# command:# Seed set to 1277377769 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493441 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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:CPU_time= 23.276 sec, elapsed time= 23.415 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1963 20 (100.000%) # n-terminus 2 1934 333 (83.250%) # middle 1 483679 20 (100.000%) # middle 2 477517 400 (100.000%) # middle 3 471578 7988 (99.850%) # middle 4 465793 120683 (75.427%) # c-terminus 1 1917 20 (100.000%) # c-terminus 2 1889 372 (93.000%) # ss-bonds 1052 # command:CPU_time= 36.536 sec, elapsed time= 40.370 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0590 numbered 1 through 137 Created new target T0590 from T0590.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.537 sec, elapsed time= 40.407 sec. # command:# Prefix for input files set to # command:# reading script from file T0590.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l0qA expands to /projects/compbio/data/pdb/1l0q.pdb.gz 1l0qA: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: OZ1 for alphabet: pdb_atoms Bad short name: NZ2 for alphabet: pdb_atoms 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 # T0590 read from 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l0qA to template set # found chain 1l0qA in template set T0590 2 :NARDNKFNTWNDSRG 1l0qA 220 :DKYFNTVSMIDTGTN # choosing archetypes in rotamer library T0590 17 :NYWSDYEGSDENGDGIGDS 1l0qA 241 :PVGPDPAGIAVTPDGKKVY T0590 38 :AVNPEAGSMDYMPL 1l0qA 270 :VIDTATNTITATMA T0590 52 :MEYLHSSPVLPTARFTSDITEGFA 1l0qA 295 :IGSIPVQPVYPSADFKSNITSGYI T0590 76 :PLSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIR 1l0qA 321 :SEPVQFTDLSKDATEWKWDFGDGSSSKKQNPTHTYSETGIYTVRLTVSNSNGTDSQISTVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_393550864.pdb -s /var/tmp/to_scwrl_393550864.seq -o /var/tmp/from_scwrl_393550864.pdb > /var/tmp/scwrl_393550864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_393550864.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4xA expands to /projects/compbio/data/pdb/2c4x.pdb.gz 2c4xA: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 # T0590 read from 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4xA read from 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c4xA to template set # found chain 2c4xA in template set Warning: unaligning (T0590)S57 because first residue in template chain is (2c4xA)P2 T0590 58 :SPVLPTARFTSDITEGFAPLSVRFK 2c4xA 3 :ENQAPKAIFTFSPEDPVTDENVVFN T0590 83 :DFSENATSRLWMFGDGN 2c4xA 33 :DEDGTIAYYVWDFGDGY T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNENDS 2c4xA 52 :TSTTPTITYKYKNPGTYKVKLIVTDNQGA T0590 129 :DSASVTIR 2c4xA 82 :SSFTATIK Number of specific fragments extracted= 4 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_745794909.pdb -s /var/tmp/to_scwrl_745794909.seq -o /var/tmp/from_scwrl_745794909.pdb > /var/tmp/scwrl_745794909.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_745794909.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b4rA expands to /projects/compbio/data/pdb/1b4r.pdb.gz 1b4rA:# T0590 read from 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4rA read from 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b4rA to template set # found chain 1b4rA in template set Warning: unaligning (T0590)A64 because first residue in template chain is (1b4rA)A8 T0590 65 :RFTSDITEGFAPLSVRFKDFS 1b4rA 9 :TLVGPHGPLASGQLAAFHIAA T0590 86 :ENATSRLWMFGDGNT 1b4rA 31 :LPVTATRWDFGDGSA T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1b4rA 49 :AAGPAASHRYVLPGRYHVTAVLALGAGSALLGTDVQV Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_233807930.pdb -s /var/tmp/to_scwrl_233807930.seq -o /var/tmp/from_scwrl_233807930.pdb > /var/tmp/scwrl_233807930.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_233807930.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2yrlA expands to /projects/compbio/data/pdb/2yrl.pdb.gz 2yrlA:# T0590 read from 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yrlA read from 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2yrlA to template set # found chain 2yrlA in template set T0590 59 :PVLPTARFTSDITEGFAPLSVRF 2yrlA 6 :SGQADAGPDKELTLPVDSTTLDG T0590 83 :DFSENATSRLWMFGDGN 2yrlA 32 :SDDQKIISYLWEKTQGP T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNEND 2yrlA 55 :NANSSVATVTGLQVGTYVFTLTVKDERN T0590 128 :SDSASVTI 2yrlA 84 :QSQSSVNV Number of specific fragments extracted= 4 number of extra gaps= 0 total=16 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_319729774.pdb -s /var/tmp/to_scwrl_319729774.seq -o /var/tmp/from_scwrl_319729774.pdb > /var/tmp/scwrl_319729774.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_319729774.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ejjX expands to /projects/compbio/data/pdb/3ejj.pdb.gz 3ejjX:# T0590 read from 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ejjX read from 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ejjX to template set # found chain 3ejjX in template set T0590 58 :SPVLPTARFTSD 3ejjX 199 :HPEPPQIKLEPS T0590 70 :ITEGFAPLSVRF 3ejjX 215 :IRGEAAQIVCSA T0590 82 :KDFSENATSRLWMFGDGNTSDSP 3ejjX 250 :SDFQDNYYKKVRALSLNAVDFQD T0590 113 :EGEY 3ejjX 273 :AGIY T0590 119 :SLIVSNENDSDSASVTI 3ejjX 277 :SCVASNDVGTRTATMNF Number of specific fragments extracted= 5 number of extra gaps= 0 total=21 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_21840258.pdb -s /var/tmp/to_scwrl_21840258.seq -o /var/tmp/from_scwrl_21840258.pdb > /var/tmp/scwrl_21840258.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_21840258.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2kpnA expands to /projects/compbio/data/pdb/2kpn.pdb.gz 2kpnA:# T0590 read from 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kpnA read from 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kpnA to template set # found chain 2kpnA in template set T0590 12 :NDSRG 2kpnA 36 :IDKED T0590 17 :NYWSDYEG 2kpnA 42 :DLTSKIKV T0590 25 :SDENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVLP 2kpnA 53 :VDTTKAGTYVLTYTVTDSKGHEVTAKQTVTVKVREEVK Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_826817222.pdb -s /var/tmp/to_scwrl_826817222.seq -o /var/tmp/from_scwrl_826817222.pdb > /var/tmp/scwrl_826817222.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_826817222.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cvsC/T0590-1cvsC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cvsC expands to /projects/compbio/data/pdb/1cvs.pdb.gz 1cvsC:# T0590 read from 1cvsC/T0590-1cvsC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cvsC read from 1cvsC/T0590-1cvsC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cvsC to template set # found chain 1cvsC in template set T0590 8 :FNTWNDSRG 1cvsC 187 :TLRWLKNGK T0590 17 :NYWSDYEGSDEN 1cvsC 200 :DHRIGGYKVRYA T0590 29 :GDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVLPTA 1cvsC 222 :PSDKGNYTCIVENEYGSINHTYQLDVVERSPHRPIL T0590 65 :RFTSDIT 1cvsC 274 :EFMCKVY T0590 72 :EGFAPLSVRFK 1cvsC 282 :DPQPHIQWLKH T0590 83 :DFSENATSRLWMFGDGNT 1cvsC 301 :GPDNLPYVQILKTAGVNT T0590 101 :SDSPSPL 1cvsC 326 :LHLRNVS T0590 113 :EGEYIV 1cvsC 336 :AGEYTC T0590 121 :IVSNENDSDSASVTIR 1cvsC 342 :LAGNSIGLSHHSAWLT Number of specific fragments extracted= 9 number of extra gaps= 0 total=33 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_1852489139.pdb -s /var/tmp/to_scwrl_1852489139.seq -o /var/tmp/from_scwrl_1852489139.pdb > /var/tmp/scwrl_1852489139.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1852489139.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kldA/T0590-3kldA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3kldA expands to /projects/compbio/data/pdb/3kld.pdb.gz 3kldA:# T0590 read from 3kldA/T0590-3kldA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kldA read from 3kldA/T0590-3kldA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kldA to template set # found chain 3kldA in template set T0590 87 :NATSRLWMFGDGNT 3kldA 253 :PVPTILWRRADGKP T0590 101 :SDSPSPLHTFFN 3kldA 273 :RHKSNGILEIPN T0590 113 :EGEYIV 3kldA 290 :AGSYEC T0590 121 :IVSNENDSDSASVTIR 3kldA 296 :VAENSRGKNVAKGQLT Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_959991137.pdb -s /var/tmp/to_scwrl_959991137.seq -o /var/tmp/from_scwrl_959991137.pdb > /var/tmp/scwrl_959991137.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_959991137.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cs6A/T0590-1cs6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0590 read from 1cs6A/T0590-1cs6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cs6A read from 1cs6A/T0590-1cs6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cs6A in training set T0590 8 :FNTWNDSRG 1cs6A 139 :SYRWLLNEF T0590 17 :NYWSDYEGSDEN 1cs6A 150 :FIPADGRRFVSQ T0590 29 :GDGIGDSAYAVNPEAGSMDYMPLMEYLH 1cs6A 175 :DLGNYSCFATSHIDFITKSVFSKFSQLS T0590 57 :SSPVLPTARFTSDIT 1cs6A 206 :EDARQYAPSIKAKFP T0590 72 :EGFAPLSVRFK 1cs6A 228 :GQMVTLECFAF T0590 85 :SENATSRLWMFGDGNT 1cs6A 239 :GNPVPQIKWRKLDGSQ T0590 101 :SDSPSPLHTFFN 1cs6A 258 :WLSSEPLLHIQN T0590 113 :EGEYIV 1cs6A 275 :EGTYEC T0590 121 :IVSNENDSDSASVTIRA 1cs6A 281 :EAENIKGRDTYQGRIII Number of specific fragments extracted= 9 number of extra gaps= 0 total=46 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_458239666.pdb -s /var/tmp/to_scwrl_458239666.seq -o /var/tmp/from_scwrl_458239666.pdb > /var/tmp/scwrl_458239666.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_458239666.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jllA/T0590-2jllA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2jllA expands to /projects/compbio/data/pdb/2jll.pdb.gz 2jllA:Skipped atom 2879, because occupancy 0.45 <= existing 0.550 in 2jllA Skipped atom 2880, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2881, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2882, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2883, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2884, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2885, because occupancy 0.450 <= existing 0.550 in 2jllA Skipped atom 2886, because occupancy 0.450 <= existing 0.550 in 2jllA # T0590 read from 2jllA/T0590-2jllA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jllA read from 2jllA/T0590-2jllA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2jllA to template set # found chain 2jllA in template set Warning: unaligning (T0590)E72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2jllA)G606 Warning: unaligning (T0590)G73 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2jllA)G606 T0590 3 :ARDNKFNTWNDSRG 2jllA 537 :VASEIWKIVRSHGV T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMP 2jllA 559 :LEPNTTYEIRVAAVNGKGQGDYSK T0590 51 :LMEYLHSSPVLPTARFTSDIT 2jllA 584 :EIFQTLPVREPSPPSIHGQPS T0590 74 :F 2jllA 607 :K T0590 76 :PLSVRFKDFS 2jllA 608 :SFKLSITKQD T0590 86 :ENATSRLWMF 2jllA 621 :APILEYIVKY T0590 100 :TSDSPSPLHTFFN 2jllA 643 :KVQGNKDHIILEH T0590 113 :EGEYIVSLIVSNEND 2jllA 659 :TMGYEVQITAANRLG T0590 128 :SDSASVTI 2jllA 675 :SEPTVYEF T0590 136 :RA 2jllA 685 :PP Number of specific fragments extracted= 10 number of extra gaps= 1 total=56 # request to SCWRL produces command: ulimit -t 124 ; scwrl4 -t -i /var/tmp/to_scwrl_497477246.pdb -s /var/tmp/to_scwrl_497477246.seq -o /var/tmp/from_scwrl_497477246.pdb > /var/tmp/scwrl_497477246.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_497477246.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.470 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 10390.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 10390.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 10390.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 10390.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 10390.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.868 rmsd (weighted)= 3.704 (unweighted)= 30.871 superimposing iter= 1 total_weight= 3518.505 rmsd (weighted)= 1.177 (unweighted)= 30.662 superimposing iter= 2 total_weight= 2112.758 rmsd (weighted)= 0.596 (unweighted)= 30.568 superimposing iter= 3 total_weight= 990.806 rmsd (weighted)= 0.462 (unweighted)= 30.521 superimposing iter= 4 total_weight= 728.870 rmsd (weighted)= 0.418 (unweighted)= 30.490 superimposing iter= 5 total_weight= 674.245 rmsd (weighted)= 0.394 (unweighted)= 30.469 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.798 rmsd (weighted)= 3.274 (unweighted)= 36.045 superimposing iter= 1 total_weight= 1850.586 rmsd (weighted)= 1.668 (unweighted)= 36.375 superimposing iter= 2 total_weight= 977.264 rmsd (weighted)= 1.239 (unweighted)= 36.508 superimposing iter= 3 total_weight= 701.482 rmsd (weighted)= 1.103 (unweighted)= 36.566 superimposing iter= 4 total_weight= 602.164 rmsd (weighted)= 1.062 (unweighted)= 36.599 superimposing iter= 5 total_weight= 578.633 rmsd (weighted)= 1.044 (unweighted)= 36.622 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.833 rmsd (weighted)= 5.610 (unweighted)= 38.495 superimposing iter= 1 total_weight= 2609.144 rmsd (weighted)= 2.318 (unweighted)= 38.185 superimposing iter= 2 total_weight= 1355.311 rmsd (weighted)= 1.480 (unweighted)= 38.068 superimposing iter= 3 total_weight= 815.454 rmsd (weighted)= 1.231 (unweighted)= 37.984 superimposing iter= 4 total_weight= 737.262 rmsd (weighted)= 1.083 (unweighted)= 37.932 superimposing iter= 5 total_weight= 687.865 rmsd (weighted)= 0.990 (unweighted)= 37.904 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.739 rmsd (weighted)= 9.516 (unweighted)= 84.526 superimposing iter= 1 total_weight= 2214.716 rmsd (weighted)= 4.109 (unweighted)= 84.932 superimposing iter= 2 total_weight= 1311.796 rmsd (weighted)= 2.421 (unweighted)= 84.640 superimposing iter= 3 total_weight= 975.333 rmsd (weighted)= 1.692 (unweighted)= 84.714 superimposing iter= 4 total_weight= 778.535 rmsd (weighted)= 1.340 (unweighted)= 84.869 superimposing iter= 5 total_weight= 648.741 rmsd (weighted)= 1.166 (unweighted)= 84.968 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.532 rmsd (weighted)= 12.044 (unweighted)= 36.902 superimposing iter= 1 total_weight= 686.856 rmsd (weighted)= 8.722 (unweighted)= 37.008 superimposing iter= 2 total_weight= 450.168 rmsd (weighted)= 7.855 (unweighted)= 37.047 superimposing iter= 3 total_weight= 438.611 rmsd (weighted)= 7.177 (unweighted)= 36.938 superimposing iter= 4 total_weight= 419.405 rmsd (weighted)= 6.708 (unweighted)= 36.733 superimposing iter= 5 total_weight= 390.300 rmsd (weighted)= 6.488 (unweighted)= 36.498 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.318 rmsd (weighted)= 17.214 (unweighted)= 61.789 superimposing iter= 1 total_weight= 1704.924 rmsd (weighted)= 12.476 (unweighted)= 62.842 superimposing iter= 2 total_weight= 1071.790 rmsd (weighted)= 11.491 (unweighted)= 63.487 superimposing iter= 3 total_weight= 1026.235 rmsd (weighted)= 10.855 (unweighted)= 63.884 superimposing iter= 4 total_weight= 1002.867 rmsd (weighted)= 10.392 (unweighted)= 64.121 superimposing iter= 5 total_weight= 962.373 rmsd (weighted)= 10.157 (unweighted)= 64.266 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.527 rmsd (weighted)= 4.626 (unweighted)= 80.704 superimposing iter= 1 total_weight= 1095.243 rmsd (weighted)= 2.510 (unweighted)= 80.220 superimposing iter= 2 total_weight= 744.157 rmsd (weighted)= 1.671 (unweighted)= 80.032 superimposing iter= 3 total_weight= 638.849 rmsd (weighted)= 1.232 (unweighted)= 80.039 superimposing iter= 4 total_weight= 512.024 rmsd (weighted)= 1.025 (unweighted)= 80.084 superimposing iter= 5 total_weight= 456.844 rmsd (weighted)= 0.908 (unweighted)= 80.105 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.355 rmsd (weighted)= 15.750 (unweighted)= 22.211 superimposing iter= 1 total_weight= 2087.025 rmsd (weighted)= 10.452 (unweighted)= 22.432 superimposing iter= 2 total_weight= 1135.896 rmsd (weighted)= 9.534 (unweighted)= 22.471 superimposing iter= 3 total_weight= 1004.562 rmsd (weighted)= 9.268 (unweighted)= 22.468 superimposing iter= 4 total_weight= 979.839 rmsd (weighted)= 9.127 (unweighted)= 22.461 superimposing iter= 5 total_weight= 971.623 rmsd (weighted)= 9.028 (unweighted)= 22.456 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.274 rmsd (weighted)= 14.840 (unweighted)= 31.447 superimposing iter= 1 total_weight= 2121.563 rmsd (weighted)= 9.354 (unweighted)= 31.319 superimposing iter= 2 total_weight= 1167.642 rmsd (weighted)= 8.061 (unweighted)= 31.536 superimposing iter= 3 total_weight= 1095.353 rmsd (weighted)= 7.139 (unweighted)= 32.248 superimposing iter= 4 total_weight= 1166.377 rmsd (weighted)= 6.034 (unweighted)= 33.763 superimposing iter= 5 total_weight= 1314.905 rmsd (weighted)= 4.722 (unweighted)= 35.723 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.470 rmsd (weighted)= 7.217 (unweighted)= 10.316 superimposing iter= 1 total_weight= 3266.799 rmsd (weighted)= 3.909 (unweighted)= 10.419 superimposing iter= 2 total_weight= 1342.348 rmsd (weighted)= 3.399 (unweighted)= 10.515 superimposing iter= 3 total_weight= 1157.023 rmsd (weighted)= 3.194 (unweighted)= 10.608 superimposing iter= 4 total_weight= 1130.427 rmsd (weighted)= 3.042 (unweighted)= 10.687 superimposing iter= 5 total_weight= 1110.038 rmsd (weighted)= 2.927 (unweighted)= 10.753 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.868 rmsd (weighted)= 4.574 (unweighted)= 32.947 superimposing iter= 1 total_weight= 1924.418 rmsd (weighted)= 2.472 (unweighted)= 33.473 superimposing iter= 2 total_weight= 880.329 rmsd (weighted)= 2.031 (unweighted)= 33.587 superimposing iter= 3 total_weight= 697.696 rmsd (weighted)= 1.881 (unweighted)= 33.628 superimposing iter= 4 total_weight= 645.849 rmsd (weighted)= 1.813 (unweighted)= 33.641 superimposing iter= 5 total_weight= 624.309 rmsd (weighted)= 1.779 (unweighted)= 33.643 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.806 rmsd (weighted)= 4.282 (unweighted)= 34.134 superimposing iter= 1 total_weight= 1319.060 rmsd (weighted)= 2.735 (unweighted)= 34.442 superimposing iter= 2 total_weight= 712.803 rmsd (weighted)= 2.422 (unweighted)= 34.623 superimposing iter= 3 total_weight= 617.835 rmsd (weighted)= 2.309 (unweighted)= 34.748 superimposing iter= 4 total_weight= 589.705 rmsd (weighted)= 2.255 (unweighted)= 34.830 superimposing iter= 5 total_weight= 583.480 rmsd (weighted)= 2.214 (unweighted)= 34.887 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.833 rmsd (weighted)= 4.887 (unweighted)= 37.305 superimposing iter= 1 total_weight= 1271.952 rmsd (weighted)= 3.236 (unweighted)= 37.180 superimposing iter= 2 total_weight= 694.766 rmsd (weighted)= 2.925 (unweighted)= 37.168 superimposing iter= 3 total_weight= 678.832 rmsd (weighted)= 2.690 (unweighted)= 37.186 superimposing iter= 4 total_weight= 671.008 rmsd (weighted)= 2.496 (unweighted)= 37.210 superimposing iter= 5 total_weight= 656.662 rmsd (weighted)= 2.346 (unweighted)= 37.232 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.739 rmsd (weighted)= 7.436 (unweighted)= 79.518 superimposing iter= 1 total_weight= 1738.478 rmsd (weighted)= 3.782 (unweighted)= 79.420 superimposing iter= 2 total_weight= 812.203 rmsd (weighted)= 2.955 (unweighted)= 79.254 superimposing iter= 3 total_weight= 624.920 rmsd (weighted)= 2.656 (unweighted)= 79.189 superimposing iter= 4 total_weight= 568.258 rmsd (weighted)= 2.514 (unweighted)= 79.128 superimposing iter= 5 total_weight= 541.163 rmsd (weighted)= 2.444 (unweighted)= 79.053 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.556 rmsd (weighted)= 9.501 (unweighted)= 34.745 superimposing iter= 1 total_weight= 696.511 rmsd (weighted)= 7.009 (unweighted)= 34.443 superimposing iter= 2 total_weight= 420.638 rmsd (weighted)= 6.711 (unweighted)= 34.212 superimposing iter= 3 total_weight= 402.333 rmsd (weighted)= 6.577 (unweighted)= 34.097 superimposing iter= 4 total_weight= 404.397 rmsd (weighted)= 6.437 (unweighted)= 34.047 superimposing iter= 5 total_weight= 405.659 rmsd (weighted)= 6.300 (unweighted)= 34.014 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.341 rmsd (weighted)= 14.217 (unweighted)= 59.864 superimposing iter= 1 total_weight= 1912.182 rmsd (weighted)= 9.756 (unweighted)= 60.367 superimposing iter= 2 total_weight= 1204.709 rmsd (weighted)= 8.552 (unweighted)= 60.649 superimposing iter= 3 total_weight= 1094.451 rmsd (weighted)= 7.902 (unweighted)= 60.804 superimposing iter= 4 total_weight= 1007.342 rmsd (weighted)= 7.618 (unweighted)= 60.891 superimposing iter= 5 total_weight= 967.366 rmsd (weighted)= 7.495 (unweighted)= 60.943 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.527 rmsd (weighted)= 4.610 (unweighted)= 83.632 superimposing iter= 1 total_weight= 1190.980 rmsd (weighted)= 2.464 (unweighted)= 83.799 superimposing iter= 2 total_weight= 542.678 rmsd (weighted)= 2.017 (unweighted)= 83.803 superimposing iter= 3 total_weight= 410.961 rmsd (weighted)= 1.907 (unweighted)= 83.838 superimposing iter= 4 total_weight= 384.781 rmsd (weighted)= 1.865 (unweighted)= 83.875 superimposing iter= 5 total_weight= 375.250 rmsd (weighted)= 1.848 (unweighted)= 83.906 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.387 rmsd (weighted)= 13.196 (unweighted)= 19.119 superimposing iter= 1 total_weight= 2258.216 rmsd (weighted)= 8.418 (unweighted)= 19.392 superimposing iter= 2 total_weight= 1258.916 rmsd (weighted)= 7.378 (unweighted)= 19.474 superimposing iter= 3 total_weight= 1029.889 rmsd (weighted)= 7.169 (unweighted)= 19.513 superimposing iter= 4 total_weight= 992.957 rmsd (weighted)= 7.097 (unweighted)= 19.536 superimposing iter= 5 total_weight= 984.529 rmsd (weighted)= 7.059 (unweighted)= 19.552 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.306 rmsd (weighted)= 9.920 (unweighted)= 28.284 superimposing iter= 1 total_weight= 1917.499 rmsd (weighted)= 6.706 (unweighted)= 28.207 superimposing iter= 2 total_weight= 1179.162 rmsd (weighted)= 5.846 (unweighted)= 28.168 superimposing iter= 3 total_weight= 1028.476 rmsd (weighted)= 5.473 (unweighted)= 28.151 superimposing iter= 4 total_weight= 980.433 rmsd (weighted)= 5.251 (unweighted)= 28.157 superimposing iter= 5 total_weight= 966.901 rmsd (weighted)= 5.069 (unweighted)= 28.198 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.470 rmsd (weighted)= 7.488 (unweighted)= 10.556 superimposing iter= 1 total_weight= 2659.086 rmsd (weighted)= 4.575 (unweighted)= 10.625 superimposing iter= 2 total_weight= 1275.654 rmsd (weighted)= 4.095 (unweighted)= 10.695 superimposing iter= 3 total_weight= 1126.950 rmsd (weighted)= 3.909 (unweighted)= 10.761 superimposing iter= 4 total_weight= 1091.491 rmsd (weighted)= 3.795 (unweighted)= 10.825 superimposing iter= 5 total_weight= 1072.015 rmsd (weighted)= 3.718 (unweighted)= 10.889 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.868 rmsd (weighted)= 4.619 (unweighted)= 35.694 superimposing iter= 1 total_weight= 1887.078 rmsd (weighted)= 2.517 (unweighted)= 36.405 superimposing iter= 2 total_weight= 883.980 rmsd (weighted)= 2.067 (unweighted)= 36.540 superimposing iter= 3 total_weight= 705.427 rmsd (weighted)= 1.911 (unweighted)= 36.602 superimposing iter= 4 total_weight= 645.104 rmsd (weighted)= 1.851 (unweighted)= 36.643 superimposing iter= 5 total_weight= 620.794 rmsd (weighted)= 1.829 (unweighted)= 36.673 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.806 rmsd (weighted)= 4.206 (unweighted)= 33.874 superimposing iter= 1 total_weight= 1272.411 rmsd (weighted)= 2.743 (unweighted)= 34.137 superimposing iter= 2 total_weight= 699.841 rmsd (weighted)= 2.446 (unweighted)= 34.360 superimposing iter= 3 total_weight= 637.749 rmsd (weighted)= 2.293 (unweighted)= 34.514 superimposing iter= 4 total_weight= 619.816 rmsd (weighted)= 2.186 (unweighted)= 34.610 superimposing iter= 5 total_weight= 600.485 rmsd (weighted)= 2.121 (unweighted)= 34.670 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.833 rmsd (weighted)= 4.868 (unweighted)= 38.353 superimposing iter= 1 total_weight= 1285.690 rmsd (weighted)= 3.205 (unweighted)= 38.185 superimposing iter= 2 total_weight= 678.570 rmsd (weighted)= 2.938 (unweighted)= 38.136 superimposing iter= 3 total_weight= 653.290 rmsd (weighted)= 2.756 (unweighted)= 38.145 superimposing iter= 4 total_weight= 659.264 rmsd (weighted)= 2.581 (unweighted)= 38.175 superimposing iter= 5 total_weight= 662.154 rmsd (weighted)= 2.416 (unweighted)= 38.208 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.739 rmsd (weighted)= 7.533 (unweighted)= 75.227 superimposing iter= 1 total_weight= 1831.097 rmsd (weighted)= 3.700 (unweighted)= 75.104 superimposing iter= 2 total_weight= 839.578 rmsd (weighted)= 2.844 (unweighted)= 74.941 superimposing iter= 3 total_weight= 622.497 rmsd (weighted)= 2.566 (unweighted)= 74.810 superimposing iter= 4 total_weight= 562.411 rmsd (weighted)= 2.445 (unweighted)= 74.643 superimposing iter= 5 total_weight= 544.193 rmsd (weighted)= 2.371 (unweighted)= 74.470 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.556 rmsd (weighted)= 8.656 (unweighted)= 35.859 superimposing iter= 1 total_weight= 812.677 rmsd (weighted)= 5.894 (unweighted)= 36.135 superimposing iter= 2 total_weight= 442.065 rmsd (weighted)= 5.523 (unweighted)= 36.322 superimposing iter= 3 total_weight= 396.542 rmsd (weighted)= 5.473 (unweighted)= 36.448 superimposing iter= 4 total_weight= 391.897 rmsd (weighted)= 5.457 (unweighted)= 36.547 superimposing iter= 5 total_weight= 390.913 rmsd (weighted)= 5.449 (unweighted)= 36.643 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.341 rmsd (weighted)= 13.651 (unweighted)= 59.753 superimposing iter= 1 total_weight= 2015.637 rmsd (weighted)= 9.124 (unweighted)= 60.184 superimposing iter= 2 total_weight= 1255.314 rmsd (weighted)= 7.814 (unweighted)= 60.443 superimposing iter= 3 total_weight= 1131.371 rmsd (weighted)= 7.071 (unweighted)= 60.587 superimposing iter= 4 total_weight= 1032.904 rmsd (weighted)= 6.706 (unweighted)= 60.660 superimposing iter= 5 total_weight= 983.993 rmsd (weighted)= 6.521 (unweighted)= 60.694 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.527 rmsd (weighted)= 4.388 (unweighted)= 85.020 superimposing iter= 1 total_weight= 1234.712 rmsd (weighted)= 2.297 (unweighted)= 85.080 superimposing iter= 2 total_weight= 550.283 rmsd (weighted)= 1.860 (unweighted)= 85.044 superimposing iter= 3 total_weight= 434.198 rmsd (weighted)= 1.708 (unweighted)= 85.039 superimposing iter= 4 total_weight= 398.594 rmsd (weighted)= 1.640 (unweighted)= 85.044 superimposing iter= 5 total_weight= 386.898 rmsd (weighted)= 1.599 (unweighted)= 85.051 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.387 rmsd (weighted)= 12.897 (unweighted)= 19.191 superimposing iter= 1 total_weight= 2376.222 rmsd (weighted)= 8.033 (unweighted)= 19.450 superimposing iter= 2 total_weight= 1253.929 rmsd (weighted)= 7.051 (unweighted)= 19.559 superimposing iter= 3 total_weight= 1043.306 rmsd (weighted)= 6.803 (unweighted)= 19.616 superimposing iter= 4 total_weight= 994.885 rmsd (weighted)= 6.726 (unweighted)= 19.653 superimposing iter= 5 total_weight= 982.800 rmsd (weighted)= 6.693 (unweighted)= 19.682 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.306 rmsd (weighted)= 8.946 (unweighted)= 28.965 superimposing iter= 1 total_weight= 2014.492 rmsd (weighted)= 5.904 (unweighted)= 28.823 superimposing iter= 2 total_weight= 1186.492 rmsd (weighted)= 5.145 (unweighted)= 28.734 superimposing iter= 3 total_weight= 1018.129 rmsd (weighted)= 4.856 (unweighted)= 28.679 superimposing iter= 4 total_weight= 965.011 rmsd (weighted)= 4.710 (unweighted)= 28.638 superimposing iter= 5 total_weight= 952.814 rmsd (weighted)= 4.597 (unweighted)= 28.608 superimposing iter= 0 total_weight= 1.470 rmsd (weighted)= 7.990 (unweighted)= 10.951 superimposing iter= 1 total_weight= 2411.928 rmsd (weighted)= 5.161 (unweighted)= 10.998 superimposing iter= 2 total_weight= 1213.900 rmsd (weighted)= 4.747 (unweighted)= 11.051 superimposing iter= 3 total_weight= 1097.825 rmsd (weighted)= 4.596 (unweighted)= 11.108 superimposing iter= 4 total_weight= 1074.340 rmsd (weighted)= 4.500 (unweighted)= 11.168 superimposing iter= 5 total_weight= 1066.382 rmsd (weighted)= 4.421 (unweighted)= 11.234 superimposing iter= 0 total_weight= 0.868 rmsd (weighted)= 4.573 (unweighted)= 39.073 superimposing iter= 1 total_weight= 1934.414 rmsd (weighted)= 2.457 (unweighted)= 39.868 superimposing iter= 2 total_weight= 900.685 rmsd (weighted)= 1.996 (unweighted)= 40.036 superimposing iter= 3 total_weight= 717.330 rmsd (weighted)= 1.828 (unweighted)= 40.148 superimposing iter= 4 total_weight= 651.805 rmsd (weighted)= 1.761 (unweighted)= 40.249 superimposing iter= 5 total_weight= 628.689 rmsd (weighted)= 1.727 (unweighted)= 40.331 superimposing iter= 0 total_weight= 0.806 rmsd (weighted)= 4.132 (unweighted)= 33.304 superimposing iter= 1 total_weight= 1285.221 rmsd (weighted)= 2.681 (unweighted)= 33.529 superimposing iter= 2 total_weight= 710.910 rmsd (weighted)= 2.374 (unweighted)= 33.742 superimposing iter= 3 total_weight= 649.808 rmsd (weighted)= 2.206 (unweighted)= 33.897 superimposing iter= 4 total_weight= 630.361 rmsd (weighted)= 2.085 (unweighted)= 33.994 superimposing iter= 5 total_weight= 604.352 rmsd (weighted)= 2.015 (unweighted)= 34.052 superimposing iter= 0 total_weight= 0.833 rmsd (weighted)= 4.774 (unweighted)= 38.355 superimposing iter= 1 total_weight= 1307.481 rmsd (weighted)= 3.121 (unweighted)= 38.155 superimposing iter= 2 total_weight= 671.598 rmsd (weighted)= 2.879 (unweighted)= 38.100 superimposing iter= 3 total_weight= 648.696 rmsd (weighted)= 2.710 (unweighted)= 38.113 superimposing iter= 4 total_weight= 671.469 rmsd (weighted)= 2.511 (unweighted)= 38.155 superimposing iter= 5 total_weight= 679.718 rmsd (weighted)= 2.318 (unweighted)= 38.199 superimposing iter= 0 total_weight= 0.739 rmsd (weighted)= 7.493 (unweighted)= 71.100 superimposing iter= 1 total_weight= 1911.808 rmsd (weighted)= 3.585 (unweighted)= 70.833 superimposing iter= 2 total_weight= 861.127 rmsd (weighted)= 2.718 (unweighted)= 70.550 superimposing iter= 3 total_weight= 642.928 rmsd (weighted)= 2.410 (unweighted)= 70.377 superimposing iter= 4 total_weight= 580.262 rmsd (weighted)= 2.257 (unweighted)= 70.242 superimposing iter= 5 total_weight= 560.495 rmsd (weighted)= 2.153 (unweighted)= 70.142 superimposing iter= 0 total_weight= 0.556 rmsd (weighted)= 8.461 (unweighted)= 36.697 superimposing iter= 1 total_weight= 822.255 rmsd (weighted)= 5.712 (unweighted)= 37.051 superimposing iter= 2 total_weight= 449.979 rmsd (weighted)= 5.302 (unweighted)= 37.278 superimposing iter= 3 total_weight= 397.915 rmsd (weighted)= 5.243 (unweighted)= 37.434 superimposing iter= 4 total_weight= 392.090 rmsd (weighted)= 5.224 (unweighted)= 37.580 superimposing iter= 5 total_weight= 391.993 rmsd (weighted)= 5.205 (unweighted)= 37.742 superimposing iter= 0 total_weight= 1.341 rmsd (weighted)= 13.397 (unweighted)= 59.467 superimposing iter= 1 total_weight= 2124.898 rmsd (weighted)= 8.702 (unweighted)= 59.853 superimposing iter= 2 total_weight= 1274.225 rmsd (weighted)= 7.381 (unweighted)= 60.090 superimposing iter= 3 total_weight= 1165.360 rmsd (weighted)= 6.573 (unweighted)= 60.226 superimposing iter= 4 total_weight= 1051.882 rmsd (weighted)= 6.169 (unweighted)= 60.294 superimposing iter= 5 total_weight= 991.376 rmsd (weighted)= 5.971 (unweighted)= 60.324 superimposing iter= 0 total_weight= 0.527 rmsd (weighted)= 4.256 (unweighted)= 85.396 superimposing iter= 1 total_weight= 1265.480 rmsd (weighted)= 2.203 (unweighted)= 85.370 superimposing iter= 2 total_weight= 563.875 rmsd (weighted)= 1.762 (unweighted)= 85.274 superimposing iter= 3 total_weight= 444.921 rmsd (weighted)= 1.598 (unweighted)= 85.219 superimposing iter= 4 total_weight= 404.740 rmsd (weighted)= 1.521 (unweighted)= 85.181 superimposing iter= 5 total_weight= 387.268 rmsd (weighted)= 1.481 (unweighted)= 85.154 superimposing iter= 0 total_weight= 1.387 rmsd (weighted)= 12.790 (unweighted)= 19.063 superimposing iter= 1 total_weight= 2509.973 rmsd (weighted)= 7.733 (unweighted)= 19.318 superimposing iter= 2 total_weight= 1251.810 rmsd (weighted)= 6.776 (unweighted)= 19.440 superimposing iter= 3 total_weight= 1036.784 rmsd (weighted)= 6.542 (unweighted)= 19.508 superimposing iter= 4 total_weight= 994.744 rmsd (weighted)= 6.455 (unweighted)= 19.558 superimposing iter= 5 total_weight= 982.819 rmsd (weighted)= 6.412 (unweighted)= 19.597 superimposing iter= 0 total_weight= 1.306 rmsd (weighted)= 8.416 (unweighted)= 29.157 superimposing iter= 1 total_weight= 2058.233 rmsd (weighted)= 5.483 (unweighted)= 28.992 superimposing iter= 2 total_weight= 1194.423 rmsd (weighted)= 4.759 (unweighted)= 28.886 superimposing iter= 3 total_weight= 1008.939 rmsd (weighted)= 4.507 (unweighted)= 28.819 superimposing iter= 4 total_weight= 962.155 rmsd (weighted)= 4.372 (unweighted)= 28.770 superimposing iter= 5 total_weight= 952.158 rmsd (weighted)= 4.264 (unweighted)= 28.731 # command:# Printing sheets for alignments to T0590.undertaker-align.sheets # command: