# 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 T0314 numbered 1 through 106 Created new target T0314 from T0314.a2m # command:CPU_time= 6.165 sec, elapsed time= 6.224 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vemA/T0314-1vemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vemA expands to /projects/compbio/data/pdb/1vem.pdb.gz 1vemA:Skipped atom 2616, because occupancy 0.5 <= 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/T0314-1vemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vemA read from 1vemA/T0314-1vemA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vemA to template set # found chain 1vemA in template set T0314 23 :RKTGRYIVRFSEDSFGMDVADDSIT 1vemA 432 :TIGDTVYITGNRAELGSWDTKQYPI # choosing archetypes in rotamer library 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=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 1vemA/T0314-1vemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1vemA/T0314-1vemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vemA read from 1vemA/T0314-1vemA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=9 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 1vemA/T0314-1vemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1vemA/T0314-1vemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vemA read from 1vemA/T0314-1vemA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vemA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=9 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/T0314-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0314-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0314-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=14 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 2cb2A/T0314-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 2cb2A/T0314-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0314-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=19 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 2cb2A/T0314-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 2cb2A/T0314-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0314-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=24 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 1din/T0314-1din-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1din expands to /projects/compbio/data/pdb/1din.pdb.gz 1din:Warning: there is no chain 1din will retry with 1dinA Skipped atom 360, because occupancy 0.400 <= existing 0.600 in 1din # T0314 read from 1din/T0314-1din-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1din read from 1din/T0314-1din-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1din to template set # found chain 1din in template 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=26 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 1din/T0314-1din-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1din/T0314-1din-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1din read from 1din/T0314-1din-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1din in template 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=28 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 1din/T0314-1din-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1din/T0314-1din-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1din read from 1din/T0314-1din-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1din in template 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=30 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 1zi8A/T0314-1zi8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zi8A expands to /projects/compbio/data/pdb/1zi8.pdb.gz 1zi8A:# T0314 read from 1zi8A/T0314-1zi8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zi8A read from 1zi8A/T0314-1zi8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zi8A to template set # 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=32 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 1zi8A/T0314-1zi8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1zi8A/T0314-1zi8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zi8A read from 1zi8A/T0314-1zi8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=34 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 1zi8A/T0314-1zi8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1zi8A/T0314-1zi8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zi8A read from 1zi8A/T0314-1zi8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=36 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 2f1kA/T0314-2f1kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f1kA expands to /projects/compbio/data/pdb/2f1k.pdb.gz 2f1kA:Skipped atom 152, because occupancy 0.400 <= 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/T0314-2f1kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f1kA read from 2f1kA/T0314-2f1kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=40 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 2f1kA/T0314-2f1kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 2f1kA/T0314-2f1kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f1kA read from 2f1kA/T0314-2f1kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=44 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 2f1kA/T0314-2f1kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 2f1kA/T0314-2f1kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f1kA read from 2f1kA/T0314-2f1kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=48 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 1ig5A/T0314-1ig5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ig5A expands to /projects/compbio/data/pdb/1ig5.pdb.gz 1ig5A:# T0314 read from 1ig5A/T0314-1ig5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ig5A read from 1ig5A/T0314-1ig5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ig5A to template set # found chain 1ig5A in template 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=51 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 1ig5A/T0314-1ig5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1ig5A/T0314-1ig5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ig5A read from 1ig5A/T0314-1ig5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ig5A in template set T0314 63 :RLGREQLQILLEQNINERLNIGEP 1ig5A 22 :QLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=52 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 1ig5A/T0314-1ig5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1ig5A/T0314-1ig5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ig5A read from 1ig5A/T0314-1ig5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ig5A in template set T0314 61 :VMRLGREQLQILLEQNINERLNIGEP 1ig5A 20 :PNQLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=53 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 1kshA/T0314-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0314-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0314-1kshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kshA to template set # found chain 1kshA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=53 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kshA/T0314-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1kshA/T0314-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0314-1kshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=55 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 1kshA/T0314-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1kshA/T0314-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kshA read from 1kshA/T0314-1kshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=61 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 1itcA/T0314-1itcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1itcA expands to /projects/compbio/data/pdb/1itc.pdb.gz 1itcA:# T0314 read from 1itcA/T0314-1itcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1itcA read from 1itcA/T0314-1itcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1itcA to template set # 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=65 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 1itcA/T0314-1itcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1itcA/T0314-1itcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1itcA read from 1itcA/T0314-1itcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=70 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 1itcA/T0314-1itcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1itcA/T0314-1itcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1itcA read from 1itcA/T0314-1itcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1itcA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=70 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wjxA/T0314-1wjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wjxA expands to /projects/compbio/data/pdb/1wjx.pdb.gz 1wjxA:# T0314 read from 1wjxA/T0314-1wjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wjxA read from 1wjxA/T0314-1wjxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wjxA to template set # found chain 1wjxA in template 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=76 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 1wjxA/T0314-1wjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1wjxA/T0314-1wjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wjxA read from 1wjxA/T0314-1wjxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wjxA in template 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=82 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 1wjxA/T0314-1wjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1wjxA/T0314-1wjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wjxA read from 1wjxA/T0314-1wjxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wjxA in template 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=88 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 1g5bA/T0314-1g5bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1g5bA expands to /projects/compbio/data/pdb/1g5b.pdb.gz 1g5bA:# T0314 read from 1g5bA/T0314-1g5bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g5bA read from 1g5bA/T0314-1g5bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1g5bA to template set # 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=91 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 1g5bA/T0314-1g5bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1g5bA/T0314-1g5bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g5bA read from 1g5bA/T0314-1g5bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=93 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 1g5bA/T0314-1g5bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0314 read from 1g5bA/T0314-1g5bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g5bA read from 1g5bA/T0314-1g5bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=95 Will force an alignment to be made, even if fragment is small Number of alignments=27 # command:CPU_time= 10.718 sec, elapsed time= 11.480 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 27 Adding 5565 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.732 sec, elapsed time= 11.497 sec. # command:Reading probabilities from T0314.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 4.510 Optimizing... Probability sum: -216.968, CN propb: -216.968 weights: 0.310 constraints: 211 # command:CPU_time= 12.534 sec, elapsed time= 13.319 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 211 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 211 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 197 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 197 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 4345 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 4345 # command:CPU_time= 12.617 sec, elapsed time= 13.495 sec. # command: