# command:# Seed set to 1276594524 # 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= 24.181 sec, elapsed time= 29.552 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= 37.376 sec, elapsed time= 46.451 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0581 numbered 1 through 136 Created new target T0581 from T0581.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.376 sec, elapsed time= 46.453 sec. # command:# Prefix for input files set to # command:# reading script from file T0581.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w9yA/T0581-1w9yA-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 1w9yA expands to /projects/compbio/data/pdb/1w9y.pdb.gz 1w9yA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0581 read from 1w9yA/T0581-1w9yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w9yA read from 1w9yA/T0581-1w9yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w9yA to template set # found chain 1w9yA in template set T0581 3 :RFMALALCFVLPTAAHAA 1w9yA 43 :REVMDTVEKMTKGHYKKC # choosing archetypes in rotamer library T0581 23 :KDFELSKMLEKVAKES 1w9yA 61 :MEQRFKELVASKALEG T0581 42 :TPRAIN 1w9yA 77 :VQAEVT T0581 50 :IL 1w9yA 83 :DM T0581 56 :TVEGNQLINHL 1w9yA 85 :DWESTFFLKHL T0581 68 :VRASHAERMRSNPDSVRS 1w9yA 106 :LDEEYREVMRDFAKRLEK T0581 86 :QLGDSVCSN 1w9yA 127 :ELLDLLCEN T0581 95 :TGYRQLLA 1w9yA 141 :GYLKNAFY T0581 103 :RGAILTYSFTEYKTNQP 1w9yA 151 :KGPNFGTKVSNYPPCPK T0581 122 :TERFDAG 1w9yA 168 :PDLIKGL Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_2030983689.pdb -s /var/tmp/to_scwrl_2030983689.seq -o /var/tmp/from_scwrl_2030983689.pdb > /var/tmp/scwrl_2030983689.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2030983689.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ko6A/T0581-2ko6A-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 2ko6A expands to /projects/compbio/data/pdb/2ko6.pdb.gz 2ko6A:# T0581 read from 2ko6A/T0581-2ko6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ko6A read from 2ko6A/T0581-2ko6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ko6A to template set # found chain 2ko6A in template set Warning: unaligning (T0581)P14 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2ko6A)P15 Warning: unaligning (T0581)T15 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2ko6A)P15 T0581 12 :VL 2ko6A 12 :LL T0581 16 :AAH 2ko6A 16 :AWQ T0581 21 :SLKDFELSKMLEKVAKESS 2ko6A 19 :KEPDFNLLQFLQKLAKESG T0581 40 :VGTPRAINEDIL 2ko6A 39 :DGELADLTDDIL T0581 84 :RSQL 2ko6A 51 :IYHL Number of specific fragments extracted= 5 number of extra gaps= 1 total=15 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_1911247706.pdb -s /var/tmp/to_scwrl_1911247706.seq -o /var/tmp/from_scwrl_1911247706.pdb > /var/tmp/scwrl_1911247706.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1911247706.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dy0A/T0581-3dy0A-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 3dy0A expands to /projects/compbio/data/pdb/3dy0.pdb.gz 3dy0A:Skipped atom 4, because occupancy 0.5 <= existing 0.500 in 3dy0A Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 242, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1132, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1134, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1146, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1408, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1410, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1412, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1414, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1882, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1884, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1886, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1888, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1897, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1899, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1901, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1903, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1905, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1922, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1924, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1926, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1953, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1955, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1961, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2246, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2248, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2250, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2252, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2254, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2256, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2258, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2260, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2262, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2285, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2308, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2310, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2312, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2314, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2316, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2318, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2498, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2500, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2502, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2504, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2506, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2520, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2522, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2524, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2605, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2607, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2609, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2611, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2613, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2615, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2617, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2690, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2692, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2694, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2696, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2698, because occupancy 0.500 <= existing 0.500 in 3dy0A Skipped atom 2700, because occupancy 0.500 <= existing 0.500 in 3dy0A # T0581 read from 3dy0A/T0581-3dy0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dy0A read from 3dy0A/T0581-3dy0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dy0A to template set # found chain 3dy0A in template set T0581 2 :SRFMALALCFVLPTAAHAA 3dy0A 53 :ISMSLAMLSLGAGSSTKMQ T0581 21 :SLKDFELSKMLEKVAKESSVGTP 3dy0A 82 :KSSEKELHRGFQQLLQELNQPRD T0581 54 :GYTVE 3dy0A 105 :GFQLS T0581 59 :GNQLINH 3dy0A 111 :GNALFTD T0581 66 :LSVRASHAERMRS 3dy0A 120 :VDLQDTFVSAMKT T0581 79 :NPDSVRSQLGDSVC 3dy0A 145 :DSAGAMKQINDYVA T0581 100 :LLARG 3dy0A 159 :KQTKG T0581 106 :ILTYSFTEYKTNQPVATERFDAGSCRIQGKK 3dy0A 180 :MVNYIFFKAKWETSFNHKGTQEQDFYVTSET Number of specific fragments extracted= 8 number of extra gaps= 0 total=23 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_1130501576.pdb -s /var/tmp/to_scwrl_1130501576.seq -o /var/tmp/from_scwrl_1130501576.pdb > /var/tmp/scwrl_1130501576.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1130501576.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f8mA/T0581-3f8mA-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 3f8mA expands to /projects/compbio/data/pdb/3f8m.pdb.gz 3f8mA:Skipped atom 135, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 139, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 141, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 143, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 145, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 147, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 149, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 151, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 510, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 514, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 516, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 518, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 520, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 524, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 3f8mA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 965, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 969, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 971, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 973, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 975, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1027, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1031, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1033, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1035, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1037, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1039, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1085, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1089, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 3f8mA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 3f8mA Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 3f8mA # T0581 read from 3f8mA/T0581-3f8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f8mA read from 3f8mA/T0581-3f8mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f8mA to template set # found chain 3f8mA in template set Warning: unaligning (T0581)L22 because first residue in template chain is (3f8mA)L10 T0581 23 :KDFELSKMLEKVAKESSVGTPRAINEDI 3f8mA 11 :KHQVVRAELDRMLDGMRIGDPFPAEREI T0581 73 :AERMRSNPDSVRSQL 3f8mA 39 :AEQFEVARETVRQAL T0581 98 :RQLLARGAIL 3f8mA 54 :RELLIDGRVE T0581 114 :YKTNQPVAT 3f8mA 64 :RRGRTTVVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=27 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_873845385.pdb -s /var/tmp/to_scwrl_873845385.seq -o /var/tmp/from_scwrl_873845385.pdb > /var/tmp/scwrl_873845385.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_873845385.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zk7A/T0581-2zk7A-simplesw-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2zk7A expands to /projects/compbio/data/pdb/2zk7.pdb.gz 2zk7A:# T0581 read from 2zk7A/T0581-2zk7A-simplesw-adpstyle1.a2m # 2zk7A read from 2zk7A/T0581-2zk7A-simplesw-adpstyle1.a2m # adding 2zk7A to template set # found chain 2zk7A in template set T0581 34 :VAKESSVGTPRAINEDILDQGYTVEGNQLINHLSVRASHAERMRSNPDSVRSQL 2zk7A 11 :IVTGASMGIGRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASI Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_2033948937.pdb -s /var/tmp/to_scwrl_2033948937.seq -o /var/tmp/from_scwrl_2033948937.pdb > /var/tmp/scwrl_2033948937.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2033948937.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g20E/1cp2A-T0581-fssp-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g20E expands to /projects/compbio/data/pdb/1g20.pdb.gz 1g20E:# T0581 read from 1g20E/1cp2A-T0581-fssp-local-adpstyle5.a2m # 1g20E read from 1g20E/1cp2A-T0581-fssp-local-adpstyle5.a2m # adding 1g20E to template set # found chain 1g20E in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2vk1A/T0581-2vk1A-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2vk1A expands to /projects/compbio/data/pdb/2vk1.pdb.gz 2vk1A:# T0581 read from 2vk1A/T0581-2vk1A-t04-global-adpstyle1.a2m # 2vk1A read from 2vk1A/T0581-2vk1A-t04-global-adpstyle1.a2m # adding 2vk1A to template set # found chain 2vk1A in template set Warning: unaligning (T0581)S2 because first residue in template chain is (2vk1A)S2 T0581 3 :RFMALALCF 2vk1A 3 :EITLGKYLF T0581 29 :KMLEKVAKESSVGTPRAINEDILDQGYTVEGNQL 2vk1A 12 :ERLKQVNVNTVFGLPGAFNLSLLDKIYEVEGMRW T0581 63 :INHLSVRASHAERMRSNPDSVRSQLGDSV 2vk1A 76 :VGELSALNGIAGSYAEHVGVLHVVGVPSI T0581 94 :NTGYRQLLARGAILTYSFTEYKTNQP 2vk1A 105 :SAQAKQLLLHHTLGNGDFTVFHRMSA T0581 120 :VATERFDAGSCRIQGKK 2vk1A 142 :IATAPAEIDRCIRTTYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=33 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_91522424.pdb -s /var/tmp/to_scwrl_91522424.seq -o /var/tmp/from_scwrl_91522424.pdb > /var/tmp/scwrl_91522424.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_91522424.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w93A/T0581-2w93A-t04-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2w93A expands to /projects/compbio/data/pdb/2w93.pdb.gz 2w93A:# T0581 read from 2w93A/T0581-2w93A-t04-global-adpstyle1.a2m # 2w93A read from 2w93A/T0581-2w93A-t04-global-adpstyle1.a2m # adding 2w93A to template set # found chain 2w93A in template set Warning: unaligning (T0581)S2 because first residue in template chain is (2w93A)S2 T0581 3 :RFMALALCF 2w93A 3 :EITLGKYLF T0581 29 :KMLEKVAKESSVGTPRAINEDILDQGYTVEGNQL 2w93A 12 :ERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRW T0581 63 :INHLSVRASHAERMRSNPDSVRSQLGDSV 2w93A 76 :VGELSALNGIAGSYAEHVGVLHVVGVPSI T0581 94 :NTGYRQLLARGAILTYSFTEYKTNQP 2w93A 105 :SSQAKQLLLHHTLGNGDFTVFHRMSA T0581 120 :VATERFDAGSCRIQGKK 2w93A 142 :IATAPAEIDRCIRTTYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=38 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_1939556538.pdb -s /var/tmp/to_scwrl_1939556538.seq -o /var/tmp/from_scwrl_1939556538.pdb > /var/tmp/scwrl_1939556538.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1939556538.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fzdA/T0581-1fzdA-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 1fzdA expands to /projects/compbio/data/pdb/1fzd.pdb.gz 1fzdA:# T0581 read from 1fzdA/T0581-1fzdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fzdA read from 1fzdA/T0581-1fzdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fzdA to template set # found chain 1fzdA in template set T0581 93 :SNTGYRQLLARGAILTYSFTEYKTNQP 1fzdA 691 :GNDYLHLLTQRGSVLRVELEDWAGNEA Number of specific fragments extracted= 1 number of extra gaps= 0 total=39 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_358196947.pdb -s /var/tmp/to_scwrl_358196947.seq -o /var/tmp/from_scwrl_358196947.pdb > /var/tmp/scwrl_358196947.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_358196947.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3huiA/T0581-3huiA-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 3huiA expands to /projects/compbio/data/pdb/3hui.pdb.gz 3huiA:# T0581 read from 3huiA/T0581-3huiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3huiA read from 3huiA/T0581-3huiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3huiA to template set # found chain 3huiA in template set T0581 41 :GTPRAINEDILDQGYTVEGN 3huiA 61 :GGPSPMEEDMLDFGYDVRPN T0581 61 :QLINHLSVRAS 3huiA 82 :RLSCQIKVSNE T0581 102 :ARGAILT 3huiA 93 :LDGLIVT Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 # request to SCWRL produces command: ulimit -t 123 ; scwrl4 -t -i /var/tmp/to_scwrl_1688225683.pdb -s /var/tmp/to_scwrl_1688225683.seq -o /var/tmp/from_scwrl_1688225683.pdb > /var/tmp/scwrl_1688225683.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1688225683.pdb Number of alignments=9 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.260 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 8730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 8730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 8730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 8730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 8730.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.375 rmsd (weighted)= 13.412 (unweighted)= 45.985 superimposing iter= 1 total_weight= 743.338 rmsd (weighted)= 7.175 (unweighted)= 50.471 superimposing iter= 2 total_weight= 463.618 rmsd (weighted)= 5.240 (unweighted)= 51.433 superimposing iter= 3 total_weight= 312.951 rmsd (weighted)= 4.744 (unweighted)= 51.464 superimposing iter= 4 total_weight= 275.522 rmsd (weighted)= 4.591 (unweighted)= 51.348 superimposing iter= 5 total_weight= 269.000 rmsd (weighted)= 4.506 (unweighted)= 51.209 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.102 rmsd (weighted)= 16.022 (unweighted)= 42.577 superimposing iter= 1 total_weight= 1609.877 rmsd (weighted)= 10.927 (unweighted)= 41.927 superimposing iter= 2 total_weight= 824.755 rmsd (weighted)= 10.492 (unweighted)= 41.700 superimposing iter= 3 total_weight= 778.925 rmsd (weighted)= 10.377 (unweighted)= 41.634 superimposing iter= 4 total_weight= 771.017 rmsd (weighted)= 10.317 (unweighted)= 41.617 superimposing iter= 5 total_weight= 768.494 rmsd (weighted)= 10.275 (unweighted)= 41.614 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.630 rmsd (weighted)= 19.544 (unweighted)= 57.404 superimposing iter= 1 total_weight= 596.198 rmsd (weighted)= 16.227 (unweighted)= 64.139 superimposing iter= 2 total_weight= 549.128 rmsd (weighted)= 14.245 (unweighted)= 69.194 superimposing iter= 3 total_weight= 516.214 rmsd (weighted)= 12.912 (unweighted)= 72.587 superimposing iter= 4 total_weight= 496.668 rmsd (weighted)= 11.954 (unweighted)= 74.354 superimposing iter= 5 total_weight= 485.155 rmsd (weighted)= 11.207 (unweighted)= 75.375 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.495 rmsd (weighted)= 14.972 (unweighted)= 113.782 superimposing iter= 1 total_weight= 733.470 rmsd (weighted)= 9.952 (unweighted)= 111.323 superimposing iter= 2 total_weight= 403.821 rmsd (weighted)= 9.114 (unweighted)= 110.095 superimposing iter= 3 total_weight= 352.495 rmsd (weighted)= 8.958 (unweighted)= 109.412 superimposing iter= 4 total_weight= 349.965 rmsd (weighted)= 8.844 (unweighted)= 109.093 superimposing iter= 5 total_weight= 354.365 rmsd (weighted)= 8.682 (unweighted)= 109.026 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.079 rmsd (weighted)= 18.462 (unweighted)= 46.902 superimposing iter= 1 total_weight= 1853.907 rmsd (weighted)= 11.389 (unweighted)= 46.763 superimposing iter= 2 total_weight= 1008.585 rmsd (weighted)= 9.701 (unweighted)= 46.679 superimposing iter= 3 total_weight= 843.703 rmsd (weighted)= 9.071 (unweighted)= 46.618 superimposing iter= 4 total_weight= 794.875 rmsd (weighted)= 8.752 (unweighted)= 46.549 superimposing iter= 5 total_weight= 777.543 rmsd (weighted)= 8.544 (unweighted)= 46.472 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.079 rmsd (weighted)= 18.452 (unweighted)= 37.734 superimposing iter= 1 total_weight= 1859.623 rmsd (weighted)= 11.364 (unweighted)= 37.620 superimposing iter= 2 total_weight= 1007.757 rmsd (weighted)= 9.683 (unweighted)= 37.546 superimposing iter= 3 total_weight= 842.598 rmsd (weighted)= 9.060 (unweighted)= 37.490 superimposing iter= 4 total_weight= 796.280 rmsd (weighted)= 8.734 (unweighted)= 37.421 superimposing iter= 5 total_weight= 778.528 rmsd (weighted)= 8.522 (unweighted)= 37.334 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.311 rmsd (weighted)= 7.166 (unweighted)= 56.799 superimposing iter= 1 total_weight= 677.598 rmsd (weighted)= 3.697 (unweighted)= 56.591 superimposing iter= 2 total_weight= 344.295 rmsd (weighted)= 2.860 (unweighted)= 56.366 superimposing iter= 3 total_weight= 259.643 rmsd (weighted)= 2.576 (unweighted)= 56.086 superimposing iter= 4 total_weight= 242.799 rmsd (weighted)= 2.416 (unweighted)= 55.863 superimposing iter= 5 total_weight= 243.822 rmsd (weighted)= 2.267 (unweighted)= 55.741 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.329 rmsd (weighted)= 12.787 (unweighted)= 87.792 superimposing iter= 1 total_weight= 423.238 rmsd (weighted)= 9.033 (unweighted)= 88.172 superimposing iter= 2 total_weight= 282.553 rmsd (weighted)= 7.922 (unweighted)= 88.138 superimposing iter= 3 total_weight= 311.585 rmsd (weighted)= 6.576 (unweighted)= 87.992 superimposing iter= 4 total_weight= 322.075 rmsd (weighted)= 5.364 (unweighted)= 87.860 superimposing iter= 5 total_weight= 280.931 rmsd (weighted)= 4.705 (unweighted)= 87.735 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.260 rmsd (weighted)= 10.528 (unweighted)= 33.138 superimposing iter= 1 total_weight= 2306.485 rmsd (weighted)= 6.311 (unweighted)= 33.299 superimposing iter= 2 total_weight= 1133.963 rmsd (weighted)= 5.497 (unweighted)= 33.369 superimposing iter= 3 total_weight= 928.372 rmsd (weighted)= 5.305 (unweighted)= 33.403 superimposing iter= 4 total_weight= 883.512 rmsd (weighted)= 5.251 (unweighted)= 33.421 superimposing iter= 5 total_weight= 871.994 rmsd (weighted)= 5.233 (unweighted)= 33.431 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.448 rmsd (weighted)= 7.003 (unweighted)= 36.202 superimposing iter= 1 total_weight= 640.633 rmsd (weighted)= 4.769 (unweighted)= 36.048 superimposing iter= 2 total_weight= 371.504 rmsd (weighted)= 4.315 (unweighted)= 36.035 superimposing iter= 3 total_weight= 331.111 rmsd (weighted)= 4.145 (unweighted)= 36.054 superimposing iter= 4 total_weight= 319.686 rmsd (weighted)= 4.058 (unweighted)= 36.074 superimposing iter= 5 total_weight= 312.296 rmsd (weighted)= 4.019 (unweighted)= 36.089 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.302 rmsd (weighted)= 13.841 (unweighted)= 24.373 superimposing iter= 1 total_weight= 1686.451 rmsd (weighted)= 9.579 (unweighted)= 24.730 superimposing iter= 2 total_weight= 1261.484 rmsd (weighted)= 7.885 (unweighted)= 25.008 superimposing iter= 3 total_weight= 1092.939 rmsd (weighted)= 7.050 (unweighted)= 25.136 superimposing iter= 4 total_weight= 992.004 rmsd (weighted)= 6.644 (unweighted)= 25.180 superimposing iter= 5 total_weight= 936.479 rmsd (weighted)= 6.454 (unweighted)= 25.190 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.700 rmsd (weighted)= 11.380 (unweighted)= 60.223 superimposing iter= 1 total_weight= 897.247 rmsd (weighted)= 7.985 (unweighted)= 62.281 superimposing iter= 2 total_weight= 678.653 rmsd (weighted)= 6.580 (unweighted)= 63.237 superimposing iter= 3 total_weight= 593.902 rmsd (weighted)= 5.881 (unweighted)= 63.579 superimposing iter= 4 total_weight= 514.927 rmsd (weighted)= 5.669 (unweighted)= 63.755 superimposing iter= 5 total_weight= 498.495 rmsd (weighted)= 5.563 (unweighted)= 63.864 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.603 rmsd (weighted)= 9.654 (unweighted)= 97.131 superimposing iter= 1 total_weight= 947.738 rmsd (weighted)= 6.167 (unweighted)= 97.541 superimposing iter= 2 total_weight= 528.465 rmsd (weighted)= 5.384 (unweighted)= 97.963 superimposing iter= 3 total_weight= 454.942 rmsd (weighted)= 5.096 (unweighted)= 98.353 superimposing iter= 4 total_weight= 444.726 rmsd (weighted)= 4.883 (unweighted)= 98.736 superimposing iter= 5 total_weight= 440.685 rmsd (weighted)= 4.697 (unweighted)= 99.104 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 10.393 (unweighted)= 30.854 superimposing iter= 1 total_weight= 1922.409 rmsd (weighted)= 6.947 (unweighted)= 31.109 superimposing iter= 2 total_weight= 1121.003 rmsd (weighted)= 6.165 (unweighted)= 31.269 superimposing iter= 3 total_weight= 986.222 rmsd (weighted)= 5.852 (unweighted)= 31.351 superimposing iter= 4 total_weight= 929.713 rmsd (weighted)= 5.725 (unweighted)= 31.392 superimposing iter= 5 total_weight= 907.135 rmsd (weighted)= 5.670 (unweighted)= 31.412 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 10.389 (unweighted)= 15.860 superimposing iter= 1 total_weight= 1905.579 rmsd (weighted)= 6.979 (unweighted)= 15.988 superimposing iter= 2 total_weight= 1112.303 rmsd (weighted)= 6.219 (unweighted)= 16.082 superimposing iter= 3 total_weight= 984.020 rmsd (weighted)= 5.910 (unweighted)= 16.130 superimposing iter= 4 total_weight= 928.573 rmsd (weighted)= 5.785 (unweighted)= 16.153 superimposing iter= 5 total_weight= 906.438 rmsd (weighted)= 5.732 (unweighted)= 16.164 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.311 rmsd (weighted)= 7.900 (unweighted)= 48.682 superimposing iter= 1 total_weight= 507.157 rmsd (weighted)= 5.029 (unweighted)= 48.936 superimposing iter= 2 total_weight= 295.234 rmsd (weighted)= 4.276 (unweighted)= 49.104 superimposing iter= 3 total_weight= 243.549 rmsd (weighted)= 4.012 (unweighted)= 49.263 superimposing iter= 4 total_weight= 226.969 rmsd (weighted)= 3.901 (unweighted)= 49.368 superimposing iter= 5 total_weight= 222.317 rmsd (weighted)= 3.836 (unweighted)= 49.439 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.417 rmsd (weighted)= 7.087 (unweighted)= 70.650 superimposing iter= 1 total_weight= 496.403 rmsd (weighted)= 5.270 (unweighted)= 70.637 superimposing iter= 2 total_weight= 324.053 rmsd (weighted)= 4.918 (unweighted)= 70.645 superimposing iter= 3 total_weight= 295.649 rmsd (weighted)= 4.816 (unweighted)= 70.637 superimposing iter= 4 total_weight= 289.606 rmsd (weighted)= 4.769 (unweighted)= 70.626 superimposing iter= 5 total_weight= 287.900 rmsd (weighted)= 4.737 (unweighted)= 70.615 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.260 rmsd (weighted)= 11.162 (unweighted)= 33.597 superimposing iter= 1 total_weight= 2184.067 rmsd (weighted)= 6.887 (unweighted)= 33.817 superimposing iter= 2 total_weight= 1124.340 rmsd (weighted)= 6.010 (unweighted)= 33.866 superimposing iter= 3 total_weight= 951.974 rmsd (weighted)= 5.717 (unweighted)= 33.861 superimposing iter= 4 total_weight= 898.354 rmsd (weighted)= 5.604 (unweighted)= 33.848 superimposing iter= 5 total_weight= 878.563 rmsd (weighted)= 5.556 (unweighted)= 33.835 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.448 rmsd (weighted)= 6.953 (unweighted)= 35.149 superimposing iter= 1 total_weight= 673.277 rmsd (weighted)= 4.592 (unweighted)= 34.984 superimposing iter= 2 total_weight= 380.184 rmsd (weighted)= 4.102 (unweighted)= 34.900 superimposing iter= 3 total_weight= 323.565 rmsd (weighted)= 3.987 (unweighted)= 34.845 superimposing iter= 4 total_weight= 308.376 rmsd (weighted)= 3.973 (unweighted)= 34.801 superimposing iter= 5 total_weight= 305.652 rmsd (weighted)= 3.977 (unweighted)= 34.765 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.302 rmsd (weighted)= 13.695 (unweighted)= 23.744 superimposing iter= 1 total_weight= 1810.340 rmsd (weighted)= 9.130 (unweighted)= 24.049 superimposing iter= 2 total_weight= 1332.111 rmsd (weighted)= 7.321 (unweighted)= 24.262 superimposing iter= 3 total_weight= 1107.897 rmsd (weighted)= 6.505 (unweighted)= 24.354 superimposing iter= 4 total_weight= 984.545 rmsd (weighted)= 6.153 (unweighted)= 24.394 superimposing iter= 5 total_weight= 920.834 rmsd (weighted)= 6.024 (unweighted)= 24.413 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.700 rmsd (weighted)= 10.617 (unweighted)= 59.636 superimposing iter= 1 total_weight= 907.150 rmsd (weighted)= 7.398 (unweighted)= 60.922 superimposing iter= 2 total_weight= 700.816 rmsd (weighted)= 5.994 (unweighted)= 61.517 superimposing iter= 3 total_weight= 589.525 rmsd (weighted)= 5.357 (unweighted)= 61.749 superimposing iter= 4 total_weight= 528.902 rmsd (weighted)= 5.078 (unweighted)= 61.880 superimposing iter= 5 total_weight= 510.385 rmsd (weighted)= 4.912 (unweighted)= 61.957 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.603 rmsd (weighted)= 9.760 (unweighted)= 98.155 superimposing iter= 1 total_weight= 1000.310 rmsd (weighted)= 6.105 (unweighted)= 98.687 superimposing iter= 2 total_weight= 494.430 rmsd (weighted)= 5.506 (unweighted)= 99.140 superimposing iter= 3 total_weight= 471.817 rmsd (weighted)= 5.111 (unweighted)= 99.502 superimposing iter= 4 total_weight= 472.243 rmsd (weighted)= 4.743 (unweighted)= 99.832 superimposing iter= 5 total_weight= 466.457 rmsd (weighted)= 4.427 (unweighted)= 100.058 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 9.799 (unweighted)= 30.765 superimposing iter= 1 total_weight= 2076.127 rmsd (weighted)= 6.282 (unweighted)= 30.983 superimposing iter= 2 total_weight= 1157.585 rmsd (weighted)= 5.491 (unweighted)= 31.087 superimposing iter= 3 total_weight= 969.640 rmsd (weighted)= 5.259 (unweighted)= 31.140 superimposing iter= 4 total_weight= 919.067 rmsd (weighted)= 5.177 (unweighted)= 31.167 superimposing iter= 5 total_weight= 901.381 rmsd (weighted)= 5.146 (unweighted)= 31.180 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 9.806 (unweighted)= 15.731 superimposing iter= 1 total_weight= 2051.961 rmsd (weighted)= 6.328 (unweighted)= 15.892 superimposing iter= 2 total_weight= 1150.367 rmsd (weighted)= 5.548 (unweighted)= 15.974 superimposing iter= 3 total_weight= 970.061 rmsd (weighted)= 5.313 (unweighted)= 16.017 superimposing iter= 4 total_weight= 917.943 rmsd (weighted)= 5.232 (unweighted)= 16.038 superimposing iter= 5 total_weight= 902.019 rmsd (weighted)= 5.197 (unweighted)= 16.049 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.311 rmsd (weighted)= 7.505 (unweighted)= 49.948 superimposing iter= 1 total_weight= 491.288 rmsd (weighted)= 4.881 (unweighted)= 50.248 superimposing iter= 2 total_weight= 281.095 rmsd (weighted)= 4.252 (unweighted)= 50.458 superimposing iter= 3 total_weight= 243.840 rmsd (weighted)= 3.993 (unweighted)= 50.592 superimposing iter= 4 total_weight= 227.256 rmsd (weighted)= 3.891 (unweighted)= 50.678 superimposing iter= 5 total_weight= 221.520 rmsd (weighted)= 3.841 (unweighted)= 50.743 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.417 rmsd (weighted)= 6.796 (unweighted)= 70.800 superimposing iter= 1 total_weight= 506.770 rmsd (weighted)= 5.007 (unweighted)= 70.535 superimposing iter= 2 total_weight= 320.711 rmsd (weighted)= 4.691 (unweighted)= 70.395 superimposing iter= 3 total_weight= 295.465 rmsd (weighted)= 4.589 (unweighted)= 70.310 superimposing iter= 4 total_weight= 289.863 rmsd (weighted)= 4.535 (unweighted)= 70.251 superimposing iter= 5 total_weight= 287.487 rmsd (weighted)= 4.502 (unweighted)= 70.207 superimposing iter= 0 total_weight= 1.260 rmsd (weighted)= 11.383 (unweighted)= 33.728 superimposing iter= 1 total_weight= 2117.447 rmsd (weighted)= 7.137 (unweighted)= 33.952 superimposing iter= 2 total_weight= 1111.066 rmsd (weighted)= 6.265 (unweighted)= 33.985 superimposing iter= 3 total_weight= 941.801 rmsd (weighted)= 5.990 (unweighted)= 33.965 superimposing iter= 4 total_weight= 894.791 rmsd (weighted)= 5.880 (unweighted)= 33.943 superimposing iter= 5 total_weight= 877.779 rmsd (weighted)= 5.829 (unweighted)= 33.926 superimposing iter= 0 total_weight= 0.448 rmsd (weighted)= 6.933 (unweighted)= 34.838 superimposing iter= 1 total_weight= 708.283 rmsd (weighted)= 4.455 (unweighted)= 34.635 superimposing iter= 2 total_weight= 391.246 rmsd (weighted)= 3.922 (unweighted)= 34.491 superimposing iter= 3 total_weight= 329.098 rmsd (weighted)= 3.780 (unweighted)= 34.384 superimposing iter= 4 total_weight= 315.000 rmsd (weighted)= 3.727 (unweighted)= 34.301 superimposing iter= 5 total_weight= 309.804 rmsd (weighted)= 3.707 (unweighted)= 34.226 superimposing iter= 0 total_weight= 1.302 rmsd (weighted)= 13.713 (unweighted)= 23.565 superimposing iter= 1 total_weight= 1865.256 rmsd (weighted)= 9.014 (unweighted)= 23.814 superimposing iter= 2 total_weight= 1321.900 rmsd (weighted)= 7.262 (unweighted)= 23.988 superimposing iter= 3 total_weight= 1083.932 rmsd (weighted)= 6.522 (unweighted)= 24.074 superimposing iter= 4 total_weight= 963.966 rmsd (weighted)= 6.229 (unweighted)= 24.122 superimposing iter= 5 total_weight= 915.186 rmsd (weighted)= 6.114 (unweighted)= 24.150 superimposing iter= 0 total_weight= 0.700 rmsd (weighted)= 10.420 (unweighted)= 59.283 superimposing iter= 1 total_weight= 928.452 rmsd (weighted)= 7.197 (unweighted)= 60.191 superimposing iter= 2 total_weight= 673.410 rmsd (weighted)= 5.974 (unweighted)= 60.574 superimposing iter= 3 total_weight= 580.236 rmsd (weighted)= 5.390 (unweighted)= 60.810 superimposing iter= 4 total_weight= 532.622 rmsd (weighted)= 5.096 (unweighted)= 61.031 superimposing iter= 5 total_weight= 513.808 rmsd (weighted)= 4.913 (unweighted)= 61.223 superimposing iter= 0 total_weight= 0.603 rmsd (weighted)= 9.893 (unweighted)= 98.954 superimposing iter= 1 total_weight= 1085.404 rmsd (weighted)= 5.946 (unweighted)= 99.384 superimposing iter= 2 total_weight= 524.124 rmsd (weighted)= 5.224 (unweighted)= 99.663 superimposing iter= 3 total_weight= 467.874 rmsd (weighted)= 4.876 (unweighted)= 99.888 superimposing iter= 4 total_weight= 455.270 rmsd (weighted)= 4.611 (unweighted)= 100.061 superimposing iter= 5 total_weight= 446.553 rmsd (weighted)= 4.402 (unweighted)= 100.175 superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 9.594 (unweighted)= 30.692 superimposing iter= 1 total_weight= 2107.862 rmsd (weighted)= 6.093 (unweighted)= 30.870 superimposing iter= 2 total_weight= 1171.972 rmsd (weighted)= 5.289 (unweighted)= 30.942 superimposing iter= 3 total_weight= 970.153 rmsd (weighted)= 5.062 (unweighted)= 30.977 superimposing iter= 4 total_weight= 914.284 rmsd (weighted)= 4.993 (unweighted)= 30.995 superimposing iter= 5 total_weight= 898.439 rmsd (weighted)= 4.969 (unweighted)= 31.004 superimposing iter= 0 total_weight= 1.296 rmsd (weighted)= 9.607 (unweighted)= 15.660 superimposing iter= 1 total_weight= 2089.783 rmsd (weighted)= 6.134 (unweighted)= 15.804 superimposing iter= 2 total_weight= 1154.010 rmsd (weighted)= 5.363 (unweighted)= 15.871 superimposing iter= 3 total_weight= 967.309 rmsd (weighted)= 5.137 (unweighted)= 15.907 superimposing iter= 4 total_weight= 916.725 rmsd (weighted)= 5.059 (unweighted)= 15.925 superimposing iter= 5 total_weight= 899.801 rmsd (weighted)= 5.029 (unweighted)= 15.934 superimposing iter= 0 total_weight= 0.311 rmsd (weighted)= 7.484 (unweighted)= 50.146 superimposing iter= 1 total_weight= 486.374 rmsd (weighted)= 4.900 (unweighted)= 50.460 superimposing iter= 2 total_weight= 275.833 rmsd (weighted)= 4.316 (unweighted)= 50.645 superimposing iter= 3 total_weight= 242.150 rmsd (weighted)= 4.075 (unweighted)= 50.762 superimposing iter= 4 total_weight= 226.441 rmsd (weighted)= 3.984 (unweighted)= 50.842 superimposing iter= 5 total_weight= 221.205 rmsd (weighted)= 3.943 (unweighted)= 50.905 superimposing iter= 0 total_weight= 0.417 rmsd (weighted)= 6.691 (unweighted)= 71.024 superimposing iter= 1 total_weight= 523.651 rmsd (weighted)= 4.848 (unweighted)= 70.672 superimposing iter= 2 total_weight= 327.359 rmsd (weighted)= 4.495 (unweighted)= 70.446 superimposing iter= 3 total_weight= 300.400 rmsd (weighted)= 4.363 (unweighted)= 70.280 superimposing iter= 4 total_weight= 293.597 rmsd (weighted)= 4.286 (unweighted)= 70.138 superimposing iter= 5 total_weight= 288.547 rmsd (weighted)= 4.246 (unweighted)= 70.004 # command:# Printing sheets for alignments to T0581.undertaker-align.sheets # command: