# 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 T0358 numbered 1 through 87 Created new target T0358 from T0358.a2m # command:CPU_time= 6.236 sec, elapsed time= 6.305 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f4qA/T0358-2f4qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f4qA expands to /projects/compbio/data/pdb/2f4q.pdb.gz 2f4qA:Skipped atom 593, because occupancy 0.5 <= existing 0.500 in 2f4qA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 936, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1821, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2133, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2135, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2139, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2296, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2300, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2344, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2348, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0358 read from 2f4qA/T0358-2f4qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f4qA read from 2f4qA/T0358-2f4qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f4qA to template set # found chain 2f4qA in template set T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 49 :PAYQDVYVSPDAENELQAFGRDAAGRLQYRYH # choosing archetypes in rotamer library T0358 54 :NFEPDAG 2f4qA 83 :FVQAGAL Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 2f4qA/T0358-2f4qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2f4qA/T0358-2f4qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f4qA read from 2f4qA/T0358-2f4qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f4qA in template set T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 49 :PAYQDVYVSPDAENELQAFGRDAAGRLQYRYH T0358 57 :PDA 2f4qA 81 :PDF Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 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 2f4qA/T0358-2f4qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2f4qA/T0358-2f4qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f4qA read from 2f4qA/T0358-2f4qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f4qA in template set T0358 23 :TYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 50 :AYQDVYVSPDAENELQAFGRDAAGRLQYRYH T0358 57 :P 2f4qA 81 :P Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 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 1yaxA/T0358-1yaxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yaxA expands to /projects/compbio/data/pdb/1yax.pdb.gz 1yaxA:# T0358 read from 1yaxA/T0358-1yaxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yaxA read from 1yaxA/T0358-1yaxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yaxA to template set # found chain 1yaxA in template set T0358 13 :TRRQAQAVTTTYS 1yaxA 52 :LRGESNLFYTLAK T0358 26 :NITLEDDQ 1yaxA 69 :KISVELPE T0358 34 :GSHFRLVVRDTEGRMVWRAWNF 1yaxA 81 :QSPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTDTATRLE 1yaxA 103 :PWLIKSIQPEWLKTNGFHEIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=10 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 1yaxA/T0358-1yaxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1yaxA/T0358-1yaxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yaxA read from 1yaxA/T0358-1yaxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yaxA in template set T0358 12 :FTRRQAQAVTTTYS 1yaxA 51 :LLRGESNLFYTLAK T0358 26 :NITLEDDQG 1yaxA 69 :KISVELPEN T0358 35 :SHFRLVVRDTEGRMVWRAWNF 1yaxA 82 :SPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTDTATRLE 1yaxA 103 :PWLIKSIQPEWLKTNGFHEIE Number of specific fragments extracted= 4 number of extra gaps= 0 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 1yaxA/T0358-1yaxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1yaxA/T0358-1yaxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yaxA read from 1yaxA/T0358-1yaxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yaxA in template set T0358 14 :RRQAQAVTTTY 1yaxA 53 :RGESNLFYTLA T0358 25 :SNITLEDDQG 1yaxA 68 :NKISVELPEN T0358 35 :SHFRLVVRDTEGRMVWRAWNF 1yaxA 82 :SPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTD 1yaxA 103 :PWLIKSIQPEWLKTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 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 2a2pA/T0358-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a2pA expands to /projects/compbio/data/pdb/2a2p.pdb.gz 2a2pA:# T0358 read from 2a2pA/T0358-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0358-2a2pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a2pA to template set # found chain 2a2pA in template set T0358 12 :FTRRQAQAVT 2a2pA 52 :RLKEVKAFVT T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEP 2a2pA 65 :QLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQM T0358 59 :AGEGLNRYIRTSGIRTDTATRLE 2a2pA 101 :TRDEINALVQELGFYRKSAPEAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 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 2a2pA/T0358-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2a2pA/T0358-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0358-2a2pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2pA in template set T0358 8 :PP 2a2pA 51 :NR T0358 13 :TRRQAQAVT 2a2pA 53 :LKEVKAFVT T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEPD 2a2pA 65 :QLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQMT T0358 60 :GEGLNRYIRTSGIRTDTATRL 2a2pA 102 :RDEINALVQELGFYRKSAPEA Number of specific fragments extracted= 4 number of extra gaps= 0 total=25 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 2a2pA/T0358-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2a2pA/T0358-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a2pA read from 2a2pA/T0358-2a2pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a2pA in template set T0358 9 :PGPFTR 2a2pA 47 :GCQLNR T0358 15 :RQAQAV 2a2pA 54 :KEVKAF T0358 21 :TTTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEP 2a2pA 64 :IQLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQM T0358 59 :AGEGLNRYIRTSGIRTDTA 2a2pA 101 :TRDEINALVQELGFYRKSA Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 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 1lktA/T0358-1lktA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lktA expands to /projects/compbio/data/pdb/1lkt.pdb.gz 1lktA:# T0358 read from 1lktA/T0358-1lktA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lktA read from 1lktA/T0358-1lktA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lktA to template set # found chain 1lktA in template set T0358 25 :SNITLEDDQGSHFRL 1lktA 47 :IPVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 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 1lktA/T0358-1lktA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1lktA/T0358-1lktA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lktA read from 1lktA/T0358-1lktA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lktA in template set T0358 25 :SNITLEDDQGSHFRL 1lktA 47 :IPVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 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 1lktA/T0358-1lktA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1lktA/T0358-1lktA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lktA read from 1lktA/T0358-1lktA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lktA in template set T0358 26 :NITLEDDQGSHFRL 1lktA 48 :PVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=35 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 1vq2A/T0358-1vq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vq2A expands to /projects/compbio/data/pdb/1vq2.pdb.gz 1vq2A:# T0358 read from 1vq2A/T0358-1vq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq2A read from 1vq2A/T0358-1vq2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vq2A to template set # found chain 1vq2A in template set Warning: unaligning (T0358)T76 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vq2A)R83 T0358 35 :SHFRLVVRD 1vq2A 22 :WKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIRTD 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWLLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=37 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 1vq2A/T0358-1vq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1vq2A/T0358-1vq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq2A read from 1vq2A/T0358-1vq2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vq2A in template set Warning: unaligning (T0358)T76 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vq2A)R83 T0358 14 :RRQAQAVTTTYSNITLE 1vq2A 4 :STVLQIAYLVSQESKCC T0358 34 :GSHFRLVVRD 1vq2A 21 :SWKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIRTD 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWLLN Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 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 1vq2A/T0358-1vq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1vq2A/T0358-1vq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vq2A read from 1vq2A/T0358-1vq2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vq2A in template set T0358 14 :RRQAQAVTTTYSNITLE 1vq2A 4 :STVLQIAYLVSQESKCC T0358 34 :GSHFRLVVRD 1vq2A 21 :SWKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIR 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWL Number of specific fragments extracted= 3 number of extra gaps= 0 total=43 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 2c3vA/T0358-2c3vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c3vA expands to /projects/compbio/data/pdb/2c3v.pdb.gz 2c3vA:Bad short name: I1 for alphabet: pdb_atoms Bad short name: I2 for alphabet: pdb_atoms Bad short name: I1 for alphabet: pdb_atoms Bad short name: I1 for alphabet: pdb_atoms Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2c3vA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2c3vA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 2c3vA # T0358 read from 2c3vA/T0358-2c3vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3vA read from 2c3vA/T0358-2c3vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c3vA to template set # found chain 2c3vA in template set Warning: unaligning (T0358)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3vA)V128 Warning: unaligning (T0358)S25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3vA)V128 T0358 26 :NITLEDDQGSHFRLVVRDTEGRMV 2c3vA 129 :KVTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=44 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 2c3vA/T0358-2c3vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2c3vA/T0358-2c3vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3vA read from 2c3vA/T0358-2c3vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3vA in template set Warning: unaligning (T0358)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3vA)V128 Warning: unaligning (T0358)S25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3vA)V128 T0358 26 :NITLEDDQGSHFRLVVRDTEGRMV 2c3vA 129 :KVTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=45 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 2c3vA/T0358-2c3vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2c3vA/T0358-2c3vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3vA read from 2c3vA/T0358-2c3vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3vA in template set T0358 27 :ITLEDDQGSHFRLVVRDTEGRMV 2c3vA 130 :VTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=46 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 1tp6A/T0358-1tp6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tp6A expands to /projects/compbio/data/pdb/1tp6.pdb.gz 1tp6A:# T0358 read from 1tp6A/T0358-1tp6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tp6A read from 1tp6A/T0358-1tp6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tp6A to template set # found chain 1tp6A in template set T0358 28 :TLEDDQGSHFRL 1tp6A 93 :IQSDAAGRSERL T0358 40 :VVRDTEGRMVWRA 1tp6A 109 :LHRDDEGRLYWRH Number of specific fragments extracted= 2 number of extra gaps= 0 total=48 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 1tp6A/T0358-1tp6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1tp6A/T0358-1tp6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tp6A read from 1tp6A/T0358-1tp6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tp6A in template set T0358 37 :FRLVVRDTEGRMVWRAW 1tp6A 106 :TVVLHRDDEGRLYWRHL Number of specific fragments extracted= 1 number of extra gaps= 0 total=49 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 1tp6A/T0358-1tp6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1tp6A/T0358-1tp6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tp6A read from 1tp6A/T0358-1tp6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tp6A in template set T0358 36 :HFRLVVRDTEGRMVWRAW 1tp6A 105 :STVVLHRDDEGRLYWRHL Number of specific fragments extracted= 1 number of extra gaps= 0 total=50 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 1zkdA/T0358-1zkdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zkdA expands to /projects/compbio/data/pdb/1zkd.pdb.gz 1zkdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0358 read from 1zkdA/T0358-1zkdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkdA read from 1zkdA/T0358-1zkdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zkdA to template set # found chain 1zkdA in template set T0358 27 :ITLEDDQGSHFRLVVRDTEGRMVWRAWNFEPD 1zkdA 166 :QAIKRETGWHERVIEIGASGELVFGVAADPIP T0358 71 :GIRTDTATRLEHHHH 1zkdA 198 :GFEALLPPLARLSPP 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=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zkdA/T0358-1zkdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1zkdA/T0358-1zkdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkdA read from 1zkdA/T0358-1zkdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkdA in template set T0358 10 :GPFTRRQAQAVTTTYSNITLEDD 1zkdA 120 :NPVLRQKQQTLLAGIRNIHWHDS T0358 33 :QGSHFRLVVRDTEGRMVWRAWNFEP 1zkdA 172 :TGWHERVIEIGASGELVFGVAADPI T0358 70 :SGIRTDTATRLEHHHH 1zkdA 197 :PGFEALLPPLARLSPP Number of specific fragments extracted= 3 number of extra gaps= 0 total=55 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 1zkdA/T0358-1zkdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1zkdA/T0358-1zkdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkdA read from 1zkdA/T0358-1zkdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkdA in template set T0358 33 :QGSHFRLVVRDTEGRMVWRAW 1zkdA 172 :TGWHERVIEIGASGELVFGVA T0358 54 :NFEPDAGEGL 1zkdA 194 :DPIPGFEALL Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 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 1ffyA/T0358-1ffyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ffyA expands to /projects/compbio/data/pdb/1ffy.pdb.gz 1ffyA:# T0358 read from 1ffyA/T0358-1ffyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffyA read from 1ffyA/T0358-1ffyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ffyA to template set # found chain 1ffyA in template set T0358 25 :SNITLED 1ffyA 856 :SQVKVVD T0358 32 :DQ 1ffyA 866 :DQ T0358 35 :SHFRLVVRDTEGRMVWRAWNFEPDAG 1ffyA 872 :EHGDIVIEHADGEKCERCWNYSEDLG T0358 61 :EGLNRYIRT 1ffyA 907 :PRCQQVVKS Number of specific fragments extracted= 4 number of extra gaps= 0 total=61 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 1ffyA/T0358-1ffyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1ffyA/T0358-1ffyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffyA read from 1ffyA/T0358-1ffyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ffyA in template set T0358 41 :VRDTEGRMV 1ffyA 466 :FYAENGEII T0358 55 :FEPDAGEGLNRYIRTSG 1ffyA 475 :MTKETVNHVADLFAEHG Number of specific fragments extracted= 2 number of extra gaps= 0 total=63 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 1ffyA/T0358-1ffyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1ffyA/T0358-1ffyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ffyA read from 1ffyA/T0358-1ffyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ffyA in template set T0358 13 :TRRQAQAVTTTYSN 1ffyA 434 :VNWGKTRIYNMVRD T0358 28 :TLEDDQGSHFRLVVRDTEGRMVW 1ffyA 453 :ISRQRVWGVPLPVFYAENGEIIM T0358 56 :EPDAGEGLNRYIRTSGI 1ffyA 476 :TKETVNHVADLFAEHGS Number of specific fragments extracted= 3 number of extra gaps= 0 total=66 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 1iscA/T0358-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iscA expands to /projects/compbio/data/pdb/1isc.pdb.gz 1iscA:# T0358 read from 1iscA/T0358-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0358-1iscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iscA to template set # found chain 1iscA in template set T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iscA/T0358-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1iscA/T0358-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0358-1iscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iscA in template set T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 2 number of extra gaps= 0 total=70 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iscA/T0358-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1iscA/T0358-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iscA read from 1iscA/T0358-1iscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iscA in template set T0358 6 :LLPP 1iscA 80 :LAPN T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 3 number of extra gaps= 0 total=73 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0358-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yx1A expands to /projects/compbio/data/pdb/1yx1.pdb.gz 1yx1A:Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 232, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 236, because occupancy 0.450 <= existing 0.450 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1128, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1130, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1134, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1401, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1463, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1465, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1467, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1469, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1471, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1475, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1694, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1yx1A # T0358 read from 1yx1A/T0358-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0358-1yx1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yx1A to template set # found chain 1yx1A in template set T0358 13 :TRRQAQAVTTTYSNITL 1yx1A 172 :ADEAALRLGRYVGYVHC T0358 38 :RLVVRDTEGRMVW 1yx1A 189 :KAVIRNRDGKLVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=75 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0358-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1yx1A/T0358-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0358-1yx1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx1A in template set T0358 13 :TRRQAQAVTTTYSNITL 1yx1A 172 :ADEAALRLGRYVGYVHC T0358 38 :RLVVRDTEGRMVW 1yx1A 189 :KAVIRNRDGKLVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=77 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/T0358-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1yx1A/T0358-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yx1A read from 1yx1A/T0358-1yx1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yx1A in template set T0358 17 :AQAVTTTYSNITL 1yx1A 173 :DEAALRLGRYVGY T0358 36 :HFRLVVRDTEGRMVWRAW 1yx1A 187 :HCKAVIRNRDGKLVAVPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=79 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cr5A/T0358-2cr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cr5A expands to /projects/compbio/data/pdb/2cr5.pdb.gz 2cr5A:# T0358 read from 2cr5A/T0358-2cr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cr5A read from 2cr5A/T0358-2cr5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cr5A to template set # found chain 2cr5A in template set T0358 2 :TQSVLLPPGPF 2cr5A 7 :GEVPDLPEEPS T0358 31 :DDQGSHFRLVVRDTEGRMVWRA 2cr5A 18 :ETAEEVVTVALRCPNGRVLRRR T0358 54 :NFEPDAGEGLNRYIRTSGIRTDTATRLEHHH 2cr5A 40 :FFKSWNSQVLLDWMMKVGYHKSLYRLSTSFP Number of specific fragments extracted= 3 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cr5A/T0358-2cr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2cr5A/T0358-2cr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cr5A read from 2cr5A/T0358-2cr5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cr5A in template set T0358 2 :TQSVLLPPGPF 2cr5A 7 :GEVPDLPEEPS T0358 31 :DDQGSHFRLVVRDTEGRMVWRA 2cr5A 18 :ETAEEVVTVALRCPNGRVLRRR T0358 54 :NFEPDAGEGLNRYIRTSGIRTDTAT 2cr5A 40 :FFKSWNSQVLLDWMMKVGYHKSLYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cr5A/T0358-2cr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 2cr5A/T0358-2cr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cr5A read from 2cr5A/T0358-2cr5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cr5A in template set T0358 6 :LLPPGP 2cr5A 11 :DLPEEP T0358 30 :EDDQGSHFRLVVRDTEGRMVWRAWNFEPD 2cr5A 17 :SETAEEVVTVALRCPNGRVLRRRFFKSWN T0358 60 :GEGLNRYIRTSGIRTD 2cr5A 46 :SQVLLDWMMKVGYHKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=88 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m93C/T0358-1m93C-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m93C expands to /projects/compbio/data/pdb/1m93.pdb.gz 1m93C:Skipped atom 2447, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2449, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2451, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2453, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2455, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2557, because occupancy 0.440 <= existing 0.560 in 1m93C # T0358 read from 1m93C/T0358-1m93C-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93C read from 1m93C/T0358-1m93C-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m93C to template set # found chain 1m93C in template set Warning: unaligning (T0358)D58 because last residue in template chain is (1m93C)T339 T0358 30 :EDDQ 1m93C 313 :SADH T0358 36 :HFRLVVRDTEGRMVWRAWNFEP 1m93C 317 :PFIYVIRHVDGKILFVGRYSSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=90 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m93C/T0358-1m93C-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1m93C/T0358-1m93C-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93C read from 1m93C/T0358-1m93C-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m93C in template set T0358 36 :HFRLVVRDTEGRMVWRAW 1m93C 317 :PFIYVIRHVDGKILFVGR Number of specific fragments extracted= 1 number of extra gaps= 0 total=91 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m93C/T0358-1m93C-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0358 read from 1m93C/T0358-1m93C-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m93C read from 1m93C/T0358-1m93C-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m93C in template set T0358 36 :HFRLVVRDTEGRMVW 1m93C 317 :PFIYVIRHVDGKILF Number of specific fragments extracted= 1 number of extra gaps= 0 total=92 Will force an alignment to be made, even if fragment is small Number of alignments=39 # command:CPU_time= 11.119 sec, elapsed time= 11.867 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 39 Adding 3741 constraints to all_contacts Done adding distance constraints # command:CPU_time= 11.131 sec, elapsed time= 11.879 sec. # command:Reading probabilities from T0358.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 11.359 Optimizing... Probability sum: -173.500, CN propb: -173.500 weights: 0.182 constraints: 161 # command:CPU_time= 11.825 sec, elapsed time= 12.604 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 161 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 161 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 166 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 166 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 2754 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 2754 # command:CPU_time= 11.876 sec, elapsed time= 12.728 sec. # command: