Starting phenix.real_space_refine on Fri Mar 6 13:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jqn_9875/03_2026/6jqn_9875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jqn_9875/03_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_9875/03_2026/6jqn_9875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jqn_9875/03_2026/6jqn_9875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jqn_9875/03_2026/6jqn_9875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jqn_9875/03_2026/6jqn_9875.map" } 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-dev-5986/lib/python3.9/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: 7.08, per 1000 atoms: 0.23 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 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: 1.17 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: 6.65 Time building geometry restraints manager: 3.72 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: 18924 28.90 - 57.80: 588 57.80 - 86.70: 86 86.70 - 115.60: 7 115.60 - 144.50: 3 Dihedral angle restraints: 19608 sinusoidal: 8088 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 19605 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: 6.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.470 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 13.287 144.502 12204 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 covalent geometry : bond 0.00779 (31932) covalent geometry : angle 1.04967 (43428) hydrogen bonds : bond 0.17319 ( 1200) hydrogen bonds : angle 8.59354 ( 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 : 1.247 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: 0.2315 time to fit residues: 272.4122 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 : 0.767 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 261 ASN 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 409 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: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.102434 restraints weight = 44058.591| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.89 r_work: 0.3041 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31932 Z= 0.147 Angle : 0.614 7.684 43428 Z= 0.315 Chirality : 0.044 0.207 4914 Planarity : 0.006 0.053 5610 Dihedral : 12.613 135.761 5154 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.23 % Allowed : 8.38 % Favored : 90.39 % 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: -2.66 (0.12), residues: 4056 helix: -0.82 (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 0.031 0.002 PHE C 595 TRP 0.019 0.002 TRP E 651 HIS 0.012 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00327 (31932) covalent geometry : angle 0.61365 (43428) hydrogen bonds : bond 0.03676 ( 1200) hydrogen bonds : angle 5.79831 ( 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 479 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 440 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7950 (tp30) cc_final: 0.7661 (tp30) REVERT: B 41 MET cc_start: 0.8553 (mmt) cc_final: 0.8288 (mmt) REVERT: B 309 ASN cc_start: 0.8640 (m110) cc_final: 0.8345 (m110) REVERT: B 321 LYS cc_start: 0.8723 (mttp) cc_final: 0.7906 (mtpp) REVERT: B 333 LYS cc_start: 0.8325 (mttt) cc_final: 0.7932 (mttp) REVERT: B 505 MET cc_start: 0.9157 (tpp) cc_final: 0.8849 (mmp) REVERT: B 631 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8582 (mttt) REVERT: C 20 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7770 (mtm-85) REVERT: C 51 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (tttp) REVERT: C 321 LYS cc_start: 0.8723 (mttp) cc_final: 0.7726 (ttpp) REVERT: C 333 LYS cc_start: 0.8339 (mttt) cc_final: 0.7966 (mttp) REVERT: C 410 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7838 (tpp80) REVERT: C 538 ASP cc_start: 0.8489 (m-30) cc_final: 0.8268 (m-30) REVERT: D 321 LYS cc_start: 0.8756 (mttp) cc_final: 0.8524 (mtmt) REVERT: E 166 GLU cc_start: 0.8288 (pp20) cc_final: 0.8001 (pp20) REVERT: E 309 ASN cc_start: 0.8557 (m110) cc_final: 0.8310 (m110) REVERT: E 321 LYS cc_start: 0.8966 (mttp) cc_final: 0.8144 (ttpp) REVERT: E 333 LYS cc_start: 0.8366 (mttt) cc_final: 0.7847 (mmmt) REVERT: E 465 SER cc_start: 0.8819 (m) cc_final: 0.8315 (p) REVERT: E 654 GLU cc_start: 0.8050 (tt0) cc_final: 0.7783 (mp0) REVERT: F 83 TYR cc_start: 0.8327 (m-80) cc_final: 0.8080 (m-80) REVERT: F 221 HIS cc_start: 0.8489 (m170) cc_final: 0.8209 (m170) REVERT: F 285 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7636 (ptp-170) REVERT: F 345 ASP cc_start: 0.8435 (m-30) cc_final: 0.8057 (m-30) REVERT: F 351 ASN cc_start: 0.9034 (m110) cc_final: 0.8806 (m-40) REVERT: F 511 LYS cc_start: 0.8900 (mttt) cc_final: 0.8654 (mtpt) REVERT: F 528 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.7851 (mmp80) outliers start: 39 outliers final: 16 residues processed: 468 average time/residue: 0.2250 time to fit residues: 161.2615 Evaluate side-chains 356 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 51 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: 1.9990 chunk 77 optimal weight: 4.9990 chunk 290 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 193 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN C 155 ASN C 659 HIS ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN D 463 HIS D 500 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 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 = 0.3549 r_free = 0.3549 target = 0.128966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101022 restraints weight = 44338.449| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.89 r_work: 0.3041 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31932 Z= 0.142 Angle : 0.569 8.380 43428 Z= 0.290 Chirality : 0.043 0.164 4914 Planarity : 0.005 0.048 5610 Dihedral : 11.808 131.750 5154 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.48 % Allowed : 9.83 % 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: -1.94 (0.12), residues: 4056 helix: 0.04 (0.14), residues: 1380 sheet: -2.58 (0.17), residues: 768 loop : -1.65 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 116 TYR 0.018 0.001 TYR B 564 PHE 0.029 0.002 PHE F 595 TRP 0.015 0.002 TRP C 124 HIS 0.008 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00323 (31932) covalent geometry : angle 0.56868 (43428) hydrogen bonds : bond 0.03180 ( 1200) hydrogen bonds : angle 5.29041 ( 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 434 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 387 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.7862 (tp30) cc_final: 0.7614 (tp30) REVERT: A 528 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8616 (mtt-85) REVERT: A 644 LYS cc_start: 0.8572 (mptm) cc_final: 0.8337 (mmmt) REVERT: B 41 MET cc_start: 0.8508 (mmt) cc_final: 0.8296 (mmt) REVERT: B 321 LYS cc_start: 0.8674 (mttp) cc_final: 0.8208 (mtpp) REVERT: B 358 CYS cc_start: 0.8056 (t) cc_final: 0.7840 (t) REVERT: B 505 MET cc_start: 0.9177 (tpp) cc_final: 0.8870 (mmp) REVERT: C 321 LYS cc_start: 0.8741 (mttp) cc_final: 0.7878 (ttpp) REVERT: C 333 LYS cc_start: 0.8278 (mttt) cc_final: 0.7907 (mttp) REVERT: C 345 ASP cc_start: 0.8534 (m-30) cc_final: 0.8294 (m-30) REVERT: C 538 ASP cc_start: 0.8485 (m-30) cc_final: 0.8251 (m-30) REVERT: D 40 ASP cc_start: 0.7311 (p0) cc_final: 0.7093 (p0) REVERT: D 50 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: D 59 MET cc_start: 0.9408 (mtp) cc_final: 0.9168 (mtm) REVERT: D 285 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7637 (ptp-170) REVERT: D 321 LYS cc_start: 0.8742 (mttp) cc_final: 0.8509 (mtmt) REVERT: D 334 MET cc_start: 0.8352 (ttm) cc_final: 0.8152 (ttp) REVERT: E 166 GLU cc_start: 0.8240 (pp20) cc_final: 0.7926 (pp20) REVERT: E 309 ASN cc_start: 0.8498 (m110) cc_final: 0.8295 (m110) REVERT: E 321 LYS cc_start: 0.8969 (mttp) cc_final: 0.8118 (ttpp) REVERT: E 465 SER cc_start: 0.8790 (m) cc_final: 0.8279 (p) REVERT: E 654 GLU cc_start: 0.8130 (tt0) cc_final: 0.7891 (mp0) REVERT: F 7 PHE cc_start: 0.8415 (t80) cc_final: 0.8189 (t80) REVERT: F 281 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7734 (tmm160) REVERT: F 511 LYS cc_start: 0.8898 (mttt) cc_final: 0.8621 (mtpt) REVERT: F 528 ARG cc_start: 0.8870 (mtt-85) cc_final: 0.7877 (mmp80) REVERT: F 607 TYR cc_start: 0.8941 (t80) cc_final: 0.8702 (t80) outliers start: 47 outliers final: 28 residues processed: 423 average time/residue: 0.2045 time to fit residues: 136.3849 Evaluate side-chains 357 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 328 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 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 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 622 ASP Chi-restraints excluded: chain E residue 656 PHE 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 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: 2.9990 chunk 331 optimal weight: 0.0470 chunk 281 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 358 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 339 ASN F 450 GLN F 525 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097006 restraints weight = 44215.155| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.88 r_work: 0.2965 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31932 Z= 0.227 Angle : 0.630 8.661 43428 Z= 0.317 Chirality : 0.046 0.160 4914 Planarity : 0.005 0.049 5610 Dihedral : 11.773 136.012 5154 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.21 % Allowed : 10.93 % Favored : 86.86 % 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: -1.75 (0.13), residues: 4056 helix: 0.23 (0.14), residues: 1416 sheet: -2.47 (0.17), residues: 726 loop : -1.64 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 116 TYR 0.017 0.002 TYR C 110 PHE 0.026 0.002 PHE F 595 TRP 0.020 0.002 TRP A 124 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00530 (31932) covalent geometry : angle 0.62991 (43428) hydrogen bonds : bond 0.03365 ( 1200) hydrogen bonds : angle 5.20354 ( 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 428 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 358 time to evaluate : 0.894 Fit side-chains REVERT: A 282 GLU cc_start: 0.7879 (tp30) cc_final: 0.7575 (tp30) REVERT: A 285 ARG cc_start: 0.8213 (ptp-170) cc_final: 0.7874 (ptp-170) REVERT: A 522 ASP cc_start: 0.7509 (p0) cc_final: 0.6799 (m-30) REVERT: A 654 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 166 GLU cc_start: 0.8493 (pp20) cc_final: 0.8044 (pp20) REVERT: B 309 ASN cc_start: 0.8732 (m-40) cc_final: 0.8401 (m110) REVERT: B 321 LYS cc_start: 0.8578 (mttp) cc_final: 0.7813 (mtpp) REVERT: B 333 LYS cc_start: 0.8375 (mttt) cc_final: 0.7937 (mttp) REVERT: B 334 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8779 (ttm) REVERT: C 321 LYS cc_start: 0.8607 (mttp) cc_final: 0.7708 (ttpp) REVERT: C 333 LYS cc_start: 0.8303 (mttt) cc_final: 0.7839 (mttp) REVERT: C 341 GLU cc_start: 0.7602 (tp30) cc_final: 0.7280 (tp30) REVERT: C 345 ASP cc_start: 0.8595 (m-30) cc_final: 0.8359 (m-30) REVERT: C 538 ASP cc_start: 0.8604 (m-30) cc_final: 0.8330 (m-30) REVERT: D 50 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: D 127 ASP cc_start: 0.8246 (m-30) cc_final: 0.7885 (m-30) REVERT: D 321 LYS cc_start: 0.8767 (mttp) cc_final: 0.8560 (mtmt) REVERT: D 334 MET cc_start: 0.8439 (ttm) cc_final: 0.8146 (ttm) REVERT: E 166 GLU cc_start: 0.8308 (pp20) cc_final: 0.7937 (pp20) REVERT: E 321 LYS cc_start: 0.8951 (mttp) cc_final: 0.7935 (ttpp) REVERT: E 465 SER cc_start: 0.8945 (m) cc_final: 0.8407 (p) REVERT: E 632 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8290 (mtp-110) REVERT: E 654 GLU cc_start: 0.8301 (tt0) cc_final: 0.8035 (mp0) REVERT: F 7 PHE cc_start: 0.8470 (t80) cc_final: 0.8252 (t80) REVERT: F 32 TRP cc_start: 0.7830 (m100) cc_final: 0.7015 (m100) REVERT: F 40 ASP cc_start: 0.7358 (p0) cc_final: 0.7088 (p0) REVERT: F 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: F 81 ARG cc_start: 0.8171 (ptp-170) cc_final: 0.7966 (ptp-170) REVERT: F 281 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7745 (tmm160) REVERT: F 511 LYS cc_start: 0.8969 (mttt) cc_final: 0.8627 (mtmt) outliers start: 70 outliers final: 43 residues processed: 412 average time/residue: 0.2061 time to fit residues: 132.7486 Evaluate side-chains 371 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL 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 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 202 LEU 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 89 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 220 ASP 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 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: 4.9990 chunk 286 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 339 ASN B 155 ASN B 158 ASN 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 339 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 191 GLN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096832 restraints weight = 44372.096| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.88 r_work: 0.2964 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31932 Z= 0.201 Angle : 0.603 8.872 43428 Z= 0.303 Chirality : 0.045 0.164 4914 Planarity : 0.005 0.047 5610 Dihedral : 11.546 136.538 5154 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.21 % Allowed : 11.94 % Favored : 85.85 % 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: -1.55 (0.13), residues: 4056 helix: 0.44 (0.14), residues: 1416 sheet: -2.37 (0.17), residues: 726 loop : -1.57 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 116 TYR 0.014 0.002 TYR C 110 PHE 0.026 0.002 PHE F 595 TRP 0.013 0.002 TRP A 124 HIS 0.006 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00469 (31932) covalent geometry : angle 0.60292 (43428) hydrogen bonds : bond 0.03161 ( 1200) hydrogen bonds : angle 5.06437 ( 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 430 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 1.099 Fit side-chains REVERT: A 40 ASP cc_start: 0.7551 (p0) cc_final: 0.7149 (p0) REVERT: A 282 GLU cc_start: 0.7932 (tp30) cc_final: 0.7660 (tp30) REVERT: A 522 ASP cc_start: 0.7657 (p0) cc_final: 0.6936 (m-30) REVERT: A 567 MET cc_start: 0.8474 (mmp) cc_final: 0.7962 (mmm) REVERT: B 166 GLU cc_start: 0.8394 (pp20) cc_final: 0.7976 (pp20) REVERT: B 309 ASN cc_start: 0.8737 (m-40) cc_final: 0.8408 (m110) REVERT: B 321 LYS cc_start: 0.8628 (mttp) cc_final: 0.7395 (ttpt) REVERT: B 333 LYS cc_start: 0.8395 (mttt) cc_final: 0.7854 (mttp) REVERT: B 341 GLU cc_start: 0.7397 (tp30) cc_final: 0.6952 (tp30) REVERT: B 433 GLN cc_start: 0.8324 (tp40) cc_final: 0.8053 (tp-100) REVERT: C 321 LYS cc_start: 0.8612 (mttp) cc_final: 0.7686 (ttpp) REVERT: C 333 LYS cc_start: 0.8321 (mttt) cc_final: 0.7878 (mttp) REVERT: C 341 GLU cc_start: 0.7546 (tp30) cc_final: 0.7172 (tp30) REVERT: C 345 ASP cc_start: 0.8589 (m-30) cc_final: 0.8280 (m-30) REVERT: C 467 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9075 (mm) REVERT: C 538 ASP cc_start: 0.8594 (m-30) cc_final: 0.8316 (m-30) REVERT: D 50 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: D 321 LYS cc_start: 0.8787 (mttp) cc_final: 0.8554 (mtmt) REVERT: D 551 ASP cc_start: 0.8549 (m-30) cc_final: 0.8322 (m-30) REVERT: E 118 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9095 (mp) REVERT: E 166 GLU cc_start: 0.8282 (pp20) cc_final: 0.8028 (pp20) REVERT: E 191 GLN cc_start: 0.8433 (tt0) cc_final: 0.8189 (tt0) REVERT: E 321 LYS cc_start: 0.8915 (mttp) cc_final: 0.7926 (ttpp) REVERT: E 465 SER cc_start: 0.8984 (m) cc_final: 0.8433 (p) REVERT: E 654 GLU cc_start: 0.8326 (tt0) cc_final: 0.8059 (mp0) REVERT: F 32 TRP cc_start: 0.7842 (m100) cc_final: 0.6926 (m100) REVERT: F 40 ASP cc_start: 0.7177 (p0) cc_final: 0.6857 (p0) REVERT: F 50 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: F 281 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7784 (tmm160) REVERT: F 351 ASN cc_start: 0.9064 (m110) cc_final: 0.8757 (m-40) REVERT: F 361 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6694 (ttt-90) REVERT: F 511 LYS cc_start: 0.8977 (mttt) cc_final: 0.8621 (mtmt) outliers start: 70 outliers final: 52 residues processed: 415 average time/residue: 0.2058 time to fit residues: 134.0694 Evaluate side-chains 387 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 331 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER 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 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 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 118 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 402 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 50 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 281 ARG 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 81 ARG 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 168 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 220 ASP 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 402 THR Chi-restraints excluded: chain F residue 490 VAL 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: 2.9990 chunk 283 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 297 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 397 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 158 ASN 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 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098034 restraints weight = 43999.579| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.87 r_work: 0.2996 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31932 Z= 0.153 Angle : 0.569 9.187 43428 Z= 0.286 Chirality : 0.043 0.154 4914 Planarity : 0.004 0.048 5610 Dihedral : 11.240 134.837 5154 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.30 % Allowed : 12.60 % Favored : 85.10 % 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: -1.33 (0.13), residues: 4056 helix: 0.68 (0.14), residues: 1398 sheet: -2.28 (0.17), residues: 726 loop : -1.44 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 116 TYR 0.014 0.002 TYR E 564 PHE 0.026 0.002 PHE F 595 TRP 0.011 0.001 TRP E 651 HIS 0.004 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00353 (31932) covalent geometry : angle 0.56874 (43428) hydrogen bonds : bond 0.02943 ( 1200) hydrogen bonds : angle 4.94513 ( 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 433 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 1.003 Fit side-chains REVERT: A 40 ASP cc_start: 0.7290 (p0) cc_final: 0.7076 (p0) REVERT: A 116 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8161 (mtp-110) REVERT: A 189 LEU cc_start: 0.8480 (tp) cc_final: 0.8173 (tp) REVERT: A 282 GLU cc_start: 0.7913 (tp30) cc_final: 0.7613 (tp30) REVERT: A 522 ASP cc_start: 0.7645 (p0) cc_final: 0.6882 (m-30) REVERT: A 540 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9259 (tp) REVERT: A 654 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 166 GLU cc_start: 0.8351 (pp20) cc_final: 0.8038 (pp20) REVERT: B 309 ASN cc_start: 0.8729 (m-40) cc_final: 0.8415 (m110) REVERT: B 321 LYS cc_start: 0.8543 (mttp) cc_final: 0.7390 (ttpt) REVERT: B 333 LYS cc_start: 0.8344 (mttt) cc_final: 0.7836 (mttp) REVERT: B 341 GLU cc_start: 0.7444 (tp30) cc_final: 0.7123 (tp30) REVERT: B 433 GLN cc_start: 0.8275 (tp40) cc_final: 0.7995 (tp-100) REVERT: C 166 GLU cc_start: 0.8299 (pp20) cc_final: 0.8004 (pp20) REVERT: C 321 LYS cc_start: 0.8571 (mttp) cc_final: 0.7647 (ttpp) REVERT: C 333 LYS cc_start: 0.8299 (mttt) cc_final: 0.7863 (mttp) REVERT: C 341 GLU cc_start: 0.7606 (tp30) cc_final: 0.7239 (tp30) REVERT: C 345 ASP cc_start: 0.8601 (m-30) cc_final: 0.8273 (m-30) REVERT: C 467 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9031 (mm) REVERT: C 538 ASP cc_start: 0.8532 (m-30) cc_final: 0.8247 (m-30) REVERT: D 40 ASP cc_start: 0.7266 (p0) cc_final: 0.7057 (p0) REVERT: D 50 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: D 59 MET cc_start: 0.9382 (mtp) cc_final: 0.9132 (mtm) REVERT: D 127 ASP cc_start: 0.8324 (m-30) cc_final: 0.8049 (m-30) REVERT: D 189 LEU cc_start: 0.8474 (tp) cc_final: 0.8240 (tp) REVERT: D 321 LYS cc_start: 0.8783 (mttp) cc_final: 0.8529 (mtmt) REVERT: D 334 MET cc_start: 0.8147 (ttm) cc_final: 0.7746 (ttm) REVERT: D 551 ASP cc_start: 0.8598 (m-30) cc_final: 0.8336 (m-30) REVERT: E 321 LYS cc_start: 0.8865 (mttp) cc_final: 0.7713 (ttpp) REVERT: E 465 SER cc_start: 0.8990 (m) cc_final: 0.8446 (p) REVERT: E 467 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9154 (mm) REVERT: E 654 GLU cc_start: 0.8285 (tt0) cc_final: 0.7995 (mp0) REVERT: F 32 TRP cc_start: 0.7831 (m100) cc_final: 0.6991 (m100) REVERT: F 50 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: F 281 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7882 (tmm160) REVERT: F 511 LYS cc_start: 0.8968 (mttt) cc_final: 0.8601 (mtmt) outliers start: 73 outliers final: 46 residues processed: 420 average time/residue: 0.2078 time to fit residues: 136.2896 Evaluate side-chains 384 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER 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 A residue 654 GLU Chi-restraints excluded: chain B residue 31 LEU 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 112 SER Chi-restraints excluded: chain C residue 202 LEU 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 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 524 ILE 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 220 ASP 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 Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 30 optimal weight: 0.4980 chunk 278 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 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: 0.9980 chunk 144 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN A 659 HIS B 155 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 = 0.3499 r_free = 0.3499 target = 0.125347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097124 restraints weight = 44311.682| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.88 r_work: 0.2982 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31932 Z= 0.182 Angle : 0.591 9.278 43428 Z= 0.297 Chirality : 0.044 0.163 4914 Planarity : 0.005 0.056 5610 Dihedral : 11.204 136.496 5154 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.65 % Allowed : 12.67 % Favored : 84.69 % 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: -1.24 (0.13), residues: 4056 helix: 0.74 (0.14), residues: 1398 sheet: -2.19 (0.18), residues: 726 loop : -1.40 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 116 TYR 0.014 0.002 TYR E 607 PHE 0.025 0.002 PHE F 595 TRP 0.012 0.001 TRP E 32 HIS 0.004 0.001 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00423 (31932) covalent geometry : angle 0.59128 (43428) hydrogen bonds : bond 0.03039 ( 1200) hydrogen bonds : angle 4.93969 ( 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 431 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 1.225 Fit side-chains REVERT: A 282 GLU cc_start: 0.7933 (tp30) cc_final: 0.7612 (tp30) REVERT: A 522 ASP cc_start: 0.7669 (p0) cc_final: 0.6943 (m-30) REVERT: A 540 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9262 (tp) REVERT: A 654 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 166 GLU cc_start: 0.8386 (pp20) cc_final: 0.8012 (pp20) REVERT: B 309 ASN cc_start: 0.8731 (m-40) cc_final: 0.8429 (m110) REVERT: B 321 LYS cc_start: 0.8611 (mttp) cc_final: 0.7466 (ttpt) REVERT: B 333 LYS cc_start: 0.8338 (mttt) cc_final: 0.7899 (mttp) REVERT: B 341 GLU cc_start: 0.7514 (tp30) cc_final: 0.7221 (tp30) REVERT: B 433 GLN cc_start: 0.8300 (tp40) cc_final: 0.8011 (tp-100) REVERT: B 642 GLU cc_start: 0.7491 (pm20) cc_final: 0.7118 (pm20) REVERT: C 321 LYS cc_start: 0.8566 (mttp) cc_final: 0.7555 (ttpp) REVERT: C 333 LYS cc_start: 0.8294 (mttt) cc_final: 0.7848 (mttp) REVERT: C 341 GLU cc_start: 0.7685 (tp30) cc_final: 0.7285 (tp30) REVERT: C 345 ASP cc_start: 0.8615 (m-30) cc_final: 0.8250 (m-30) REVERT: C 467 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9057 (mm) REVERT: D 40 ASP cc_start: 0.7260 (p0) cc_final: 0.7059 (p0) REVERT: D 50 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: D 59 MET cc_start: 0.9404 (mtp) cc_final: 0.9150 (mtm) REVERT: D 127 ASP cc_start: 0.8293 (m-30) cc_final: 0.8024 (m-30) REVERT: D 189 LEU cc_start: 0.8543 (tp) cc_final: 0.8286 (tp) REVERT: D 321 LYS cc_start: 0.8747 (mttp) cc_final: 0.8478 (mtmt) REVERT: D 334 MET cc_start: 0.8276 (ttm) cc_final: 0.7867 (ttm) REVERT: D 551 ASP cc_start: 0.8613 (m-30) cc_final: 0.8354 (m-30) REVERT: E 118 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9124 (mp) REVERT: E 465 SER cc_start: 0.9007 (m) cc_final: 0.8447 (p) REVERT: E 467 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9170 (mm) REVERT: E 654 GLU cc_start: 0.8334 (tt0) cc_final: 0.8057 (mp0) REVERT: F 33 GLU cc_start: 0.7940 (pt0) cc_final: 0.7736 (tt0) REVERT: F 50 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: F 281 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7904 (tmm160) REVERT: F 511 LYS cc_start: 0.8967 (mttt) cc_final: 0.8585 (mtmt) outliers start: 84 outliers final: 58 residues processed: 414 average time/residue: 0.2134 time to fit residues: 137.9331 Evaluate side-chains 402 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 337 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER 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 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 202 LEU Chi-restraints excluded: chain B residue 319 LEU 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 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 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 193 MET 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 81 ARG 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 256 GLU Chi-restraints excluded: chain E residue 332 VAL 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 533 GLU 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: 2.9990 chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 360 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 332 optimal weight: 0.3980 chunk 185 optimal weight: 0.2980 chunk 164 optimal weight: 4.9990 chunk 155 optimal weight: 0.0030 chunk 189 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 158 ASN B 191 GLN ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** 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 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099288 restraints weight = 44216.702| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.88 r_work: 0.3015 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3436 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= 0.124 Angle : 0.559 9.438 43428 Z= 0.281 Chirality : 0.043 0.202 4914 Planarity : 0.004 0.054 5610 Dihedral : 10.872 133.730 5154 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.02 % Allowed : 13.61 % Favored : 84.37 % 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: -1.12 (0.13), residues: 4056 helix: 0.88 (0.14), residues: 1398 sheet: -2.17 (0.18), residues: 708 loop : -1.35 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 116 TYR 0.020 0.001 TYR E 607 PHE 0.025 0.001 PHE F 595 TRP 0.011 0.001 TRP E 651 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00282 (31932) covalent geometry : angle 0.55860 (43428) hydrogen bonds : bond 0.02776 ( 1200) hydrogen bonds : angle 4.83328 ( 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 444 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 1.188 Fit side-chains REVERT: A 40 ASP cc_start: 0.7280 (p0) cc_final: 0.7065 (p0) REVERT: A 96 SER cc_start: 0.8969 (t) cc_final: 0.8485 (t) REVERT: A 282 GLU cc_start: 0.7953 (tp30) cc_final: 0.7673 (tp30) REVERT: A 361 ARG cc_start: 0.6804 (mmm-85) cc_final: 0.6449 (mtm180) REVERT: A 522 ASP cc_start: 0.7642 (p0) cc_final: 0.6846 (m-30) REVERT: A 540 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9249 (tp) REVERT: B 166 GLU cc_start: 0.8306 (pp20) cc_final: 0.8105 (pp20) REVERT: B 309 ASN cc_start: 0.8749 (m-40) cc_final: 0.8448 (m110) REVERT: B 333 LYS cc_start: 0.8314 (mttt) cc_final: 0.7916 (mttp) REVERT: B 341 GLU cc_start: 0.7536 (tp30) cc_final: 0.7311 (tp30) REVERT: C 333 LYS cc_start: 0.8277 (mttt) cc_final: 0.7855 (mttp) REVERT: C 341 GLU cc_start: 0.7693 (tp30) cc_final: 0.7319 (tp30) REVERT: C 345 ASP cc_start: 0.8569 (m-30) cc_final: 0.8199 (m-30) REVERT: C 505 MET cc_start: 0.9099 (tpp) cc_final: 0.8825 (mmp) REVERT: C 538 ASP cc_start: 0.8493 (m-30) cc_final: 0.8228 (m-30) REVERT: D 46 GLN cc_start: 0.8426 (mm110) cc_final: 0.8094 (mm-40) REVERT: D 50 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: D 59 MET cc_start: 0.9367 (mtp) cc_final: 0.9063 (mtm) REVERT: D 110 TYR cc_start: 0.9038 (m-80) cc_final: 0.8666 (m-80) REVERT: D 127 ASP cc_start: 0.8322 (m-30) cc_final: 0.7993 (m-30) REVERT: D 189 LEU cc_start: 0.8411 (tp) cc_final: 0.8211 (tp) REVERT: D 321 LYS cc_start: 0.8765 (mttp) cc_final: 0.8484 (mtmt) REVERT: D 334 MET cc_start: 0.8064 (ttm) cc_final: 0.7723 (ttm) REVERT: D 551 ASP cc_start: 0.8584 (m-30) cc_final: 0.8381 (m-30) REVERT: E 118 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9096 (mp) REVERT: E 465 SER cc_start: 0.8969 (m) cc_final: 0.8448 (p) REVERT: E 467 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9130 (mm) REVERT: E 654 GLU cc_start: 0.8290 (tt0) cc_final: 0.7848 (mt-10) REVERT: F 32 TRP cc_start: 0.7853 (m100) cc_final: 0.7008 (m100) REVERT: F 50 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: F 281 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7885 (tmm160) REVERT: F 511 LYS cc_start: 0.8915 (mttt) cc_final: 0.8545 (mtmt) outliers start: 64 outliers final: 43 residues processed: 427 average time/residue: 0.2064 time to fit residues: 138.9294 Evaluate side-chains 388 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 340 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL 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 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 319 LEU 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 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 426 THR 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 193 MET 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 31 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 118 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 332 VAL 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 469 GLN Chi-restraints excluded: chain F residue 533 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 37 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 158 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 339 ASN ** E 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 HIS F 659 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096080 restraints weight = 44305.238| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.87 r_work: 0.2960 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31932 Z= 0.232 Angle : 0.639 9.108 43428 Z= 0.321 Chirality : 0.046 0.218 4914 Planarity : 0.005 0.065 5610 Dihedral : 11.162 138.628 5154 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.21 % Allowed : 13.55 % 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: -1.19 (0.13), residues: 4056 helix: 0.75 (0.14), residues: 1398 sheet: -2.17 (0.17), residues: 738 loop : -1.33 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.023 0.002 TYR E 607 PHE 0.025 0.002 PHE F 595 TRP 0.018 0.002 TRP F 97 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00544 (31932) covalent geometry : angle 0.63915 (43428) hydrogen bonds : bond 0.03211 ( 1200) hydrogen bonds : angle 4.97313 ( 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 423 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 1.121 Fit side-chains REVERT: A 40 ASP cc_start: 0.7286 (p0) cc_final: 0.7031 (p0) REVERT: A 96 SER cc_start: 0.9011 (t) cc_final: 0.8538 (t) REVERT: A 282 GLU cc_start: 0.7961 (tp30) cc_final: 0.7669 (tp30) REVERT: A 540 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9254 (tp) REVERT: B 166 GLU cc_start: 0.8347 (pp20) cc_final: 0.8102 (pp20) REVERT: B 220 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8512 (t0) REVERT: B 309 ASN cc_start: 0.8746 (m-40) cc_final: 0.8468 (m110) REVERT: B 321 LYS cc_start: 0.8607 (mttp) cc_final: 0.7447 (ttpp) REVERT: B 333 LYS cc_start: 0.8306 (mttt) cc_final: 0.7888 (mttp) REVERT: B 341 GLU cc_start: 0.7628 (tp30) cc_final: 0.7366 (tp30) REVERT: C 166 GLU cc_start: 0.8275 (pp20) cc_final: 0.7905 (pp20) REVERT: C 220 ASP cc_start: 0.8751 (m-30) cc_final: 0.8512 (m-30) REVERT: C 321 LYS cc_start: 0.8576 (mttp) cc_final: 0.7547 (ttpp) REVERT: C 333 LYS cc_start: 0.8349 (mttt) cc_final: 0.7892 (mttp) REVERT: C 341 GLU cc_start: 0.7734 (tp30) cc_final: 0.7304 (tp30) REVERT: C 345 ASP cc_start: 0.8585 (m-30) cc_final: 0.8194 (m-30) REVERT: C 467 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9087 (mm) REVERT: C 538 ASP cc_start: 0.8571 (m-30) cc_final: 0.8297 (m-30) REVERT: D 46 GLN cc_start: 0.8365 (mm110) cc_final: 0.8028 (mm-40) REVERT: D 50 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: D 127 ASP cc_start: 0.8333 (m-30) cc_final: 0.8094 (m-30) REVERT: D 189 LEU cc_start: 0.8547 (tp) cc_final: 0.8322 (tp) REVERT: D 321 LYS cc_start: 0.8766 (mttp) cc_final: 0.8503 (mtmt) REVERT: D 334 MET cc_start: 0.8325 (ttm) cc_final: 0.7933 (ttm) REVERT: D 551 ASP cc_start: 0.8624 (m-30) cc_final: 0.8422 (m-30) REVERT: E 118 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9163 (mp) REVERT: E 321 LYS cc_start: 0.8879 (mttp) cc_final: 0.7791 (ttpp) REVERT: E 465 SER cc_start: 0.9026 (m) cc_final: 0.8470 (p) REVERT: E 467 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9188 (mm) REVERT: E 654 GLU cc_start: 0.8363 (tt0) cc_final: 0.8099 (mp0) REVERT: F 50 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: F 281 ARG cc_start: 0.8151 (ttm170) cc_final: 0.7898 (tmm160) REVERT: F 511 LYS cc_start: 0.9014 (mttt) cc_final: 0.8630 (mtmt) outliers start: 70 outliers final: 58 residues processed: 409 average time/residue: 0.2123 time to fit residues: 135.4209 Evaluate side-chains 403 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 189 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 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 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 202 LEU 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 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 193 MET 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 35 THR 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 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 332 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 241 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 281 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 155 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 ** 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 = 0.3504 r_free = 0.3504 target = 0.125677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097540 restraints weight = 44083.027| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.87 r_work: 0.2963 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31932 Z= 0.166 Angle : 0.598 9.639 43428 Z= 0.302 Chirality : 0.044 0.253 4914 Planarity : 0.005 0.063 5610 Dihedral : 10.993 137.113 5154 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.05 % Allowed : 13.77 % Favored : 84.18 % 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: -1.13 (0.13), residues: 4056 helix: 0.82 (0.14), residues: 1398 sheet: -2.18 (0.17), residues: 762 loop : -1.27 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.023 0.002 TYR E 607 PHE 0.025 0.002 PHE F 595 TRP 0.020 0.001 TRP F 97 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00386 (31932) covalent geometry : angle 0.59835 (43428) hydrogen bonds : bond 0.02996 ( 1200) hydrogen bonds : angle 4.90219 ( 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 422 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 357 time to evaluate : 1.125 Fit side-chains REVERT: A 40 ASP cc_start: 0.7172 (p0) cc_final: 0.6949 (p0) REVERT: A 96 SER cc_start: 0.8984 (t) cc_final: 0.8485 (t) REVERT: A 282 GLU cc_start: 0.7942 (tp30) cc_final: 0.7647 (tp30) REVERT: A 540 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9236 (tp) REVERT: B 220 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8458 (t0) REVERT: B 309 ASN cc_start: 0.8737 (m-40) cc_final: 0.8466 (m110) REVERT: B 321 LYS cc_start: 0.8553 (mttp) cc_final: 0.7471 (ttpp) REVERT: B 333 LYS cc_start: 0.8301 (mttt) cc_final: 0.7882 (mttp) REVERT: B 341 GLU cc_start: 0.7659 (tp30) cc_final: 0.7424 (tp30) REVERT: C 166 GLU cc_start: 0.8241 (pp20) cc_final: 0.7950 (pp20) REVERT: C 220 ASP cc_start: 0.8772 (m-30) cc_final: 0.8534 (m-30) REVERT: C 321 LYS cc_start: 0.8553 (mttp) cc_final: 0.7514 (ttpp) REVERT: C 333 LYS cc_start: 0.8252 (mttt) cc_final: 0.7783 (mttp) REVERT: C 341 GLU cc_start: 0.7741 (tp30) cc_final: 0.7353 (tp30) REVERT: C 345 ASP cc_start: 0.8507 (m-30) cc_final: 0.8122 (m-30) REVERT: C 467 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9068 (mm) REVERT: C 538 ASP cc_start: 0.8512 (m-30) cc_final: 0.8244 (m-30) REVERT: D 46 GLN cc_start: 0.8357 (mm110) cc_final: 0.8032 (mm-40) REVERT: D 50 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: D 59 MET cc_start: 0.9408 (mtp) cc_final: 0.9148 (mtm) REVERT: D 127 ASP cc_start: 0.8275 (m-30) cc_final: 0.8031 (m-30) REVERT: D 189 LEU cc_start: 0.8498 (tp) cc_final: 0.8285 (tp) REVERT: D 321 LYS cc_start: 0.8751 (mttp) cc_final: 0.8460 (mtmt) REVERT: D 334 MET cc_start: 0.8229 (ttm) cc_final: 0.7862 (ttm) REVERT: E 118 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9132 (mp) REVERT: E 465 SER cc_start: 0.8990 (m) cc_final: 0.8446 (p) REVERT: E 467 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9151 (mm) REVERT: E 654 GLU cc_start: 0.8378 (tt0) cc_final: 0.7910 (mt-10) REVERT: F 50 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: F 281 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7884 (tmm160) REVERT: F 511 LYS cc_start: 0.8980 (mttt) cc_final: 0.8600 (mtmt) outliers start: 65 outliers final: 53 residues processed: 408 average time/residue: 0.2189 time to fit residues: 139.1121 Evaluate side-chains 394 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 158 ASN 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 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 118 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 202 LEU 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 193 MET 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 467 LEU 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 35 THR Chi-restraints excluded: chain E residue 81 ARG 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 256 GLU 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 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: 9.9990 chunk 323 optimal weight: 3.9990 chunk 317 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 191 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 191 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.123284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.095369 restraints weight = 44586.016| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.81 r_work: 0.2945 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31932 Z= 0.142 Angle : 0.588 11.988 43428 Z= 0.295 Chirality : 0.043 0.243 4914 Planarity : 0.005 0.064 5610 Dihedral : 10.820 136.068 5154 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.11 % Allowed : 13.89 % Favored : 83.99 % 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: -1.09 (0.13), residues: 4056 helix: 0.88 (0.14), residues: 1398 sheet: -2.19 (0.17), residues: 780 loop : -1.22 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.022 0.001 TYR E 607 PHE 0.025 0.001 PHE F 595 TRP 0.020 0.001 TRP F 97 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00326 (31932) covalent geometry : angle 0.58839 (43428) hydrogen bonds : bond 0.02876 ( 1200) hydrogen bonds : angle 4.84253 ( 3513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8285.96 seconds wall clock time: 142 minutes 19.66 seconds (8539.66 seconds total)