# command:# Seed set to 1275251015 # 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= 23.315 sec, elapsed time= 23.821 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= 36.532 sec, elapsed time= 40.673 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0557 numbered 1 through 145 Created new target T0557 from T0557.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.533 sec, elapsed time= 40.675 sec. # command:# Prefix for input files set to # command:# reading script from file T0557.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lmmA/T0557-3lmmA-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 3lmmA expands to /projects/compbio/data/pdb/3lmm.pdb.gz 3lmmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0557 read from 3lmmA/T0557-3lmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmmA read from 3lmmA/T0557-3lmmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lmmA to template set # found chain 3lmmA in template set T0557 5 :TDLLDELNA 3lmmA 16 :IAQVESILA # choosing archetypes in rotamer library T0557 14 :VDESARIEAKRA 3lmmA 34 :TKETQSVDFKEE T0557 26 :SDMGKSVMETVIAFANEP 3lmmA 62 :PEAADKLADEVACMANTP T0557 46 :DGGYLLLGVD 3lmmA 80 :GGGALIVGIE T0557 60 :DKGD 3lmmA 90 :DKTG T0557 65 :VYRPVGLP 3lmmA 94 :RIIGTELD T0557 78 :QRDLASQCASML 3lmmA 102 :IDWLRQGIFTRI T0557 93 :LRPEMQLEQVGGKTLLVVYVPEA 3lmmA 115 :VAPDVVAKRVLGQRVLAIYVAAA T0557 119 :HKPIYKKA 3lmmA 138 :AEPIEDTS T0557 131 :GGAYRRIGSSDQRC 3lmmA 146 :DRLRWRVGDSCRPV Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1488424862.pdb -s /var/tmp/to_scwrl_1488424862.seq -o /var/tmp/from_scwrl_1488424862.pdb > /var/tmp/scwrl_1488424862.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1488424862.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wcuA/T0557-1wcuA-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 1wcuA expands to /projects/compbio/data/pdb/1wcu.pdb.gz 1wcuA:Skipped atom 258, because occupancy 0.5 <= existing 0.500 in 1wcuA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 668, because occupancy 0.000 <= existing 0.500 in 1wcuA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1wcuA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1wcuA # T0557 read from 1wcuA/T0557-1wcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wcuA read from 1wcuA/T0557-1wcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wcuA to template set # found chain 1wcuA in template set Warning: unaligning (T0557)R19 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)I48 Warning: unaligning (T0557)I20 because of BadResidue code BAD_PEPTIDE at template residue (1wcuA)I48 Warning: unaligning (T0557)T106 because of BadResidue code BAD_PEPTIDE in next template residue (1wcuA)F114 T0557 14 :VDESA 1wcuA 42 :PDEYG T0557 21 :EAKRA 1wcuA 49 :SLKNL T0557 26 :SDM 1wcuA 55 :SNY T0557 41 :NE 1wcuA 58 :YG T0557 46 :DGGYLLLGVDWAINDK 1wcuA 60 :KGGCIYLQVKTETEGL T0557 62 :GDTVYRPVGLPD 1wcuA 77 :KVQGVRGYDETE T0557 87 :SMLNVALRPEMQLEQV 1wcuA 91 :NVGSFRSSSDFTEYKF T0557 103 :GGK 1wcuA 110 :DEY T0557 107 :LLVVYVPEAD 1wcuA 116 :RIIVQDGPAS T0557 119 :HKPIYKK 1wcuA 126 :NIPIYMR T0557 132 :GAYRRIGSSD 1wcuA 133 :YIIYSTGSCD Number of specific fragments extracted= 11 number of extra gaps= 2 total=21 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1141510349.pdb -s /var/tmp/to_scwrl_1141510349.seq -o /var/tmp/from_scwrl_1141510349.pdb > /var/tmp/scwrl_1141510349.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1141510349.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzgA/T0557-1yzgA-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 1yzgA expands to /projects/compbio/data/pdb/1yzg.pdb.gz 1yzgA:# T0557 read from 1yzgA/T0557-1yzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yzgA read from 1yzgA/T0557-1yzgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yzgA to template set # found chain 1yzgA in template set Warning: unaligning (T0557)A86 because of BadResidue code BAD_PEPTIDE in next template residue (1yzgA)V42 Warning: unaligning (T0557)S87 because of BadResidue code BAD_PEPTIDE at template residue (1yzgA)V42 T0557 46 :DGGYLLLGV 1yzgA 16 :EHKVIIVGL T0557 67 :RPVG 1yzgA 25 :DNAG T0557 74 :PDKVQRDLASQC 1yzgA 29 :KTTILYQFLMNE T0557 88 :MLNVALRPEMQLEQVGGKTLLVVYVPEADVTH 1yzgA 43 :HTSPTIGSNVEEIVVKNTHFLMWDIGGQESLR Number of specific fragments extracted= 4 number of extra gaps= 1 total=25 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_676136152.pdb -s /var/tmp/to_scwrl_676136152.seq -o /var/tmp/from_scwrl_676136152.pdb > /var/tmp/scwrl_676136152.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_676136152.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vlmA/T0557-1vlmA-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 1vlmA expands to /projects/compbio/data/pdb/1vlm.pdb.gz 1vlmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1022, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 1vlmA Skipped atom 1032, because occupancy 0.500 <= existing 0.500 in 1vlmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0557 read from 1vlmA/T0557-1vlmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vlmA read from 1vlmA/T0557-1vlmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vlmA to template set # found chain 1vlmA in template set Warning: unaligning (T0557)V54 because of BadResidue code BAD_PEPTIDE in next template residue (1vlmA)V128 Warning: unaligning (T0557)D55 because of BadResidue code BAD_PEPTIDE at template residue (1vlmA)V128 Warning: unaligning (T0557)D63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1vlmA)V146 Warning: unaligning (T0557)R67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1vlmA)V146 Warning: unaligning (T0557)D73 because of BadResidue code BAD_PEPTIDE at template residue (1vlmA)S155 T0557 27 :DMGKSVMETVIAFA 1vlmA 104 :DDPERALKEAYRIL T0557 42 :E 1vlmA 118 :K T0557 46 :DGGYLLLG 1vlmA 119 :KGGYLIVG T0557 56 :WAI 1vlmA 129 :DRE T0557 60 :DKG 1vlmA 141 :NKE T0557 68 :PV 1vlmA 147 :FY T0557 70 :GL 1vlmA 150 :NA T0557 74 :PDK 1vlmA 156 :TEE T0557 81 :LASQCAS 1vlmA 159 :LMDLMRK T0557 88 :MLN 1vlmA 167 :GFE T0557 96 :EMQLEQV 1vlmA 170 :EFKVVQT T0557 113 :PEADVTHKPIYKKATGLPGGAYRRIG 1vlmA 180 :HPSELSEIEPVKEGYGEGAFVVIRGT Number of specific fragments extracted= 12 number of extra gaps= 2 total=37 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1121244246.pdb -s /var/tmp/to_scwrl_1121244246.seq -o /var/tmp/from_scwrl_1121244246.pdb > /var/tmp/scwrl_1121244246.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1121244246.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hh1A/T0557-1hh1A-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 1hh1A expands to /projects/compbio/data/pdb/1hh1.pdb.gz 1hh1A:Skipped atom 406, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 407, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 408, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 409, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 410, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 411, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 412, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 413, because occupancy 0.330 <= existing 0.670 in 1hh1A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1hh1A Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 1hh1A # T0557 read from 1hh1A/T0557-1hh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hh1A read from 1hh1A/T0557-1hh1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hh1A to template set # found chain 1hh1A in template set Warning: unaligning (T0557)D55 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hh1A)K93 Warning: unaligning (T0557)D60 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hh1A)K93 Warning: unaligning (T0557)N90 because last residue in template chain is (1hh1A)D140 T0557 27 :D 1hh1A 64 :G T0557 28 :MGKSVMETVIAFA 1hh1A 68 :VRREQAEGIIEFA T0557 46 :DGGYLLLGV 1hh1A 83 :SGGSLFLGV T0557 61 :KGDTVYRPV 1hh1A 94 :PGVLKFIPF T0557 70 :GLP 1hh1A 118 :EIE T0557 73 :DPDKVQRDLASQCASML 1hh1A 123 :DLEDLVRLVEAKISRTL Number of specific fragments extracted= 6 number of extra gaps= 1 total=43 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_929448628.pdb -s /var/tmp/to_scwrl_929448628.seq -o /var/tmp/from_scwrl_929448628.pdb > /var/tmp/scwrl_929448628.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_929448628.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3citA/T0557-3citA-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 3citA expands to /projects/compbio/data/pdb/3cit.pdb.gz 3citA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 445, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 447, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 449, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 451, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 453, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 455, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 457, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 459, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 461, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 3citA Skipped atom 962, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 964, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 966, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 968, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 970, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 972, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 974, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 976, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 978, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1187, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1191, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1193, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1195, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1197, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1199, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1201, because occupancy 0.400 <= existing 0.600 in 3citA Skipped atom 1203, because occupancy 0.400 <= existing 0.600 in 3citA # T0557 read from 3citA/T0557-3citA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3citA read from 3citA/T0557-3citA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3citA to template set # found chain 3citA in template set Warning: unaligning (T0557)I58 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3citA)N72 Warning: unaligning (T0557)G62 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3citA)N72 T0557 5 :TDLLDELNAVD 3citA 32 :VDTGQELIQLP T0557 27 :D 3citA 44 :E T0557 28 :MGKSVMETVIAF 3citA 46 :MRKCVLQRACAF T0557 43 :PGLDGGYLLL 3citA 58 :VAMDHGLLLE T0557 57 :A 3citA 68 :W T0557 63 :DTVYRPVGLP 3citA 73 :GVQTTARHGS T0557 74 :PDKV 3citA 83 :KERL T0557 87 :SMLNVALR 3citA 87 :STLETTAD T0557 95 :PEMQLEQVGGK 3citA 98 :IGPQWLERPGT T0557 106 :TLLVVYVPEAD 3citA 112 :CVLLLPLRGAD T0557 119 :HKP 3citA 123 :EGS T0557 131 :GGAYRRIGSSDQRC 3citA 126 :FGTLVLANSVAISA Number of specific fragments extracted= 12 number of extra gaps= 0 total=55 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_81039054.pdb -s /var/tmp/to_scwrl_81039054.seq -o /var/tmp/from_scwrl_81039054.pdb > /var/tmp/scwrl_81039054.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_81039054.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw7A/T0557-1hw7A-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 1hw7A expands to /projects/compbio/data/pdb/1hw7.pdb.gz 1hw7A:Skipped atom 702, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 704, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 706, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 708, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 710, because occupancy 0.480 <= existing 0.520 in 1hw7A Skipped atom 712, because occupancy 0.480 <= existing 0.520 in 1hw7A # T0557 read from 1hw7A/T0557-1hw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw7A read from 1hw7A/T0557-1hw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hw7A to template set # found chain 1hw7A in template set Warning: unaligning (T0557)S26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hw7A)E99 Warning: unaligning (T0557)D27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hw7A)E99 T0557 25 :A 1hw7A 97 :Q T0557 28 :MGK 1hw7A 100 :IPE T0557 31 :SVMETV 1hw7A 105 :DLKTLV T0557 46 :DGGYLLLGVDWA 1hw7A 111 :GNGYVVITITPS T0557 60 :DKGDT 1hw7A 123 :EGERY T0557 65 :VYRPVGLPD 1hw7A 129 :GVVGLEGDT T0557 77 :VQRDLASQCASMLNVALRPEMQLEQVGGKTLLVVYV 1hw7A 138 :LAACLEDYFMRSEQLPTRLFIRTGDVDGKPAAGGML Number of specific fragments extracted= 7 number of extra gaps= 1 total=62 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1533802387.pdb -s /var/tmp/to_scwrl_1533802387.seq -o /var/tmp/from_scwrl_1533802387.pdb > /var/tmp/scwrl_1533802387.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1533802387.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1skoB/T0557-1skoB-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 1skoB expands to /projects/compbio/data/pdb/1sko.pdb.gz 1skoB:# T0557 read from 1skoB/T0557-1skoB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1skoB read from 1skoB/T0557-1skoB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1skoB to template set # found chain 1skoB in template set Warning: unaligning (T0557)G29 because first residue in template chain is (1skoB)P3 Warning: unaligning (T0557)Y66 because of BadResidue code BAD_PEPTIDE in next template residue (1skoB)S34 Warning: unaligning (T0557)R67 because of BadResidue code BAD_PEPTIDE at template residue (1skoB)S34 Warning: unaligning (T0557)L71 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1skoB)T39 Warning: unaligning (T0557)P72 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1skoB)T39 Warning: unaligning (T0557)D73 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1skoB)D40 Warning: unaligning (T0557)N90 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1skoB)N58 Warning: unaligning (T0557)V91 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1skoB)N58 Warning: unaligning (T0557)A92 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1skoB)G59 Warning: unaligning (T0557)L93 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1skoB)N60 Warning: unaligning (T0557)R94 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1skoB)A62 T0557 30 :KSVMETVIA 1skoB 4 :KALTQVLSQ T0557 40 :ANE 1skoB 13 :ANT T0557 46 :DGGYLLLGVD 1skoB 16 :GGVQSTLLLN T0557 60 :DKGDT 1skoB 26 :NEGSL T0557 65 :V 1skoB 32 :A T0557 68 :PVG 1skoB 35 :GYG T0557 74 :PDKVQRDLASQCASML 1skoB 41 :ARVTAAIASNIWAAYD T0557 95 :PEMQLEQVGGKTLLVVYVP 1skoB 68 :LKFILMDCMEGRVAITRVA T0557 131 :GGAYRRIGSSDQ 1skoB 87 :NLLLCMYAKETV Number of specific fragments extracted= 9 number of extra gaps= 3 total=71 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1727179746.pdb -s /var/tmp/to_scwrl_1727179746.seq -o /var/tmp/from_scwrl_1727179746.pdb > /var/tmp/scwrl_1727179746.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1727179746.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pqzA/T0557-1pqzA-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 1pqzA expands to /projects/compbio/data/pdb/1pqz.pdb.gz 1pqzA:# T0557 read from 1pqzA/T0557-1pqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pqzA read from 1pqzA/T0557-1pqzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pqzA to template set # found chain 1pqzA in template set T0557 5 :TDLLDELNAVD 1pqzA 73 :QAELDKMQNNS T0557 16 :ESARIEAKRA 1pqzA 87 :GVKTVQLDVG T0557 26 :SD 1pqzA 99 :SK T0557 54 :VDWAINDKGD 1pqzA 101 :IEKHYAYDGN T0557 68 :PVGLP 1pqzA 111 :ETEDD T0557 73 :DPDKVQRDL 1pqzA 123 :RARDCQKKL T0557 82 :ASQCASML 1pqzA 135 :RKLVLASA T0557 91 :VALRPEMQLEQV 1pqzA 143 :VSPQLEVERRSS T0557 103 :GGKTLLVVYVPE 1pqzA 157 :EGGMRLRCFARD T0557 115 :AD 1pqzA 172 :AD T0557 119 :HKPIYKKATG 1pqzA 174 :LEIRWWKDDG T0557 129 :LPGGAYRRIG 1pqzA 202 :GQGLYQKHID Number of specific fragments extracted= 12 number of extra gaps= 0 total=83 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1057199336.pdb -s /var/tmp/to_scwrl_1057199336.seq -o /var/tmp/from_scwrl_1057199336.pdb > /var/tmp/scwrl_1057199336.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1057199336.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v2bA/T0557-1v2bA-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 # T0557 read from 1v2bA/T0557-1v2bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2bA read from 1v2bA/T0557-1v2bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v2bA in training set Warning: unaligning (T0557)A92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v2bA)A107 Warning: unaligning (T0557)E114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1v2bA)G141 Warning: unaligning (T0557)K120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1v2bA)G141 T0557 64 :TVYRPVGLPDPDKV 1v2bA 61 :VAITPTDKKSITDF T0557 78 :QRDLASQCAS 1v2bA 77 :PEQFLSQVDY T0557 93 :LR 1v2bA 108 :VA T0557 95 :PEMQLEQVGGKTLLVVYV 1v2bA 114 :LETSTAEVGGKQYYYLSI T0557 113 :P 1v2bA 134 :R T0557 121 :PIYKKAT 1v2bA 147 :VTATVND T0557 131 :GGAYRRI 1v2bA 154 :GKLYICK Number of specific fragments extracted= 7 number of extra gaps= 0 total=90 # request to SCWRL produces command: ulimit -t 131 ; scwrl4 -t -i /var/tmp/to_scwrl_1722658195.pdb -s /var/tmp/to_scwrl_1722658195.seq -o /var/tmp/from_scwrl_1722658195.pdb > /var/tmp/scwrl_1722658195.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1722658195.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.250 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 8990.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 8990.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 8990.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 8990.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 8990.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.843 rmsd (weighted)= 15.551 (unweighted)= 63.579 superimposing iter= 1 total_weight= 1445.045 rmsd (weighted)= 9.709 (unweighted)= 64.321 superimposing iter= 2 total_weight= 796.088 rmsd (weighted)= 8.343 (unweighted)= 64.690 superimposing iter= 3 total_weight= 691.481 rmsd (weighted)= 7.734 (unweighted)= 65.000 superimposing iter= 4 total_weight= 671.158 rmsd (weighted)= 7.303 (unweighted)= 65.254 superimposing iter= 5 total_weight= 663.096 rmsd (weighted)= 6.963 (unweighted)= 65.433 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.499 rmsd (weighted)= 13.272 (unweighted)= 55.079 superimposing iter= 1 total_weight= 808.452 rmsd (weighted)= 8.558 (unweighted)= 55.340 superimposing iter= 2 total_weight= 506.347 rmsd (weighted)= 7.061 (unweighted)= 55.175 superimposing iter= 3 total_weight= 467.653 rmsd (weighted)= 6.103 (unweighted)= 55.073 superimposing iter= 4 total_weight= 435.989 rmsd (weighted)= 5.483 (unweighted)= 55.006 superimposing iter= 5 total_weight= 418.277 rmsd (weighted)= 5.049 (unweighted)= 54.978 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.677 rmsd (weighted)= 15.969 (unweighted)= 85.642 superimposing iter= 1 total_weight= 1201.823 rmsd (weighted)= 9.168 (unweighted)= 84.011 superimposing iter= 2 total_weight= 1001.075 rmsd (weighted)= 5.814 (unweighted)= 83.616 superimposing iter= 3 total_weight= 797.509 rmsd (weighted)= 4.247 (unweighted)= 83.513 superimposing iter= 4 total_weight= 686.659 rmsd (weighted)= 3.423 (unweighted)= 83.531 superimposing iter= 5 total_weight= 573.189 rmsd (weighted)= 3.076 (unweighted)= 83.559 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.476 rmsd (weighted)= 11.046 (unweighted)= 60.988 superimposing iter= 1 total_weight= 642.451 rmsd (weighted)= 7.678 (unweighted)= 62.458 superimposing iter= 2 total_weight= 510.674 rmsd (weighted)= 6.111 (unweighted)= 62.964 superimposing iter= 3 total_weight= 451.160 rmsd (weighted)= 5.215 (unweighted)= 63.048 superimposing iter= 4 total_weight= 402.523 rmsd (weighted)= 4.737 (unweighted)= 63.040 superimposing iter= 5 total_weight= 361.692 rmsd (weighted)= 4.552 (unweighted)= 63.037 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.892 rmsd (weighted)= 15.943 (unweighted)= 70.574 superimposing iter= 1 total_weight= 1578.054 rmsd (weighted)= 9.820 (unweighted)= 67.264 superimposing iter= 2 total_weight= 865.505 rmsd (weighted)= 8.329 (unweighted)= 65.754 superimposing iter= 3 total_weight= 723.808 rmsd (weighted)= 7.774 (unweighted)= 65.125 superimposing iter= 4 total_weight= 666.719 rmsd (weighted)= 7.581 (unweighted)= 64.907 superimposing iter= 5 total_weight= 643.659 rmsd (weighted)= 7.529 (unweighted)= 64.814 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.671 rmsd (weighted)= 13.627 (unweighted)= 62.585 superimposing iter= 1 total_weight= 1047.347 rmsd (weighted)= 8.700 (unweighted)= 60.494 superimposing iter= 2 total_weight= 819.779 rmsd (weighted)= 6.224 (unweighted)= 60.886 superimposing iter= 3 total_weight= 827.759 rmsd (weighted)= 4.569 (unweighted)= 61.888 superimposing iter= 4 total_weight= 643.141 rmsd (weighted)= 3.889 (unweighted)= 62.648 superimposing iter= 5 total_weight= 553.212 rmsd (weighted)= 3.599 (unweighted)= 63.089 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.755 rmsd (weighted)= 15.124 (unweighted)= 61.658 superimposing iter= 1 total_weight= 1187.657 rmsd (weighted)= 9.822 (unweighted)= 61.013 superimposing iter= 2 total_weight= 684.905 rmsd (weighted)= 8.591 (unweighted)= 60.736 superimposing iter= 3 total_weight= 590.384 rmsd (weighted)= 8.102 (unweighted)= 60.539 superimposing iter= 4 total_weight= 584.063 rmsd (weighted)= 7.680 (unweighted)= 60.415 superimposing iter= 5 total_weight= 569.001 rmsd (weighted)= 7.365 (unweighted)= 60.306 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 0.902 rmsd (weighted)= 21.866 (unweighted)= 55.318 superimposing iter= 1 total_weight= 1269.971 rmsd (weighted)= 15.181 (unweighted)= 57.547 superimposing iter= 2 total_weight= 820.441 rmsd (weighted)= 13.242 (unweighted)= 58.943 superimposing iter= 3 total_weight= 788.091 rmsd (weighted)= 11.795 (unweighted)= 59.812 superimposing iter= 4 total_weight= 797.583 rmsd (weighted)= 10.444 (unweighted)= 60.278 superimposing iter= 5 total_weight= 788.624 rmsd (weighted)= 9.311 (unweighted)= 60.375 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.560 rmsd (weighted)= 10.932 (unweighted)= 84.970 superimposing iter= 1 total_weight= 1634.899 rmsd (weighted)= 4.847 (unweighted)= 85.057 superimposing iter= 2 total_weight= 861.600 rmsd (weighted)= 3.207 (unweighted)= 84.812 superimposing iter= 3 total_weight= 550.862 rmsd (weighted)= 2.723 (unweighted)= 84.477 superimposing iter= 4 total_weight= 445.100 rmsd (weighted)= 2.577 (unweighted)= 84.120 superimposing iter= 5 total_weight= 435.268 rmsd (weighted)= 2.467 (unweighted)= 83.764 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.250 rmsd (weighted)= 8.510 (unweighted)= 40.874 superimposing iter= 1 total_weight= 2215.989 rmsd (weighted)= 5.223 (unweighted)= 40.782 superimposing iter= 2 total_weight= 1223.293 rmsd (weighted)= 4.430 (unweighted)= 40.727 superimposing iter= 3 total_weight= 990.357 rmsd (weighted)= 4.200 (unweighted)= 40.693 superimposing iter= 4 total_weight= 926.133 rmsd (weighted)= 4.122 (unweighted)= 40.675 superimposing iter= 5 total_weight= 908.358 rmsd (weighted)= 4.088 (unweighted)= 40.666 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.951 rmsd (weighted)= 11.763 (unweighted)= 53.860 superimposing iter= 1 total_weight= 1246.307 rmsd (weighted)= 8.590 (unweighted)= 53.911 superimposing iter= 2 total_weight= 777.500 rmsd (weighted)= 8.030 (unweighted)= 54.521 superimposing iter= 3 total_weight= 709.631 rmsd (weighted)= 7.863 (unweighted)= 55.260 superimposing iter= 4 total_weight= 701.818 rmsd (weighted)= 7.742 (unweighted)= 56.023 superimposing iter= 5 total_weight= 708.278 rmsd (weighted)= 7.587 (unweighted)= 56.759 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.602 rmsd (weighted)= 10.144 (unweighted)= 40.988 superimposing iter= 1 total_weight= 1161.849 rmsd (weighted)= 6.061 (unweighted)= 41.446 superimposing iter= 2 total_weight= 514.206 rmsd (weighted)= 5.536 (unweighted)= 41.601 superimposing iter= 3 total_weight= 447.252 rmsd (weighted)= 5.426 (unweighted)= 41.685 superimposing iter= 4 total_weight= 440.812 rmsd (weighted)= 5.354 (unweighted)= 41.718 superimposing iter= 5 total_weight= 439.812 rmsd (weighted)= 5.288 (unweighted)= 41.709 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.826 rmsd (weighted)= 11.637 (unweighted)= 78.508 superimposing iter= 1 total_weight= 1137.639 rmsd (weighted)= 8.094 (unweighted)= 77.697 superimposing iter= 2 total_weight= 789.508 rmsd (weighted)= 6.872 (unweighted)= 77.374 superimposing iter= 3 total_weight= 709.358 rmsd (weighted)= 6.202 (unweighted)= 77.185 superimposing iter= 4 total_weight= 681.187 rmsd (weighted)= 5.732 (unweighted)= 77.097 superimposing iter= 5 total_weight= 654.645 rmsd (weighted)= 5.412 (unweighted)= 77.084 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.540 rmsd (weighted)= 8.979 (unweighted)= 48.067 superimposing iter= 1 total_weight= 1111.489 rmsd (weighted)= 5.060 (unweighted)= 48.227 superimposing iter= 2 total_weight= 573.589 rmsd (weighted)= 4.086 (unweighted)= 48.305 superimposing iter= 3 total_weight= 438.444 rmsd (weighted)= 3.800 (unweighted)= 48.334 superimposing iter= 4 total_weight= 399.217 rmsd (weighted)= 3.708 (unweighted)= 48.343 superimposing iter= 5 total_weight= 387.402 rmsd (weighted)= 3.674 (unweighted)= 48.343 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.012 rmsd (weighted)= 10.791 (unweighted)= 60.121 superimposing iter= 1 total_weight= 1939.266 rmsd (weighted)= 6.386 (unweighted)= 60.124 superimposing iter= 2 total_weight= 976.648 rmsd (weighted)= 5.453 (unweighted)= 60.227 superimposing iter= 3 total_weight= 786.583 rmsd (weighted)= 5.210 (unweighted)= 60.261 superimposing iter= 4 total_weight= 738.076 rmsd (weighted)= 5.142 (unweighted)= 60.262 superimposing iter= 5 total_weight= 722.787 rmsd (weighted)= 5.128 (unweighted)= 60.246 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 12.566 (unweighted)= 57.519 superimposing iter= 1 total_weight= 1499.001 rmsd (weighted)= 7.385 (unweighted)= 58.566 superimposing iter= 2 total_weight= 684.127 rmsd (weighted)= 6.521 (unweighted)= 59.328 superimposing iter= 3 total_weight= 618.648 rmsd (weighted)= 6.064 (unweighted)= 59.713 superimposing iter= 4 total_weight= 586.274 rmsd (weighted)= 5.792 (unweighted)= 59.882 superimposing iter= 5 total_weight= 565.198 rmsd (weighted)= 5.632 (unweighted)= 59.970 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.808 rmsd (weighted)= 11.312 (unweighted)= 59.752 superimposing iter= 1 total_weight= 1468.781 rmsd (weighted)= 6.774 (unweighted)= 59.818 superimposing iter= 2 total_weight= 820.228 rmsd (weighted)= 5.590 (unweighted)= 59.907 superimposing iter= 3 total_weight= 649.722 rmsd (weighted)= 5.217 (unweighted)= 59.986 superimposing iter= 4 total_weight= 592.693 rmsd (weighted)= 5.103 (unweighted)= 60.043 superimposing iter= 5 total_weight= 576.030 rmsd (weighted)= 5.062 (unweighted)= 60.080 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.069 rmsd (weighted)= 17.696 (unweighted)= 44.334 superimposing iter= 1 total_weight= 1722.152 rmsd (weighted)= 11.475 (unweighted)= 44.913 superimposing iter= 2 total_weight= 1042.573 rmsd (weighted)= 9.745 (unweighted)= 45.141 superimposing iter= 3 total_weight= 912.679 rmsd (weighted)= 8.879 (unweighted)= 45.253 superimposing iter= 4 total_weight= 837.234 rmsd (weighted)= 8.453 (unweighted)= 45.314 superimposing iter= 5 total_weight= 801.591 rmsd (weighted)= 8.225 (unweighted)= 45.351 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.634 rmsd (weighted)= 7.822 (unweighted)= 74.910 superimposing iter= 1 total_weight= 1153.073 rmsd (weighted)= 4.798 (unweighted)= 74.931 superimposing iter= 2 total_weight= 589.015 rmsd (weighted)= 4.203 (unweighted)= 75.002 superimposing iter= 3 total_weight= 500.698 rmsd (weighted)= 4.002 (unweighted)= 75.062 superimposing iter= 4 total_weight= 485.933 rmsd (weighted)= 3.870 (unweighted)= 75.106 superimposing iter= 5 total_weight= 479.374 rmsd (weighted)= 3.768 (unweighted)= 75.130 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.250 rmsd (weighted)= 9.905 (unweighted)= 41.771 superimposing iter= 1 total_weight= 2062.659 rmsd (weighted)= 6.295 (unweighted)= 41.305 superimposing iter= 2 total_weight= 1311.521 rmsd (weighted)= 5.122 (unweighted)= 41.171 superimposing iter= 3 total_weight= 1066.195 rmsd (weighted)= 4.663 (unweighted)= 41.128 superimposing iter= 4 total_weight= 956.314 rmsd (weighted)= 4.492 (unweighted)= 41.108 superimposing iter= 5 total_weight= 919.514 rmsd (weighted)= 4.416 (unweighted)= 41.098 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 0.951 rmsd (weighted)= 10.598 (unweighted)= 55.529 superimposing iter= 1 total_weight= 1320.537 rmsd (weighted)= 7.459 (unweighted)= 56.178 superimposing iter= 2 total_weight= 817.443 rmsd (weighted)= 6.758 (unweighted)= 56.733 superimposing iter= 3 total_weight= 743.550 rmsd (weighted)= 6.447 (unweighted)= 57.060 superimposing iter= 4 total_weight= 715.939 rmsd (weighted)= 6.282 (unweighted)= 57.232 superimposing iter= 5 total_weight= 700.482 rmsd (weighted)= 6.195 (unweighted)= 57.312 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 0.602 rmsd (weighted)= 8.433 (unweighted)= 43.836 superimposing iter= 1 total_weight= 1022.253 rmsd (weighted)= 5.365 (unweighted)= 43.855 superimposing iter= 2 total_weight= 526.407 rmsd (weighted)= 4.828 (unweighted)= 43.797 superimposing iter= 3 total_weight= 457.578 rmsd (weighted)= 4.665 (unweighted)= 43.722 superimposing iter= 4 total_weight= 443.530 rmsd (weighted)= 4.579 (unweighted)= 43.663 superimposing iter= 5 total_weight= 439.454 rmsd (weighted)= 4.517 (unweighted)= 43.623 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 0.826 rmsd (weighted)= 10.271 (unweighted)= 78.573 superimposing iter= 1 total_weight= 1200.152 rmsd (weighted)= 7.058 (unweighted)= 78.503 superimposing iter= 2 total_weight= 688.458 rmsd (weighted)= 6.476 (unweighted)= 78.431 superimposing iter= 3 total_weight= 672.128 rmsd (weighted)= 6.022 (unweighted)= 78.398 superimposing iter= 4 total_weight= 680.738 rmsd (weighted)= 5.573 (unweighted)= 78.426 superimposing iter= 5 total_weight= 663.535 rmsd (weighted)= 5.232 (unweighted)= 78.485 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 0.540 rmsd (weighted)= 8.094 (unweighted)= 47.669 superimposing iter= 1 total_weight= 966.667 rmsd (weighted)= 4.913 (unweighted)= 47.657 superimposing iter= 2 total_weight= 499.459 rmsd (weighted)= 4.259 (unweighted)= 47.722 superimposing iter= 3 total_weight= 443.308 rmsd (weighted)= 3.939 (unweighted)= 47.747 superimposing iter= 4 total_weight= 426.374 rmsd (weighted)= 3.723 (unweighted)= 47.722 superimposing iter= 5 total_weight= 414.133 rmsd (weighted)= 3.574 (unweighted)= 47.677 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.012 rmsd (weighted)= 8.935 (unweighted)= 61.780 superimposing iter= 1 total_weight= 1736.889 rmsd (weighted)= 5.627 (unweighted)= 61.647 superimposing iter= 2 total_weight= 935.972 rmsd (weighted)= 4.906 (unweighted)= 61.630 superimposing iter= 3 total_weight= 802.229 rmsd (weighted)= 4.631 (unweighted)= 61.581 superimposing iter= 4 total_weight= 765.355 rmsd (weighted)= 4.476 (unweighted)= 61.533 superimposing iter= 5 total_weight= 737.098 rmsd (weighted)= 4.405 (unweighted)= 61.502 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 12.311 (unweighted)= 59.589 superimposing iter= 1 total_weight= 1499.507 rmsd (weighted)= 7.201 (unweighted)= 59.126 superimposing iter= 2 total_weight= 685.278 rmsd (weighted)= 6.337 (unweighted)= 59.030 superimposing iter= 3 total_weight= 585.007 rmsd (weighted)= 6.049 (unweighted)= 58.943 superimposing iter= 4 total_weight= 569.504 rmsd (weighted)= 5.856 (unweighted)= 58.878 superimposing iter= 5 total_weight= 560.792 rmsd (weighted)= 5.715 (unweighted)= 58.835 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 0.808 rmsd (weighted)= 9.199 (unweighted)= 55.978 superimposing iter= 1 total_weight= 1650.687 rmsd (weighted)= 5.291 (unweighted)= 56.641 superimposing iter= 2 total_weight= 726.922 rmsd (weighted)= 4.662 (unweighted)= 57.020 superimposing iter= 3 total_weight= 635.552 rmsd (weighted)= 4.401 (unweighted)= 57.231 superimposing iter= 4 total_weight= 606.436 rmsd (weighted)= 4.255 (unweighted)= 57.338 superimposing iter= 5 total_weight= 590.705 rmsd (weighted)= 4.170 (unweighted)= 57.392 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.069 rmsd (weighted)= 16.063 (unweighted)= 44.069 superimposing iter= 1 total_weight= 1845.216 rmsd (weighted)= 9.900 (unweighted)= 44.502 superimposing iter= 2 total_weight= 1144.913 rmsd (weighted)= 7.947 (unweighted)= 44.613 superimposing iter= 3 total_weight= 907.766 rmsd (weighted)= 7.208 (unweighted)= 44.634 superimposing iter= 4 total_weight= 819.207 rmsd (weighted)= 6.897 (unweighted)= 44.636 superimposing iter= 5 total_weight= 782.798 rmsd (weighted)= 6.757 (unweighted)= 44.635 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 0.634 rmsd (weighted)= 8.620 (unweighted)= 76.264 superimposing iter= 1 total_weight= 1211.280 rmsd (weighted)= 5.121 (unweighted)= 75.925 superimposing iter= 2 total_weight= 622.104 rmsd (weighted)= 4.349 (unweighted)= 75.806 superimposing iter= 3 total_weight= 499.291 rmsd (weighted)= 4.140 (unweighted)= 75.737 superimposing iter= 4 total_weight= 467.998 rmsd (weighted)= 4.074 (unweighted)= 75.698 superimposing iter= 5 total_weight= 460.062 rmsd (weighted)= 4.046 (unweighted)= 75.675 superimposing iter= 0 total_weight= 1.250 rmsd (weighted)= 10.593 (unweighted)= 41.717 superimposing iter= 1 total_weight= 2036.647 rmsd (weighted)= 6.803 (unweighted)= 41.238 superimposing iter= 2 total_weight= 1235.037 rmsd (weighted)= 5.719 (unweighted)= 41.072 superimposing iter= 3 total_weight= 1033.750 rmsd (weighted)= 5.292 (unweighted)= 41.004 superimposing iter= 4 total_weight= 944.062 rmsd (weighted)= 5.133 (unweighted)= 40.966 superimposing iter= 5 total_weight= 912.594 rmsd (weighted)= 5.066 (unweighted)= 40.944 superimposing iter= 0 total_weight= 0.951 rmsd (weighted)= 9.808 (unweighted)= 55.074 superimposing iter= 1 total_weight= 1313.696 rmsd (weighted)= 6.946 (unweighted)= 55.789 superimposing iter= 2 total_weight= 790.814 rmsd (weighted)= 6.394 (unweighted)= 56.352 superimposing iter= 3 total_weight= 738.210 rmsd (weighted)= 6.115 (unweighted)= 56.639 superimposing iter= 4 total_weight= 717.397 rmsd (weighted)= 5.943 (unweighted)= 56.772 superimposing iter= 5 total_weight= 703.875 rmsd (weighted)= 5.837 (unweighted)= 56.834 superimposing iter= 0 total_weight= 0.602 rmsd (weighted)= 7.838 (unweighted)= 44.409 superimposing iter= 1 total_weight= 969.884 rmsd (weighted)= 5.132 (unweighted)= 44.493 superimposing iter= 2 total_weight= 511.067 rmsd (weighted)= 4.687 (unweighted)= 44.436 superimposing iter= 3 total_weight= 458.285 rmsd (weighted)= 4.528 (unweighted)= 44.337 superimposing iter= 4 total_weight= 448.701 rmsd (weighted)= 4.422 (unweighted)= 44.242 superimposing iter= 5 total_weight= 440.377 rmsd (weighted)= 4.359 (unweighted)= 44.166 superimposing iter= 0 total_weight= 0.826 rmsd (weighted)= 9.525 (unweighted)= 79.353 superimposing iter= 1 total_weight= 1188.519 rmsd (weighted)= 6.625 (unweighted)= 79.681 superimposing iter= 2 total_weight= 658.976 rmsd (weighted)= 6.252 (unweighted)= 79.791 superimposing iter= 3 total_weight= 616.885 rmsd (weighted)= 6.106 (unweighted)= 79.804 superimposing iter= 4 total_weight= 607.465 rmsd (weighted)= 6.012 (unweighted)= 79.780 superimposing iter= 5 total_weight= 602.589 rmsd (weighted)= 5.943 (unweighted)= 79.745 superimposing iter= 0 total_weight= 0.540 rmsd (weighted)= 7.690 (unweighted)= 46.012 superimposing iter= 1 total_weight= 890.717 rmsd (weighted)= 4.864 (unweighted)= 46.218 superimposing iter= 2 total_weight= 489.206 rmsd (weighted)= 4.244 (unweighted)= 46.293 superimposing iter= 3 total_weight= 463.166 rmsd (weighted)= 3.826 (unweighted)= 46.338 superimposing iter= 4 total_weight= 441.792 rmsd (weighted)= 3.535 (unweighted)= 46.369 superimposing iter= 5 total_weight= 423.283 rmsd (weighted)= 3.340 (unweighted)= 46.398 superimposing iter= 0 total_weight= 1.012 rmsd (weighted)= 8.209 (unweighted)= 61.968 superimposing iter= 1 total_weight= 1703.708 rmsd (weighted)= 5.216 (unweighted)= 61.931 superimposing iter= 2 total_weight= 926.881 rmsd (weighted)= 4.559 (unweighted)= 61.915 superimposing iter= 3 total_weight= 798.864 rmsd (weighted)= 4.309 (unweighted)= 61.902 superimposing iter= 4 total_weight= 748.358 rmsd (weighted)= 4.212 (unweighted)= 61.887 superimposing iter= 5 total_weight= 729.018 rmsd (weighted)= 4.173 (unweighted)= 61.876 superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 12.475 (unweighted)= 59.265 superimposing iter= 1 total_weight= 1548.905 rmsd (weighted)= 7.123 (unweighted)= 59.085 superimposing iter= 2 total_weight= 710.412 rmsd (weighted)= 6.145 (unweighted)= 59.134 superimposing iter= 3 total_weight= 590.641 rmsd (weighted)= 5.836 (unweighted)= 59.185 superimposing iter= 4 total_weight= 567.485 rmsd (weighted)= 5.663 (unweighted)= 59.215 superimposing iter= 5 total_weight= 555.919 rmsd (weighted)= 5.555 (unweighted)= 59.221 superimposing iter= 0 total_weight= 0.808 rmsd (weighted)= 8.438 (unweighted)= 54.115 superimposing iter= 1 total_weight= 1580.243 rmsd (weighted)= 4.961 (unweighted)= 54.757 superimposing iter= 2 total_weight= 743.421 rmsd (weighted)= 4.317 (unweighted)= 55.165 superimposing iter= 3 total_weight= 649.840 rmsd (weighted)= 4.032 (unweighted)= 55.419 superimposing iter= 4 total_weight= 614.529 rmsd (weighted)= 3.876 (unweighted)= 55.566 superimposing iter= 5 total_weight= 592.739 rmsd (weighted)= 3.794 (unweighted)= 55.649 superimposing iter= 0 total_weight= 1.069 rmsd (weighted)= 15.789 (unweighted)= 44.004 superimposing iter= 1 total_weight= 1749.908 rmsd (weighted)= 9.962 (unweighted)= 44.445 superimposing iter= 2 total_weight= 1146.642 rmsd (weighted)= 7.959 (unweighted)= 44.596 superimposing iter= 3 total_weight= 921.083 rmsd (weighted)= 7.154 (unweighted)= 44.639 superimposing iter= 4 total_weight= 826.382 rmsd (weighted)= 6.810 (unweighted)= 44.654 superimposing iter= 5 total_weight= 783.445 rmsd (weighted)= 6.666 (unweighted)= 44.659 superimposing iter= 0 total_weight= 0.634 rmsd (weighted)= 9.193 (unweighted)= 76.412 superimposing iter= 1 total_weight= 1226.737 rmsd (weighted)= 5.425 (unweighted)= 76.031 superimposing iter= 2 total_weight= 630.935 rmsd (weighted)= 4.577 (unweighted)= 75.874 superimposing iter= 3 total_weight= 503.963 rmsd (weighted)= 4.335 (unweighted)= 75.739 superimposing iter= 4 total_weight= 477.702 rmsd (weighted)= 4.221 (unweighted)= 75.643 superimposing iter= 5 total_weight= 466.820 rmsd (weighted)= 4.159 (unweighted)= 75.581 # command:# Printing sheets for alignments to T0557.undertaker-align.sheets # command: