# 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 T0382 numbered 1 through 123 Created new target T0382 from T0382.a2m # command:CPU_time= 6.243 sec, elapsed time= 6.312 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9uA/T0382-2a9uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a9uA expands to /projects/compbio/data/pdb/2a9u.pdb.gz 2a9uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0382 read from 2a9uA/T0382-2a9uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9uA read from 2a9uA/T0382-2a9uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a9uA to template set # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDG 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPD # choosing archetypes in rotamer library T0382 58 :QRTALLSLFEYPNMQVRLQAAKLT 2a9uA 82 :QQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVS 2a9uA 111 :LRYEEAEVRKKLEEKDR Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 2a9uA/T0382-2a9uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 2a9uA/T0382-2a9uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9uA read from 2a9uA/T0382-2a9uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDGD 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPDF T0382 58 :QRTALLSLFEYPNMQVRLQAAKLT 2a9uA 82 :QQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVSS 2a9uA 111 :LRYEEAEVRKKLEEKDRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 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 2a9uA/T0382-2a9uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 2a9uA/T0382-2a9uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a9uA read from 2a9uA/T0382-2a9uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDG 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPD T0382 57 :DQRTALLSLFEYPNMQVRLQAAKLT 2a9uA 81 :QQQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVS 2a9uA 111 :LRYEEAEVRKKLEEKDR Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 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 1h5zA/T0382-1h5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h5zA expands to /projects/compbio/data/pdb/1h5z.pdb.gz 1h5zA:# T0382 read from 1h5zA/T0382-1h5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h5zA read from 1h5zA/T0382-1h5zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h5zA to template set # found chain 1h5zA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLG 1h5zA 235 :ETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1h5zA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 69 :P 1h5zA 303 :Q T0382 71 :MQVRLQAAKLTLAV 1h5zA 304 :IPQLENVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 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 1h5zA/T0382-1h5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1h5zA/T0382-1h5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h5zA read from 1h5zA/T0382-1h5zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h5zA in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1h5zA 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGD 1h5zA 267 :WTLIELMRHRDAYAAVIDELDELYGD T0382 62 :LLSLFEYPNMQVR 1h5zA 296 :VSFHALRQIPQLE T0382 76 :QAAK 1h5zA 309 :NVLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=17 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 1h5zA/T0382-1h5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1h5zA/T0382-1h5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h5zA read from 1h5zA/T0382-1h5zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h5zA in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDD 1h5zA 234 :AETGTPRFSADEITGMFISMMFAGHH T0382 28 :ALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1h5zA 263 :GTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1h5zA 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=20 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 2a5dB/T0382-2a5dB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a5dB/T0382-2a5dB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a5dB/T0382-2a5dB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5eA/T0382-1s5eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5eA/T0382-1s5eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5eA/T0382-1s5eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u13A/T0382-1u13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u13A expands to /projects/compbio/data/pdb/1u13.pdb.gz 1u13A:# T0382 read from 1u13A/T0382-1u13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u13A read from 1u13A/T0382-1u13A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u13A to template set # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLF 1u13A 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHAL T0382 68 :YPN 1u13A 302 :RQI T0382 72 :QVRLQAAKLTLAVA 1u13A 305 :PQLENVLKETLRLH Number of specific fragments extracted= 4 number of extra gaps= 0 total=24 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 1u13A/T0382-1u13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1u13A/T0382-1u13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u13A read from 1u13A/T0382-1u13A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGD 1u13A 267 :WTLIELMRHRDAYAAVIDELDELYGD T0382 62 :LLSLFEYPNMQVR 1u13A 296 :VSFHALRQIPQLE T0382 76 :QAAKLTLAV 1u13A 309 :NVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=28 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 1u13A/T0382-1u13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1u13A/T0382-1u13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u13A read from 1u13A/T0382-1u13A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDD 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHH T0382 28 :ALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1u13A 263 :GTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1u13A 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=31 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 1x8vA/T0382-1x8vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x8vA expands to /projects/compbio/data/pdb/1x8v.pdb.gz 1x8vA:# T0382 read from 1x8vA/T0382-1x8vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8vA read from 1x8vA/T0382-1x8vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x8vA to template set # found chain 1x8vA in template set T0382 8 :QMTTQDLVALFAKVTVEQDDALLG 1x8vA 240 :RFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1x8vA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 69 :PN 1x8vA 303 :QI T0382 72 :QVRLQAAKLTLAV 1x8vA 305 :PQLENVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=35 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 1x8vA/T0382-1x8vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1x8vA/T0382-1x8vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8vA read from 1x8vA/T0382-1x8vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x8vA in template set Warning: unaligning (T0382)L6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x8vA)T238 T0382 7 :HQMTTQDLVALFAKVTVEQDDALLG 1x8vA 239 :PRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKAR 1x8vA 267 :WTLIELMRHRDAYAAVIDELDEL T0382 97 :VSSKW 1x8vA 290 :YGDGR Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 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 1x8vA/T0382-1x8vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1x8vA/T0382-1x8vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x8vA read from 1x8vA/T0382-1x8vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x8vA in template set Warning: unaligning (T0382)L6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x8vA)T238 T0382 7 :HQMTTQDLVALFAKVTVEQDDALLG 1x8vA 239 :PRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1x8vA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1x8vA 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=41 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 1yn9A/T0382-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yn9A expands to /projects/compbio/data/pdb/1yn9.pdb.gz 1yn9A:Skipped atom 2, because occupancy 0.4 <= existing 0.600 in 1yn9A Skipped atom 4, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 6, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 8, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 10, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 12, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 14, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 16, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 175, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 177, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 596, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 598, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 600, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 635, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 637, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 639, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 641, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 643, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 645, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 647, because occupancy 0.300 <= existing 0.700 in 1yn9A Skipped atom 941, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 943, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 945, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 947, because occupancy 0.400 <= existing 0.600 in 1yn9A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1yn9A Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1yn9A # T0382 read from 1yn9A/T0382-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0382-1yn9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yn9A to template set # found chain 1yn9A in template set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 33 :QISRFNRL 1yn9A 69 :DGVHFLRA T0382 41 :FGVMAEIADELKA 1yn9A 93 :ESIVQEFIDTVKE T0382 54 :RDGD 1yn9A 110 :CPGM T0382 66 :FEYPNMQVRLQAAKLTLAV 1yn9A 119 :CTHGINRTGYMVCRYLMHT T0382 85 :APVKAREQLEAIVSSKW 1yn9A 141 :APQEAIDRFEKARGHKI T0382 107 :DAGMCLDLL 1yn9A 158 :ERQNYVQDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=48 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 1yn9A/T0382-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1yn9A/T0382-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0382-1yn9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yn9A in template set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 33 :QISRFNR 1yn9A 69 :DGVHFLR T0382 42 :GVMAEIADELKA 1yn9A 94 :SIVQEFIDTVKE T0382 54 :RDGD 1yn9A 110 :CPGM T0382 66 :FEYPNMQVRLQAAKLTLAV 1yn9A 119 :CTHGINRTGYMVCRYLMHT T0382 85 :APVKAREQLEAIVSSKW 1yn9A 141 :APQEAIDRFEKARGHKI T0382 107 :DAGMCLDLL 1yn9A 158 :ERQNYVQDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=55 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 1yn9A/T0382-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1yn9A/T0382-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yn9A read from 1yn9A/T0382-1yn9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yn9A in template set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 23 :VEQDDA 1yn9A 71 :VHFLRA T0382 33 :QISRFNRLFGVMAEIADE 1yn9A 92 :PESIVQEFIDTVKEFTEK T0382 54 :RDG 1yn9A 110 :CPG T0382 67 :EYPNMQVRLQAAKLTLA 1yn9A 120 :THGINRTGYMVCRYLMH T0382 84 :VAPVKAREQLEAIVSSKWFP 1yn9A 140 :IAPQEAIDRFEKARGHKIER T0382 109 :GMCLDL 1yn9A 160 :QNYVQD Number of specific fragments extracted= 7 number of extra gaps= 0 total=62 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 1favA/T0382-1favA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1favA expands to /projects/compbio/data/pdb/1fav.pdb.gz 1favA:# T0382 read from 1favA/T0382-1favA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1favA read from 1favA/T0382-1favA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1favA to template set # found chain 1favA in template set T0382 27 :DALLGNQISRFNRLFGVMAEIA 1favA 7 :EEILSKIYHIENEIARIKKLIG T0382 57 :DQRTALLSLFEYPNMQVRLQAAKLTLAVAPVKAREQLEAI 1favA 29 :EARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQAR Number of specific fragments extracted= 2 number of extra gaps= 0 total=64 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 1favA/T0382-1favA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1favA/T0382-1favA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1favA read from 1favA/T0382-1favA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1favA in template set T0382 24 :EQDDALLGNQISRFNRLFGVMAEIADELKA 1favA 10 :LSKIYHIENEIARIKKLIGEARQLLSGIVQ T0382 58 :QRT 1favA 40 :QQN T0382 70 :NMQVRLQAAKLTLAVAPVKAREQLEAIVS 1favA 43 :NLLRAIEAQQHLLQLTVWGIKQLQARILA Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 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 1favA/T0382-1favA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1favA/T0382-1favA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1favA read from 1favA/T0382-1favA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1favA in template set T0382 12 :QDLVALF 1favA 7 :EEILSKI T0382 19 :AKVTVEQDDALLGNQISRFNRLFGVMAEIADE 1favA 16 :IENEIARIKKLIGEARQLLSGIVQQQNNLLRA T0382 75 :LQAAKLTLAVAPVKAREQLEAIVS 1favA 48 :IEAQQHLLQLTVWGIKQLQARILA Number of specific fragments extracted= 3 number of extra gaps= 0 total=70 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 1ea1A/T0382-1ea1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ea1A expands to /projects/compbio/data/pdb/1ea1.pdb.gz 1ea1A:# T0382 read from 1ea1A/T0382-1ea1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea1A read from 1ea1A/T0382-1ea1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ea1A to template set # found chain 1ea1A in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQ 1ea1A 235 :ETGTPRFSADEITGMFISMMFAG T0382 26 :DDALLGNQISRFNRLFGVMA 1ea1A 261 :SSGTASWTLIELMRHRDAYA T0382 88 :KAREQLEAIVSSK 1ea1A 281 :AVIDELDELYGDG 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=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ea1A/T0382-1ea1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1ea1A/T0382-1ea1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea1A read from 1ea1A/T0382-1ea1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ea1A in template set T0382 8 :QMT 1ea1A 160 :QLD T0382 16 :ALFAKVTVEQDD 1ea1A 163 :GRFAKLYHELER T0382 28 :AL 1ea1A 180 :AY T0382 30 :LGNQISRFNRLFGVMAEIADELKAR 1ea1A 184 :PYLPIESFRRRDEARNGLVALVADI T0382 55 :DGDQRTALLSLF 1ea1A 219 :DKSDRDMLDVLI T0382 67 :EYPNMQVRLQ 1ea1A 240 :RFSADEITGM T0382 77 :AAKLTLAVAP 1ea1A 265 :ASWTLIELMR T0382 87 :VKAREQLEAIVSSKW 1ea1A 280 :AAVIDELDELYGDGR Number of specific fragments extracted= 8 number of extra gaps= 0 total=81 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 1ea1A/T0382-1ea1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1ea1A/T0382-1ea1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ea1A read from 1ea1A/T0382-1ea1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ea1A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVE 1ea1A 234 :AETGTPRFSADEITGMFISMMFA T0382 25 :QDDALLGNQISRFNRLFGVMAEIADELKARDGDQRTA 1ea1A 260 :TSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSV T0382 63 :LSLFEYPNMQVR 1ea1A 297 :SFHALRQIPQLE T0382 76 :QAAKLTLAVAP 1ea1A 309 :NVLKETLRLHP Number of specific fragments extracted= 4 number of extra gaps= 0 total=85 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 1hjp/T0382-1hjp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hjp expands to /projects/compbio/data/pdb/1hjp.pdb.gz 1hjp:Warning: there is no chain 1hjp will retry with 1hjpA # T0382 read from 1hjp/T0382-1hjp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjp read from 1hjp/T0382-1hjp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hjp to template set # found chain 1hjp in template set Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 7 :HQMTTQDLVALFAKV 1hjp 79 :NGVGPKLALAILSGM T0382 22 :TVEQDDALLGNQI 1hjp 95 :AQQFVNAVEREEV T0382 35 :SRFNRL 1hjp 119 :KTAERL T0382 44 :MAEIADELKARDGD 1hjp 125 :IVEMKDRFKGLHGD T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLEA 1hjp 172 :YKPQEASRMVSK T0382 101 :WFPQAGDAGMCLDLL 1hjp 184 :IARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=92 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 1hjp/T0382-1hjp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1hjp/T0382-1hjp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjp read from 1hjp/T0382-1hjp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjp in template set Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 8 :QMTTQDLVALF 1hjp 92 :GMSAQQFVNAV T0382 30 :LGNQI 1hjp 103 :EREEV T0382 35 :SRFNRL 1hjp 119 :KTAERL T0382 44 :MAEIADELKARDGD 1hjp 125 :IVEMKDRFKGLHGD T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLE 1hjp 172 :YKPQEASRMVS T0382 100 :KWFPQAGDAGMCLDLL 1hjp 183 :KIARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=99 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 1hjp/T0382-1hjp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0382 read from 1hjp/T0382-1hjp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjp read from 1hjp/T0382-1hjp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjp in template set Warning: unaligning (T0382)R59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hjp)D158 Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 9 :MTTQDLVALF 1hjp 93 :MSAQQFVNAV T0382 28 :ALL 1hjp 109 :ALV T0382 35 :SRFNRLF 1hjp 119 :KTAERLI T0382 45 :AEIADELKARDGDQ 1hjp 126 :VEMKDRFKGLHGDL T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLEA 1hjp 172 :YKPQEASRMVSK T0382 101 :WFPQAGDAGMCLDLL 1hjp 184 :IARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=106 Will force an alignment to be made, even if fragment is small Number of alignments=24 # command:CPU_time= 10.902 sec, elapsed time= 11.520 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 24 Adding 7503 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.920 sec, elapsed time= 11.539 sec. # command:Reading probabilities from T0382.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 4.879 Optimizing... Probability sum: -246.934, CN propb: -246.934 weights: 0.254 constraints: 169 # command:CPU_time= 11.545 sec, elapsed time= 12.172 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 169 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 169 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 183 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 183 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 6203 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 6203 # command:CPU_time= 11.665 sec, elapsed time= 12.403 sec. # command: