# command:# Seed set to 1273741212 # 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= 23.472 sec, elapsed time= 24.375 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= 36.685 sec, elapsed time= 40.953 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0517 numbered 1 through 159 Created new target T0517 from T0517.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.686 sec, elapsed time= 40.954 sec. # command:# Prefix for input files set to # command:# reading script from file T0517.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qs7A/T0517-2qs7A-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 2qs7A expands to /projects/compbio/data/pdb/2qs7.pdb.gz 2qs7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 256, because occupancy 0.5 <= existing 0.500 in 2qs7A Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 621, because occupancy 0.370 <= existing 0.380 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2qs7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 850, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 854, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 856, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 2qs7A Skipped atom 991, because occupancy 0.500 <= existing 0.500 in 2qs7A # T0517 read from 2qs7A/T0517-2qs7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qs7A read from 2qs7A/T0517-2qs7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qs7A to template set # found chain 2qs7A in template set Warning: unaligning (T0517)N3 because first residue in template chain is (2qs7A)K6 T0517 4 :KKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQA 2qs7A 7 :KKLSIIVFSGTIDKLMPVGILTSGAAASGYEVNLFFTFWGLQAITKRSLNSQQPPQIDKNY # choosing archetypes in rotamer library T0517 84 :GGIGKKMLLEM 2qs7A 68 :EQMGPIMMQKM T0517 96 :KEEKAPKLSDLLSGARKKE 2qs7A 79 :QEMKYPMWHQLVQQAKEIG T0517 115 :VKFYACQLSVEIMGFKKEELFPEVQ 2qs7A 99 :VKVFACSTTMEFFGIKREDLAEFVD T0517 140 :IMDVKEYLKNALESDLQL 2qs7A 125 :VVGVATFLDRAEGGTTLF Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1758548177.pdb -s /var/tmp/to_scwrl_1758548177.seq -o /var/tmp/from_scwrl_1758548177.pdb > /var/tmp/scwrl_1758548177.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1758548177.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jx7A/T0517-1jx7A-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 1jx7A expands to /projects/compbio/data/pdb/1jx7.pdb.gz 1jx7A: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 # T0517 read from 1jx7A/T0517-1jx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx7A read from 1jx7A/T0517-1jx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jx7A to template set # found chain 1jx7A in template set T0517 5 :KMNLLLFSGDY 1jx7A 2 :QKIVIVANGAP T0517 16 :DKALASLIIANAARE 1jx7A 16 :ESLFNSLRLAIALRE T0517 32 :EIEVTIFCAFWGLLLLRDPEKASQ 1jx7A 34 :NLDLRLFLMSDAVTAGLRGQKPGE T0517 100 :APKLSDLLSGARKKEVKFYACQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 1jx7A 58 :GYNIQQMLEILTAQNVPVKLCKTCTDGRGISTLPLIDGVEIGTLVELAQWTLSADKVLTF Number of specific fragments extracted= 4 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_2051227876.pdb -s /var/tmp/to_scwrl_2051227876.seq -o /var/tmp/from_scwrl_2051227876.pdb > /var/tmp/scwrl_2051227876.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2051227876.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pd2A/T0517-2pd2A-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 2pd2A expands to /projects/compbio/data/pdb/2pd2.pdb.gz 2pd2A:# T0517 read from 2pd2A/T0517-2pd2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pd2A read from 2pd2A/T0517-2pd2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pd2A to template set # found chain 2pd2A in template set T0517 7 :NLLLFSGDYDKALASLIIANAARE 2pd2A 2 :KVVVQIKDFDKVPQALRSVINLYN T0517 32 :EIEVTIFCAFWGLLLLRDP 2pd2A 29 :DAEIEVVLHQSAIKALLKD T0517 101 :PKLSDLLSGARKKEVKFYACQLSVEIMGFKKEELFPEVQIM 2pd2A 48 :SDTRSIIEDLIKKNILIVGCENSIRSQNLSHDQLIPGIKIV T0517 142 :DVKEYLKNALESDLQLF 2pd2A 90 :SGVGEIVRKQSEGWIYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1063514654.pdb -s /var/tmp/to_scwrl_1063514654.seq -o /var/tmp/from_scwrl_1063514654.pdb > /var/tmp/scwrl_1063514654.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1063514654.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fb6A/T0517-2fb6A-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 2fb6A expands to /projects/compbio/data/pdb/2fb6.pdb.gz 2fb6A:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 235, because occupancy 0.350 <= existing 0.350 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 458, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 462, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 464, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 466, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 468, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 470, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 569, because occupancy 0.300 <= existing 0.700 in 2fb6A Skipped atom 573, because occupancy 0.300 <= existing 0.700 in 2fb6A Skipped atom 575, because occupancy 0.300 <= existing 0.700 in 2fb6A Skipped atom 577, because occupancy 0.300 <= existing 0.700 in 2fb6A Skipped atom 579, because occupancy 0.300 <= existing 0.700 in 2fb6A Skipped atom 582, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 586, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 588, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 590, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 592, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 594, because occupancy 0.400 <= existing 0.600 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 613, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 617, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 619, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 621, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 623, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 625, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 754, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 758, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 760, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 779, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 783, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 785, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 787, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 790, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 794, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 796, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 798, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 800, because occupancy 0.400 <= existing 0.600 in 2fb6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 906, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 910, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 912, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 914, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 967, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 971, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 973, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 975, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 977, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 979, because occupancy 0.400 <= existing 0.600 in 2fb6A Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fb6A Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fb6A # T0517 read from 2fb6A/T0517-2fb6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fb6A read from 2fb6A/T0517-2fb6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fb6A to template set # found chain 2fb6A in template set T0517 2 :ENKKMNLLLFSGDYDKAL 2fb6A 3 :ANDKLTILWTTDNKDTVF T0517 24 :IANAAREM 2fb6A 23 :LAMYALNS T0517 32 :EI 2fb6A 34 :GW T0517 34 :EVTIFCAFWGLLLLRDPEK 2fb6A 38 :HINIILWGASVKLVANDTQ T0517 103 :LSDLLSGARKKEVKFYACQLSVEIMG 2fb6A 57 :VQTEILEMLQSGITIEACQDCCENFG T0517 137 :EVQIMDVKEYLKNALESDLQLF 2fb6A 91 :GITVRYMGIPLTEYLKNGEKIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=19 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1227659566.pdb -s /var/tmp/to_scwrl_1227659566.seq -o /var/tmp/from_scwrl_1227659566.pdb > /var/tmp/scwrl_1227659566.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1227659566.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hy5C/T0517-2hy5C-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 2hy5C expands to /projects/compbio/data/pdb/2hy5.pdb.gz 2hy5C:# T0517 read from 2hy5C/T0517-2hy5C-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hy5C read from 2hy5C/T0517-2hy5C-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hy5C to template set # found chain 2hy5C in template set T0517 7 :NLLLFSGDY 2hy5C 403 :ILHTVNKSP T0517 16 :DKALASL 2hy5C 415 :NSLESCL T0517 34 :EVTIFCAFWGLLLLRDPE 2hy5C 427 :GASVLLFEDGIYAALAGT T0517 102 :KLSDLLSGA 2hy5C 445 :RVESQVTEA T0517 113 :KE 2hy5C 454 :LG T0517 115 :VKFYACQLSVEIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI 2hy5C 457 :LKLYVLGPDLKARGFSDERVIPGISVVDYAGFVDLTTECDTVQAW Number of specific fragments extracted= 6 number of extra gaps= 0 total=25 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1007951681.pdb -s /var/tmp/to_scwrl_1007951681.seq -o /var/tmp/from_scwrl_1007951681.pdb > /var/tmp/scwrl_1007951681.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1007951681.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zxxA/T0517-1zxxA-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 1zxxA expands to /projects/compbio/data/pdb/1zxx.pdb.gz 1zxxA:# T0517 read from 1zxxA/T0517-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0517-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zxxA to template set # found chain 1zxxA in template set T0517 4 :KKMNLLLFSGDYDKALASL 1zxxA 2 :KRIGILTSGGDAPGMNAAV T0517 23 :IIANAAREMEIEV 1zxxA 22 :AVTRVAIANGLEV T0517 38 :FCAFWGLLLLRDPEKASQ 1zxxA 35 :FGIRYGFAGLVAGDIFPL T0517 57 :DKSLYEQAFS 1zxxA 53 :ESEDVAHLIN T0517 67 :SLTPREAEELP 1zxxA 67 :FLYSARYPEFA T0517 84 :GGIGKKMLLEMMKEEKAP 1zxxA 78 :EEEGQLAGIEQLKKHGID T0517 103 :LSDLLSGARKKEVKFYACQLSVEI 1zxxA 105 :SYHGALQLTRHGFNSIGLPGTIDN T0517 135 :FPEVQ 1zxxA 130 :IPYTD T0517 140 :IMD 1zxxA 136 :TIG T0517 143 :VKEYLKNALESDLQLFI 1zxxA 150 :IDKIRDTASSHHRVFIV Number of specific fragments extracted= 10 number of extra gaps= 0 total=35 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1464550492.pdb -s /var/tmp/to_scwrl_1464550492.seq -o /var/tmp/from_scwrl_1464550492.pdb > /var/tmp/scwrl_1464550492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1464550492.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 6pfkA/T0517-6pfkA-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 6pfkA expands to /projects/compbio/data/pdb/6pfk.pdb.gz 6pfkA:Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1879, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1881, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1883, because occupancy 0.500 <= existing 0.500 in 6pfkA Skipped atom 1885, because occupancy 0.500 <= existing 0.500 in 6pfkA # T0517 read from 6pfkA/T0517-6pfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 6pfkA read from 6pfkA/T0517-6pfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 6pfkA to template set # found chain 6pfkA in template set Warning: unaligning (T0517)E30 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H30 Warning: unaligning (T0517)M31 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H30 Warning: unaligning (T0517)E51 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)I49 Warning: unaligning (T0517)K52 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)I49 Warning: unaligning (T0517)A64 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)H62 Warning: unaligning (T0517)F65 because of BadResidue code BAD_PEPTIDE at template residue (6pfkA)H62 Warning: unaligning (T0517)K80 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (6pfkA)T78 Warning: unaligning (T0517)G84 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (6pfkA)T78 Warning: unaligning (T0517)Q139 because of BadResidue code BAD_PEPTIDE in next template residue (6pfkA)F135 T0517 4 :KKMNLLLFSGDYDKALASL 6pfkA 2 :KRIGVLTSGGDSPGMNAAI T0517 23 :IIANAAR 6pfkA 22 :SVVRKAI T0517 32 :EIE 6pfkA 31 :GVE T0517 37 :IFCAFWGLLLLRDP 6pfkA 34 :VYGVYHGYAGLIAG T0517 53 :ASQEDKSLYEQ 6pfkA 50 :KKLEVGDVGDI T0517 66 :SSLTPREAEELPLS 6pfkA 63 :RGGTILYTARCPEF T0517 85 :GIGKKMLLEMMKEEKAP 6pfkA 79 :EEGQKKGIEQLKKHGIE T0517 103 :LSDLLSGARKKEVKFYACQLSVEI 6pfkA 105 :SYQGAKKLTEHGFPCVGVPGTIDN T0517 135 :FPEV 6pfkA 130 :IPGT T0517 140 :IMD 6pfkA 136 :TIG T0517 143 :VKEYLKNALES 6pfkA 146 :VIDAIDKIRDT Number of specific fragments extracted= 11 number of extra gaps= 5 total=46 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_34280187.pdb -s /var/tmp/to_scwrl_34280187.seq -o /var/tmp/from_scwrl_34280187.pdb > /var/tmp/scwrl_34280187.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_34280187.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h7eA/T0517-3h7eA-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 3h7eA expands to /projects/compbio/data/pdb/3h7e.pdb.gz 3h7eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0517 read from 3h7eA/T0517-3h7eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h7eA read from 3h7eA/T0517-3h7eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h7eA to template set # found chain 3h7eA in template set Warning: unaligning (T0517)N3 because first residue in template chain is (3h7eA)G3 Warning: unaligning (T0517)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h7eA)S44 Warning: unaligning (T0517)S54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3h7eA)S44 Warning: unaligning (T0517)P101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3h7eA)R126 T0517 4 :KKMNLLLFSGDYDKALASL 3h7eA 4 :LADVAVLYSGGKDSNYALY T0517 27 :AAREMEIEVTIFCAFWG 3h7eA 23 :WAIKNRFSVKFLVTMVS T0517 50 :PE 3h7eA 40 :EN T0517 55 :QEDKSLYEQAFSSLTP 3h7eA 45 :YMYHTINANLTDLQAR T0517 79 :SKMNLGGIGKKMLLEMMKEEKA 3h7eA 96 :AGALASKYQRKRIEKVAKELGL T0517 102 :KLSDLLSGARKKEVKFYACQ 3h7eA 127 :DAKEYMRELLNLGFKIMVVG T0517 124 :VEIMGFKKEELFPEVQ 3h7eA 147 :VSAYGLDESWLGRILD T0517 140 :IMDVKEYLK 3h7eA 166 :LEELITLNE Number of specific fragments extracted= 8 number of extra gaps= 0 total=54 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_210547724.pdb -s /var/tmp/to_scwrl_210547724.seq -o /var/tmp/from_scwrl_210547724.pdb > /var/tmp/scwrl_210547724.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_210547724.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1irxA/T0517-1irxA-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 1irxA expands to /projects/compbio/data/pdb/1irx.pdb.gz 1irxA:# T0517 read from 1irxA/T0517-1irxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1irxA read from 1irxA/T0517-1irxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1irxA to template set # found chain 1irxA in template set T0517 1 :MENKKMNLLLFSG 1irxA 17 :GEKEKYVVESGIT T0517 14 :DYDKALASLIIANAAREMEIEVTIFCAFWGLLLLR 1irxA 38 :NFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFR T0517 55 :QEDKS 1irxA 73 :KVPRN T0517 69 :TPREAEE 1irxA 78 :VPQEWKD T0517 76 :LPLSKM 1irxA 88 :MPISEV T0517 82 :NLGGIGKKMLLEM 1irxA 99 :CHESYAEHFMRKF T0517 104 :SD 1irxA 112 :EE T0517 123 :SVEIMGFK 1irxA 114 :EVEKLGIE T0517 138 :VQIMDVKEYLK 1irxA 122 :VDLLYASELYK Number of specific fragments extracted= 9 number of extra gaps= 0 total=63 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_274328867.pdb -s /var/tmp/to_scwrl_274328867.seq -o /var/tmp/from_scwrl_274328867.pdb > /var/tmp/scwrl_274328867.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_274328867.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g5tA/T0517-1g5tA-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 # T0517 read from 1g5tA/T0517-1g5tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1g5tA read from 1g5tA/T0517-1g5tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1g5tA in training set Warning: unaligning (T0517)E2 because first residue in template chain is (1g5tA)E27 T0517 3 :NKKMN 1g5tA 28 :RGIII T0517 9 :LLFSGDYDKALASLIIANAAREMEIEVTIFCA 1g5tA 33 :VFTGNGKGKTTAAFGTAARAVGHGKNVGVVQF T0517 52 :KASQEDKSLYEQAFSSL 1g5tA 65 :IKGTWPNGERNLLEPHG T0517 69 :TPREAEELPL 1g5tA 87 :MATGFTWETQ T0517 83 :LGGIGKKMLL 1g5tA 97 :NREADTAACM T0517 105 :DLLSGARK 1g5tA 107 :AVWQHGKR T0517 113 :KEVKFYACQLSVEIMG 1g5tA 119 :PLLDMVVLDELTYMVA T0517 135 :FPEVQIMDVKEYLKNALESDLQLFI 1g5tA 135 :YDYLPLEEVISALNARPGHQTVIIT Number of specific fragments extracted= 8 number of extra gaps= 0 total=71 # request to SCWRL produces command: ulimit -t 144 ; scwrl4 -t -i /var/tmp/to_scwrl_1039904229.pdb -s /var/tmp/to_scwrl_1039904229.seq -o /var/tmp/from_scwrl_1039904229.pdb > /var/tmp/scwrl_1039904229.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1039904229.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 10660.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 10660.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 10660.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 10660.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 10660.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.018 rmsd (weighted)= 3.930 (unweighted)= 63.766 superimposing iter= 1 total_weight= 3193.284 rmsd (weighted)= 1.925 (unweighted)= 63.623 superimposing iter= 2 total_weight= 1353.754 rmsd (weighted)= 1.512 (unweighted)= 63.585 superimposing iter= 3 total_weight= 967.576 rmsd (weighted)= 1.412 (unweighted)= 63.563 superimposing iter= 4 total_weight= 888.963 rmsd (weighted)= 1.378 (unweighted)= 63.549 superimposing iter= 5 total_weight= 862.542 rmsd (weighted)= 1.365 (unweighted)= 63.540 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.946 rmsd (weighted)= 4.319 (unweighted)= 43.706 superimposing iter= 1 total_weight= 3183.769 rmsd (weighted)= 1.987 (unweighted)= 43.907 superimposing iter= 2 total_weight= 1388.900 rmsd (weighted)= 1.473 (unweighted)= 43.978 superimposing iter= 3 total_weight= 1044.293 rmsd (weighted)= 1.272 (unweighted)= 44.017 superimposing iter= 4 total_weight= 928.354 rmsd (weighted)= 1.169 (unweighted)= 44.037 superimposing iter= 5 total_weight= 862.887 rmsd (weighted)= 1.115 (unweighted)= 44.044 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.870 rmsd (weighted)= 3.945 (unweighted)= 23.591 superimposing iter= 1 total_weight= 2739.313 rmsd (weighted)= 1.909 (unweighted)= 23.699 superimposing iter= 2 total_weight= 1330.288 rmsd (weighted)= 1.394 (unweighted)= 23.699 superimposing iter= 3 total_weight= 938.236 rmsd (weighted)= 1.221 (unweighted)= 23.701 superimposing iter= 4 total_weight= 918.684 rmsd (weighted)= 1.083 (unweighted)= 23.710 superimposing iter= 5 total_weight= 899.714 rmsd (weighted)= 0.972 (unweighted)= 23.719 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.834 rmsd (weighted)= 3.618 (unweighted)= 75.931 superimposing iter= 1 total_weight= 2232.001 rmsd (weighted)= 1.900 (unweighted)= 76.312 superimposing iter= 2 total_weight= 1038.439 rmsd (weighted)= 1.539 (unweighted)= 76.439 superimposing iter= 3 total_weight= 790.888 rmsd (weighted)= 1.444 (unweighted)= 76.467 superimposing iter= 4 total_weight= 742.516 rmsd (weighted)= 1.402 (unweighted)= 76.473 superimposing iter= 5 total_weight= 728.130 rmsd (weighted)= 1.375 (unweighted)= 76.472 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.147 rmsd (weighted)= 17.140 (unweighted)= 35.637 superimposing iter= 1 total_weight= 2372.859 rmsd (weighted)= 10.553 (unweighted)= 35.271 superimposing iter= 2 total_weight= 1234.874 rmsd (weighted)= 9.190 (unweighted)= 35.142 superimposing iter= 3 total_weight= 1050.074 rmsd (weighted)= 8.736 (unweighted)= 35.093 superimposing iter= 4 total_weight= 993.396 rmsd (weighted)= 8.558 (unweighted)= 35.070 superimposing iter= 5 total_weight= 989.818 rmsd (weighted)= 8.410 (unweighted)= 35.060 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.055 rmsd (weighted)= 15.751 (unweighted)= 33.941 superimposing iter= 1 total_weight= 2091.457 rmsd (weighted)= 10.035 (unweighted)= 33.526 superimposing iter= 2 total_weight= 1095.052 rmsd (weighted)= 8.951 (unweighted)= 33.182 superimposing iter= 3 total_weight= 955.966 rmsd (weighted)= 8.569 (unweighted)= 32.921 superimposing iter= 4 total_weight= 928.638 rmsd (weighted)= 8.333 (unweighted)= 32.734 superimposing iter= 5 total_weight= 922.491 rmsd (weighted)= 8.139 (unweighted)= 32.610 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.035 rmsd (weighted)= 14.214 (unweighted)= 47.309 superimposing iter= 1 total_weight= 1990.486 rmsd (weighted)= 9.213 (unweighted)= 47.002 superimposing iter= 2 total_weight= 1054.875 rmsd (weighted)= 8.284 (unweighted)= 46.487 superimposing iter= 3 total_weight= 992.996 rmsd (weighted)= 7.678 (unweighted)= 46.038 superimposing iter= 4 total_weight= 991.250 rmsd (weighted)= 7.131 (unweighted)= 45.755 superimposing iter= 5 total_weight= 992.220 rmsd (weighted)= 6.625 (unweighted)= 45.564 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.769 rmsd (weighted)= 13.626 (unweighted)= 65.224 superimposing iter= 1 total_weight= 2480.187 rmsd (weighted)= 6.063 (unweighted)= 65.121 superimposing iter= 2 total_weight= 1640.940 rmsd (weighted)= 3.537 (unweighted)= 64.830 superimposing iter= 3 total_weight= 1306.449 rmsd (weighted)= 2.387 (unweighted)= 64.666 superimposing iter= 4 total_weight= 981.157 rmsd (weighted)= 1.901 (unweighted)= 64.595 superimposing iter= 5 total_weight= 769.581 rmsd (weighted)= 1.723 (unweighted)= 64.559 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.977 rmsd (weighted)= 12.740 (unweighted)= 31.339 superimposing iter= 1 total_weight= 1864.751 rmsd (weighted)= 7.997 (unweighted)= 31.662 superimposing iter= 2 total_weight= 1018.534 rmsd (weighted)= 6.978 (unweighted)= 31.980 superimposing iter= 3 total_weight= 997.266 rmsd (weighted)= 6.186 (unweighted)= 32.263 superimposing iter= 4 total_weight= 1023.101 rmsd (weighted)= 5.399 (unweighted)= 32.459 superimposing iter= 5 total_weight= 1055.317 rmsd (weighted)= 4.630 (unweighted)= 32.564 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 7.301 (unweighted)= 22.790 superimposing iter= 1 total_weight= 3189.402 rmsd (weighted)= 4.054 (unweighted)= 22.880 superimposing iter= 2 total_weight= 1368.989 rmsd (weighted)= 3.541 (unweighted)= 22.936 superimposing iter= 3 total_weight= 1121.945 rmsd (weighted)= 3.429 (unweighted)= 22.955 superimposing iter= 4 total_weight= 1098.568 rmsd (weighted)= 3.358 (unweighted)= 22.967 superimposing iter= 5 total_weight= 1102.530 rmsd (weighted)= 3.284 (unweighted)= 22.977 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.039 rmsd (weighted)= 5.086 (unweighted)= 57.903 superimposing iter= 1 total_weight= 1921.624 rmsd (weighted)= 3.361 (unweighted)= 57.616 superimposing iter= 2 total_weight= 1062.480 rmsd (weighted)= 3.035 (unweighted)= 57.531 superimposing iter= 3 total_weight= 909.738 rmsd (weighted)= 2.968 (unweighted)= 57.500 superimposing iter= 4 total_weight= 881.190 rmsd (weighted)= 2.950 (unweighted)= 57.485 superimposing iter= 5 total_weight= 875.092 rmsd (weighted)= 2.942 (unweighted)= 57.477 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.957 rmsd (weighted)= 4.736 (unweighted)= 34.565 superimposing iter= 1 total_weight= 1685.881 rmsd (weighted)= 3.217 (unweighted)= 34.604 superimposing iter= 2 total_weight= 962.751 rmsd (weighted)= 2.930 (unweighted)= 34.598 superimposing iter= 3 total_weight= 859.300 rmsd (weighted)= 2.832 (unweighted)= 34.592 superimposing iter= 4 total_weight= 833.153 rmsd (weighted)= 2.782 (unweighted)= 34.593 superimposing iter= 5 total_weight= 822.281 rmsd (weighted)= 2.752 (unweighted)= 34.598 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.901 rmsd (weighted)= 4.452 (unweighted)= 23.222 superimposing iter= 1 total_weight= 1767.569 rmsd (weighted)= 2.862 (unweighted)= 23.235 superimposing iter= 2 total_weight= 930.939 rmsd (weighted)= 2.573 (unweighted)= 23.262 superimposing iter= 3 total_weight= 812.941 rmsd (weighted)= 2.481 (unweighted)= 23.272 superimposing iter= 4 total_weight= 785.464 rmsd (weighted)= 2.433 (unweighted)= 23.268 superimposing iter= 5 total_weight= 776.523 rmsd (weighted)= 2.401 (unweighted)= 23.257 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.855 rmsd (weighted)= 4.346 (unweighted)= 77.821 superimposing iter= 1 total_weight= 1673.626 rmsd (weighted)= 2.800 (unweighted)= 77.909 superimposing iter= 2 total_weight= 873.432 rmsd (weighted)= 2.533 (unweighted)= 77.892 superimposing iter= 3 total_weight= 774.846 rmsd (weighted)= 2.437 (unweighted)= 77.882 superimposing iter= 4 total_weight= 759.870 rmsd (weighted)= 2.367 (unweighted)= 77.881 superimposing iter= 5 total_weight= 749.952 rmsd (weighted)= 2.315 (unweighted)= 77.884 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.300 rmsd (weighted)= 12.134 (unweighted)= 26.304 superimposing iter= 1 total_weight= 2990.611 rmsd (weighted)= 6.990 (unweighted)= 26.086 superimposing iter= 2 total_weight= 1448.690 rmsd (weighted)= 6.001 (unweighted)= 26.089 superimposing iter= 3 total_weight= 1220.308 rmsd (weighted)= 5.659 (unweighted)= 26.111 superimposing iter= 4 total_weight= 1139.790 rmsd (weighted)= 5.527 (unweighted)= 26.124 superimposing iter= 5 total_weight= 1110.840 rmsd (weighted)= 5.467 (unweighted)= 26.129 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.192 rmsd (weighted)= 10.270 (unweighted)= 28.935 superimposing iter= 1 total_weight= 2057.465 rmsd (weighted)= 7.004 (unweighted)= 28.846 superimposing iter= 2 total_weight= 1203.238 rmsd (weighted)= 6.333 (unweighted)= 28.843 superimposing iter= 3 total_weight= 1128.595 rmsd (weighted)= 5.939 (unweighted)= 28.847 superimposing iter= 4 total_weight= 1073.972 rmsd (weighted)= 5.718 (unweighted)= 28.841 superimposing iter= 5 total_weight= 1036.642 rmsd (weighted)= 5.605 (unweighted)= 28.831 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.145 rmsd (weighted)= 11.234 (unweighted)= 37.434 superimposing iter= 1 total_weight= 2181.547 rmsd (weighted)= 7.352 (unweighted)= 37.084 superimposing iter= 2 total_weight= 1107.416 rmsd (weighted)= 6.840 (unweighted)= 36.928 superimposing iter= 3 total_weight= 1005.235 rmsd (weighted)= 6.686 (unweighted)= 36.844 superimposing iter= 4 total_weight= 995.562 rmsd (weighted)= 6.566 (unweighted)= 36.789 superimposing iter= 5 total_weight= 993.488 rmsd (weighted)= 6.453 (unweighted)= 36.749 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.939 rmsd (weighted)= 10.615 (unweighted)= 62.156 superimposing iter= 1 total_weight= 2378.611 rmsd (weighted)= 5.746 (unweighted)= 62.076 superimposing iter= 2 total_weight= 1307.724 rmsd (weighted)= 4.366 (unweighted)= 61.914 superimposing iter= 3 total_weight= 1015.895 rmsd (weighted)= 3.802 (unweighted)= 61.803 superimposing iter= 4 total_weight= 890.184 rmsd (weighted)= 3.551 (unweighted)= 61.718 superimposing iter= 5 total_weight= 832.012 rmsd (weighted)= 3.434 (unweighted)= 61.648 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 9.699 (unweighted)= 21.313 superimposing iter= 1 total_weight= 1946.435 rmsd (weighted)= 6.737 (unweighted)= 21.204 superimposing iter= 2 total_weight= 1102.016 rmsd (weighted)= 6.259 (unweighted)= 21.138 superimposing iter= 3 total_weight= 1015.550 rmsd (weighted)= 6.063 (unweighted)= 21.108 superimposing iter= 4 total_weight= 1001.442 rmsd (weighted)= 5.915 (unweighted)= 21.101 superimposing iter= 5 total_weight= 995.742 rmsd (weighted)= 5.789 (unweighted)= 21.112 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 7.424 (unweighted)= 23.007 superimposing iter= 1 total_weight= 3141.477 rmsd (weighted)= 4.178 (unweighted)= 23.107 superimposing iter= 2 total_weight= 1358.185 rmsd (weighted)= 3.666 (unweighted)= 23.134 superimposing iter= 3 total_weight= 1130.988 rmsd (weighted)= 3.535 (unweighted)= 23.135 superimposing iter= 4 total_weight= 1093.224 rmsd (weighted)= 3.467 (unweighted)= 23.132 superimposing iter= 5 total_weight= 1100.227 rmsd (weighted)= 3.391 (unweighted)= 23.130 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.039 rmsd (weighted)= 5.173 (unweighted)= 57.816 superimposing iter= 1 total_weight= 1862.405 rmsd (weighted)= 3.483 (unweighted)= 57.529 superimposing iter= 2 total_weight= 1029.958 rmsd (weighted)= 3.195 (unweighted)= 57.428 superimposing iter= 3 total_weight= 905.866 rmsd (weighted)= 3.130 (unweighted)= 57.382 superimposing iter= 4 total_weight= 880.330 rmsd (weighted)= 3.111 (unweighted)= 57.359 superimposing iter= 5 total_weight= 874.597 rmsd (weighted)= 3.103 (unweighted)= 57.345 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.957 rmsd (weighted)= 4.881 (unweighted)= 34.364 superimposing iter= 1 total_weight= 1738.109 rmsd (weighted)= 3.277 (unweighted)= 34.317 superimposing iter= 2 total_weight= 933.379 rmsd (weighted)= 3.037 (unweighted)= 34.280 superimposing iter= 3 total_weight= 845.015 rmsd (weighted)= 2.964 (unweighted)= 34.257 superimposing iter= 4 total_weight= 824.647 rmsd (weighted)= 2.929 (unweighted)= 34.246 superimposing iter= 5 total_weight= 816.742 rmsd (weighted)= 2.909 (unweighted)= 34.241 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.901 rmsd (weighted)= 4.538 (unweighted)= 23.788 superimposing iter= 1 total_weight= 1826.833 rmsd (weighted)= 2.874 (unweighted)= 23.805 superimposing iter= 2 total_weight= 926.962 rmsd (weighted)= 2.588 (unweighted)= 23.809 superimposing iter= 3 total_weight= 821.158 rmsd (weighted)= 2.481 (unweighted)= 23.792 superimposing iter= 4 total_weight= 790.171 rmsd (weighted)= 2.425 (unweighted)= 23.769 superimposing iter= 5 total_weight= 777.503 rmsd (weighted)= 2.389 (unweighted)= 23.747 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.855 rmsd (weighted)= 4.414 (unweighted)= 78.116 superimposing iter= 1 total_weight= 1635.474 rmsd (weighted)= 2.892 (unweighted)= 78.174 superimposing iter= 2 total_weight= 839.703 rmsd (weighted)= 2.671 (unweighted)= 78.161 superimposing iter= 3 total_weight= 752.091 rmsd (weighted)= 2.609 (unweighted)= 78.155 superimposing iter= 4 total_weight= 735.369 rmsd (weighted)= 2.577 (unweighted)= 78.155 superimposing iter= 5 total_weight= 731.997 rmsd (weighted)= 2.552 (unweighted)= 78.158 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.300 rmsd (weighted)= 11.953 (unweighted)= 26.261 superimposing iter= 1 total_weight= 3257.901 rmsd (weighted)= 6.580 (unweighted)= 26.022 superimposing iter= 2 total_weight= 1513.668 rmsd (weighted)= 5.534 (unweighted)= 26.013 superimposing iter= 3 total_weight= 1214.716 rmsd (weighted)= 5.237 (unweighted)= 26.024 superimposing iter= 4 total_weight= 1127.227 rmsd (weighted)= 5.151 (unweighted)= 26.030 superimposing iter= 5 total_weight= 1104.095 rmsd (weighted)= 5.121 (unweighted)= 26.031 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.192 rmsd (weighted)= 9.995 (unweighted)= 28.968 superimposing iter= 1 total_weight= 2218.745 rmsd (weighted)= 6.562 (unweighted)= 28.956 superimposing iter= 2 total_weight= 1244.140 rmsd (weighted)= 5.841 (unweighted)= 28.973 superimposing iter= 3 total_weight= 1122.195 rmsd (weighted)= 5.501 (unweighted)= 28.981 superimposing iter= 4 total_weight= 1062.985 rmsd (weighted)= 5.330 (unweighted)= 28.978 superimposing iter= 5 total_weight= 1032.454 rmsd (weighted)= 5.243 (unweighted)= 28.967 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.145 rmsd (weighted)= 10.938 (unweighted)= 37.364 superimposing iter= 1 total_weight= 2069.146 rmsd (weighted)= 7.372 (unweighted)= 36.995 superimposing iter= 2 total_weight= 1086.467 rmsd (weighted)= 6.932 (unweighted)= 36.824 superimposing iter= 3 total_weight= 1013.799 rmsd (weighted)= 6.756 (unweighted)= 36.727 superimposing iter= 4 total_weight= 1011.881 rmsd (weighted)= 6.591 (unweighted)= 36.658 superimposing iter= 5 total_weight= 1013.825 rmsd (weighted)= 6.423 (unweighted)= 36.606 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.939 rmsd (weighted)= 10.518 (unweighted)= 62.384 superimposing iter= 1 total_weight= 2359.580 rmsd (weighted)= 5.749 (unweighted)= 62.314 superimposing iter= 2 total_weight= 1220.096 rmsd (weighted)= 4.541 (unweighted)= 62.175 superimposing iter= 3 total_weight= 977.746 rmsd (weighted)= 4.041 (unweighted)= 62.075 superimposing iter= 4 total_weight= 889.625 rmsd (weighted)= 3.784 (unweighted)= 61.998 superimposing iter= 5 total_weight= 842.152 rmsd (weighted)= 3.648 (unweighted)= 61.933 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 9.524 (unweighted)= 21.425 superimposing iter= 1 total_weight= 2002.473 rmsd (weighted)= 6.523 (unweighted)= 21.366 superimposing iter= 2 total_weight= 1098.121 rmsd (weighted)= 6.078 (unweighted)= 21.302 superimposing iter= 3 total_weight= 991.968 rmsd (weighted)= 5.966 (unweighted)= 21.251 superimposing iter= 4 total_weight= 972.453 rmsd (weighted)= 5.916 (unweighted)= 21.206 superimposing iter= 5 total_weight= 969.343 rmsd (weighted)= 5.875 (unweighted)= 21.169 superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 7.499 (unweighted)= 23.059 superimposing iter= 1 total_weight= 3147.265 rmsd (weighted)= 4.226 (unweighted)= 23.151 superimposing iter= 2 total_weight= 1335.890 rmsd (weighted)= 3.739 (unweighted)= 23.168 superimposing iter= 3 total_weight= 1137.532 rmsd (weighted)= 3.597 (unweighted)= 23.165 superimposing iter= 4 total_weight= 1099.906 rmsd (weighted)= 3.521 (unweighted)= 23.160 superimposing iter= 5 total_weight= 1100.555 rmsd (weighted)= 3.446 (unweighted)= 23.158 superimposing iter= 0 total_weight= 1.039 rmsd (weighted)= 5.181 (unweighted)= 57.882 superimposing iter= 1 total_weight= 1854.673 rmsd (weighted)= 3.500 (unweighted)= 57.612 superimposing iter= 2 total_weight= 1025.389 rmsd (weighted)= 3.219 (unweighted)= 57.509 superimposing iter= 3 total_weight= 906.374 rmsd (weighted)= 3.153 (unweighted)= 57.462 superimposing iter= 4 total_weight= 882.407 rmsd (weighted)= 3.131 (unweighted)= 57.437 superimposing iter= 5 total_weight= 875.906 rmsd (weighted)= 3.121 (unweighted)= 57.423 superimposing iter= 0 total_weight= 0.957 rmsd (weighted)= 4.897 (unweighted)= 34.225 superimposing iter= 1 total_weight= 1762.478 rmsd (weighted)= 3.271 (unweighted)= 34.175 superimposing iter= 2 total_weight= 925.856 rmsd (weighted)= 3.046 (unweighted)= 34.137 superimposing iter= 3 total_weight= 835.987 rmsd (weighted)= 2.990 (unweighted)= 34.115 superimposing iter= 4 total_weight= 823.622 rmsd (weighted)= 2.958 (unweighted)= 34.103 superimposing iter= 5 total_weight= 812.969 rmsd (weighted)= 2.945 (unweighted)= 34.097 superimposing iter= 0 total_weight= 0.901 rmsd (weighted)= 4.565 (unweighted)= 24.158 superimposing iter= 1 total_weight= 1838.311 rmsd (weighted)= 2.878 (unweighted)= 24.140 superimposing iter= 2 total_weight= 940.864 rmsd (weighted)= 2.572 (unweighted)= 24.127 superimposing iter= 3 total_weight= 811.298 rmsd (weighted)= 2.480 (unweighted)= 24.104 superimposing iter= 4 total_weight= 781.447 rmsd (weighted)= 2.437 (unweighted)= 24.077 superimposing iter= 5 total_weight= 777.047 rmsd (weighted)= 2.402 (unweighted)= 24.055 superimposing iter= 0 total_weight= 0.855 rmsd (weighted)= 4.442 (unweighted)= 78.130 superimposing iter= 1 total_weight= 1612.622 rmsd (weighted)= 2.935 (unweighted)= 78.184 superimposing iter= 2 total_weight= 834.300 rmsd (weighted)= 2.721 (unweighted)= 78.179 superimposing iter= 3 total_weight= 748.176 rmsd (weighted)= 2.666 (unweighted)= 78.179 superimposing iter= 4 total_weight= 731.295 rmsd (weighted)= 2.641 (unweighted)= 78.181 superimposing iter= 5 total_weight= 725.809 rmsd (weighted)= 2.627 (unweighted)= 78.183 superimposing iter= 0 total_weight= 1.300 rmsd (weighted)= 11.803 (unweighted)= 26.249 superimposing iter= 1 total_weight= 3358.422 rmsd (weighted)= 6.394 (unweighted)= 25.972 superimposing iter= 2 total_weight= 1534.263 rmsd (weighted)= 5.347 (unweighted)= 25.950 superimposing iter= 3 total_weight= 1205.717 rmsd (weighted)= 5.078 (unweighted)= 25.952 superimposing iter= 4 total_weight= 1129.851 rmsd (weighted)= 4.989 (unweighted)= 25.952 superimposing iter= 5 total_weight= 1101.428 rmsd (weighted)= 4.967 (unweighted)= 25.949 superimposing iter= 0 total_weight= 1.192 rmsd (weighted)= 9.866 (unweighted)= 28.956 superimposing iter= 1 total_weight= 2281.071 rmsd (weighted)= 6.388 (unweighted)= 28.987 superimposing iter= 2 total_weight= 1256.113 rmsd (weighted)= 5.663 (unweighted)= 29.028 superimposing iter= 3 total_weight= 1110.354 rmsd (weighted)= 5.361 (unweighted)= 29.047 superimposing iter= 4 total_weight= 1048.754 rmsd (weighted)= 5.226 (unweighted)= 29.051 superimposing iter= 5 total_weight= 1021.489 rmsd (weighted)= 5.164 (unweighted)= 29.048 superimposing iter= 0 total_weight= 1.145 rmsd (weighted)= 10.909 (unweighted)= 37.490 superimposing iter= 1 total_weight= 2055.425 rmsd (weighted)= 7.390 (unweighted)= 37.128 superimposing iter= 2 total_weight= 1094.662 rmsd (weighted)= 6.922 (unweighted)= 36.946 superimposing iter= 3 total_weight= 1028.763 rmsd (weighted)= 6.693 (unweighted)= 36.835 superimposing iter= 4 total_weight= 1028.169 rmsd (weighted)= 6.473 (unweighted)= 36.759 superimposing iter= 5 total_weight= 1029.597 rmsd (weighted)= 6.254 (unweighted)= 36.707 superimposing iter= 0 total_weight= 0.939 rmsd (weighted)= 10.538 (unweighted)= 62.363 superimposing iter= 1 total_weight= 2321.634 rmsd (weighted)= 5.826 (unweighted)= 62.298 superimposing iter= 2 total_weight= 1175.729 rmsd (weighted)= 4.693 (unweighted)= 62.173 superimposing iter= 3 total_weight= 963.075 rmsd (weighted)= 4.209 (unweighted)= 62.093 superimposing iter= 4 total_weight= 886.061 rmsd (weighted)= 3.950 (unweighted)= 62.036 superimposing iter= 5 total_weight= 838.912 rmsd (weighted)= 3.815 (unweighted)= 61.989 superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 9.375 (unweighted)= 21.490 superimposing iter= 1 total_weight= 1992.655 rmsd (weighted)= 6.431 (unweighted)= 21.451 superimposing iter= 2 total_weight= 1103.881 rmsd (weighted)= 5.979 (unweighted)= 21.400 superimposing iter= 3 total_weight= 991.856 rmsd (weighted)= 5.872 (unweighted)= 21.364 superimposing iter= 4 total_weight= 969.719 rmsd (weighted)= 5.835 (unweighted)= 21.337 superimposing iter= 5 total_weight= 964.020 rmsd (weighted)= 5.816 (unweighted)= 21.316 # command:# Printing sheets for alignments to T0517.undertaker-align.sheets # command: