Starting phenix.real_space_refine on Fri Aug 7 20:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.map" model { file = "/net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zqs_74577/08_2026/9zqs_74577.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.150 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 14598 2.51 5 N 4050 2.21 5 O 4563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23325 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "B" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "C" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "D" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "E" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "F" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3847 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Time building chain proxies: 5.14, per 1000 atoms: 0.22 Number of scatterers: 23325 At special positions: 0 Unit cell: (117.875, 112.75, 154.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4563 8.00 N 4050 7.00 C 14598 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5352 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 9 sheets defined 56.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 65 through 88 removed outlier: 4.822A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.507A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.557A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.164A pdb=" N VAL A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.506A pdb=" N PHE A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.602A pdb=" N ILE A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.582A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.748A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 553 Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.524A pdb=" N ILE B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.532A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.560A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.160A pdb=" N VAL B 255 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.510A pdb=" N PHE B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.533A pdb=" N ILE B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.582A pdb=" N LYS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 478 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.763A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 Processing helix chain 'C' and resid 65 through 88 removed outlier: 3.541A pdb=" N ILE C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.508A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.528A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.108A pdb=" N VAL C 255 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.650A pdb=" N PHE C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.532A pdb=" N ILE C 292 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.555A pdb=" N LYS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.740A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 553 Processing helix chain 'D' and resid 65 through 89 removed outlier: 4.785A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.515A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.560A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.155A pdb=" N VAL D 255 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.602A pdb=" N ILE D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.503A pdb=" N PHE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 410 through 420 removed outlier: 3.589A pdb=" N LYS D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 478 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.745A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 553 Processing helix chain 'E' and resid 65 through 89 removed outlier: 3.531A pdb=" N ILE E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 194 through 212 removed outlier: 3.519A pdb=" N LYS E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.556A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.150A pdb=" N VAL E 255 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 285 removed outlier: 3.510A pdb=" N PHE E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.533A pdb=" N ILE E 292 " --> pdb=" O SER E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 410 through 420 removed outlier: 3.552A pdb=" N LYS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 478 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.762A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 553 Processing helix chain 'F' and resid 65 through 88 removed outlier: 3.523A pdb=" N ILE F 80 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.508A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 194 through 212 removed outlier: 3.533A pdb=" N LYS F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 243 removed outlier: 3.518A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.112A pdb=" N VAL F 255 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 removed outlier: 3.647A pdb=" N PHE F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.537A pdb=" N ILE F 292 " --> pdb=" O SER F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 410 through 420 removed outlier: 3.553A pdb=" N LYS F 415 " --> pdb=" O PRO F 411 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 478 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.738A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 6.493A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ALA A 223 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY A 148 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 149 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.894A pdb=" N SER A 336 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 306 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 330 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A 303 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE A 380 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 305 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 224 removed outlier: 6.454A pdb=" N CYS B 146 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA B 223 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY B 149 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY E 149 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.813A pdb=" N SER B 336 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL B 306 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 330 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR B 303 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE B 380 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 305 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 224 removed outlier: 6.476A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA C 223 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 148 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY C 149 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY D 149 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA D 223 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY D 148 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.887A pdb=" N SER C 336 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 306 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 330 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 303 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ILE C 380 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 305 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.949A pdb=" N SER D 336 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE D 304 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 330 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL D 306 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 303 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE D 380 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 305 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.871A pdb=" N SER E 336 " --> pdb=" O TYR E 367 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL E 306 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL E 330 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR E 303 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE E 380 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL E 305 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.898A pdb=" N SER F 336 " --> pdb=" O TYR F 367 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL F 306 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL F 330 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR F 303 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE F 380 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 305 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1328 hydrogen bonds defined for protein. 3840 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: 4.55 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7692 1.34 - 1.46: 4544 1.46 - 1.58: 11146 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 23574 Sorted by residual: bond pdb=" C ILE A 328 " pdb=" O ILE A 328 " ideal model delta sigma weight residual 1.233 1.241 -0.008 1.02e-02 9.61e+03 6.53e-01 bond pdb=" CA LYS D 110 " pdb=" C LYS D 110 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.80e-01 bond pdb=" CA VAL A 175 " pdb=" C VAL A 175 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.27e-02 6.20e+03 3.54e-01 bond pdb=" CA VAL C 175 " pdb=" C VAL C 175 " ideal model delta sigma weight residual 1.523 1.530 -0.007 1.27e-02 6.20e+03 3.28e-01 bond pdb=" CA MET C 226 " pdb=" CB MET C 226 " ideal model delta sigma weight residual 1.528 1.537 -0.009 1.56e-02 4.11e+03 3.26e-01 ... (remaining 23569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 31166 1.05 - 2.09: 492 2.09 - 3.14: 122 3.14 - 4.19: 26 4.19 - 5.23: 12 Bond angle restraints: 31818 Sorted by residual: angle pdb=" N MET C 226 " pdb=" CA MET C 226 " pdb=" C MET C 226 " ideal model delta sigma weight residual 111.28 113.71 -2.43 1.09e+00 8.42e-01 4.99e+00 angle pdb=" N GLY C 407 " pdb=" CA GLY C 407 " pdb=" C GLY C 407 " ideal model delta sigma weight residual 112.34 116.47 -4.13 2.04e+00 2.40e-01 4.10e+00 angle pdb=" N GLY F 407 " pdb=" CA GLY F 407 " pdb=" C GLY F 407 " ideal model delta sigma weight residual 112.34 116.47 -4.13 2.04e+00 2.40e-01 4.09e+00 angle pdb=" N GLY A 407 " pdb=" CA GLY A 407 " pdb=" C GLY A 407 " ideal model delta sigma weight residual 112.34 116.45 -4.11 2.04e+00 2.40e-01 4.05e+00 angle pdb=" N VAL F 221 " pdb=" CA VAL F 221 " pdb=" C VAL F 221 " ideal model delta sigma weight residual 107.60 109.75 -2.15 1.07e+00 8.73e-01 4.05e+00 ... (remaining 31813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 13412 14.77 - 29.54: 561 29.54 - 44.31: 122 44.31 - 59.07: 29 59.07 - 73.84: 12 Dihedral angle restraints: 14136 sinusoidal: 5730 harmonic: 8406 Sorted by residual: dihedral pdb=" N ASN C 541 " pdb=" CA ASN C 541 " pdb=" CB ASN C 541 " pdb=" CG ASN C 541 " ideal model delta sinusoidal sigma weight residual -60.00 -117.59 57.59 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N ASN F 541 " pdb=" CA ASN F 541 " pdb=" CB ASN F 541 " pdb=" CG ASN F 541 " ideal model delta sinusoidal sigma weight residual -60.00 -117.21 57.21 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ILE F 122 " pdb=" CB ILE F 122 " pdb=" CG1 ILE F 122 " pdb=" CD1 ILE F 122 " ideal model delta sinusoidal sigma weight residual 180.00 123.06 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 14133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2075 0.028 - 0.055: 918 0.055 - 0.083: 232 0.083 - 0.110: 166 0.110 - 0.138: 65 Chirality restraints: 3456 Sorted by residual: chirality pdb=" CA ILE E 485 " pdb=" N ILE E 485 " pdb=" C ILE E 485 " pdb=" CB ILE E 485 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE F 485 " pdb=" N ILE F 485 " pdb=" C ILE F 485 " pdb=" CB ILE F 485 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE D 485 " pdb=" N ILE D 485 " pdb=" C ILE D 485 " pdb=" CB ILE D 485 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3453 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 221 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 222 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 221 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 222 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 222 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 222 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 221 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO F 222 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.022 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2853 2.75 - 3.29: 23782 3.29 - 3.83: 41704 3.83 - 4.36: 52540 4.36 - 4.90: 88393 Nonbonded interactions: 209272 Sorted by model distance: nonbonded pdb=" OG1 THR D 524 " pdb=" OD1 ASN D 541 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A 524 " pdb=" OD1 ASN A 541 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLU D 552 " pdb=" OG SER E 261 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU A 552 " pdb=" OG SER B 261 " model vdw 2.248 3.040 nonbonded pdb=" OE1 GLU E 552 " pdb=" OG SER F 261 " model vdw 2.257 3.040 ... (remaining 209267 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.720 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.002 0.018 23574 Z= 0.080 Angle : 0.389 5.234 31818 Z= 0.210 Chirality : 0.040 0.138 3456 Planarity : 0.003 0.039 4140 Dihedral : 9.148 73.844 8784 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.73 % Allowed : 2.35 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.81 (0.15), residues: 2940 helix: 1.07 (0.13), residues: 1470 sheet: 0.12 (0.27), residues: 408 loop : 0.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.007 0.001 TYR F 170 PHE 0.008 0.001 PHE D 205 TRP 0.006 0.001 TRP D 338 HIS 0.003 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.08 (23574) covalent geometry : angle 0.38944 / 0.21 (31818) hydrogen bonds : bond 0.21173 / 14.11 ( 1328) hydrogen bonds : angle 6.35364 / 4.48 ( 3840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 446 time to evaluate : 1.125 Fit side-chains REVERT: A 71 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7227 (mt-10) REVERT: A 90 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.5992 (mmpt) REVERT: A 207 MET cc_start: 0.8981 (mmm) cc_final: 0.8732 (mmm) REVERT: A 321 HIS cc_start: 0.8121 (t-90) cc_final: 0.7903 (t-90) REVERT: A 332 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6556 (tp30) REVERT: A 387 GLN cc_start: 0.8427 (mm110) cc_final: 0.7959 (mm-40) REVERT: A 399 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7440 (mmtm) REVERT: B 82 GLU cc_start: 0.7375 (tt0) cc_final: 0.7106 (tt0) REVERT: B 83 ASP cc_start: 0.7262 (m-30) cc_final: 0.6892 (m-30) REVERT: B 133 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7866 (mp0) REVERT: B 187 LYS cc_start: 0.8888 (tttm) cc_final: 0.8664 (tttt) REVERT: B 387 GLN cc_start: 0.8432 (mm110) cc_final: 0.8080 (mp10) REVERT: B 390 LYS cc_start: 0.8110 (ptmm) cc_final: 0.7533 (ptmm) REVERT: B 397 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7273 (mptt) REVERT: B 514 MET cc_start: 0.9185 (mmm) cc_final: 0.8949 (mmm) REVERT: B 519 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7206 (mtm110) REVERT: C 83 ASP cc_start: 0.7377 (m-30) cc_final: 0.7061 (m-30) REVERT: C 123 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7357 (ttm110) REVERT: C 133 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7709 (mp0) REVERT: C 168 MET cc_start: 0.9062 (tpp) cc_final: 0.8775 (tpt) REVERT: C 195 ASP cc_start: 0.8225 (m-30) cc_final: 0.8005 (m-30) REVERT: C 314 LEU cc_start: 0.8397 (tt) cc_final: 0.7943 (tm) REVERT: C 332 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6464 (tp30) REVERT: C 397 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7385 (mmtp) REVERT: C 541 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8038 (m110) REVERT: D 71 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7254 (mt-10) REVERT: D 159 ASP cc_start: 0.7864 (m-30) cc_final: 0.7620 (m-30) REVERT: D 207 MET cc_start: 0.8970 (mmm) cc_final: 0.8716 (mmm) REVERT: D 332 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6651 (tp30) REVERT: D 348 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7200 (mt) REVERT: D 387 GLN cc_start: 0.8530 (mm110) cc_final: 0.8112 (mm-40) REVERT: D 399 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7501 (mmtm) REVERT: E 83 ASP cc_start: 0.7161 (m-30) cc_final: 0.6776 (m-30) REVERT: E 87 GLU cc_start: 0.7202 (pt0) cc_final: 0.6892 (mp0) REVERT: E 133 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7866 (mp0) REVERT: E 187 LYS cc_start: 0.8907 (tttm) cc_final: 0.8690 (tttt) REVERT: E 387 GLN cc_start: 0.8458 (mm110) cc_final: 0.8103 (mp10) REVERT: E 390 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7562 (ptmm) REVERT: E 397 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7449 (mptt) REVERT: E 427 ASP cc_start: 0.7971 (p0) cc_final: 0.7767 (p0) REVERT: E 514 MET cc_start: 0.9193 (mmm) cc_final: 0.8958 (mmm) REVERT: E 519 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7183 (mtm110) REVERT: F 71 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7284 (mt-10) REVERT: F 83 ASP cc_start: 0.7296 (m-30) cc_final: 0.7001 (m-30) REVERT: F 123 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7294 (ttm110) REVERT: F 133 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7610 (mp0) REVERT: F 168 MET cc_start: 0.9018 (tpp) cc_final: 0.8724 (tpt) REVERT: F 195 ASP cc_start: 0.8281 (m-30) cc_final: 0.8045 (m-30) REVERT: F 314 LEU cc_start: 0.8203 (tt) cc_final: 0.7734 (tm) REVERT: F 332 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6270 (tp30) REVERT: F 339 ASN cc_start: 0.7163 (t0) cc_final: 0.6919 (t0) REVERT: F 348 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6301 (tp) REVERT: F 397 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7327 (mmtp) REVERT: F 541 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8018 (m110) outliers start: 18 outliers final: 4 residues processed: 454 average time/residue: 0.6883 time to fit residues: 354.2593 Evaluate side-chains 377 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 368 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 541 ASN Chi-restraints excluded: chain E residue 541 ASN Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 541 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 100 ASN B 113 ASN B 406 ASN C 192 ASN C 387 GLN E 100 ASN E 113 ASN E 406 ASN F 387 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121446 restraints weight = 23084.924| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.54 r_work: 0.3370 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23574 Z= 0.138 Angle : 0.485 5.298 31818 Z= 0.260 Chirality : 0.043 0.136 3456 Planarity : 0.004 0.041 4140 Dihedral : 4.721 56.734 3248 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.18 % Allowed : 6.07 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.53 (0.16), residues: 2940 helix: 1.94 (0.13), residues: 1494 sheet: -0.10 (0.27), residues: 420 loop : 0.24 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.010 0.001 TYR D 439 PHE 0.011 0.001 PHE D 277 TRP 0.012 0.002 TRP C 338 HIS 0.005 0.001 HIS D 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (23574) covalent geometry : angle 0.48483 / 0.26 (31818) hydrogen bonds : bond 0.04513 / 3.00 ( 1328) hydrogen bonds : angle 4.54590 / 3.24 ( 3840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 0.904 Fit side-chains REVERT: A 87 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.5959 (mp0) REVERT: A 90 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.5879 (mmpt) REVERT: A 290 MET cc_start: 0.8238 (mmm) cc_final: 0.7985 (mmp) REVERT: A 332 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6491 (tp30) REVERT: A 387 GLN cc_start: 0.8644 (mm110) cc_final: 0.8186 (mm-40) REVERT: A 399 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7597 (mmtm) REVERT: A 444 ASN cc_start: 0.8365 (t0) cc_final: 0.7901 (t0) REVERT: A 515 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: A 526 MET cc_start: 0.7834 (mmt) cc_final: 0.7508 (mmm) REVERT: B 100 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6962 (t0) REVERT: B 187 LYS cc_start: 0.9026 (tttm) cc_final: 0.8815 (tttt) REVERT: B 336 SER cc_start: 0.8394 (m) cc_final: 0.8172 (m) REVERT: B 390 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7550 (ptmm) REVERT: B 397 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7402 (mptt) REVERT: B 519 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7305 (mtm110) REVERT: B 526 MET cc_start: 0.7581 (mmt) cc_final: 0.7253 (mmm) REVERT: C 123 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7469 (ttm110) REVERT: C 311 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6962 (t0) REVERT: C 321 HIS cc_start: 0.8083 (t70) cc_final: 0.7807 (t-170) REVERT: C 323 PHE cc_start: 0.7822 (m-80) cc_final: 0.7401 (m-80) REVERT: C 332 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6381 (tp30) REVERT: C 397 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7612 (mmtp) REVERT: D 76 ARG cc_start: 0.7710 (ttt90) cc_final: 0.7228 (ttm-80) REVERT: D 290 MET cc_start: 0.8251 (mmm) cc_final: 0.7968 (mmp) REVERT: D 332 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6796 (tp30) REVERT: D 387 GLN cc_start: 0.8583 (mm110) cc_final: 0.8169 (mm-40) REVERT: D 399 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7572 (mmtm) REVERT: D 444 ASN cc_start: 0.8366 (t0) cc_final: 0.7904 (t0) REVERT: D 526 MET cc_start: 0.7764 (mmt) cc_final: 0.7442 (mmm) REVERT: E 100 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.6947 (t0) REVERT: E 187 LYS cc_start: 0.9005 (tttm) cc_final: 0.8794 (tttt) REVERT: E 390 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7570 (ptmm) REVERT: E 397 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7409 (mptt) REVERT: E 519 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7285 (mtm110) REVERT: E 526 MET cc_start: 0.7586 (mmt) cc_final: 0.7246 (mmm) REVERT: F 71 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7418 (mm-30) REVERT: F 123 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7412 (ttm110) REVERT: F 311 ASN cc_start: 0.7510 (OUTLIER) cc_final: 0.7016 (t0) REVERT: F 321 HIS cc_start: 0.8092 (t70) cc_final: 0.7819 (t-170) REVERT: F 323 PHE cc_start: 0.7817 (m-80) cc_final: 0.7389 (m-80) REVERT: F 332 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6503 (tp30) REVERT: F 339 ASN cc_start: 0.7599 (t0) cc_final: 0.7375 (t0) REVERT: F 348 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6825 (tp) outliers start: 54 outliers final: 9 residues processed: 391 average time/residue: 0.6917 time to fit residues: 307.0449 Evaluate side-chains 361 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 344 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 292 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 141 GLN C 387 GLN D 541 ASN E 113 ASN F 387 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122161 restraints weight = 23008.131| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.54 r_work: 0.3306 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 23574 Z= 0.121 Angle : 0.456 5.329 31818 Z= 0.243 Chirality : 0.042 0.151 3456 Planarity : 0.004 0.040 4140 Dihedral : 4.051 48.979 3234 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.54 % Allowed : 8.41 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.16), residues: 2940 helix: 2.17 (0.13), residues: 1524 sheet: -0.17 (0.27), residues: 420 loop : 0.22 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.007 0.001 TYR F 439 PHE 0.010 0.001 PHE B 277 TRP 0.013 0.002 TRP C 338 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (23574) covalent geometry : angle 0.45576 / 0.24 (31818) hydrogen bonds : bond 0.03940 / 2.62 ( 1328) hydrogen bonds : angle 4.30537 / 3.07 ( 3840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: A 90 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5932 (mmpt) REVERT: A 103 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7529 (mtt90) REVERT: A 290 MET cc_start: 0.8205 (mmm) cc_final: 0.7424 (mmm) REVERT: A 332 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6662 (tp30) REVERT: A 387 GLN cc_start: 0.8530 (mm110) cc_final: 0.8096 (mm-40) REVERT: A 399 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7118 (mmtm) REVERT: A 444 ASN cc_start: 0.8338 (t0) cc_final: 0.7880 (t0) REVERT: A 515 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: A 526 MET cc_start: 0.7853 (mmt) cc_final: 0.7515 (mmm) REVERT: B 159 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: B 336 SER cc_start: 0.8367 (m) cc_final: 0.8145 (m) REVERT: B 390 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7551 (ptmm) REVERT: B 397 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7388 (mptt) REVERT: B 519 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7350 (mtp180) REVERT: B 526 MET cc_start: 0.7513 (mmt) cc_final: 0.7157 (mmm) REVERT: C 123 ARG cc_start: 0.7957 (ttt180) cc_final: 0.7469 (ttm110) REVERT: C 311 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.6840 (t0) REVERT: C 319 TYR cc_start: 0.8568 (m-80) cc_final: 0.8313 (m-80) REVERT: C 321 HIS cc_start: 0.8051 (t70) cc_final: 0.7761 (t-170) REVERT: C 323 PHE cc_start: 0.7740 (m-80) cc_final: 0.7278 (m-80) REVERT: C 332 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6564 (tp30) REVERT: D 76 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7287 (ttm-80) REVERT: D 290 MET cc_start: 0.8216 (mmm) cc_final: 0.7432 (mmm) REVERT: D 332 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6813 (tp30) REVERT: D 387 GLN cc_start: 0.8544 (mm110) cc_final: 0.8056 (mm-40) REVERT: D 444 ASN cc_start: 0.8350 (t0) cc_final: 0.7889 (t0) REVERT: D 526 MET cc_start: 0.7751 (mmt) cc_final: 0.7422 (mmm) REVERT: E 159 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: E 390 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7546 (ptmm) REVERT: E 397 LYS cc_start: 0.7743 (mmmt) cc_final: 0.7380 (mptt) REVERT: E 503 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8319 (ttpt) REVERT: E 519 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7322 (mtp180) REVERT: E 526 MET cc_start: 0.7524 (mmt) cc_final: 0.7154 (mmm) REVERT: F 71 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7472 (mm-30) REVERT: F 123 ARG cc_start: 0.7868 (ttt180) cc_final: 0.7419 (ttm110) REVERT: F 311 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.6956 (t0) REVERT: F 319 TYR cc_start: 0.8574 (m-80) cc_final: 0.8368 (m-80) REVERT: F 321 HIS cc_start: 0.8040 (t70) cc_final: 0.7763 (t-170) REVERT: F 323 PHE cc_start: 0.7742 (m-80) cc_final: 0.7275 (m-80) REVERT: F 332 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6566 (tp30) REVERT: F 339 ASN cc_start: 0.7674 (t0) cc_final: 0.7207 (t0) REVERT: F 348 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6742 (tp) outliers start: 38 outliers final: 13 residues processed: 367 average time/residue: 0.6927 time to fit residues: 288.2949 Evaluate side-chains 356 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 335 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 263 optimal weight: 0.0770 chunk 246 optimal weight: 0.6980 chunk 277 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 387 GLN F 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.164809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123163 restraints weight = 21981.382| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.55 r_work: 0.3181 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23574 Z= 0.104 Angle : 0.434 5.315 31818 Z= 0.232 Chirality : 0.041 0.148 3456 Planarity : 0.003 0.040 4140 Dihedral : 3.961 49.453 3234 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.02 % Allowed : 8.86 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.87 (0.16), residues: 2940 helix: 2.37 (0.13), residues: 1518 sheet: -0.17 (0.26), residues: 420 loop : 0.18 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.007 0.001 TYR E 439 PHE 0.010 0.001 PHE B 309 TRP 0.012 0.002 TRP C 338 HIS 0.004 0.001 HIS D 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (23574) covalent geometry : angle 0.43357 / 0.23 (31818) hydrogen bonds : bond 0.03538 / 2.35 ( 1328) hydrogen bonds : angle 4.15503 / 2.96 ( 3840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.902 Fit side-chains REVERT: A 87 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: A 90 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.5944 (mmpt) REVERT: A 103 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7396 (mtt90) REVERT: A 290 MET cc_start: 0.8021 (mmm) cc_final: 0.7221 (mmm) REVERT: A 332 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6607 (tp30) REVERT: A 387 GLN cc_start: 0.8484 (mm110) cc_final: 0.8039 (mm-40) REVERT: A 399 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7045 (mmtm) REVERT: A 444 ASN cc_start: 0.8393 (t0) cc_final: 0.7942 (t0) REVERT: A 526 MET cc_start: 0.7760 (mmt) cc_final: 0.7373 (mpp) REVERT: B 336 SER cc_start: 0.8323 (m) cc_final: 0.8112 (m) REVERT: B 390 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7490 (ptmm) REVERT: B 397 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7272 (mptt) REVERT: B 519 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7219 (mtp180) REVERT: B 526 MET cc_start: 0.7517 (mmt) cc_final: 0.7177 (mmm) REVERT: C 123 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7376 (ttm110) REVERT: C 311 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6826 (t0) REVERT: C 319 TYR cc_start: 0.8446 (m-80) cc_final: 0.8235 (m-80) REVERT: C 323 PHE cc_start: 0.7632 (m-80) cc_final: 0.7114 (m-80) REVERT: C 332 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6454 (tp30) REVERT: C 414 ASP cc_start: 0.8182 (m-30) cc_final: 0.7956 (m-30) REVERT: C 444 ASN cc_start: 0.8358 (t0) cc_final: 0.7957 (t0) REVERT: D 76 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7408 (ttm-80) REVERT: D 87 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: D 123 ARG cc_start: 0.7741 (tpt-90) cc_final: 0.7532 (tpt-90) REVERT: D 290 MET cc_start: 0.8023 (mmm) cc_final: 0.7192 (mmm) REVERT: D 332 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6848 (tp30) REVERT: D 387 GLN cc_start: 0.8494 (mm110) cc_final: 0.8053 (mm-40) REVERT: D 399 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7379 (mmtm) REVERT: D 444 ASN cc_start: 0.8395 (t0) cc_final: 0.7935 (t0) REVERT: D 519 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7297 (mmm160) REVERT: D 526 MET cc_start: 0.7751 (mmt) cc_final: 0.7374 (mpp) REVERT: E 141 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8539 (mm-40) REVERT: E 159 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: E 326 LYS cc_start: 0.7376 (ttmt) cc_final: 0.7164 (ttpp) REVERT: E 390 LYS cc_start: 0.8058 (ptmm) cc_final: 0.7497 (ptmm) REVERT: E 397 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7311 (mptt) REVERT: E 503 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8272 (ttpt) REVERT: E 519 ARG cc_start: 0.8248 (mmm160) cc_final: 0.7211 (mtp180) REVERT: E 526 MET cc_start: 0.7508 (mmt) cc_final: 0.7163 (mmm) REVERT: F 71 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7448 (mm-30) REVERT: F 123 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7331 (ttm110) REVERT: F 311 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6846 (t0) REVERT: F 319 TYR cc_start: 0.8463 (m-80) cc_final: 0.8256 (m-80) REVERT: F 323 PHE cc_start: 0.7646 (m-80) cc_final: 0.7155 (m-80) REVERT: F 332 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6451 (tp30) REVERT: F 339 ASN cc_start: 0.7488 (t0) cc_final: 0.6961 (t0) REVERT: F 444 ASN cc_start: 0.8350 (t0) cc_final: 0.7955 (t0) outliers start: 50 outliers final: 14 residues processed: 379 average time/residue: 0.6851 time to fit residues: 293.9662 Evaluate side-chains 367 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 346 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 311 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 214 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117377 restraints weight = 22920.223| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.53 r_work: 0.3282 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23574 Z= 0.247 Angle : 0.554 5.404 31818 Z= 0.295 Chirality : 0.047 0.145 3456 Planarity : 0.004 0.043 4140 Dihedral : 4.456 19.833 3232 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.27 % Allowed : 9.30 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.44 (0.15), residues: 2940 helix: 1.94 (0.13), residues: 1524 sheet: -0.19 (0.26), residues: 408 loop : 0.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.016 0.002 TYR A 319 PHE 0.014 0.002 PHE D 283 TRP 0.017 0.003 TRP C 338 HIS 0.009 0.002 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (23574) covalent geometry : angle 0.55360 / 0.30 (31818) hydrogen bonds : bond 0.04614 / 3.08 ( 1328) hydrogen bonds : angle 4.43137 / 3.16 ( 3840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: A 90 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.5936 (mmpt) REVERT: A 290 MET cc_start: 0.8153 (mmm) cc_final: 0.7476 (mmm) REVERT: A 332 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6645 (tp30) REVERT: A 387 GLN cc_start: 0.8506 (mm110) cc_final: 0.8023 (mm-40) REVERT: A 414 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: A 526 MET cc_start: 0.7852 (mmt) cc_final: 0.7497 (mpp) REVERT: B 336 SER cc_start: 0.8368 (m) cc_final: 0.8165 (m) REVERT: B 390 LYS cc_start: 0.8019 (ptmm) cc_final: 0.7442 (ptmm) REVERT: B 519 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7315 (mtm110) REVERT: B 526 MET cc_start: 0.7539 (mmt) cc_final: 0.7211 (mmm) REVERT: C 123 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7642 (ttm110) REVERT: C 311 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7105 (t0) REVERT: C 321 HIS cc_start: 0.8152 (t70) cc_final: 0.7889 (t-170) REVERT: C 323 PHE cc_start: 0.7842 (m-80) cc_final: 0.7316 (m-80) REVERT: C 332 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6388 (tp30) REVERT: C 399 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (mmpt) REVERT: D 76 ARG cc_start: 0.7741 (ttt90) cc_final: 0.7430 (ttm-80) REVERT: D 290 MET cc_start: 0.8173 (mmm) cc_final: 0.7464 (mmm) REVERT: D 332 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6709 (tp30) REVERT: D 347 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: D 387 GLN cc_start: 0.8517 (mm110) cc_final: 0.8051 (mm-40) REVERT: D 515 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8252 (tm-30) REVERT: D 526 MET cc_start: 0.7811 (mmt) cc_final: 0.7462 (mpp) REVERT: E 141 GLN cc_start: 0.8878 (mp-120) cc_final: 0.8567 (mm-40) REVERT: E 326 LYS cc_start: 0.7502 (ttmt) cc_final: 0.7285 (ttpp) REVERT: E 390 LYS cc_start: 0.8042 (ptmm) cc_final: 0.7446 (ptmm) REVERT: E 519 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7288 (mtm110) REVERT: E 526 MET cc_start: 0.7541 (mmt) cc_final: 0.7202 (mmm) REVERT: F 71 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7487 (mm-30) REVERT: F 123 ARG cc_start: 0.8179 (ttt180) cc_final: 0.7696 (ttm110) REVERT: F 311 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.7086 (t0) REVERT: F 321 HIS cc_start: 0.8138 (t70) cc_final: 0.7890 (t-170) REVERT: F 323 PHE cc_start: 0.7855 (m-80) cc_final: 0.7373 (m-80) REVERT: F 332 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6340 (tp30) REVERT: F 399 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7958 (mmpt) outliers start: 56 outliers final: 21 residues processed: 393 average time/residue: 0.7446 time to fit residues: 329.8665 Evaluate side-chains 383 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 399 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 12 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 266 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 GLN C 541 ASN D 141 GLN F 339 ASN F 541 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121087 restraints weight = 23065.551| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.54 r_work: 0.3292 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23574 Z= 0.121 Angle : 0.458 5.315 31818 Z= 0.245 Chirality : 0.042 0.142 3456 Planarity : 0.004 0.043 4140 Dihedral : 4.099 19.625 3232 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.78 % Allowed : 10.84 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.65 (0.16), residues: 2940 helix: 2.23 (0.13), residues: 1524 sheet: -0.43 (0.26), residues: 420 loop : 0.08 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.007 0.001 TYR C 170 PHE 0.015 0.001 PHE C 309 TRP 0.012 0.002 TRP C 338 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23574) covalent geometry : angle 0.45819 / 0.24 (31818) hydrogen bonds : bond 0.03672 / 2.44 ( 1328) hydrogen bonds : angle 4.20604 / 3.00 ( 3840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: A 90 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.5973 (mmpt) REVERT: A 290 MET cc_start: 0.8100 (mmm) cc_final: 0.7406 (mmm) REVERT: A 332 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6669 (tp30) REVERT: A 387 GLN cc_start: 0.8547 (mm110) cc_final: 0.8198 (mm-40) REVERT: A 444 ASN cc_start: 0.8272 (t0) cc_final: 0.7866 (t0) REVERT: A 519 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7314 (mmm160) REVERT: A 526 MET cc_start: 0.7808 (mmt) cc_final: 0.7395 (mpp) REVERT: B 100 ASN cc_start: 0.7713 (t0) cc_final: 0.7404 (m-40) REVERT: B 336 SER cc_start: 0.8317 (m) cc_final: 0.8102 (m) REVERT: B 390 LYS cc_start: 0.7971 (ptmm) cc_final: 0.7410 (ptmm) REVERT: B 519 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7293 (mtp180) REVERT: B 526 MET cc_start: 0.7484 (mmt) cc_final: 0.7152 (mmm) REVERT: C 123 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7485 (ttm110) REVERT: C 311 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.6951 (t0) REVERT: C 321 HIS cc_start: 0.8049 (t70) cc_final: 0.7804 (t-170) REVERT: C 323 PHE cc_start: 0.7748 (m-80) cc_final: 0.7252 (m-80) REVERT: C 332 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6355 (tp30) REVERT: C 444 ASN cc_start: 0.8272 (t0) cc_final: 0.7820 (t0) REVERT: C 504 ASP cc_start: 0.8394 (m-30) cc_final: 0.8158 (m-30) REVERT: C 541 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8438 (m110) REVERT: C 552 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: D 76 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7417 (ttm-80) REVERT: D 87 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6172 (mp0) REVERT: D 290 MET cc_start: 0.8096 (mmm) cc_final: 0.7348 (mmm) REVERT: D 332 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6737 (tp30) REVERT: D 347 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: D 387 GLN cc_start: 0.8544 (mm110) cc_final: 0.8128 (mm-40) REVERT: D 519 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7340 (mmm160) REVERT: D 526 MET cc_start: 0.7763 (mmt) cc_final: 0.7386 (mpp) REVERT: E 100 ASN cc_start: 0.7713 (t0) cc_final: 0.7407 (m-40) REVERT: E 390 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7481 (ptmm) REVERT: E 519 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7261 (mtp180) REVERT: E 526 MET cc_start: 0.7485 (mmt) cc_final: 0.7144 (mmm) REVERT: F 71 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7445 (mm-30) REVERT: F 123 ARG cc_start: 0.8038 (ttt180) cc_final: 0.7571 (ttm110) REVERT: F 311 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7074 (t0) REVERT: F 321 HIS cc_start: 0.8035 (t70) cc_final: 0.7761 (t-170) REVERT: F 323 PHE cc_start: 0.7782 (m-80) cc_final: 0.7272 (m-80) REVERT: F 332 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6332 (tp30) REVERT: F 339 ASN cc_start: 0.7735 (t0) cc_final: 0.7505 (t0) REVERT: F 414 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: F 444 ASN cc_start: 0.8288 (t0) cc_final: 0.7825 (t0) REVERT: F 504 ASP cc_start: 0.8374 (m-30) cc_final: 0.8132 (m-30) REVERT: F 541 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8417 (m110) outliers start: 44 outliers final: 17 residues processed: 376 average time/residue: 0.6809 time to fit residues: 289.6566 Evaluate side-chains 362 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 335 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 541 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 249 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 ASN D 541 ASN F 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118799 restraints weight = 23034.011| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.55 r_work: 0.3295 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23574 Z= 0.179 Angle : 0.499 5.350 31818 Z= 0.267 Chirality : 0.044 0.142 3456 Planarity : 0.004 0.043 4140 Dihedral : 4.285 19.080 3232 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 11.12 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.54 (0.16), residues: 2940 helix: 2.11 (0.13), residues: 1524 sheet: -0.29 (0.26), residues: 408 loop : -0.01 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 101 TYR 0.011 0.002 TYR A 319 PHE 0.015 0.002 PHE A 323 TRP 0.015 0.002 TRP C 338 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (23574) covalent geometry : angle 0.49906 / 0.27 (31818) hydrogen bonds : bond 0.04073 / 2.71 ( 1328) hydrogen bonds : angle 4.27354 / 3.05 ( 3840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 90 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.5970 (mmpt) REVERT: A 290 MET cc_start: 0.8158 (mmm) cc_final: 0.7511 (mmm) REVERT: A 332 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6711 (tp30) REVERT: A 387 GLN cc_start: 0.8540 (mm110) cc_final: 0.8077 (mm-40) REVERT: A 515 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 519 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7385 (mmm160) REVERT: A 526 MET cc_start: 0.7848 (mmt) cc_final: 0.7502 (mpp) REVERT: A 533 ASP cc_start: 0.8335 (t0) cc_final: 0.8042 (t70) REVERT: B 336 SER cc_start: 0.8357 (m) cc_final: 0.8152 (m) REVERT: B 390 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7437 (ptmm) REVERT: B 519 ARG cc_start: 0.8274 (mmm160) cc_final: 0.7292 (mtp180) REVERT: B 526 MET cc_start: 0.7523 (mmt) cc_final: 0.7233 (mmm) REVERT: C 123 ARG cc_start: 0.8025 (ttt180) cc_final: 0.7570 (ttm110) REVERT: C 311 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7050 (t0) REVERT: C 321 HIS cc_start: 0.8123 (t70) cc_final: 0.7855 (t-170) REVERT: C 323 PHE cc_start: 0.7845 (m-80) cc_final: 0.7334 (m-80) REVERT: C 332 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6459 (tp30) REVERT: C 541 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (m110) REVERT: D 76 ARG cc_start: 0.7706 (ttt90) cc_final: 0.7320 (ttm-80) REVERT: D 290 MET cc_start: 0.8116 (mmm) cc_final: 0.7467 (mmm) REVERT: D 332 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6668 (tp30) REVERT: D 347 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: D 387 GLN cc_start: 0.8560 (mm110) cc_final: 0.8071 (mm-40) REVERT: D 515 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 519 ARG cc_start: 0.7839 (mtm110) cc_final: 0.7384 (mmm160) REVERT: D 526 MET cc_start: 0.7794 (mmt) cc_final: 0.7454 (mpp) REVERT: E 390 LYS cc_start: 0.8001 (ptmm) cc_final: 0.7407 (ptmm) REVERT: E 519 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7285 (mtp180) REVERT: E 526 MET cc_start: 0.7523 (mmt) cc_final: 0.7227 (mmm) REVERT: F 71 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7476 (mm-30) REVERT: F 123 ARG cc_start: 0.8095 (ttt180) cc_final: 0.7628 (ttm110) REVERT: F 311 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7113 (t0) REVERT: F 321 HIS cc_start: 0.8114 (t70) cc_final: 0.7865 (t-170) REVERT: F 323 PHE cc_start: 0.7851 (m-80) cc_final: 0.7343 (m-80) REVERT: F 332 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6429 (tp30) REVERT: F 339 ASN cc_start: 0.7753 (t0) cc_final: 0.7269 (t0) REVERT: F 414 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: F 541 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8479 (m110) outliers start: 54 outliers final: 29 residues processed: 373 average time/residue: 0.6924 time to fit residues: 291.4680 Evaluate side-chains 374 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 541 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 190 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 ASN F 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119731 restraints weight = 22889.227| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.54 r_work: 0.3309 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23574 Z= 0.149 Angle : 0.480 5.332 31818 Z= 0.257 Chirality : 0.043 0.141 3456 Planarity : 0.004 0.042 4140 Dihedral : 4.217 19.004 3232 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.14 % Allowed : 11.41 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.59 (0.16), residues: 2940 helix: 2.17 (0.13), residues: 1524 sheet: -0.34 (0.26), residues: 408 loop : -0.01 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 123 TYR 0.009 0.001 TYR A 319 PHE 0.016 0.001 PHE A 323 TRP 0.014 0.002 TRP D 129 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (23574) covalent geometry : angle 0.47959 / 0.26 (31818) hydrogen bonds : bond 0.03871 / 2.57 ( 1328) hydrogen bonds : angle 4.23134 / 3.02 ( 3840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 343 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: A 90 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5967 (mmpt) REVERT: A 290 MET cc_start: 0.8133 (mmm) cc_final: 0.7486 (mmm) REVERT: A 332 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6668 (tp30) REVERT: A 387 GLN cc_start: 0.8546 (mm110) cc_final: 0.8139 (mm-40) REVERT: A 519 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7361 (mmm160) REVERT: A 526 MET cc_start: 0.7850 (mmt) cc_final: 0.7442 (mpp) REVERT: B 87 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: B 100 ASN cc_start: 0.7760 (t0) cc_final: 0.7448 (m-40) REVERT: B 336 SER cc_start: 0.8332 (m) cc_final: 0.8128 (m) REVERT: B 390 LYS cc_start: 0.8012 (ptmm) cc_final: 0.7445 (ptmm) REVERT: B 476 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7356 (ttp80) REVERT: B 519 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7283 (mtp180) REVERT: B 526 MET cc_start: 0.7527 (mmt) cc_final: 0.7235 (mmm) REVERT: C 123 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7536 (ttm110) REVERT: C 311 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7099 (t0) REVERT: C 321 HIS cc_start: 0.8081 (t70) cc_final: 0.7818 (t-170) REVERT: C 323 PHE cc_start: 0.7844 (m-80) cc_final: 0.7340 (m-80) REVERT: C 332 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6432 (tp30) REVERT: C 414 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: C 541 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8437 (m110) REVERT: C 552 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: D 76 ARG cc_start: 0.7717 (ttt90) cc_final: 0.7397 (ttm-80) REVERT: D 87 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: D 290 MET cc_start: 0.8121 (mmm) cc_final: 0.7439 (mmm) REVERT: D 332 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6657 (tp30) REVERT: D 347 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: D 387 GLN cc_start: 0.8555 (mm110) cc_final: 0.8133 (mm-40) REVERT: D 519 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7384 (mmm160) REVERT: D 526 MET cc_start: 0.7781 (mmt) cc_final: 0.7403 (mpp) REVERT: E 100 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: E 390 LYS cc_start: 0.8000 (ptmm) cc_final: 0.7410 (ptmm) REVERT: E 476 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7384 (ttp80) REVERT: E 519 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7278 (mtp180) REVERT: E 526 MET cc_start: 0.7513 (mmt) cc_final: 0.7213 (mmm) REVERT: F 71 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7485 (mm-30) REVERT: F 123 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7618 (ttm110) REVERT: F 311 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7128 (t0) REVERT: F 321 HIS cc_start: 0.8076 (t70) cc_final: 0.7786 (t-170) REVERT: F 323 PHE cc_start: 0.7834 (m-80) cc_final: 0.7334 (m-80) REVERT: F 332 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6424 (tp30) REVERT: F 339 ASN cc_start: 0.7757 (t0) cc_final: 0.7275 (t0) REVERT: F 414 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: F 541 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8390 (m110) outliers start: 53 outliers final: 30 residues processed: 375 average time/residue: 0.6885 time to fit residues: 291.3626 Evaluate side-chains 380 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 337 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 541 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 288 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 ASN F 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.166039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120253 restraints weight = 23010.448| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.55 r_work: 0.3318 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23574 Z= 0.135 Angle : 0.468 5.315 31818 Z= 0.251 Chirality : 0.043 0.141 3456 Planarity : 0.004 0.042 4140 Dihedral : 4.158 19.097 3232 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.14 % Allowed : 11.61 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.60 (0.16), residues: 2940 helix: 2.23 (0.13), residues: 1524 sheet: -0.54 (0.26), residues: 420 loop : 0.05 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 123 TYR 0.008 0.001 TYR F 170 PHE 0.016 0.001 PHE A 323 TRP 0.014 0.002 TRP D 129 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (23574) covalent geometry : angle 0.46830 / 0.25 (31818) hydrogen bonds : bond 0.03748 / 2.49 ( 1328) hydrogen bonds : angle 4.18511 / 2.99 ( 3840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: A 90 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5988 (mmpt) REVERT: A 290 MET cc_start: 0.8078 (mmm) cc_final: 0.7434 (mmm) REVERT: A 332 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6659 (tp30) REVERT: A 387 GLN cc_start: 0.8589 (mm110) cc_final: 0.8222 (mm-40) REVERT: A 519 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7368 (mmm160) REVERT: A 526 MET cc_start: 0.7833 (mmt) cc_final: 0.7477 (mpp) REVERT: B 87 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: B 100 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7448 (m-40) REVERT: B 336 SER cc_start: 0.8327 (m) cc_final: 0.8122 (m) REVERT: B 390 LYS cc_start: 0.8007 (ptmm) cc_final: 0.7438 (ptmm) REVERT: B 476 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.7378 (ttp80) REVERT: B 519 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7274 (mtp180) REVERT: B 526 MET cc_start: 0.7542 (mmt) cc_final: 0.7259 (mmm) REVERT: C 123 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7510 (ttm110) REVERT: C 311 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6988 (t0) REVERT: C 323 PHE cc_start: 0.7799 (m-80) cc_final: 0.7285 (m-80) REVERT: C 332 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6451 (tp30) REVERT: C 414 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: C 541 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8404 (m110) REVERT: C 552 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: D 76 ARG cc_start: 0.7704 (ttt90) cc_final: 0.7390 (ttm-80) REVERT: D 87 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: D 290 MET cc_start: 0.8081 (mmm) cc_final: 0.7391 (mmm) REVERT: D 332 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6685 (tp30) REVERT: D 347 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: D 387 GLN cc_start: 0.8585 (mm110) cc_final: 0.8170 (mm-40) REVERT: D 519 ARG cc_start: 0.7815 (mtm110) cc_final: 0.7356 (mmt180) REVERT: D 526 MET cc_start: 0.7765 (mmt) cc_final: 0.7433 (mpp) REVERT: E 100 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.7456 (m-40) REVERT: E 390 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7404 (ptmm) REVERT: E 476 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7417 (ttp80) REVERT: E 519 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7277 (mtp180) REVERT: E 526 MET cc_start: 0.7537 (mmt) cc_final: 0.7248 (mmm) REVERT: F 71 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7496 (mm-30) REVERT: F 123 ARG cc_start: 0.8067 (ttt180) cc_final: 0.7603 (ttm110) REVERT: F 311 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7070 (t0) REVERT: F 321 HIS cc_start: 0.8070 (t70) cc_final: 0.7826 (t-170) REVERT: F 323 PHE cc_start: 0.7805 (m-80) cc_final: 0.7296 (m-80) REVERT: F 332 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6463 (tp30) REVERT: F 339 ASN cc_start: 0.7788 (t0) cc_final: 0.7318 (t0) REVERT: F 414 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: F 444 ASN cc_start: 0.8249 (t0) cc_final: 0.7992 (t0) REVERT: F 504 ASP cc_start: 0.8376 (m-30) cc_final: 0.8171 (m-30) REVERT: F 541 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8343 (m110) outliers start: 53 outliers final: 29 residues processed: 378 average time/residue: 0.6647 time to fit residues: 284.7535 Evaluate side-chains 383 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 541 ASN Chi-restraints excluded: chain C residue 552 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain F residue 541 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 144 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 541 ASN F 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118613 restraints weight = 23059.501| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.54 r_work: 0.3293 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23574 Z= 0.188 Angle : 0.512 5.366 31818 Z= 0.274 Chirality : 0.045 0.140 3456 Planarity : 0.004 0.043 4140 Dihedral : 4.345 18.850 3232 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.02 % Allowed : 11.97 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.50 (0.16), residues: 2940 helix: 2.08 (0.13), residues: 1524 sheet: -0.36 (0.25), residues: 414 loop : -0.02 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 123 TYR 0.012 0.002 TYR A 319 PHE 0.018 0.002 PHE B 309 TRP 0.021 0.003 TRP A 129 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (23574) covalent geometry : angle 0.51218 / 0.27 (31818) hydrogen bonds : bond 0.04129 / 2.74 ( 1328) hydrogen bonds : angle 4.27267 / 3.05 ( 3840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 90 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.5892 (mmpt) REVERT: A 290 MET cc_start: 0.8123 (mmm) cc_final: 0.7471 (mmm) REVERT: A 332 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6685 (tp30) REVERT: A 387 GLN cc_start: 0.8546 (mm110) cc_final: 0.8087 (mm-40) REVERT: A 519 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7390 (mmm160) REVERT: A 526 MET cc_start: 0.7850 (mmt) cc_final: 0.7497 (mpp) REVERT: B 87 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: B 100 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7434 (m-40) REVERT: B 373 GLU cc_start: 0.7579 (mp0) cc_final: 0.7352 (mt-10) REVERT: B 390 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7455 (ptmm) REVERT: B 476 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.7406 (ttp80) REVERT: B 519 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7286 (mtp180) REVERT: B 526 MET cc_start: 0.7524 (mmt) cc_final: 0.7233 (mmm) REVERT: C 123 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7711 (ttm110) REVERT: C 311 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7124 (t0) REVERT: C 319 TYR cc_start: 0.8542 (m-80) cc_final: 0.8335 (m-80) REVERT: C 321 HIS cc_start: 0.8152 (t70) cc_final: 0.7873 (t-170) REVERT: C 323 PHE cc_start: 0.7867 (m-80) cc_final: 0.7325 (m-80) REVERT: C 332 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6469 (tp30) REVERT: C 399 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7876 (mmpt) REVERT: C 414 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: D 76 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7410 (ttm-80) REVERT: D 290 MET cc_start: 0.8121 (mmm) cc_final: 0.7534 (mmm) REVERT: D 332 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6669 (tp30) REVERT: D 347 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: D 387 GLN cc_start: 0.8554 (mm110) cc_final: 0.8065 (mm-40) REVERT: D 519 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7343 (mmt180) REVERT: D 526 MET cc_start: 0.7795 (mmt) cc_final: 0.7458 (mpp) REVERT: E 100 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: E 390 LYS cc_start: 0.8047 (ptmm) cc_final: 0.7451 (ptmm) REVERT: E 476 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7440 (ttp80) REVERT: E 519 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7285 (mtp180) REVERT: E 526 MET cc_start: 0.7521 (mmt) cc_final: 0.7222 (mmm) REVERT: F 71 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7515 (mm-30) REVERT: F 123 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7661 (ttm110) REVERT: F 311 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7096 (t0) REVERT: F 321 HIS cc_start: 0.8127 (t70) cc_final: 0.7876 (t-170) REVERT: F 323 PHE cc_start: 0.7860 (m-80) cc_final: 0.7331 (m-80) REVERT: F 332 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6488 (tp30) REVERT: F 339 ASN cc_start: 0.7783 (t0) cc_final: 0.7326 (t0) REVERT: F 414 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7500 (m-30) outliers start: 50 outliers final: 29 residues processed: 379 average time/residue: 0.6762 time to fit residues: 289.7225 Evaluate side-chains 385 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 345 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 98 LYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 399 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain F residue 225 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 81 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 173 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120944 restraints weight = 22928.535| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.55 r_work: 0.3291 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23574 Z= 0.125 Angle : 0.464 5.292 31818 Z= 0.249 Chirality : 0.042 0.140 3456 Planarity : 0.004 0.043 4140 Dihedral : 4.109 18.921 3232 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.62 % Allowed : 12.54 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.64 (0.16), residues: 2940 helix: 2.31 (0.13), residues: 1518 sheet: -0.60 (0.25), residues: 420 loop : 0.03 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 123 TYR 0.011 0.001 TYR C 319 PHE 0.021 0.001 PHE C 309 TRP 0.013 0.002 TRP A 129 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (23574) covalent geometry : angle 0.46362 / 0.25 (31818) hydrogen bonds : bond 0.03644 / 2.42 ( 1328) hydrogen bonds : angle 4.15011 / 2.96 ( 3840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9012.00 seconds wall clock time: 154 minutes 22.31 seconds (9262.31 seconds total)