Starting phenix.real_space_refine on Mon Jul 6 04:56:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oz6_17299/07_2026/8oz6_17299.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 132 5.49 5 S 96 5.16 5 C 20236 2.51 5 N 5300 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "H" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Time building chain proxies: 6.84, per 1000 atoms: 0.21 Number of scatterers: 32004 At special positions: 0 Unit cell: (177.87, 208.12, 165.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 132 15.00 O 6240 8.00 N 5300 7.00 C 20236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 985.9 milliseconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 28 sheets defined 39.3% alpha, 14.3% beta 11 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.825A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.081A pdb=" N ARG A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 158 removed outlier: 4.037A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU A 202 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.118A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.522A pdb=" N LYS A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.682A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 353 through 366 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.865A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.695A pdb=" N TYR B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 132 removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.546A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.537A pdb=" N ASP B 233 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 removed outlier: 4.672A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.716A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.824A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.529A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.526A pdb=" N TYR B 505 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 28 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 71 through 89 Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.928A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.558A pdb=" N GLY C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 219 through 224 removed outlier: 4.168A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 removed outlier: 4.300A pdb=" N THR C 232 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.541A pdb=" N THR C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 257 through 280 removed outlier: 3.537A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 353 through 366 removed outlier: 3.557A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 385 removed outlier: 3.797A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 23 through 30 Processing helix chain 'D' and resid 46 through 62 removed outlier: 4.095A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.642A pdb=" N PHE D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 132 removed outlier: 3.702A pdb=" N LYS D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.568A pdb=" N VAL D 162 " --> pdb=" O LYS D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.523A pdb=" N GLN D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.841A pdb=" N ALA D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 351 removed outlier: 3.858A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 removed outlier: 3.852A pdb=" N TRP D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 removed outlier: 3.710A pdb=" N ASP D 458 " --> pdb=" O GLN D 454 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 491 removed outlier: 3.789A pdb=" N ASP D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.718A pdb=" N TYR D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.626A pdb=" N GLU E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.838A pdb=" N PHE E 93 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE E 94 " --> pdb=" O ASP E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 94' Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.528A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 146 through 157 removed outlier: 3.654A pdb=" N SER E 150 " --> pdb=" O ASP E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.056A pdb=" N THR E 232 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.548A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 257 through 280 removed outlier: 3.950A pdb=" N ILE E 265 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 366 Processing helix chain 'E' and resid 369 through 385 removed outlier: 4.527A pdb=" N LYS E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 30 Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.086A pdb=" N LYS F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 104 removed outlier: 3.778A pdb=" N PHE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 132 removed outlier: 4.173A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 151 removed outlier: 3.549A pdb=" N TYR F 148 " --> pdb=" O PRO F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.692A pdb=" N GLN F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 218 Processing helix chain 'F' and resid 230 through 234 removed outlier: 3.750A pdb=" N ASP F 233 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.505A pdb=" N ALA F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 348 removed outlier: 3.518A pdb=" N TYR F 346 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 377 removed outlier: 3.596A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.837A pdb=" N LEU F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 491 removed outlier: 3.550A pdb=" N ASP F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'G' and resid 10 through 13 removed outlier: 3.801A pdb=" N ASP G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.939A pdb=" N THR G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP G 20 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 65 through 70 removed outlier: 4.612A pdb=" N GLN G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 89 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.729A pdb=" N ILE G 108 " --> pdb=" O TYR G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.898A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 138 removed outlier: 3.913A pdb=" N GLY G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 128 " --> pdb=" O TRP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 158 removed outlier: 3.678A pdb=" N PHE G 158 " --> pdb=" O TYR G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.684A pdb=" N ASP G 222 " --> pdb=" O TRP G 219 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR G 224 " --> pdb=" O TYR G 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 224' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.575A pdb=" N GLU G 231 " --> pdb=" O PRO G 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 242 through 249 removed outlier: 3.519A pdb=" N ILE G 246 " --> pdb=" O PRO G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 280 removed outlier: 4.233A pdb=" N LEU G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE G 265 " --> pdb=" O CYS G 261 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 353 through 367 removed outlier: 4.180A pdb=" N ASN G 367 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 385 removed outlier: 3.905A pdb=" N THR G 375 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.637A pdb=" N GLY H 17 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 31 Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.737A pdb=" N ILE H 52 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 53 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 97 through 106 Processing helix chain 'H' and resid 109 through 132 removed outlier: 4.028A pdb=" N LYS H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 151 removed outlier: 4.170A pdb=" N TYR H 148 " --> pdb=" O PRO H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 162 Processing helix chain 'H' and resid 205 through 214 removed outlier: 3.679A pdb=" N LEU H 214 " --> pdb=" O PHE H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.590A pdb=" N ALA H 259 " --> pdb=" O THR H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 348 removed outlier: 3.660A pdb=" N TYR H 346 " --> pdb=" O SER H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 377 removed outlier: 3.550A pdb=" N TRP H 370 " --> pdb=" O ASN H 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 376 " --> pdb=" O ALA H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 463 removed outlier: 3.578A pdb=" N ASP H 458 " --> pdb=" O GLN H 454 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 491 removed outlier: 3.630A pdb=" N ASP H 484 " --> pdb=" O LEU H 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 506 removed outlier: 3.788A pdb=" N TYR H 505 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.902A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 62 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 178 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 344 current: chain 'A' and resid 400 through 415 removed outlier: 8.367A pdb=" N LEU B 4 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 411 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR B 6 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN A 413 " --> pdb=" O TYR B 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 3 through 6 current: chain 'B' and resid 297 through 301 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 315 through 316 current: chain 'B' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 382 through 389 current: chain 'B' and resid 417 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.583A pdb=" N PHE A 305 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.513A pdb=" N GLN B 18 " --> pdb=" O PHE B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 95 removed outlier: 3.671A pdb=" N THR B 92 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 304 through 305 removed outlier: 3.655A pdb=" N PHE B 304 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 312 " --> pdb=" O PHE B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 33 removed outlier: 5.584A pdb=" N LYS C 4 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 172 removed outlier: 8.431A pdb=" N LEU D 4 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 411 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR D 6 " --> pdb=" O LYS C 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 3 through 6 current: chain 'D' and resid 298 through 305 removed outlier: 3.539A pdb=" N PHE D 304 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 312 " --> pdb=" O PHE D 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 311 through 315 current: chain 'D' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 382 through 389 current: chain 'D' and resid 417 through 420 Processing sheet with id=AB1, first strand: chain 'C' and resid 283 through 286 removed outlier: 6.297A pdb=" N THR C 291 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 325 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 334 " --> pdb=" O LYS C 328 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 177 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 402 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 401 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.588A pdb=" N THR D 92 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY D 42 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE D 142 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE D 44 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 425 through 426 removed outlier: 3.803A pdb=" N VAL D 426 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 33 removed outlier: 5.831A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 4 " --> pdb=" O CYS E 58 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE E 60 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 6 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU E 62 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER E 8 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER E 64 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB8, first strand: chain 'E' and resid 169 through 180 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 180 current: chain 'E' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 291 through 294 current: chain 'E' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 400 through 412 removed outlier: 8.672A pdb=" N LEU F 4 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 3 through 6 current: chain 'F' and resid 297 through 305 removed outlier: 3.534A pdb=" N PHE F 304 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F 312 " --> pdb=" O PHE F 304 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 311 through 315 current: chain 'F' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 382 through 389 current: chain 'F' and resid 417 through 420 Processing sheet with id=AB9, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AC2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.589A pdb=" N GLN F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 95 removed outlier: 6.328A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.921A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 32 through 33 removed outlier: 5.622A pdb=" N ILE G 5 " --> pdb=" O TRP G 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS G 4 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU G 61 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE G 6 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 63 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER G 8 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE G 118 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 165 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 165 through 178 current: chain 'G' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 291 through 294 current: chain 'G' and resid 317 through 328 removed outlier: 3.639A pdb=" N VAL G 334 " --> pdb=" O LYS G 328 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 334 through 344 current: chain 'G' and resid 400 through 415 removed outlier: 4.302A pdb=" N ASN G 413 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR H 6 " --> pdb=" O ASN G 413 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N SER G 415 " --> pdb=" O TYR H 6 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 6 current: chain 'H' and resid 297 through 305 removed outlier: 3.527A pdb=" N PHE H 304 " --> pdb=" O VAL H 312 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 311 through 316 current: chain 'H' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 382 through 389 current: chain 'H' and resid 417 through 420 Processing sheet with id=AC7, first strand: chain 'G' and resid 186 through 188 Processing sheet with id=AC8, first strand: chain 'G' and resid 304 through 305 Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 92 through 95 removed outlier: 7.099A pdb=" N SER H 41 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N LYS H 94 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 43 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLY H 42 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE H 142 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE H 44 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 139 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N PHE H 224 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL H 141 " --> pdb=" O PHE H 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 999 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3965 1.24 - 1.38: 8709 1.38 - 1.53: 15872 1.53 - 1.67: 4370 1.67 - 1.81: 148 Bond restraints: 33064 Sorted by residual: bond pdb=" CG PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.503 1.098 0.405 3.40e-02 8.65e+02 1.42e+02 bond pdb=" CG PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO F 158 " pdb=" CD PRO F 158 " ideal model delta sigma weight residual 1.503 1.151 0.352 3.40e-02 8.65e+02 1.07e+02 bond pdb=" CG PRO D 500 " pdb=" CD PRO D 500 " ideal model delta sigma weight residual 1.503 1.305 0.198 3.40e-02 8.65e+02 3.40e+01 bond pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.14e+01 ... (remaining 33059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 45141 4.33 - 8.66: 99 8.66 - 12.99: 9 12.99 - 17.33: 4 17.33 - 21.66: 3 Bond angle restraints: 45256 Sorted by residual: angle pdb=" N PRO D 378 " pdb=" CD PRO D 378 " pdb=" CG PRO D 378 " ideal model delta sigma weight residual 103.20 81.54 21.66 1.50e+00 4.44e-01 2.08e+02 angle pdb=" N PRO D 76 " pdb=" CD PRO D 76 " pdb=" CG PRO D 76 " ideal model delta sigma weight residual 103.20 82.69 20.51 1.50e+00 4.44e-01 1.87e+02 angle pdb=" N PRO F 158 " pdb=" CD PRO F 158 " pdb=" CG PRO F 158 " ideal model delta sigma weight residual 103.20 83.55 19.65 1.50e+00 4.44e-01 1.72e+02 angle pdb=" CA PRO D 378 " pdb=" N PRO D 378 " pdb=" CD PRO D 378 " ideal model delta sigma weight residual 112.00 98.26 13.74 1.40e+00 5.10e-01 9.64e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 ... (remaining 45251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 19103 35.69 - 71.37: 501 71.37 - 107.06: 33 107.06 - 142.74: 8 142.74 - 178.43: 7 Dihedral angle restraints: 19652 sinusoidal: 9144 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 21.57 178.43 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U M 9 " pdb=" C1' U M 9 " pdb=" N1 U M 9 " pdb=" C2 U M 9 " ideal model delta sinusoidal sigma weight residual -160.00 -7.26 -152.74 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U K 9 " pdb=" C1' U K 9 " pdb=" N1 U K 9 " pdb=" C2 U K 9 " ideal model delta sinusoidal sigma weight residual 200.00 48.79 151.21 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 19649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3507 0.038 - 0.076: 1040 0.076 - 0.114: 350 0.114 - 0.152: 65 0.152 - 0.190: 6 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB ILE G 239 " pdb=" CA ILE G 239 " pdb=" CG1 ILE G 239 " pdb=" CG2 ILE G 239 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA PRO D 427 " pdb=" N PRO D 427 " pdb=" C PRO D 427 " pdb=" CB PRO D 427 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA TYR D 56 " pdb=" N TYR D 56 " pdb=" C TYR D 56 " pdb=" CB TYR D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4965 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 499 " -0.065 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 500 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 254 " -0.019 2.00e-02 2.50e+03 2.26e-02 1.28e+01 pdb=" CG TRP D 254 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP D 254 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 254 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 254 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 254 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 157 " -0.063 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 158 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " -0.048 5.00e-02 4.00e+02 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 631 2.65 - 3.22: 30314 3.22 - 3.78: 52738 3.78 - 4.34: 73379 4.34 - 4.90: 112902 Nonbonded interactions: 269964 Sorted by model distance: nonbonded pdb=" OG SER C 354 " pdb=" O2' U K 8 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A 416 " pdb=" O THR B 404 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASN A 151 " pdb=" NE2 GLN A 155 " model vdw 2.131 3.120 nonbonded pdb=" OH TYR C 190 " pdb=" O ALA C 220 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR G 221 " pdb=" O TYR G 233 " model vdw 2.140 3.040 ... (remaining 269959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.250 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.405 33064 Z= 0.235 Angle : 0.745 21.656 45256 Z= 0.452 Chirality : 0.041 0.190 4968 Planarity : 0.005 0.091 5236 Dihedral : 15.906 178.426 12860 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.95 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3532 helix: 0.11 (0.15), residues: 1190 sheet: -1.09 (0.21), residues: 612 loop : -1.13 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 407 TYR 0.035 0.001 TYR D 56 PHE 0.031 0.002 PHE E 135 TRP 0.060 0.002 TRP D 254 HIS 0.007 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (33064) covalent geometry : angle 0.74490 / 0.45 (45256) hydrogen bonds : bond 0.21413 / 14.02 ( 1021) hydrogen bonds : angle 7.98308 / 5.61 ( 2798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ILE cc_start: 0.7500 (mt) cc_final: 0.7209 (mm) REVERT: A 210 TYR cc_start: 0.7786 (t80) cc_final: 0.7570 (t80) REVERT: B 118 VAL cc_start: 0.7047 (t) cc_final: 0.6819 (t) REVERT: B 478 VAL cc_start: 0.7524 (p) cc_final: 0.7266 (m) REVERT: C 122 MET cc_start: 0.6943 (tmm) cc_final: 0.6717 (tmm) REVERT: C 162 LYS cc_start: 0.6753 (mptt) cc_final: 0.5962 (mmmt) REVERT: D 290 LYS cc_start: 0.7512 (tptt) cc_final: 0.7129 (tptp) REVERT: E 287 MET cc_start: 0.3500 (tmm) cc_final: 0.3217 (tmm) REVERT: E 305 PHE cc_start: 0.8034 (t80) cc_final: 0.7645 (t80) REVERT: F 390 LYS cc_start: 0.7175 (tmtt) cc_final: 0.6936 (tmtt) REVERT: G 62 LEU cc_start: 0.8220 (tp) cc_final: 0.7975 (tp) REVERT: G 192 TRP cc_start: 0.6359 (p-90) cc_final: 0.5188 (t60) REVERT: G 193 MET cc_start: 0.5917 (mpp) cc_final: 0.3738 (mtt) REVERT: G 393 LEU cc_start: 0.8649 (mt) cc_final: 0.8302 (tp) REVERT: H 86 TRP cc_start: 0.6116 (t60) cc_final: 0.5134 (t60) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1827 time to fit residues: 125.5302 Evaluate side-chains 273 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.0470 overall best weight: 4.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 251 HIS D 446 ASN E 156 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN H 129 ASN H 329 HIS H 349 GLN H 468 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.111673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.095132 restraints weight = 201939.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.096533 restraints weight = 144747.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.097411 restraints weight = 114961.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.098264 restraints weight = 98441.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.098694 restraints weight = 87105.875| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 33064 Z= 0.217 Angle : 0.730 8.342 45256 Z= 0.385 Chirality : 0.045 0.266 4968 Planarity : 0.006 0.061 5236 Dihedral : 15.631 160.438 5572 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 1.47 % Allowed : 9.20 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3532 helix: -0.01 (0.15), residues: 1216 sheet: -1.39 (0.21), residues: 592 loop : -1.23 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 126 TYR 0.020 0.002 TYR H 411 PHE 0.025 0.002 PHE D 78 TRP 0.066 0.002 TRP D 254 HIS 0.011 0.002 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (33064) covalent geometry : angle 0.73007 / 0.39 (45256) hydrogen bonds : bond 0.06258 / 4.16 ( 1021) hydrogen bonds : angle 6.27785 / 4.47 ( 2798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7901 (t80) cc_final: 0.7688 (t80) REVERT: B 74 MET cc_start: 0.5258 (tpp) cc_final: 0.4780 (tpp) REVERT: B 118 VAL cc_start: 0.7369 (t) cc_final: 0.7142 (t) REVERT: C 122 MET cc_start: 0.7370 (tmm) cc_final: 0.7094 (tmm) REVERT: C 162 LYS cc_start: 0.6535 (mptt) cc_final: 0.5877 (mmmt) REVERT: C 395 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5616 (tmm) REVERT: C 410 PHE cc_start: 0.6378 (m-10) cc_final: 0.5899 (m-80) REVERT: D 290 LYS cc_start: 0.7732 (tptt) cc_final: 0.7372 (tptp) REVERT: D 435 MET cc_start: -0.0190 (ttp) cc_final: -0.0413 (ttp) REVERT: E 156 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: E 287 MET cc_start: 0.4998 (tmm) cc_final: 0.4527 (tmm) REVERT: E 305 PHE cc_start: 0.8345 (t80) cc_final: 0.7968 (t80) REVERT: E 373 TRP cc_start: 0.5713 (m100) cc_final: 0.5351 (m100) REVERT: F 435 MET cc_start: 0.6525 (mmm) cc_final: 0.6065 (mmm) REVERT: G 192 TRP cc_start: 0.6220 (p-90) cc_final: 0.5130 (t60) REVERT: G 193 MET cc_start: 0.5236 (mpp) cc_final: 0.4288 (mtt) REVERT: G 393 LEU cc_start: 0.8743 (mt) cc_final: 0.8511 (tp) REVERT: H 75 PHE cc_start: 0.7892 (t80) cc_final: 0.7633 (t80) REVERT: H 86 TRP cc_start: 0.6510 (t60) cc_final: 0.5516 (t60) REVERT: H 106 TYR cc_start: 0.4418 (m-80) cc_final: 0.4183 (m-10) REVERT: H 303 MET cc_start: 0.5221 (ttm) cc_final: 0.4991 (ttm) outliers start: 47 outliers final: 30 residues processed: 335 average time/residue: 0.1741 time to fit residues: 96.4700 Evaluate side-chains 304 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 336 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain H residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 304 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 153 optimal weight: 0.8980 chunk 319 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS D 322 ASN E 156 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 135 ASN G 109 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.109742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.093447 restraints weight = 202338.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.094814 restraints weight = 146042.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.095795 restraints weight = 114996.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.096366 restraints weight = 97378.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.096882 restraints weight = 87474.593| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33064 Z= 0.195 Angle : 0.687 8.717 45256 Z= 0.364 Chirality : 0.044 0.328 4968 Planarity : 0.005 0.062 5236 Dihedral : 15.793 163.212 5572 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.44 % Favored : 94.25 % Rotamer: Outliers : 1.97 % Allowed : 11.95 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3532 helix: 0.08 (0.15), residues: 1230 sheet: -1.48 (0.21), residues: 578 loop : -1.26 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 225 TYR 0.028 0.002 TYR H 397 PHE 0.044 0.002 PHE H 373 TRP 0.087 0.002 TRP D 254 HIS 0.013 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (33064) covalent geometry : angle 0.68745 / 0.36 (45256) hydrogen bonds : bond 0.05727 / 3.79 ( 1021) hydrogen bonds : angle 5.98477 / 4.27 ( 2798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7887 (t80) cc_final: 0.7661 (t80) REVERT: A 268 LEU cc_start: 0.7621 (mm) cc_final: 0.7290 (mm) REVERT: B 74 MET cc_start: 0.5506 (tpp) cc_final: 0.4947 (tpp) REVERT: B 118 VAL cc_start: 0.7431 (t) cc_final: 0.7206 (t) REVERT: C 122 MET cc_start: 0.7340 (tmm) cc_final: 0.6986 (tmm) REVERT: C 162 LYS cc_start: 0.6655 (mptt) cc_final: 0.6012 (mmmt) REVERT: C 395 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5556 (tmm) REVERT: C 410 PHE cc_start: 0.6496 (m-10) cc_final: 0.5946 (m-80) REVERT: D 398 LYS cc_start: 0.6912 (pttt) cc_final: 0.6402 (pptt) REVERT: E 135 PHE cc_start: 0.8012 (m-80) cc_final: 0.7664 (m-80) REVERT: E 257 ARG cc_start: 0.6658 (tpt90) cc_final: 0.6319 (tpt90) REVERT: E 373 TRP cc_start: 0.5936 (m100) cc_final: 0.5585 (m100) REVERT: F 81 VAL cc_start: 0.7552 (m) cc_final: 0.7160 (p) REVERT: F 272 SER cc_start: 0.4790 (p) cc_final: 0.4581 (t) REVERT: G 393 LEU cc_start: 0.8743 (mt) cc_final: 0.8543 (tp) REVERT: H 75 PHE cc_start: 0.7954 (t80) cc_final: 0.7726 (t80) REVERT: H 86 TRP cc_start: 0.6491 (t60) cc_final: 0.5413 (t60) REVERT: H 106 TYR cc_start: 0.4858 (m-80) cc_final: 0.4640 (m-10) REVERT: H 303 MET cc_start: 0.4448 (ttm) cc_final: 0.4221 (ttm) REVERT: H 435 MET cc_start: 0.5050 (tmm) cc_final: 0.0155 (ptp) REVERT: H 504 LYS cc_start: 0.7442 (mtmt) cc_final: 0.6626 (mtmm) outliers start: 63 outliers final: 42 residues processed: 336 average time/residue: 0.1680 time to fit residues: 93.1638 Evaluate side-chains 308 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 107 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 409 ASN D 302 GLN E 156 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 ASN H 430 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.109300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.093103 restraints weight = 202163.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.094447 restraints weight = 144889.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.095405 restraints weight = 114391.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.095980 restraints weight = 97110.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.096584 restraints weight = 87376.432| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33064 Z= 0.165 Angle : 0.663 10.993 45256 Z= 0.349 Chirality : 0.044 0.299 4968 Planarity : 0.005 0.064 5236 Dihedral : 15.829 161.032 5572 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.80 % Favored : 93.88 % Rotamer: Outliers : 2.35 % Allowed : 13.64 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3532 helix: 0.16 (0.15), residues: 1234 sheet: -1.49 (0.21), residues: 598 loop : -1.25 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.021 0.001 TYR D 321 PHE 0.040 0.002 PHE H 373 TRP 0.080 0.002 TRP D 254 HIS 0.010 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (33064) covalent geometry : angle 0.66289 / 0.35 (45256) hydrogen bonds : bond 0.05086 / 3.30 ( 1021) hydrogen bonds : angle 5.80373 / 4.15 ( 2798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 284 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7596 (mm) cc_final: 0.7242 (mm) REVERT: B 74 MET cc_start: 0.5700 (tpp) cc_final: 0.5021 (tpp) REVERT: B 118 VAL cc_start: 0.7247 (t) cc_final: 0.6987 (t) REVERT: C 122 MET cc_start: 0.7515 (tmm) cc_final: 0.7139 (tmm) REVERT: C 395 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.5409 (tmm) REVERT: C 410 PHE cc_start: 0.6545 (m-10) cc_final: 0.6005 (m-80) REVERT: D 137 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6624 (t0) REVERT: E 135 PHE cc_start: 0.7962 (m-80) cc_final: 0.7577 (m-80) REVERT: E 257 ARG cc_start: 0.6774 (tpt90) cc_final: 0.6294 (tpt90) REVERT: F 81 VAL cc_start: 0.7594 (m) cc_final: 0.7198 (p) REVERT: G 1 MET cc_start: 0.5794 (ppp) cc_final: 0.5558 (ppp) REVERT: G 391 PHE cc_start: 0.8115 (p90) cc_final: 0.7896 (p90) REVERT: H 86 TRP cc_start: 0.6652 (t60) cc_final: 0.5559 (t60) REVERT: H 106 TYR cc_start: 0.4840 (m-80) cc_final: 0.4625 (m-80) REVERT: H 303 MET cc_start: 0.4545 (ttm) cc_final: 0.4273 (ttm) REVERT: H 489 ILE cc_start: 0.6228 (tp) cc_final: 0.5994 (tp) outliers start: 75 outliers final: 47 residues processed: 330 average time/residue: 0.1653 time to fit residues: 91.3953 Evaluate side-chains 304 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 341 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 287 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN C 174 ASN C 367 ASN D 293 ASN D 302 GLN E 116 ASN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.106884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.090811 restraints weight = 203326.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.092175 restraints weight = 146148.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.093132 restraints weight = 115250.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.093702 restraints weight = 97892.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.094260 restraints weight = 87905.399| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33064 Z= 0.193 Angle : 0.692 9.593 45256 Z= 0.364 Chirality : 0.044 0.216 4968 Planarity : 0.005 0.065 5236 Dihedral : 15.922 162.338 5572 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.03 % Favored : 93.66 % Rotamer: Outliers : 2.91 % Allowed : 15.33 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3532 helix: 0.14 (0.15), residues: 1234 sheet: -1.77 (0.20), residues: 598 loop : -1.30 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 19 TYR 0.019 0.002 TYR D 346 PHE 0.030 0.002 PHE H 373 TRP 0.048 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (33064) covalent geometry : angle 0.69230 / 0.36 (45256) hydrogen bonds : bond 0.05286 / 3.40 ( 1021) hydrogen bonds : angle 5.81577 / 4.17 ( 2798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 276 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.7644 (mm) cc_final: 0.7302 (mm) REVERT: B 118 VAL cc_start: 0.7346 (t) cc_final: 0.7116 (t) REVERT: B 303 MET cc_start: 0.7377 (tmm) cc_final: 0.6858 (ttm) REVERT: C 122 MET cc_start: 0.7484 (tmm) cc_final: 0.7117 (tmm) REVERT: C 388 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6930 (p0) REVERT: C 395 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5564 (tmm) REVERT: C 410 PHE cc_start: 0.6459 (m-10) cc_final: 0.6096 (m-80) REVERT: D 137 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6727 (t0) REVERT: D 398 LYS cc_start: 0.6626 (pttt) cc_final: 0.6396 (pttm) REVERT: E 93 PHE cc_start: 0.7003 (t80) cc_final: 0.6420 (t80) REVERT: E 135 PHE cc_start: 0.8260 (m-80) cc_final: 0.7841 (m-80) REVERT: E 287 MET cc_start: 0.5075 (tmm) cc_final: 0.4692 (tmm) REVERT: E 309 MET cc_start: 0.4672 (tpt) cc_final: 0.4429 (tpt) REVERT: E 310 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5348 (tt) REVERT: E 373 TRP cc_start: 0.6303 (m100) cc_final: 0.5901 (m100) REVERT: F 81 VAL cc_start: 0.7651 (m) cc_final: 0.7232 (p) REVERT: G 133 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8696 (pt0) REVERT: G 309 MET cc_start: 0.5747 (tmm) cc_final: 0.5516 (tmm) REVERT: H 86 TRP cc_start: 0.6810 (t60) cc_final: 0.5593 (t60) REVERT: H 435 MET cc_start: 0.4897 (tmm) cc_final: 0.0400 (ptp) REVERT: H 489 ILE cc_start: 0.6264 (tp) cc_final: 0.6061 (tp) REVERT: H 504 LYS cc_start: 0.7457 (mtmt) cc_final: 0.7068 (mtmm) outliers start: 93 outliers final: 63 residues processed: 338 average time/residue: 0.1668 time to fit residues: 94.5978 Evaluate side-chains 320 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 34 CYS Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 370 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 507 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 232 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 29 optimal weight: 0.0070 chunk 111 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN H 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.091130 restraints weight = 202672.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.092530 restraints weight = 145565.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.093371 restraints weight = 115311.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.094214 restraints weight = 98697.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.094612 restraints weight = 87522.334| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33064 Z= 0.158 Angle : 0.662 12.943 45256 Z= 0.346 Chirality : 0.043 0.315 4968 Planarity : 0.005 0.064 5236 Dihedral : 15.903 163.077 5572 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.86 % Favored : 93.86 % Rotamer: Outliers : 2.63 % Allowed : 16.80 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3532 helix: 0.25 (0.15), residues: 1236 sheet: -1.71 (0.21), residues: 584 loop : -1.26 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.019 0.001 TYR H 346 PHE 0.030 0.002 PHE G 391 TRP 0.082 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (33064) covalent geometry : angle 0.66241 / 0.35 (45256) hydrogen bonds : bond 0.04846 / 3.11 ( 1021) hydrogen bonds : angle 5.68532 / 4.08 ( 2798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 277 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7131 (t80) cc_final: 0.6820 (t80) REVERT: A 268 LEU cc_start: 0.7635 (mm) cc_final: 0.7333 (mm) REVERT: B 118 VAL cc_start: 0.7275 (t) cc_final: 0.7025 (t) REVERT: B 303 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7031 (ttm) REVERT: C 122 MET cc_start: 0.7504 (tmm) cc_final: 0.7119 (tmm) REVERT: C 388 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6856 (p0) REVERT: C 395 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5477 (tmm) REVERT: C 410 PHE cc_start: 0.6442 (m-10) cc_final: 0.6204 (m-80) REVERT: D 137 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6688 (t0) REVERT: D 398 LYS cc_start: 0.6189 (pttt) cc_final: 0.5644 (pttp) REVERT: E 135 PHE cc_start: 0.8367 (m-80) cc_final: 0.7899 (m-80) REVERT: E 287 MET cc_start: 0.5057 (tmm) cc_final: 0.4706 (tmm) REVERT: F 81 VAL cc_start: 0.7647 (m) cc_final: 0.7238 (p) REVERT: F 101 ILE cc_start: 0.5498 (pp) cc_final: 0.5252 (pp) REVERT: G 133 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8692 (pt0) REVERT: G 287 MET cc_start: -0.0207 (tpt) cc_final: -0.0420 (tpt) REVERT: G 336 MET cc_start: 0.2937 (OUTLIER) cc_final: 0.2259 (mmt) REVERT: H 86 TRP cc_start: 0.6911 (t60) cc_final: 0.5614 (t60) REVERT: H 504 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7142 (mtmm) outliers start: 84 outliers final: 61 residues processed: 331 average time/residue: 0.1713 time to fit residues: 93.9289 Evaluate side-chains 323 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 136 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 321 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 109 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 454 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 ASN H 302 GLN ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.105944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.090005 restraints weight = 204888.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.091350 restraints weight = 146744.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.092295 restraints weight = 115463.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.092997 restraints weight = 98130.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.093451 restraints weight = 86769.942| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33064 Z= 0.187 Angle : 0.689 12.432 45256 Z= 0.362 Chirality : 0.044 0.358 4968 Planarity : 0.005 0.087 5236 Dihedral : 15.943 163.488 5572 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.46 % Favored : 93.29 % Rotamer: Outliers : 2.91 % Allowed : 17.15 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3532 helix: 0.17 (0.14), residues: 1236 sheet: -1.86 (0.20), residues: 598 loop : -1.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 295 TYR 0.026 0.002 TYR H 106 PHE 0.036 0.002 PHE F 121 TRP 0.043 0.002 TRP D 254 HIS 0.008 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (33064) covalent geometry : angle 0.68900 / 0.36 (45256) hydrogen bonds : bond 0.05056 / 3.23 ( 1021) hydrogen bonds : angle 5.73500 / 4.11 ( 2798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 264 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7181 (t80) cc_final: 0.6836 (t80) REVERT: A 268 LEU cc_start: 0.7720 (mm) cc_final: 0.7420 (mm) REVERT: B 118 VAL cc_start: 0.7391 (t) cc_final: 0.7158 (t) REVERT: B 303 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7036 (ttm) REVERT: C 122 MET cc_start: 0.7441 (tmm) cc_final: 0.7070 (tmm) REVERT: C 388 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7247 (p0) REVERT: C 395 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5521 (tmm) REVERT: C 410 PHE cc_start: 0.6650 (m-10) cc_final: 0.6071 (m-80) REVERT: D 137 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6527 (t0) REVERT: D 447 LYS cc_start: 0.4468 (OUTLIER) cc_final: 0.2873 (mmtp) REVERT: E 287 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4817 (tmm) REVERT: F 81 VAL cc_start: 0.7586 (m) cc_final: 0.7201 (p) REVERT: F 101 ILE cc_start: 0.5527 (pp) cc_final: 0.5293 (pp) REVERT: G 133 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8768 (pt0) REVERT: G 336 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.2277 (mmt) REVERT: H 86 TRP cc_start: 0.6947 (t60) cc_final: 0.5846 (t60) REVERT: H 106 TYR cc_start: 0.4121 (m-80) cc_final: 0.3714 (m-80) REVERT: H 435 MET cc_start: 0.4881 (tmm) cc_final: 0.4452 (tmm) REVERT: H 504 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7317 (mtmm) outliers start: 93 outliers final: 67 residues processed: 327 average time/residue: 0.1703 time to fit residues: 92.6159 Evaluate side-chains 329 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 86 TRP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 501 LEU Chi-restraints excluded: chain H residue 504 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 242 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS E 318 ASN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.103904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.088198 restraints weight = 205555.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.089504 restraints weight = 146860.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.090347 restraints weight = 114779.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.091001 restraints weight = 97638.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.091356 restraints weight = 87138.335| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33064 Z= 0.211 Angle : 0.729 12.868 45256 Z= 0.383 Chirality : 0.046 0.273 4968 Planarity : 0.005 0.066 5236 Dihedral : 16.083 164.291 5572 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.36 % Favored : 92.41 % Rotamer: Outliers : 3.13 % Allowed : 17.33 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3532 helix: 0.03 (0.14), residues: 1236 sheet: -1.94 (0.21), residues: 546 loop : -1.47 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.033 0.002 TYR F 65 PHE 0.032 0.002 PHE D 75 TRP 0.034 0.002 TRP D 254 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (33064) covalent geometry : angle 0.72902 / 0.38 (45256) hydrogen bonds : bond 0.05250 / 3.34 ( 1021) hydrogen bonds : angle 5.83187 / 4.20 ( 2798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 267 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7190 (t80) cc_final: 0.6838 (t80) REVERT: A 268 LEU cc_start: 0.7789 (mm) cc_final: 0.7507 (mm) REVERT: B 118 VAL cc_start: 0.7442 (t) cc_final: 0.7210 (t) REVERT: B 303 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7015 (ttm) REVERT: C 122 MET cc_start: 0.7380 (tmm) cc_final: 0.6968 (tmm) REVERT: C 388 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7074 (p0) REVERT: C 395 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5657 (tmm) REVERT: C 410 PHE cc_start: 0.6523 (m-10) cc_final: 0.5974 (m-80) REVERT: E 287 MET cc_start: 0.5483 (OUTLIER) cc_final: 0.5052 (tmm) REVERT: E 309 MET cc_start: 0.4881 (tpt) cc_final: 0.4583 (tpt) REVERT: E 310 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5321 (tt) REVERT: F 65 TYR cc_start: 0.3236 (m-80) cc_final: 0.2942 (m-80) REVERT: F 81 VAL cc_start: 0.7540 (m) cc_final: 0.7179 (p) REVERT: F 353 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6016 (m-10) REVERT: F 435 MET cc_start: 0.7039 (tpp) cc_final: 0.6802 (mmm) REVERT: G 133 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8738 (pt0) REVERT: G 336 MET cc_start: 0.2639 (OUTLIER) cc_final: 0.2010 (mmt) REVERT: H 86 TRP cc_start: 0.7082 (t60) cc_final: 0.6009 (t60) REVERT: H 161 MET cc_start: 0.1700 (mpp) cc_final: 0.1111 (ttt) REVERT: H 435 MET cc_start: 0.4752 (tmm) cc_final: 0.4476 (tmm) outliers start: 100 outliers final: 75 residues processed: 332 average time/residue: 0.1723 time to fit residues: 95.0818 Evaluate side-chains 331 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 249 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 484 ASP Chi-restraints excluded: chain H residue 501 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 359 optimal weight: 40.0000 chunk 77 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.104477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.088508 restraints weight = 203276.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.089827 restraints weight = 145304.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.090828 restraints weight = 115252.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.091269 restraints weight = 97753.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.091735 restraints weight = 89345.526| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33064 Z= 0.174 Angle : 0.708 12.848 45256 Z= 0.368 Chirality : 0.045 0.283 4968 Planarity : 0.005 0.092 5236 Dihedral : 16.099 165.260 5572 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.81 % Rotamer: Outliers : 2.88 % Allowed : 17.77 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3532 helix: 0.09 (0.15), residues: 1236 sheet: -2.01 (0.21), residues: 552 loop : -1.47 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 114 TYR 0.033 0.002 TYR H 346 PHE 0.026 0.002 PHE D 75 TRP 0.038 0.002 TRP D 254 HIS 0.011 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (33064) covalent geometry : angle 0.70802 / 0.37 (45256) hydrogen bonds : bond 0.04907 / 3.12 ( 1021) hydrogen bonds : angle 5.72427 / 4.11 ( 2798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 258 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7043 (t80) cc_final: 0.6716 (t80) REVERT: A 268 LEU cc_start: 0.7606 (mm) cc_final: 0.7330 (mm) REVERT: B 118 VAL cc_start: 0.7435 (t) cc_final: 0.7200 (t) REVERT: B 161 MET cc_start: 0.1368 (tmm) cc_final: 0.0479 (tpp) REVERT: B 219 ILE cc_start: 0.7183 (mt) cc_final: 0.6968 (mt) REVERT: B 303 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6999 (ttm) REVERT: C 122 MET cc_start: 0.7243 (tmm) cc_final: 0.6751 (tmm) REVERT: C 395 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5547 (tmm) REVERT: C 410 PHE cc_start: 0.6540 (m-10) cc_final: 0.5977 (m-80) REVERT: D 233 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7366 (p0) REVERT: E 287 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5348 (tmm) REVERT: F 81 VAL cc_start: 0.7251 (m) cc_final: 0.6906 (p) REVERT: F 353 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5962 (m-10) REVERT: F 435 MET cc_start: 0.6847 (tpp) cc_final: 0.6568 (mmm) REVERT: G 133 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8727 (pt0) REVERT: G 309 MET cc_start: 0.5834 (tmm) cc_final: 0.5633 (tmm) REVERT: G 336 MET cc_start: 0.2947 (OUTLIER) cc_final: 0.2216 (mmt) REVERT: H 36 LEU cc_start: 0.6839 (tt) cc_final: 0.6543 (mm) REVERT: H 86 TRP cc_start: 0.7015 (t60) cc_final: 0.5987 (t60) REVERT: H 161 MET cc_start: 0.1568 (mpp) cc_final: 0.0986 (ttt) outliers start: 92 outliers final: 76 residues processed: 322 average time/residue: 0.1857 time to fit residues: 98.2048 Evaluate side-chains 329 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain D residue 454 GLN Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 299 CYS Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 362 ARG Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 223 ILE Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 430 GLN Chi-restraints excluded: chain H residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 301 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 202 optimal weight: 0.0010 chunk 120 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 122 optimal weight: 0.0020 chunk 111 optimal weight: 9.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN E 358 HIS ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 226 HIS ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 GLN H 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.108062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.091978 restraints weight = 200880.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.093369 restraints weight = 142751.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.094398 restraints weight = 112062.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.094973 restraints weight = 94158.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.095537 restraints weight = 84362.599| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33064 Z= 0.131 Angle : 0.682 17.779 45256 Z= 0.349 Chirality : 0.044 0.260 4968 Planarity : 0.005 0.064 5236 Dihedral : 15.981 167.186 5572 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 2.03 % Allowed : 18.65 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3532 helix: 0.32 (0.15), residues: 1228 sheet: -1.91 (0.21), residues: 570 loop : -1.31 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 257 TYR 0.036 0.001 TYR H 397 PHE 0.022 0.002 PHE H 373 TRP 0.031 0.002 TRP D 254 HIS 0.032 0.001 HIS G 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (33064) covalent geometry : angle 0.68154 / 0.35 (45256) hydrogen bonds : bond 0.04361 / 2.74 ( 1021) hydrogen bonds : angle 5.41345 / 3.89 ( 2798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 TYR cc_start: 0.7238 (t80) cc_final: 0.6923 (t80) REVERT: A 268 LEU cc_start: 0.7569 (mm) cc_final: 0.7321 (mm) REVERT: B 25 ASP cc_start: 0.7047 (m-30) cc_final: 0.6728 (m-30) REVERT: B 118 VAL cc_start: 0.7260 (t) cc_final: 0.6989 (t) REVERT: B 303 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6766 (ttm) REVERT: C 122 MET cc_start: 0.7121 (tmm) cc_final: 0.6644 (tmm) REVERT: C 391 PHE cc_start: 0.8241 (p90) cc_final: 0.7967 (p90) REVERT: C 395 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.5010 (tmm) REVERT: C 410 PHE cc_start: 0.6584 (m-10) cc_final: 0.5971 (m-80) REVERT: D 137 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6401 (t0) REVERT: E 287 MET cc_start: 0.5561 (OUTLIER) cc_final: 0.5179 (tmm) REVERT: F 81 VAL cc_start: 0.7141 (m) cc_final: 0.6730 (p) REVERT: G 309 MET cc_start: 0.5935 (tmm) cc_final: 0.5720 (tmm) REVERT: G 336 MET cc_start: 0.2898 (OUTLIER) cc_final: 0.2242 (mmt) REVERT: H 86 TRP cc_start: 0.6938 (t60) cc_final: 0.6122 (t60) REVERT: H 243 ARG cc_start: 0.5870 (mtp180) cc_final: 0.4495 (ptp90) REVERT: H 435 MET cc_start: 0.4280 (tmm) cc_final: -0.0213 (mtt) outliers start: 65 outliers final: 43 residues processed: 316 average time/residue: 0.1955 time to fit residues: 101.5151 Evaluate side-chains 303 residues out of total 3196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 447 LYS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 87 GLN Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 234 HIS Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 321 PHE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain G residue 67 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 395 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 341 GLN Chi-restraints excluded: chain H residue 411 TYR Chi-restraints excluded: chain H residue 468 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 339 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 299 optimal weight: 4.9990 chunk 149 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 358 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 overall best weight: 2.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.106227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.090203 restraints weight = 202393.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.091594 restraints weight = 144757.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.092424 restraints weight = 113827.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.093107 restraints weight = 97241.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.093612 restraints weight = 86697.195| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33064 Z= 0.151 Angle : 0.691 14.402 45256 Z= 0.356 Chirality : 0.044 0.315 4968 Planarity : 0.005 0.066 5236 Dihedral : 15.987 166.394 5572 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.29 % Favored : 93.52 % Rotamer: Outliers : 1.69 % Allowed : 19.46 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3532 helix: 0.37 (0.15), residues: 1224 sheet: -1.73 (0.21), residues: 530 loop : -1.37 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 126 TYR 0.023 0.001 TYR H 346 PHE 0.052 0.002 PHE C 17 TRP 0.070 0.002 TRP A 175 HIS 0.011 0.001 HIS G 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (33064) covalent geometry : angle 0.69127 / 0.36 (45256) hydrogen bonds : bond 0.04511 / 2.86 ( 1021) hydrogen bonds : angle 5.54106 / 3.98 ( 2798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.02 seconds wall clock time: 96 minutes 26.97 seconds (5786.97 seconds total)