Starting phenix.real_space_refine on Mon Sep 14 15:10:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jqn_9875/09_2026/6jqn_9875.cif" } resolution = 3.1 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 36 5.49 5 S 156 5.16 5 C 19644 2.51 5 N 5508 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31278 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'CO8': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.34, per 1000 atoms: 0.20 Number of scatterers: 31278 At special positions: 0 Unit cell: (178.08, 174.9, 108.12, 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 156 16.00 P 36 15.00 O 5934 8.00 N 5508 7.00 C 19644 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 41 sheets defined 37.9% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 40 through 58 removed outlier: 4.085A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.108A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.604A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.229A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.837A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.983A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.527A pdb=" N ALA A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 502 through 511 removed outlier: 4.028A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.515A pdb=" N LEU A 534 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.540A pdb=" N ALA A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.636A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 58 removed outlier: 4.012A pdb=" N ALA B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.627A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.612A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 118 removed outlier: 3.997A pdb=" N LEU B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.326A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.112A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 4.027A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.575A pdb=" N GLY B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 273 through 289 removed outlier: 3.781A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.918A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 317 " --> pdb=" O ASP B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 354 Processing helix chain 'B' and resid 410 through 418 Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.703A pdb=" N ALA B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.888A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.732A pdb=" N ALA B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.718A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 58 removed outlier: 3.890A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.676A pdb=" N SER C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 87 removed outlier: 4.141A pdb=" N PHE C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 92 through 118 removed outlier: 3.520A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.505A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 186 through 199 removed outlier: 4.105A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.744A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 289 removed outlier: 3.969A pdb=" N ALA C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.667A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 485 through 489 removed outlier: 3.507A pdb=" N ALA C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 removed outlier: 3.947A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 560 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.621A pdb=" N ALA C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 removed outlier: 3.548A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 58 removed outlier: 3.967A pdb=" N ALA D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Proline residue: D 54 - end of helix Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.607A pdb=" N SER D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 92 through 117 Processing helix chain 'D' and resid 161 through 174 removed outlier: 4.209A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.306A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.745A pdb=" N GLN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 273 through 289 removed outlier: 3.959A pdb=" N ALA D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.545A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 removed outlier: 3.706A pdb=" N ALA D 393 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 394 " --> pdb=" O VAL D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 390 through 394' Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.586A pdb=" N ALA D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.870A pdb=" N ALA D 489 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.973A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 568 through 574 removed outlier: 3.517A pdb=" N ALA D 572 " --> pdb=" O ASP D 568 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.545A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 58 removed outlier: 3.516A pdb=" N ALA E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.714A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 3.656A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 92 through 118 removed outlier: 3.781A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 removed outlier: 4.288A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.161A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.940A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 241 removed outlier: 3.541A pdb=" N GLY E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 273 through 289 removed outlier: 3.971A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 307 through 320 Processing helix chain 'E' and resid 339 through 354 Processing helix chain 'E' and resid 410 through 418 Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.650A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 485 through 489 removed outlier: 3.639A pdb=" N ALA E 489 " --> pdb=" O GLY E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 removed outlier: 3.902A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 569 through 574 removed outlier: 3.610A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.611A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 596 " --> pdb=" O ALA E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 58 removed outlier: 4.051A pdb=" N ALA F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Proline residue: F 54 - end of helix Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.825A pdb=" N GLU F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 92 through 117 removed outlier: 3.812A pdb=" N LEU F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 174 removed outlier: 4.327A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.334A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.659A pdb=" N VAL F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 273 through 289 removed outlier: 3.925A pdb=" N ALA F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 Processing helix chain 'F' and resid 307 through 320 Processing helix chain 'F' and resid 339 through 354 Processing helix chain 'F' and resid 411 through 418 Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.540A pdb=" N ALA F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 485 through 489 removed outlier: 3.521A pdb=" N ARG F 488 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 489 " --> pdb=" O GLY F 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 485 through 489' Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.048A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 529 Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 574 removed outlier: 3.693A pdb=" N ALA F 573 " --> pdb=" O LYS F 569 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 574 " --> pdb=" O ILE F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.704A pdb=" N ALA F 592 " --> pdb=" O LEU F 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.771A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.672A pdb=" N GLY B 425 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 452 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 427 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN B 261 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 299 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N MET B 404 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 301 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 378 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU B 403 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.652A pdb=" N ALA A 178 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 152 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 228 " --> pdb=" O THR A 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.661A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.661A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 469 through 472 removed outlier: 5.289A pdb=" N LEU A 470 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 485 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 541 removed outlier: 3.616A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.465A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.796A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.506A pdb=" N ILE B 180 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 228 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU B 256 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 545 through 547 removed outlier: 6.523A pdb=" N GLU B 650 " --> pdb=" O LYS B 631 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB6, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.875A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AB8, first strand: chain 'C' and resid 124 through 125 removed outlier: 6.634A pdb=" N GLY D 425 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN D 261 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG D 299 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR D 378 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU D 403 " --> pdb=" O THR D 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.237A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 228 " --> pdb=" O THR C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.455A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 539 through 541 Processing sheet with id=AC3, first strand: chain 'C' and resid 539 through 541 removed outlier: 5.031A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 671 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AC5, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.864A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AC7, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.437A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 539 through 541 removed outlier: 3.697A pdb=" N ASP D 622 " --> pdb=" O MET D 547 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 539 through 541 removed outlier: 5.089A pdb=" N VAL D 626 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE D 656 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 628 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU D 654 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS D 630 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA D 652 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 671 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AD2, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.919A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AD4, first strand: chain 'E' and resid 124 through 125 removed outlier: 8.027A pdb=" N ILE F 449 " --> pdb=" O ARG E 496 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA E 498 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE F 451 " --> pdb=" O ALA E 498 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN E 500 " --> pdb=" O ILE F 451 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS F 262 " --> pdb=" O THR F 426 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL F 428 " --> pdb=" O CYS F 262 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 264 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN F 261 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARG F 299 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR F 378 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU F 403 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.510A pdb=" N ILE E 180 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 228 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 402 through 404 removed outlier: 6.440A pdb=" N ARG E 299 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N MET E 404 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 301 " --> pdb=" O MET E 404 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 545 through 547 removed outlier: 5.110A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 545 through 547 removed outlier: 5.110A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU E 665 " --> pdb=" O LEU E 612 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 612 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 667 " --> pdb=" O GLU E 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AE1, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.909A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 130 through 131 Processing sheet with id=AE3, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.361A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 539 through 541 removed outlier: 3.632A pdb=" N ASP F 622 " --> pdb=" O MET F 547 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 539 through 541 removed outlier: 6.458A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) 1252 hydrogen bonds defined for protein. 3513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.54 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9153 1.33 - 1.45: 4937 1.45 - 1.57: 17530 1.57 - 1.69: 66 1.69 - 1.81: 246 Bond restraints: 31932 Sorted by residual: bond pdb=" O2B NAP D 801 " pdb=" P2B NAP D 801 " ideal model delta sigma weight residual 1.736 1.604 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" O2B NAP A 801 " pdb=" P2B NAP A 801 " ideal model delta sigma weight residual 1.736 1.604 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" O2B NAP F 801 " pdb=" P2B NAP F 801 " ideal model delta sigma weight residual 1.736 1.605 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" O2B NAP E 801 " pdb=" P2B NAP E 801 " ideal model delta sigma weight residual 1.736 1.605 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" O2B NAP C 801 " pdb=" P2B NAP C 801 " ideal model delta sigma weight residual 1.736 1.605 0.131 2.00e-02 2.50e+03 4.26e+01 ... (remaining 31927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 42076 2.62 - 5.23: 1107 5.23 - 7.85: 153 7.85 - 10.47: 70 10.47 - 13.08: 22 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C TRP D 513 " pdb=" N VAL D 514 " pdb=" CA VAL D 514 " ideal model delta sigma weight residual 121.97 113.86 8.11 1.80e+00 3.09e-01 2.03e+01 angle pdb=" O3A CO8 E 802 " pdb=" P1A CO8 E 802 " pdb=" O5B CO8 E 802 " ideal model delta sigma weight residual 99.28 112.36 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C TRP F 513 " pdb=" N VAL F 514 " pdb=" CA VAL F 514 " ideal model delta sigma weight residual 121.97 114.27 7.70 1.80e+00 3.09e-01 1.83e+01 angle pdb=" O3A CO8 C 802 " pdb=" P1A CO8 C 802 " pdb=" O5B CO8 C 802 " ideal model delta sigma weight residual 99.28 111.79 -12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" C TRP E 513 " pdb=" N VAL E 514 " pdb=" CA VAL E 514 " ideal model delta sigma weight residual 121.97 114.59 7.38 1.80e+00 3.09e-01 1.68e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 18781 28.90 - 57.80: 499 57.80 - 86.70: 42 86.70 - 115.60: 7 115.60 - 144.50: 3 Dihedral angle restraints: 19332 sinusoidal: 7812 harmonic: 11520 Sorted by residual: dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASP B 522 " pdb=" C ASP B 522 " pdb=" N ARG B 523 " pdb=" CA ARG B 523 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP D 522 " pdb=" C ASP D 522 " pdb=" N ARG D 523 " pdb=" CA ARG D 523 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 19329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3610 0.057 - 0.114: 1087 0.114 - 0.171: 180 0.171 - 0.227: 29 0.227 - 0.284: 8 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C1B NAP F 801 " pdb=" C2B NAP F 801 " pdb=" N9A NAP F 801 " pdb=" O4B NAP F 801 " both_signs ideal model delta sigma weight residual False 2.31 2.59 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1B NAP E 801 " pdb=" C2B NAP E 801 " pdb=" N9A NAP E 801 " pdb=" O4B NAP E 801 " both_signs ideal model delta sigma weight residual False 2.31 2.57 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C1B NAP B 801 " pdb=" C2B NAP B 801 " pdb=" N9A NAP B 801 " pdb=" O4B NAP B 801 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4911 not shown) Planarity restraints: 5610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CO8 C 802 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C9P CO8 C 802 " -0.070 2.00e-02 2.50e+03 pdb=" CAP CO8 C 802 " 0.103 2.00e-02 2.50e+03 pdb=" N8P CO8 C 802 " -0.539 2.00e-02 2.50e+03 pdb=" O9P CO8 C 802 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P CO8 E 802 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C9P CO8 E 802 " 0.066 2.00e-02 2.50e+03 pdb=" CAP CO8 E 802 " -0.155 2.00e-02 2.50e+03 pdb=" N8P CO8 E 802 " 0.506 2.00e-02 2.50e+03 pdb=" O9P CO8 E 802 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P CO8 A 802 " 0.271 2.00e-02 2.50e+03 2.33e-01 6.77e+02 pdb=" C9P CO8 A 802 " -0.051 2.00e-02 2.50e+03 pdb=" CAP CO8 A 802 " -0.020 2.00e-02 2.50e+03 pdb=" N8P CO8 A 802 " -0.395 2.00e-02 2.50e+03 pdb=" O9P CO8 A 802 " 0.196 2.00e-02 2.50e+03 ... (remaining 5607 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8156 2.80 - 3.32: 27695 3.32 - 3.85: 54805 3.85 - 4.37: 64265 4.37 - 4.90: 112493 Nonbonded interactions: 267414 Sorted by model distance: nonbonded pdb=" OG SER D 19 " pdb=" OE1 GLU D 33 " model vdw 2.274 3.040 nonbonded pdb=" O6A CO8 C 802 " pdb=" OAP CO8 C 802 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 607 " pdb=" O9A CO8 B 802 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 607 " pdb=" O9A CO8 A 802 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR F 607 " pdb=" O8A CO8 E 802 " model vdw 2.310 3.040 ... (remaining 267409 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 679) selection = (chain 'B' and resid 2 through 679) selection = (chain 'C' and resid 2 through 679) selection = (chain 'D' and resid 2 through 679) selection = (chain 'E' and resid 2 through 679) selection = (chain 'F' and resid 2 through 679) } 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 individual isotropic 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.330 Find NCS groups from input model: 0.640 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.008 0.132 31932 Z= 0.354 Angle : 1.050 13.084 43428 Z= 0.500 Chirality : 0.055 0.284 4914 Planarity : 0.010 0.300 5610 Dihedral : 12.236 144.502 11928 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.15 (0.10), residues: 4056 helix: -2.76 (0.10), residues: 1374 sheet: -3.27 (0.15), residues: 810 loop : -2.35 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 361 TYR 0.022 0.003 TYR E 666 PHE 0.021 0.003 PHE B 563 TRP 0.049 0.004 TRP F 124 HIS 0.009 0.002 HIS A 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.35 (31932) covalent geometry : angle 1.04967 / 0.50 (43428) hydrogen bonds : bond 0.17319 / 11.94 ( 1200) hydrogen bonds : angle 8.59354 / 5.94 ( 3513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 784 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7446 (tp30) cc_final: 0.7205 (tp30) REVERT: A 414 GLN cc_start: 0.7911 (mt0) cc_final: 0.7706 (mt0) REVERT: A 547 MET cc_start: 0.8456 (mmt) cc_final: 0.8187 (mmt) REVERT: B 196 SER cc_start: 0.8921 (m) cc_final: 0.8706 (t) REVERT: B 202 LEU cc_start: 0.8179 (mt) cc_final: 0.7969 (mt) REVERT: B 309 ASN cc_start: 0.8335 (m110) cc_final: 0.7982 (m110) REVERT: B 321 LYS cc_start: 0.8468 (mttp) cc_final: 0.8098 (mtpp) REVERT: B 333 LYS cc_start: 0.8270 (mttt) cc_final: 0.7856 (mmmt) REVERT: C 255 MET cc_start: 0.8267 (ttp) cc_final: 0.8019 (ttp) REVERT: C 309 ASN cc_start: 0.7879 (m110) cc_final: 0.7628 (m110) REVERT: C 321 LYS cc_start: 0.8467 (mttp) cc_final: 0.7490 (ttpp) REVERT: C 333 LYS cc_start: 0.8279 (mttt) cc_final: 0.7972 (mttp) REVERT: C 345 ASP cc_start: 0.8303 (m-30) cc_final: 0.8016 (m-30) REVERT: D 127 ASP cc_start: 0.7735 (m-30) cc_final: 0.7399 (m-30) REVERT: D 321 LYS cc_start: 0.8690 (mttp) cc_final: 0.8466 (mtmt) REVERT: D 414 GLN cc_start: 0.7952 (mt0) cc_final: 0.7721 (mt0) REVERT: D 511 LYS cc_start: 0.8695 (mttt) cc_final: 0.8446 (mtpt) REVERT: E 83 TYR cc_start: 0.8439 (m-80) cc_final: 0.8051 (m-80) REVERT: E 159 PHE cc_start: 0.8932 (m-80) cc_final: 0.8582 (m-80) REVERT: E 166 GLU cc_start: 0.8056 (pp20) cc_final: 0.7688 (pp20) REVERT: E 196 SER cc_start: 0.8964 (m) cc_final: 0.8750 (t) REVERT: E 309 ASN cc_start: 0.8140 (m110) cc_final: 0.7866 (m110) REVERT: E 313 ASP cc_start: 0.7413 (m-30) cc_final: 0.7213 (m-30) REVERT: E 321 LYS cc_start: 0.8766 (mttp) cc_final: 0.7757 (ttpp) REVERT: E 333 LYS cc_start: 0.8290 (mttt) cc_final: 0.7931 (mttp) REVERT: E 465 SER cc_start: 0.8567 (m) cc_final: 0.8097 (p) REVERT: E 654 GLU cc_start: 0.6907 (tt0) cc_final: 0.6582 (tm-30) REVERT: F 414 GLN cc_start: 0.7972 (mt0) cc_final: 0.7627 (mt0) REVERT: F 511 LYS cc_start: 0.8656 (mttt) cc_final: 0.8440 (mtmt) REVERT: F 547 MET cc_start: 0.8635 (mmt) cc_final: 0.8433 (mmt) outliers start: 0 outliers final: 0 residues processed: 784 average time/residue: 0.2303 time to fit residues: 273.0929 Evaluate side-chains 407 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 261 ASN B 329 GLN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 450 GLN B 463 HIS B 500 GLN B 659 HIS C 158 ASN C 339 ASN C 347 GLN C 409 GLN C 500 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 309 ASN D 329 GLN ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 46 GLN E 329 GLN E 339 ASN E 384 GLN E 409 GLN E 463 HIS E 500 GLN E 525 HIS F 339 ASN F 347 GLN F 414 GLN F 463 HIS F 492 HIS F 500 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102459 restraints weight = 44068.509| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.89 r_work: 0.3064 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31932 Z= 0.147 Angle : 0.610 7.412 43428 Z= 0.313 Chirality : 0.044 0.211 4914 Planarity : 0.006 0.049 5610 Dihedral : 10.497 135.277 4878 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.26 % Allowed : 8.29 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.65 (0.12), residues: 4056 helix: -0.81 (0.13), residues: 1380 sheet: -2.93 (0.16), residues: 798 loop : -1.84 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 281 TYR 0.014 0.002 TYR B 110 PHE 0.032 0.002 PHE C 595 TRP 0.019 0.002 TRP E 651 HIS 0.011 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (31932) covalent geometry : angle 0.60952 / 0.31 (43428) hydrogen bonds : bond 0.03804 / 2.61 ( 1200) hydrogen bonds : angle 5.80923 / 4.07 ( 3513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 444 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7953 (tp30) cc_final: 0.7664 (tp30) REVERT: B 41 MET cc_start: 0.8548 (mmt) cc_final: 0.8267 (mmt) REVERT: B 309 ASN cc_start: 0.8649 (m110) cc_final: 0.8354 (m110) REVERT: B 321 LYS cc_start: 0.8722 (mttp) cc_final: 0.7902 (mtpp) REVERT: B 333 LYS cc_start: 0.8316 (mttt) cc_final: 0.7922 (mttp) REVERT: B 505 MET cc_start: 0.9152 (tpp) cc_final: 0.8839 (mmp) REVERT: B 631 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8570 (mttt) REVERT: C 20 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7751 (mtm-85) REVERT: C 321 LYS cc_start: 0.8726 (mttp) cc_final: 0.7733 (ttpp) REVERT: C 333 LYS cc_start: 0.8338 (mttt) cc_final: 0.7964 (mttp) REVERT: C 410 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7854 (tpp80) REVERT: C 538 ASP cc_start: 0.8509 (m-30) cc_final: 0.8287 (m-30) REVERT: D 321 LYS cc_start: 0.8756 (mttp) cc_final: 0.8526 (mtmt) REVERT: E 166 GLU cc_start: 0.8288 (pp20) cc_final: 0.8004 (pp20) REVERT: E 309 ASN cc_start: 0.8555 (m110) cc_final: 0.8303 (m110) REVERT: E 321 LYS cc_start: 0.8971 (mttp) cc_final: 0.8166 (ttpp) REVERT: E 333 LYS cc_start: 0.8366 (mttt) cc_final: 0.7839 (mmmt) REVERT: E 465 SER cc_start: 0.8809 (m) cc_final: 0.8311 (p) REVERT: E 654 GLU cc_start: 0.8051 (tt0) cc_final: 0.7702 (mp0) REVERT: F 83 TYR cc_start: 0.8319 (m-80) cc_final: 0.8069 (m-80) REVERT: F 221 HIS cc_start: 0.8512 (m170) cc_final: 0.8193 (m170) REVERT: F 285 ARG cc_start: 0.7960 (ttp-110) cc_final: 0.7648 (ptp-170) REVERT: F 345 ASP cc_start: 0.8438 (m-30) cc_final: 0.8056 (m-30) REVERT: F 351 ASN cc_start: 0.9036 (m110) cc_final: 0.8802 (m-40) REVERT: F 511 LYS cc_start: 0.8909 (mttt) cc_final: 0.8667 (mtpt) REVERT: F 528 ARG cc_start: 0.8852 (mtt-85) cc_final: 0.7846 (mmp80) REVERT: F 607 TYR cc_start: 0.8972 (t80) cc_final: 0.8645 (t80) REVERT: F 644 LYS cc_start: 0.8680 (mptm) cc_final: 0.8466 (mmmt) outliers start: 40 outliers final: 17 residues processed: 473 average time/residue: 0.2274 time to fit residues: 164.9135 Evaluate side-chains 354 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 336 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 631 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 104 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 320 optimal weight: 0.0060 chunk 127 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 HIS B 155 ASN B 191 GLN B 339 ASN B 384 GLN C 155 ASN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS D 500 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 261 ASN E 659 HIS F 158 ASN F 245 ASN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101601 restraints weight = 44343.354| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.89 r_work: 0.3049 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31932 Z= 0.132 Angle : 0.564 8.728 43428 Z= 0.287 Chirality : 0.043 0.200 4914 Planarity : 0.005 0.046 5610 Dihedral : 9.861 131.835 4878 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.35 % Allowed : 9.96 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.98 (0.13), residues: 4056 helix: -0.01 (0.14), residues: 1386 sheet: -2.70 (0.16), residues: 798 loop : -1.59 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 116 TYR 0.018 0.001 TYR B 564 PHE 0.028 0.002 PHE F 595 TRP 0.015 0.002 TRP E 651 HIS 0.009 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (31932) covalent geometry : angle 0.56396 / 0.29 (43428) hydrogen bonds : bond 0.03162 / 2.15 ( 1200) hydrogen bonds : angle 5.30124 / 3.71 ( 3513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 379 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 282 GLU cc_start: 0.7871 (tp30) cc_final: 0.7603 (tp30) REVERT: A 644 LYS cc_start: 0.8546 (mptm) cc_final: 0.8315 (mmmt) REVERT: B 41 MET cc_start: 0.8514 (mmt) cc_final: 0.8281 (mmt) REVERT: B 321 LYS cc_start: 0.8680 (mttp) cc_final: 0.8210 (mtpp) REVERT: B 358 CYS cc_start: 0.8039 (t) cc_final: 0.7818 (t) REVERT: B 505 MET cc_start: 0.9170 (tpp) cc_final: 0.8859 (mmp) REVERT: C 321 LYS cc_start: 0.8730 (mttp) cc_final: 0.7835 (ttpp) REVERT: C 333 LYS cc_start: 0.8282 (mttt) cc_final: 0.7922 (mttp) REVERT: C 538 ASP cc_start: 0.8521 (m-30) cc_final: 0.8287 (m-30) REVERT: D 40 ASP cc_start: 0.7307 (p0) cc_final: 0.7081 (p0) REVERT: D 50 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: D 110 TYR cc_start: 0.9018 (m-80) cc_final: 0.8569 (m-80) REVERT: D 285 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7590 (ptp-170) REVERT: D 321 LYS cc_start: 0.8722 (mttp) cc_final: 0.8500 (mtmt) REVERT: E 166 GLU cc_start: 0.8243 (pp20) cc_final: 0.8006 (pp20) REVERT: E 309 ASN cc_start: 0.8454 (m110) cc_final: 0.8248 (m110) REVERT: E 321 LYS cc_start: 0.8959 (mttp) cc_final: 0.8108 (ttpp) REVERT: E 465 SER cc_start: 0.8774 (m) cc_final: 0.8263 (p) REVERT: E 654 GLU cc_start: 0.8108 (tt0) cc_final: 0.7821 (mp0) REVERT: F 7 PHE cc_start: 0.8426 (t80) cc_final: 0.8154 (t80) REVERT: F 281 ARG cc_start: 0.8141 (ttm170) cc_final: 0.7777 (tmm160) REVERT: F 511 LYS cc_start: 0.8883 (mttt) cc_final: 0.8611 (mtpt) REVERT: F 528 ARG cc_start: 0.8852 (mtt-85) cc_final: 0.7852 (mmp80) REVERT: F 607 TYR cc_start: 0.8937 (t80) cc_final: 0.8684 (t80) REVERT: F 644 LYS cc_start: 0.8660 (mptm) cc_final: 0.8443 (mmmt) outliers start: 43 outliers final: 23 residues processed: 412 average time/residue: 0.2156 time to fit residues: 139.6223 Evaluate side-chains 354 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 622 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 200 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 158 ASN B 339 ASN B 384 GLN B 409 GLN ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 450 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN F 525 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096006 restraints weight = 44282.331| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.88 r_work: 0.2928 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 31932 Z= 0.260 Angle : 0.653 8.206 43428 Z= 0.330 Chirality : 0.047 0.215 4914 Planarity : 0.005 0.062 5610 Dihedral : 9.966 137.638 4878 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.36 % Allowed : 11.03 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.84 (0.12), residues: 4056 helix: 0.16 (0.14), residues: 1410 sheet: -2.49 (0.17), residues: 726 loop : -1.70 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 116 TYR 0.018 0.002 TYR C 110 PHE 0.027 0.002 PHE D 595 TRP 0.022 0.002 TRP A 124 HIS 0.007 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (31932) covalent geometry : angle 0.65313 / 0.33 (43428) hydrogen bonds : bond 0.03537 / 2.39 ( 1200) hydrogen bonds : angle 5.27693 / 3.72 ( 3513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 359 time to evaluate : 1.141 Fit side-chains REVERT: A 40 ASP cc_start: 0.7528 (p0) cc_final: 0.7262 (p0) REVERT: A 50 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: A 282 GLU cc_start: 0.7890 (tp30) cc_final: 0.7633 (tp30) REVERT: A 285 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7897 (ptp-170) REVERT: A 522 ASP cc_start: 0.7512 (p0) cc_final: 0.6857 (m-30) REVERT: A 567 MET cc_start: 0.8563 (mmp) cc_final: 0.8154 (mmm) REVERT: A 654 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: B 166 GLU cc_start: 0.8493 (pp20) cc_final: 0.8039 (pp20) REVERT: B 309 ASN cc_start: 0.8746 (m-40) cc_final: 0.8400 (m110) REVERT: B 321 LYS cc_start: 0.8649 (mttp) cc_final: 0.7883 (mtpp) REVERT: B 333 LYS cc_start: 0.8392 (mttt) cc_final: 0.7951 (mttp) REVERT: C 321 LYS cc_start: 0.8612 (mttp) cc_final: 0.7673 (ttpp) REVERT: C 333 LYS cc_start: 0.8327 (mttt) cc_final: 0.7943 (mttp) REVERT: C 341 GLU cc_start: 0.7603 (tp30) cc_final: 0.7372 (tp30) REVERT: C 538 ASP cc_start: 0.8614 (m-30) cc_final: 0.8345 (m-30) REVERT: D 50 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: D 127 ASP cc_start: 0.8275 (m-30) cc_final: 0.7928 (m-30) REVERT: D 321 LYS cc_start: 0.8771 (mttp) cc_final: 0.8566 (mtmt) REVERT: E 134 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8583 (mmmt) REVERT: E 191 GLN cc_start: 0.8435 (tt0) cc_final: 0.8185 (tt0) REVERT: E 321 LYS cc_start: 0.8977 (mttp) cc_final: 0.8057 (ttpp) REVERT: E 465 SER cc_start: 0.8947 (m) cc_final: 0.8391 (p) REVERT: E 632 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8275 (mtp-110) REVERT: E 654 GLU cc_start: 0.8336 (tt0) cc_final: 0.8063 (mp0) REVERT: F 32 TRP cc_start: 0.7855 (m100) cc_final: 0.6942 (m100) REVERT: F 50 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: F 281 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7743 (tmm160) REVERT: F 511 LYS cc_start: 0.8992 (mttt) cc_final: 0.8648 (mtmt) REVERT: F 644 LYS cc_start: 0.8676 (mptm) cc_final: 0.8449 (mmmt) outliers start: 75 outliers final: 48 residues processed: 418 average time/residue: 0.2129 time to fit residues: 139.5045 Evaluate side-chains 379 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 156 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN B 158 ASN B 191 GLN B 384 GLN ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 158 ASN ** E 566 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.125837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097861 restraints weight = 44396.062| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.88 r_work: 0.2979 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31932 Z= 0.168 Angle : 0.578 8.969 43428 Z= 0.292 Chirality : 0.043 0.158 4914 Planarity : 0.005 0.067 5610 Dihedral : 9.606 135.703 4878 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.02 % Allowed : 12.16 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.57 (0.13), residues: 4056 helix: 0.50 (0.14), residues: 1398 sheet: -2.44 (0.17), residues: 750 loop : -1.57 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 361 TYR 0.013 0.002 TYR C 110 PHE 0.027 0.002 PHE F 595 TRP 0.011 0.001 TRP A 124 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (31932) covalent geometry : angle 0.57773 / 0.29 (43428) hydrogen bonds : bond 0.03063 / 2.07 ( 1200) hydrogen bonds : angle 5.05130 / 3.55 ( 3513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 361 time to evaluate : 1.083 Fit side-chains REVERT: A 189 LEU cc_start: 0.8488 (tp) cc_final: 0.8189 (tp) REVERT: A 282 GLU cc_start: 0.7876 (tp30) cc_final: 0.7585 (tp30) REVERT: A 285 ARG cc_start: 0.8241 (ptp-170) cc_final: 0.7998 (ptp-170) REVERT: A 522 ASP cc_start: 0.7542 (p0) cc_final: 0.6799 (m-30) REVERT: A 567 MET cc_start: 0.8486 (mmp) cc_final: 0.8003 (mmm) REVERT: B 166 GLU cc_start: 0.8345 (pp20) cc_final: 0.8035 (pp20) REVERT: B 309 ASN cc_start: 0.8732 (m-40) cc_final: 0.8403 (m110) REVERT: B 321 LYS cc_start: 0.8645 (mttp) cc_final: 0.7839 (mtpp) REVERT: B 333 LYS cc_start: 0.8367 (mttt) cc_final: 0.7899 (mttp) REVERT: B 341 GLU cc_start: 0.7332 (tp30) cc_final: 0.7066 (tp30) REVERT: C 321 LYS cc_start: 0.8586 (mttp) cc_final: 0.7629 (ttpp) REVERT: C 333 LYS cc_start: 0.8337 (mttt) cc_final: 0.7864 (mttp) REVERT: C 341 GLU cc_start: 0.7588 (tp30) cc_final: 0.7386 (tp30) REVERT: C 467 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9032 (mm) REVERT: C 538 ASP cc_start: 0.8577 (m-30) cc_final: 0.8297 (m-30) REVERT: D 50 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: D 321 LYS cc_start: 0.8783 (mttp) cc_final: 0.8530 (mtmt) REVERT: D 551 ASP cc_start: 0.8565 (m-30) cc_final: 0.8335 (m-30) REVERT: E 321 LYS cc_start: 0.8922 (mttp) cc_final: 0.7913 (ttpp) REVERT: E 465 SER cc_start: 0.8974 (m) cc_final: 0.8447 (p) REVERT: E 654 GLU cc_start: 0.8308 (tt0) cc_final: 0.8030 (mp0) REVERT: F 32 TRP cc_start: 0.7809 (m100) cc_final: 0.6993 (m100) REVERT: F 40 ASP cc_start: 0.7296 (p0) cc_final: 0.6982 (p0) REVERT: F 50 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: F 281 ARG cc_start: 0.8096 (ttm170) cc_final: 0.7803 (tmm160) REVERT: F 351 ASN cc_start: 0.9056 (m110) cc_final: 0.8758 (m-40) REVERT: F 511 LYS cc_start: 0.8966 (mttt) cc_final: 0.8611 (mtmt) REVERT: F 644 LYS cc_start: 0.8689 (mptm) cc_final: 0.8412 (mmmt) outliers start: 64 outliers final: 47 residues processed: 408 average time/residue: 0.2082 time to fit residues: 133.4758 Evaluate side-chains 379 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 51 optimal weight: 0.0270 chunk 283 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 397 optimal weight: 0.5980 chunk 240 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 GLN ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098739 restraints weight = 44103.797| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.88 r_work: 0.3007 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31932 Z= 0.139 Angle : 0.565 9.025 43428 Z= 0.284 Chirality : 0.043 0.154 4914 Planarity : 0.004 0.052 5610 Dihedral : 9.280 134.022 4878 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.11 % Allowed : 12.38 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.38 (0.13), residues: 4056 helix: 0.71 (0.14), residues: 1398 sheet: -2.40 (0.17), residues: 762 loop : -1.47 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 116 TYR 0.014 0.002 TYR C 607 PHE 0.026 0.002 PHE F 595 TRP 0.010 0.001 TRP E 651 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (31932) covalent geometry : angle 0.56520 / 0.28 (43428) hydrogen bonds : bond 0.02891 / 1.95 ( 1200) hydrogen bonds : angle 4.92471 / 3.47 ( 3513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7406 (p0) cc_final: 0.7064 (p0) REVERT: A 116 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8163 (mtp-110) REVERT: A 189 LEU cc_start: 0.8460 (tp) cc_final: 0.8222 (tp) REVERT: A 282 GLU cc_start: 0.7841 (tp30) cc_final: 0.7516 (tp30) REVERT: A 285 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7908 (ptp-170) REVERT: A 522 ASP cc_start: 0.7537 (p0) cc_final: 0.6772 (m-30) REVERT: A 540 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9275 (tp) REVERT: B 166 GLU cc_start: 0.8314 (pp20) cc_final: 0.8045 (pp20) REVERT: B 309 ASN cc_start: 0.8738 (m-40) cc_final: 0.8409 (m110) REVERT: B 333 LYS cc_start: 0.8341 (mttt) cc_final: 0.7872 (mttp) REVERT: B 341 GLU cc_start: 0.7499 (tp30) cc_final: 0.7192 (tp30) REVERT: C 321 LYS cc_start: 0.8568 (mttp) cc_final: 0.7646 (ttpp) REVERT: C 333 LYS cc_start: 0.8299 (mttt) cc_final: 0.7817 (mttp) REVERT: C 467 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9018 (mm) REVERT: C 538 ASP cc_start: 0.8520 (m-30) cc_final: 0.8243 (m-30) REVERT: D 50 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: D 59 MET cc_start: 0.9376 (mtp) cc_final: 0.9117 (mtm) REVERT: D 127 ASP cc_start: 0.8197 (m-30) cc_final: 0.7955 (m-30) REVERT: D 321 LYS cc_start: 0.8750 (mttp) cc_final: 0.8504 (mtmt) REVERT: D 551 ASP cc_start: 0.8568 (m-30) cc_final: 0.8307 (m-30) REVERT: E 118 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9093 (mp) REVERT: E 321 LYS cc_start: 0.8856 (mttp) cc_final: 0.7697 (ttpp) REVERT: E 465 SER cc_start: 0.8977 (m) cc_final: 0.8452 (p) REVERT: E 467 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9130 (mm) REVERT: E 654 GLU cc_start: 0.8281 (tt0) cc_final: 0.7812 (mt-10) REVERT: F 32 TRP cc_start: 0.7771 (m100) cc_final: 0.6992 (m100) REVERT: F 40 ASP cc_start: 0.7169 (p0) cc_final: 0.6891 (p0) REVERT: F 50 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: F 281 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7795 (tmm160) REVERT: F 511 LYS cc_start: 0.8939 (mttt) cc_final: 0.8569 (mtmt) REVERT: F 644 LYS cc_start: 0.8648 (mptm) cc_final: 0.8416 (mmmt) outliers start: 67 outliers final: 48 residues processed: 407 average time/residue: 0.2104 time to fit residues: 134.7767 Evaluate side-chains 383 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 329 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 30 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 47 optimal weight: 0.0040 chunk 144 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 659 HIS B 158 ASN B 191 GLN B 339 ASN ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.095931 restraints weight = 44395.311| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.87 r_work: 0.2937 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31932 Z= 0.224 Angle : 0.626 10.099 43428 Z= 0.313 Chirality : 0.045 0.153 4914 Planarity : 0.005 0.051 5610 Dihedral : 9.433 138.679 4878 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.55 % Allowed : 12.82 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.35 (0.13), residues: 4056 helix: 0.65 (0.14), residues: 1398 sheet: -2.28 (0.17), residues: 750 loop : -1.42 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 116 TYR 0.014 0.002 TYR E 110 PHE 0.025 0.002 PHE F 595 TRP 0.020 0.002 TRP F 97 HIS 0.005 0.001 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (31932) covalent geometry : angle 0.62606 / 0.31 (43428) hydrogen bonds : bond 0.03243 / 2.19 ( 1200) hydrogen bonds : angle 5.02723 / 3.54 ( 3513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 344 time to evaluate : 1.147 Fit side-chains REVERT: A 40 ASP cc_start: 0.7356 (p0) cc_final: 0.6951 (p0) REVERT: A 189 LEU cc_start: 0.8488 (tp) cc_final: 0.8208 (tp) REVERT: A 282 GLU cc_start: 0.7891 (tp30) cc_final: 0.7602 (tp30) REVERT: A 522 ASP cc_start: 0.7668 (p0) cc_final: 0.6931 (m-30) REVERT: A 540 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9247 (tp) REVERT: B 166 GLU cc_start: 0.8393 (pp20) cc_final: 0.8010 (pp20) REVERT: B 309 ASN cc_start: 0.8737 (m-40) cc_final: 0.8417 (m110) REVERT: B 321 LYS cc_start: 0.8682 (mttp) cc_final: 0.7348 (ttpt) REVERT: B 333 LYS cc_start: 0.8349 (mttt) cc_final: 0.7880 (mttp) REVERT: B 341 GLU cc_start: 0.7502 (tp30) cc_final: 0.7249 (tp30) REVERT: C 16 ARG cc_start: 0.6903 (mmp80) cc_final: 0.6669 (mmp80) REVERT: C 134 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8555 (mmmt) REVERT: C 321 LYS cc_start: 0.8589 (mttp) cc_final: 0.7674 (ttpp) REVERT: C 333 LYS cc_start: 0.8335 (mttt) cc_final: 0.7880 (mttp) REVERT: C 334 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: C 467 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9133 (mm) REVERT: D 40 ASP cc_start: 0.7325 (p0) cc_final: 0.7086 (p0) REVERT: D 50 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: D 321 LYS cc_start: 0.8773 (mttp) cc_final: 0.8504 (mtmt) REVERT: D 551 ASP cc_start: 0.8592 (m-30) cc_final: 0.8310 (m-30) REVERT: E 118 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9160 (mp) REVERT: E 134 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8584 (mmmt) REVERT: E 158 ASN cc_start: 0.8738 (m110) cc_final: 0.8524 (m-40) REVERT: E 166 GLU cc_start: 0.8383 (pp20) cc_final: 0.8006 (pp20) REVERT: E 321 LYS cc_start: 0.8852 (mttp) cc_final: 0.7770 (ttpp) REVERT: E 465 SER cc_start: 0.9034 (m) cc_final: 0.8472 (p) REVERT: E 467 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9193 (mm) REVERT: E 654 GLU cc_start: 0.8362 (tt0) cc_final: 0.8091 (mp0) REVERT: F 50 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: F 281 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7907 (tmm160) REVERT: F 511 LYS cc_start: 0.9012 (mttt) cc_final: 0.8635 (mtmt) REVERT: F 644 LYS cc_start: 0.8623 (mptm) cc_final: 0.8393 (mmmt) outliers start: 81 outliers final: 55 residues processed: 406 average time/residue: 0.2023 time to fit residues: 130.4500 Evaluate side-chains 390 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 44 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 185 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 155 optimal weight: 0.0370 chunk 189 optimal weight: 1.9990 overall best weight: 1.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097407 restraints weight = 44237.882| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.87 r_work: 0.2973 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31932 Z= 0.170 Angle : 0.593 9.918 43428 Z= 0.298 Chirality : 0.044 0.196 4914 Planarity : 0.005 0.056 5610 Dihedral : 9.246 137.219 4878 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.49 % Allowed : 13.26 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.13), residues: 4056 helix: 0.74 (0.14), residues: 1398 sheet: -2.23 (0.17), residues: 750 loop : -1.38 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 116 TYR 0.018 0.002 TYR E 607 PHE 0.025 0.002 PHE F 595 TRP 0.017 0.001 TRP F 97 HIS 0.005 0.001 HIS C 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (31932) covalent geometry : angle 0.59267 / 0.30 (43428) hydrogen bonds : bond 0.03019 / 2.04 ( 1200) hydrogen bonds : angle 4.95229 / 3.49 ( 3513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 347 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7868 (tp30) cc_final: 0.7546 (tp30) REVERT: A 285 ARG cc_start: 0.8296 (ptp-170) cc_final: 0.8081 (ptp-170) REVERT: A 361 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6522 (ttt180) REVERT: A 522 ASP cc_start: 0.7608 (p0) cc_final: 0.6906 (m-30) REVERT: A 540 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9242 (tp) REVERT: B 166 GLU cc_start: 0.8358 (pp20) cc_final: 0.8022 (pp20) REVERT: B 309 ASN cc_start: 0.8723 (m-40) cc_final: 0.8416 (m110) REVERT: B 333 LYS cc_start: 0.8342 (mttt) cc_final: 0.7928 (mttp) REVERT: B 339 ASN cc_start: 0.8090 (m-40) cc_final: 0.7841 (m-40) REVERT: B 341 GLU cc_start: 0.7556 (tp30) cc_final: 0.7300 (tp30) REVERT: C 134 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8554 (mmmt) REVERT: C 166 GLU cc_start: 0.8299 (pp20) cc_final: 0.8013 (pp20) REVERT: C 220 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: C 321 LYS cc_start: 0.8554 (mttp) cc_final: 0.7548 (ttpp) REVERT: C 333 LYS cc_start: 0.8298 (mttt) cc_final: 0.7856 (mttp) REVERT: C 467 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9068 (mm) REVERT: C 538 ASP cc_start: 0.8503 (m-30) cc_final: 0.8240 (m-30) REVERT: D 46 GLN cc_start: 0.8432 (mm110) cc_final: 0.8103 (mm-40) REVERT: D 50 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: D 59 MET cc_start: 0.9386 (mtp) cc_final: 0.9142 (mtm) REVERT: D 189 LEU cc_start: 0.8408 (tp) cc_final: 0.8161 (tp) REVERT: D 321 LYS cc_start: 0.8724 (mttp) cc_final: 0.8470 (mtmt) REVERT: E 118 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9143 (mp) REVERT: E 166 GLU cc_start: 0.8297 (pp20) cc_final: 0.7988 (pp20) REVERT: E 465 SER cc_start: 0.8996 (m) cc_final: 0.8445 (p) REVERT: E 467 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9145 (mm) REVERT: E 654 GLU cc_start: 0.8339 (tt0) cc_final: 0.8057 (mp0) REVERT: F 50 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: F 281 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7905 (tmm160) REVERT: F 511 LYS cc_start: 0.8957 (mttt) cc_final: 0.8568 (mtmt) REVERT: F 644 LYS cc_start: 0.8603 (mptm) cc_final: 0.8374 (mmmt) outliers start: 79 outliers final: 54 residues processed: 406 average time/residue: 0.2069 time to fit residues: 132.2331 Evaluate side-chains 397 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 336 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 381 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN B 46 GLN B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 450 GLN ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 463 HIS ** 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 = 0.3511 r_free = 0.3511 target = 0.126253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.098267 restraints weight = 44221.336| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.87 r_work: 0.3000 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31932 Z= 0.146 Angle : 0.583 9.968 43428 Z= 0.294 Chirality : 0.044 0.225 4914 Planarity : 0.004 0.059 5610 Dihedral : 9.063 136.136 4878 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.17 % Allowed : 13.71 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.21 (0.13), residues: 4056 helix: 0.82 (0.14), residues: 1398 sheet: -2.27 (0.17), residues: 780 loop : -1.33 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 116 TYR 0.025 0.002 TYR E 607 PHE 0.025 0.001 PHE F 595 TRP 0.020 0.001 TRP F 97 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (31932) covalent geometry : angle 0.58318 / 0.29 (43428) hydrogen bonds : bond 0.02906 / 1.95 ( 1200) hydrogen bonds : angle 4.87247 / 3.42 ( 3513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 351 time to evaluate : 1.163 Fit side-chains REVERT: A 282 GLU cc_start: 0.7870 (tp30) cc_final: 0.7535 (tp30) REVERT: A 285 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.8056 (ptp-170) REVERT: A 522 ASP cc_start: 0.7649 (p0) cc_final: 0.6839 (m-30) REVERT: A 540 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9253 (tp) REVERT: B 166 GLU cc_start: 0.8326 (pp20) cc_final: 0.8035 (pp20) REVERT: B 220 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8475 (t0) REVERT: B 309 ASN cc_start: 0.8738 (m-40) cc_final: 0.8432 (m110) REVERT: B 333 LYS cc_start: 0.8308 (mttt) cc_final: 0.7912 (mttp) REVERT: B 341 GLU cc_start: 0.7528 (tp30) cc_final: 0.7316 (tp30) REVERT: C 134 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8554 (mmmt) REVERT: C 220 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8488 (m-30) REVERT: C 321 LYS cc_start: 0.8559 (mttp) cc_final: 0.7532 (ttpp) REVERT: C 333 LYS cc_start: 0.8342 (mttt) cc_final: 0.7891 (mttp) REVERT: C 467 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9054 (mm) REVERT: C 538 ASP cc_start: 0.8487 (m-30) cc_final: 0.8209 (m-30) REVERT: D 32 TRP cc_start: 0.8160 (m100) cc_final: 0.7842 (m100) REVERT: D 46 GLN cc_start: 0.8369 (mm110) cc_final: 0.8087 (mm-40) REVERT: D 50 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: D 59 MET cc_start: 0.9372 (mtp) cc_final: 0.9096 (mtm) REVERT: D 321 LYS cc_start: 0.8698 (mttp) cc_final: 0.8435 (mtmt) REVERT: E 118 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9116 (mp) REVERT: E 158 ASN cc_start: 0.8477 (m110) cc_final: 0.8230 (m-40) REVERT: E 166 GLU cc_start: 0.8232 (pp20) cc_final: 0.7978 (pp20) REVERT: E 465 SER cc_start: 0.8970 (m) cc_final: 0.8430 (p) REVERT: E 467 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9124 (mm) REVERT: E 654 GLU cc_start: 0.8359 (tt0) cc_final: 0.7888 (mt-10) REVERT: F 50 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: F 193 MET cc_start: 0.8711 (ttm) cc_final: 0.8501 (ttm) REVERT: F 281 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7899 (tmm160) REVERT: F 511 LYS cc_start: 0.8953 (mttt) cc_final: 0.8577 (mtmt) REVERT: F 644 LYS cc_start: 0.8595 (mptm) cc_final: 0.8363 (mmmt) outliers start: 69 outliers final: 54 residues processed: 404 average time/residue: 0.2081 time to fit residues: 132.6901 Evaluate side-chains 391 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 241 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 281 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.126444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.098462 restraints weight = 44057.270| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.87 r_work: 0.3001 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31932 Z= 0.148 Angle : 0.593 10.004 43428 Z= 0.299 Chirality : 0.044 0.254 4914 Planarity : 0.004 0.064 5610 Dihedral : 8.994 136.272 4878 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 13.96 % Favored : 83.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.14 (0.13), residues: 4056 helix: 0.85 (0.14), residues: 1398 sheet: -2.18 (0.17), residues: 774 loop : -1.30 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 116 TYR 0.024 0.002 TYR E 607 PHE 0.025 0.002 PHE F 595 TRP 0.021 0.001 TRP F 97 HIS 0.004 0.001 HIS D 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (31932) covalent geometry : angle 0.59331 / 0.30 (43428) hydrogen bonds : bond 0.02904 / 1.96 ( 1200) hydrogen bonds : angle 4.85879 / 3.41 ( 3513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 1.141 Fit side-chains REVERT: A 282 GLU cc_start: 0.7884 (tp30) cc_final: 0.7542 (tp30) REVERT: A 285 ARG cc_start: 0.8300 (ptp-170) cc_final: 0.8071 (ptp-170) REVERT: A 522 ASP cc_start: 0.7666 (p0) cc_final: 0.6857 (m-30) REVERT: A 540 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9251 (tp) REVERT: B 166 GLU cc_start: 0.8306 (pp20) cc_final: 0.8020 (pp20) REVERT: B 220 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8454 (t0) REVERT: B 309 ASN cc_start: 0.8744 (m-40) cc_final: 0.8452 (m110) REVERT: B 333 LYS cc_start: 0.8288 (mttt) cc_final: 0.7882 (mttm) REVERT: B 341 GLU cc_start: 0.7515 (tp30) cc_final: 0.7204 (tp30) REVERT: C 134 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8539 (mmmt) REVERT: C 220 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8492 (m-30) REVERT: C 321 LYS cc_start: 0.8542 (mttp) cc_final: 0.7494 (ttpp) REVERT: C 333 LYS cc_start: 0.8319 (mttt) cc_final: 0.7900 (mttp) REVERT: C 467 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9065 (mm) REVERT: C 505 MET cc_start: 0.9127 (tpp) cc_final: 0.8851 (mmp) REVERT: C 538 ASP cc_start: 0.8495 (m-30) cc_final: 0.8218 (m-30) REVERT: D 32 TRP cc_start: 0.8167 (m100) cc_final: 0.7845 (m100) REVERT: D 46 GLN cc_start: 0.8367 (mm110) cc_final: 0.8074 (mm-40) REVERT: D 50 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: D 59 MET cc_start: 0.9401 (mtp) cc_final: 0.9133 (mtm) REVERT: D 321 LYS cc_start: 0.8696 (mttp) cc_final: 0.8442 (mtmt) REVERT: E 118 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9112 (mp) REVERT: E 166 GLU cc_start: 0.8155 (pp20) cc_final: 0.7930 (pp20) REVERT: E 465 SER cc_start: 0.8995 (m) cc_final: 0.8464 (p) REVERT: E 467 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9146 (mm) REVERT: E 654 GLU cc_start: 0.8307 (tt0) cc_final: 0.8007 (mp0) REVERT: F 50 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 83 TYR cc_start: 0.8370 (m-80) cc_final: 0.8127 (m-80) REVERT: F 193 MET cc_start: 0.8642 (ttm) cc_final: 0.8421 (ttm) REVERT: F 281 ARG cc_start: 0.8169 (ttm170) cc_final: 0.7898 (tmm160) REVERT: F 511 LYS cc_start: 0.8967 (mttt) cc_final: 0.8589 (mtmt) REVERT: F 644 LYS cc_start: 0.8597 (mptm) cc_final: 0.8367 (mmmt) outliers start: 68 outliers final: 57 residues processed: 400 average time/residue: 0.2049 time to fit residues: 129.5309 Evaluate side-chains 392 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 327 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 656 PHE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 533 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 225 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 129 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN D 339 ASN ** D 463 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.096802 restraints weight = 44620.423| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.81 r_work: 0.2969 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31932 Z= 0.121 Angle : 0.567 9.549 43428 Z= 0.286 Chirality : 0.043 0.237 4914 Planarity : 0.004 0.061 5610 Dihedral : 8.807 134.468 4878 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.98 % Allowed : 13.99 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.00 (0.13), residues: 4056 helix: 0.98 (0.14), residues: 1392 sheet: -2.07 (0.18), residues: 726 loop : -1.28 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 116 TYR 0.031 0.002 TYR C 607 PHE 0.024 0.001 PHE F 595 TRP 0.021 0.001 TRP F 97 HIS 0.004 0.001 HIS D 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (31932) covalent geometry : angle 0.56744 / 0.29 (43428) hydrogen bonds : bond 0.02761 / 1.86 ( 1200) hydrogen bonds : angle 4.78092 / 3.35 ( 3513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8553.32 seconds wall clock time: 147 minutes 9.75 seconds (8829.75 seconds total)