumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1gumA/T0304-1gumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gumA read from 1gumA/T0304-1gumA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gumA in template set T0304 33 :RLVQEGNRLHYLADRAGIRGL 1gumA 64 :KLVQTRSILHYIADKHNLFGK T0304 55 :SDADAYHLDQAFPLLMKQLELMLT 1gumA 85 :NLKERTLIDMYVEGTLDLLELLIM Number of specific fragments extracted= 2 number of extra gaps= 0 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gaiA/T0304-2gaiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gaiA expands to /projects/compbio/data/pdb/2gai.pdb.gz 2gaiA:Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1549, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1780, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1782, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2019, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2025, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2462, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2464, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2466, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2468, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2631, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2633, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 2635, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3105, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3107, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3109, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3383, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3385, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 3387, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4164, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4166, because occupancy 0.500 <= existing 0.500 in 2gaiA Skipped atom 4168, because occupancy 0.500 <= existing 0.500 in 2gaiA # T0304 read from 2gaiA/T0304-2gaiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaiA read from 2gaiA/T0304-2gaiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gaiA to template set # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=26 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gaiA/T0304-2gaiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 2gaiA/T0304-2gaiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaiA read from 2gaiA/T0304-2gaiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gaiA/T0304-2gaiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 2gaiA/T0304-2gaiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaiA read from 2gaiA/T0304-2gaiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gaiA in template set T0304 65 :AFPLLMKQLELMLTS 2gaiA 172 :TLKLVCDREREILRF T0304 83 :NPRHQHTVTLYAKGLTCKADT 2gaiA 187 :VPKKYHRITVNFDGLTAEIDV Number of specific fragments extracted= 2 number of extra gaps= 0 total=30 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z9lA/T0304-1z9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z9lA expands to /projects/compbio/data/pdb/1z9l.pdb.gz 1z9lA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 371, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 808, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 810, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 1z9lA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 1z9lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0304 read from 1z9lA/T0304-1z9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z9lA read from 1z9lA/T0304-1z9lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z9lA to template set # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z9lA/T0304-1z9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1z9lA/T0304-1z9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z9lA read from 1z9lA/T0304-1z9lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z9lA/T0304-1z9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1z9lA/T0304-1z9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z9lA read from 1z9lA/T0304-1z9lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z9lA in template set T0304 80 :GELNPRHQHTVTLYAKGLTCKADTLSSCDYVYLAVYPTPEMKN 1z9lA 59 :GVIDPGSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISD Number of specific fragments extracted= 1 number of extra gaps= 0 total=33 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaeA/T0304-1kaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kaeA expands to /projects/compbio/data/pdb/1kae.pdb.gz 1kaeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1816, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2035, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2037, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2039, because occupancy 0.500 <= existing 0.500 in 1kaeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2059, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2061, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2063, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2065, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2067, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2069, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2557, because occupancy 0.500 <= existing 0.500 in 1kaeA Skipped atom 2825, because occupancy 0.500 <= existing 0.500 in 1kaeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0304 read from 1kaeA/T0304-1kaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kaeA read from 1kaeA/T0304-1kaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kaeA to template set # found chain 1kaeA in template set Warning: unaligning (T0304)R17 because of BadResidue code BAD_PEPTIDE at template residue (1kaeA)T61 T0304 18 :PWWGLPCT 1kaeA 62 :TVTALKVS T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYHLD 1kaeA 80 :LSDELKQAMA T0304 68 :LLMKQLELMLTSGELNPRHQH 1kaeA 90 :VAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPEM 1kaeA 122 :RPVASVGLYIPGGSAP Number of specific fragments extracted= 6 number of extra gaps= 1 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaeA/T0304-1kaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1kaeA/T0304-1kaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kaeA read from 1kaeA/T0304-1kaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kaeA in template set Warning: unaligning (T0304)R17 because of BadResidue code BAD_PEPTIDE at template residue (1kaeA)T61 T0304 18 :PWWGLPCT 1kaeA 62 :TVTALKVS T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYHLD 1kaeA 80 :LSDELKQAMA T0304 68 :LLMKQLELMLTSGELNPRHQH 1kaeA 90 :VAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPEM 1kaeA 122 :RPVASVGLYIPGGSAP Number of specific fragments extracted= 6 number of extra gaps= 1 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaeA/T0304-1kaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1kaeA/T0304-1kaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kaeA read from 1kaeA/T0304-1kaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kaeA in template set T0304 38 :GNRLHYLADR 1kaeA 70 :AEEIAAASER T0304 54 :FSDADAYH 1kaeA 80 :LSDELKQA T0304 66 :FPLLMKQLELMLTSGELNPRHQH 1kaeA 88 :MAVAVKNIETFHTAQKLPPVDVE T0304 93 :YAKGLTCKADT 1kaeA 111 :TQPGVRCQQVT T0304 105 :SSCDYVYLAVYPTPE 1kaeA 122 :RPVASVGLYIPGGSA Number of specific fragments extracted= 5 number of extra gaps= 0 total=50 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zemA/T0304-1zemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zemA expands to /projects/compbio/data/pdb/1zem.pdb.gz 1zemA:# T0304 read from 1zemA/T0304-1zemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zemA read from 1zemA/T0304-1zemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zemA to template set # found chain 1zemA in template set T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=52 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zemA/T0304-1zemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1zemA/T0304-1zemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zemA read from 1zemA/T0304-1zemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zemA in template set T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=54 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zemA/T0304-1zemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1zemA/T0304-1zemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zemA read from 1zemA/T0304-1zemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zemA in template set T0304 31 :GARLVQEG 1zemA 33 :AIALLDMN T0304 39 :NRLHYLADR 1zemA 42 :EALEKAEAS T0304 48 :AGIRGLF 1zemA 54 :KGVEARS T0304 55 :SDAD 1zemA 64 :DVTS T0304 63 :DQAFPLLMKQLELML 1zemA 68 :EEAVIGTVDSVVRDF T0304 80 :GELN 1zemA 83 :GKID Number of specific fragments extracted= 6 number of extra gaps= 0 total=60 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj2A/T0304-1lj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lj2A expands to /projects/compbio/data/pdb/1lj2.pdb.gz 1lj2A:# T0304 read from 1lj2A/T0304-1lj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj2A read from 1lj2A/T0304-1lj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lj2A to template set # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=61 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj2A/T0304-1lj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1lj2A/T0304-1lj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj2A read from 1lj2A/T0304-1lj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj2A/T0304-1lj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1lj2A/T0304-1lj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj2A read from 1lj2A/T0304-1lj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj2A in template set T0304 59 :AYHLDQAFPLLMKQLELMLTSGELNP 1lj2A 231 :ERDLQNKIGSLTSSIEWYLRSMELDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=63 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpkA/T0304-1vpkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpkA expands to /projects/compbio/data/pdb/1vpk.pdb.gz 1vpkA:Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1961, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1973, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 1977, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2409, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2411, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2413, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2415, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2800, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2804, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2806, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2810, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2812, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2814, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2816, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2818, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2820, because occupancy 0.500 <= existing 0.500 in 1vpkA Skipped atom 2822, because occupancy 0.500 <= existing 0.500 in 1vpkA # T0304 read from 1vpkA/T0304-1vpkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpkA read from 1vpkA/T0304-1vpkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpkA to template set # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAVY 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVMP Number of specific fragments extracted= 2 number of extra gaps= 0 total=65 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpkA/T0304-1vpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1vpkA/T0304-1vpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpkA read from 1vpkA/T0304-1vpkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAVY 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVMP Number of specific fragments extracted= 2 number of extra gaps= 0 total=67 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpkA/T0304-1vpkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0304 read from 1vpkA/T0304-1vpkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpkA read from 1vpkA/T0304-1vpkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpkA in template set T0304 68 :LLMKQLELMLT 1vpkA 321 :KFIEDVLKHIE T0304 85 :RHQHTVTLYAKGLTCKADTLSSCDYVYLAV 1vpkA 332 :TEEIEMNFVDSTSPCQINPLDISGYLYIVM Number of specific fragments extracted= 2 number of extra gaps= 0 total=69 Will force an alignment to be made, even if fragment is small Number of alignments=28 # command:CPU_time= 11.317 sec, elapsed time= 12.147 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 28 Adding 7381 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.333 sec, elapsed time= 12.165 sec. # command:Reading probabilities from T0304.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 4.166 Optimizing... Probability sum: -316.576, CN propb: -316.576 weights: 0.332 constraints: 149 # command:CPU_time= 11.390 sec, elapsed time= 12.246 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 149 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 149 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 37 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 37 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 6255 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 6255 # command:CPU_time= 11.509 sec, elapsed time= 12.466 sec. # command: