# 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 T0306 numbered 1 through 95 Created new target T0306 from T0306.a2m # command:CPU_time= 6.364 sec, elapsed time= 6.617 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ae0X/T0306-2ae0X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ae0X expands to /projects/compbio/data/pdb/2ae0.pdb.gz 2ae0X:# T0306 read from 2ae0X/T0306-2ae0X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae0X read from 2ae0X/T0306-2ae0X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ae0X to template set # found chain 2ae0X in template set T0306 12 :CTVRHHGLAHDKLLMVEMI 2ae0X 258 :VASDRSIIPPGTTLLAEVP # choosing archetypes in rotamer library T0306 31 :DPQGNPDG 2ae0X 279 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLVS 2ae0X 291 :RLMVALDVGGAIKGQHFDIYQ T0306 60 :GSSARQAHKSETSPVDLCVI 2ae0X 314 :GPEAGHRAGWYNHYGRVWVL 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 2ae0X/T0306-2ae0X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2ae0X/T0306-2ae0X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae0X read from 2ae0X/T0306-2ae0X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ae0X in template set T0306 12 :CTVRHHGLAHDKLLMVEMI 2ae0X 258 :VASDRSIIPPGTTLLAEVP T0306 31 :DPQGNPDG 2ae0X 279 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLV 2ae0X 291 :RLMVALDVGGAIKGQHFDIY T0306 60 :GSSARQAHKSETSPVDLCVI 2ae0X 314 :GPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ae0X/T0306-2ae0X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2ae0X/T0306-2ae0X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ae0X read from 2ae0X/T0306-2ae0X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ae0X in template set T0306 11 :VCTVRHHGLAHDKLLMVEMI 2ae0X 257 :SVASDRSIIPPGTTLLAEVP T0306 31 :DPQGNPDGQC 2ae0X 279 :DNNGKFNGQY T0306 41 :AVAIDNIGAGTGEWVLLV 2ae0X 293 :MVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2ae0X 313 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 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 2gaeA/T0306-2gaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gaeA expands to /projects/compbio/data/pdb/2gae.pdb.gz 2gaeA:# T0306 read from 2gaeA/T0306-2gaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaeA read from 2gaeA/T0306-2gaeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gaeA to template set # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 12 :CTVRHHGLAHDKLLM 2gaeA 278 :VASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDG 2gaeA 299 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLVS 2gaeA 311 :RLMVALDVGGAIKGQHFDIYQ T0306 60 :GSSARQAHKSETSPVDLCVI 2gaeA 334 :GPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=17 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 2gaeA/T0306-2gaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2gaeA/T0306-2gaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaeA read from 2gaeA/T0306-2gaeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 12 :CTVRHHGLAHDKLLM 2gaeA 278 :VASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDG 2gaeA 299 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLV 2gaeA 311 :RLMVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2gaeA 333 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=22 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 2gaeA/T0306-2gaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2gaeA/T0306-2gaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gaeA read from 2gaeA/T0306-2gaeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 11 :VCTVRHHGLAHDKLLM 2gaeA 277 :SVASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDGQC 2gaeA 299 :DNNGKFNGQY T0306 41 :AVAIDNIGAGTGEWVLLV 2gaeA 313 :MVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2gaeA 333 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=27 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 2c3mA/T0306-2c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c3mA expands to /projects/compbio/data/pdb/2c3m.pdb.gz 2c3mA:# T0306 read from 2c3mA/T0306-2c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3mA read from 2c3mA/T0306-2c3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c3mA to template set # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSG 2c3mA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVIGIV 2c3mA 284 :EEVINHLAAKGEKIGLIKVRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 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 2c3mA/T0306-2c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2c3mA/T0306-2c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3mA read from 2c3mA/T0306-2c3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSG 2c3mA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVIGIV 2c3mA 284 :EEVINHLAAKGEKIGLIKVRLY 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=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3mA/T0306-2c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 2c3mA/T0306-2c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c3mA read from 2c3mA/T0306-2c3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 2c3mA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAHKSETSPVDLCVIGIVD 2c3mA 286 :VINHLAAKGEKIGLIKVRLYR 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=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v04A/T0306-1v04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v04A expands to /projects/compbio/data/pdb/1v04.pdb.gz 1v04A:# T0306 read from 1v04A/T0306-1v04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v04A read from 1v04A/T0306-1v04A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v04A to template set # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 9 :QIVCTV 1v04A 234 :YVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :AGT 1v04A 273 :VDP T0306 52 :GEWVLLVSGSSARQAH 1v04A 278 :GDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGIVDEVVSGGQV 1v04A 296 :AENPPGSEVLRIQDILSEEPKV Number of specific fragments extracted= 7 number of extra gaps= 2 total=40 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 1v04A/T0306-1v04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1v04A/T0306-1v04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v04A read from 1v04A/T0306-1v04A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 9 :QIVCTV 1v04A 234 :YVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :AGT 1v04A 273 :VDP T0306 52 :GEWVLLVSGSSARQAH 1v04A 278 :GDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGIVDEVVSGGQV 1v04A 296 :AENPPGSEVLRIQDILSEEPKV Number of specific fragments extracted= 7 number of extra gaps= 2 total=47 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 1v04A/T0306-1v04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1v04A/T0306-1v04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v04A read from 1v04A/T0306-1v04A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 8 :GQIVCTV 1v04A 233 :KYVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :A 1v04A 273 :V T0306 50 :GTGEWVLLVSGSSARQAH 1v04A 276 :VTGDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGI 1v04A 296 :AENPPGSEVLRI T0306 83 :DEVVSGGQ 1v04A 308 :QDILSEEP Number of specific fragments extracted= 8 number of extra gaps= 2 total=55 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 1b0pA/T0306-1b0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b0pA expands to /projects/compbio/data/pdb/1b0p.pdb.gz 1b0pA:# T0306 read from 1b0pA/T0306-1b0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0pA read from 1b0pA/T0306-1b0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b0pA to template set # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSG 1b0pA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVI 1b0pA 284 :EEVINHLAAKGEKIGLIKV 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=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0pA/T0306-1b0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1b0pA/T0306-1b0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0pA read from 1b0pA/T0306-1b0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSG 1b0pA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVI 1b0pA 284 :EEVINHLAAKGEKIGLIKV Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 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 1b0pA/T0306-1b0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1b0pA/T0306-1b0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b0pA read from 1b0pA/T0306-1b0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 1b0pA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAHKSETSPVDLCVIGIV 1b0pA 286 :VINHLAAKGEKIGLIKVRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 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 1kekA/T0306-1kekA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kekA expands to /projects/compbio/data/pdb/1kek.pdb.gz 1kekA:# T0306 read from 1kekA/T0306-1kekA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kekA read from 1kekA/T0306-1kekA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kekA to template set # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSSAR 1kekA 261 :FDYVGAPDAERVIVSMGSSCE T0306 65 :QAHKSETSPVDLCVIG 1kekA 288 :NHLAAKGEKIGLIKVR 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=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kekA/T0306-1kekA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1kekA/T0306-1kekA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kekA read from 1kekA/T0306-1kekA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSSAR 1kekA 261 :FDYVGAPDAERVIVSMGSSCE T0306 65 :QAHKSETSPVDLCVI 1kekA 288 :NHLAAKGEKIGLIKV Number of specific fragments extracted= 2 number of extra gaps= 0 total=65 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kekA/T0306-1kekA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1kekA/T0306-1kekA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kekA read from 1kekA/T0306-1kekA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 1kekA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAH 1kekA 287 :INHLA T0306 69 :SETSPVDLCVIGIV 1kekA 292 :AKGEKIGLIKVRLY Number of specific fragments extracted= 3 number of extra gaps= 0 total=68 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 1wucA/T0306-1wucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wucA expands to /projects/compbio/data/pdb/1wuc.pdb.gz 1wucA:Skipped atom 479, because occupancy 0.5 <= existing 0.500 in 1wucA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 1wucA # T0306 read from 1wucA/T0306-1wucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wucA read from 1wucA/T0306-1wucA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wucA to template set # found chain 1wucA in template set T0306 20 :AHDKLLMVEMIDPQGN 1wucA 45 :DDKRFVLVDITTTSKK T0306 39 :QCAVAIDNIG 1wucA 61 :TVKVAIDVTD T0306 76 :LCVIGIVDEVVS 1wucA 71 :VYVVGYQDKWDG T0306 90 :QVI 1wucA 83 :KDR Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 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 1wucA/T0306-1wucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1wucA/T0306-1wucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wucA read from 1wucA/T0306-1wucA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wucA in template set T0306 20 :AHDKLLMVEMIDPQGN 1wucA 45 :DDKRFVLVDITTTSKK T0306 39 :QCAVAIDNIG 1wucA 61 :TVKVAIDVTD T0306 76 :LCVIGIVDEVVS 1wucA 71 :VYVVGYQDKWDG T0306 90 :QVI 1wucA 83 :KDR Number of specific fragments extracted= 4 number of extra gaps= 0 total=76 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 1wucA/T0306-1wucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1wucA/T0306-1wucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wucA read from 1wucA/T0306-1wucA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wucA in template set T0306 21 :HDKLLMVEMIDPQGN 1wucA 46 :DKRFVLVDITTTSKK T0306 39 :QCAVAIDN 1wucA 61 :TVKVAIDV T0306 74 :VDLCVIGIVDEV 1wucA 69 :TDVYVVGYQDKW T0306 88 :GGQVIF 1wucA 81 :DGKDRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=80 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 1wi1A/T0306-1wi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wi1A expands to /projects/compbio/data/pdb/1wi1.pdb.gz 1wi1A:# T0306 read from 1wi1A/T0306-1wi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wi1A read from 1wi1A/T0306-1wi1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wi1A to template set # found chain 1wi1A in template set T0306 3 :LAVVT 1wi1A 32 :LVQVS T0306 8 :GQIVCTVRHHGLAHDKLL 1wi1A 39 :TFAMCSYREKKAEPQELL T0306 27 :VEMIDPQGNPDG 1wi1A 63 :VDYTDPQPGLEG T0306 39 :QCAVAI 1wi1A 77 :AFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSP 1wi1A 103 :QAMYRATGQSHKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=86 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 1wi1A/T0306-1wi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1wi1A/T0306-1wi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wi1A read from 1wi1A/T0306-1wi1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wi1A in template set T0306 3 :LAVVT 1wi1A 32 :LVQVS T0306 8 :GQIVCTVRHHGLAHDKLL 1wi1A 39 :TFAMCSYREKKAEPQELL T0306 27 :VEMIDPQGNPDG 1wi1A 63 :VDYTDPQPGLEG T0306 39 :QCAVAI 1wi1A 77 :AFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSP 1wi1A 103 :QAMYRATGQSHKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=92 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 1wi1A/T0306-1wi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1wi1A/T0306-1wi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wi1A read from 1wi1A/T0306-1wi1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wi1A in template set T0306 2 :KLAVVTG 1wi1A 31 :VLVQVSQ T0306 9 :QIVCTVRHHGLAHDKLL 1wi1A 40 :FAMCSYREKKAEPQELL T0306 27 :VEMIDPQGN 1wi1A 63 :VDYTDPQPG T0306 36 :PDGQCAVAI 1wi1A 74 :GGRAFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSPV 1wi1A 103 :QAMYRATGQSHKPV Number of specific fragments extracted= 6 number of extra gaps= 0 total=98 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 1pgl1/T0306-1pgl1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pgl1 expands to /projects/compbio/data/pdb/1pgl.pdb.gz 1pgl1:# T0306 read from 1pgl1/T0306-1pgl1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pgl1 read from 1pgl1/T0306-1pgl1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pgl1 to template set # found chain 1pgl1 in template set T0306 17 :HGLAHDKLLMVE 1pgl1 4 :QQTVWNQMATVR T0306 30 :IDPQGNPD 1pgl1 16 :TPLNFDSS T0306 38 :GQCAVAIDNIGAG 1pgl1 26 :SFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAH 1pgl1 44 :TGDWITLVQNSPISNLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=102 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 1pgl1/T0306-1pgl1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1pgl1/T0306-1pgl1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pgl1 read from 1pgl1/T0306-1pgl1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pgl1 in template set T0306 17 :HGLAHDKLLMVE 1pgl1 4 :QQTVWNQMATVR T0306 30 :IDPQGNPD 1pgl1 16 :TPLNFDSS T0306 38 :GQCAVAIDNIGAG 1pgl1 26 :SFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAH 1pgl1 44 :TGDWITLVQNSPISNLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=106 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 1pgl1/T0306-1pgl1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1pgl1/T0306-1pgl1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pgl1 read from 1pgl1/T0306-1pgl1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pgl1 in template set T0306 21 :HDKLLMVE 1pgl1 8 :WNQMATVR T0306 30 :IDPQGN 1pgl1 16 :TPLNFD T0306 36 :PDGQCAVAIDNIGAG 1pgl1 24 :KQSFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAHKS 1pgl1 44 :TGDWITLVQNSPISNLLRV T0306 74 :VDLCVIGIVDEVVSG 1pgl1 67 :KGCLMVKVVMSGNAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=111 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 1mrj/T0306-1mrj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mrj expands to /projects/compbio/data/pdb/1mrj.pdb.gz 1mrj:Warning: there is no chain 1mrj will retry with 1mrjA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1mrj Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1mrj # T0306 read from 1mrj/T0306-1mrj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrj read from 1mrj/T0306-1mrj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mrj to template set # found chain 1mrj in template set Warning: unaligning (T0306)K23 because of BadResidue code BAD_PEPTIDE at template residue (1mrj)R46 T0306 12 :CTVRHHGLAH 1mrj 34 :IPLLRSSLPG T0306 24 :LLMVEMIDPQGN 1mrj 47 :YALIHLTNYADE T0306 39 :QCAVAID 1mrj 59 :TISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 1 total=115 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 1mrj/T0306-1mrj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1mrj/T0306-1mrj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrj read from 1mrj/T0306-1mrj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mrj in template set Warning: unaligning (T0306)K23 because of BadResidue code BAD_PEPTIDE at template residue (1mrj)R46 T0306 12 :CTVRHHGLAH 1mrj 34 :IPLLRSSLPG T0306 24 :LLMVEMIDPQGN 1mrj 47 :YALIHLTNYADE T0306 39 :QCAVAID 1mrj 59 :TISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 1 total=119 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 1mrj/T0306-1mrj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0306 read from 1mrj/T0306-1mrj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrj read from 1mrj/T0306-1mrj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mrj in template set T0306 23 :KLLMVE 1mrj 48 :ALIHLT T0306 31 :DPQG 1mrj 54 :NYAD T0306 38 :GQCAVAID 1mrj 58 :ETISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 0 total=123 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 13.007 sec, elapsed time= 14.117 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 4465 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.023 sec, elapsed time= 14.133 sec. # command:Reading probabilities from T0306.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 9.313 Optimizing... Probability sum: -178.884, CN propb: -178.884 weights: 0.260 constraints: 348 # command:CPU_time= 13.268 sec, elapsed time= 14.386 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 348 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 348 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 138 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 138 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 3255 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 3255 # command:CPU_time= 13.334 sec, elapsed time= 14.545 sec. # command: