Starting phenix.real_space_refine on Wed Jun 18 14:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuj_45935/06_2025/9cuj_45935.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.076 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 20 5.49 5 S 160 5.16 5 C 14288 2.51 5 N 3336 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21557 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "B" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "D" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 477 Unusual residues: {' CA': 1, 'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1, 'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 13.28, per 1000 atoms: 0.62 Number of scatterers: 21557 At special positions: 0 Unit cell: (131.97, 131.97, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 20 15.00 O 3752 8.00 N 3336 7.00 C 14288 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: 5.33 Conformation dependent library (CDL) restraints added in 2.5 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 67.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.675A pdb=" N SER A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.572A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.867A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.009A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.579A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.550A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.531A pdb=" N LEU B 612 " --> pdb=" O PRO B 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.007A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.581A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.582A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU C 612 " --> pdb=" O PRO C 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.747A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.577A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.690A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1010 hydrogen bonds defined for protein. 2922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3204 1.30 - 1.43: 5461 1.43 - 1.56: 12808 1.56 - 1.69: 175 1.69 - 1.81: 272 Bond restraints: 21920 Sorted by residual: bond pdb=" C29 POV A 803 " pdb="C210 POV A 803 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV D 809 " pdb="C210 POV D 809 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 805 " pdb="C210 POV C 805 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 808 " pdb="C210 POV C 808 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 ... (remaining 21915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 28517 3.25 - 6.50: 676 6.50 - 9.75: 159 9.75 - 12.99: 68 12.99 - 16.24: 16 Bond angle restraints: 29436 Sorted by residual: angle pdb=" C GLU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 121.54 133.83 -12.29 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 121.54 133.82 -12.28 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C29 POV A 806 " pdb="C210 POV A 806 " pdb="C211 POV A 806 " ideal model delta sigma weight residual 127.67 111.43 16.24 3.00e+00 1.11e-01 2.93e+01 ... (remaining 29431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 13225 30.26 - 60.52: 696 60.52 - 90.78: 69 90.78 - 121.04: 14 121.04 - 151.30: 12 Dihedral angle restraints: 14016 sinusoidal: 6880 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASP C 69 " pdb=" C ASP C 69 " pdb=" N CYS C 70 " pdb=" CA CYS C 70 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP B 69 " pdb=" C ASP B 69 " pdb=" N CYS B 70 " pdb=" CA CYS B 70 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP A 69 " pdb=" C ASP A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2767 0.074 - 0.148: 395 0.148 - 0.222: 30 0.222 - 0.296: 0 0.296 - 0.370: 12 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 3201 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 805 " 0.299 2.00e-02 2.50e+03 2.99e-01 8.96e+02 pdb=" C29 POV B 805 " -0.297 2.00e-02 2.50e+03 pdb="C210 POV B 805 " -0.302 2.00e-02 2.50e+03 pdb="C211 POV B 805 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 809 " -0.292 2.00e-02 2.50e+03 2.93e-01 8.58e+02 pdb=" C29 POV D 809 " 0.288 2.00e-02 2.50e+03 pdb="C210 POV D 809 " 0.298 2.00e-02 2.50e+03 pdb="C211 POV D 809 " -0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 803 " -0.287 2.00e-02 2.50e+03 2.90e-01 8.43e+02 pdb=" C29 POV A 803 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV A 803 " 0.302 2.00e-02 2.50e+03 pdb="C211 POV A 803 " -0.293 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5834 2.81 - 3.33: 17911 3.33 - 3.86: 33584 3.86 - 4.38: 43816 4.38 - 4.90: 72872 Nonbonded interactions: 174017 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU A 535 " pdb=" O HOH A 901 " model vdw 2.312 3.040 ... (remaining 174012 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 806)) selection = (chain 'B' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) } 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=0.45 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: 1.210 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.080 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.011 0.219 21920 Z= 0.533 Angle : 1.393 16.244 29436 Z= 0.640 Chirality : 0.054 0.370 3204 Planarity : 0.013 0.299 3552 Dihedral : 17.597 151.303 9408 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.51 % Allowed : 3.02 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.66 (0.11), residues: 2432 helix: -4.26 (0.06), residues: 1456 sheet: -2.58 (0.65), residues: 76 loop : -2.56 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 629 HIS 0.012 0.003 HIS C 522 PHE 0.028 0.003 PHE B 169 TYR 0.027 0.003 TYR A 377 ARG 0.008 0.001 ARG A 589 Details of bonding type rmsd hydrogen bonds : bond 0.33578 ( 1010) hydrogen bonds : angle 9.45382 ( 2922) covalent geometry : bond 0.01125 (21920) covalent geometry : angle 1.39314 (29436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 500 time to evaluate : 2.196 Fit side-chains REVERT: A 47 SER cc_start: 0.6063 (m) cc_final: 0.5480 (p) REVERT: A 93 GLU cc_start: 0.6607 (mp0) cc_final: 0.6277 (mt-10) REVERT: A 96 MET cc_start: 0.5079 (mtm) cc_final: 0.4695 (mtm) REVERT: A 110 MET cc_start: 0.6739 (mtt) cc_final: 0.6473 (mtt) REVERT: A 139 ARG cc_start: 0.6568 (mtt-85) cc_final: 0.6211 (mpt180) REVERT: A 177 GLU cc_start: 0.7095 (mp0) cc_final: 0.6571 (mp0) REVERT: A 311 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5162 (m) REVERT: A 375 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 379 THR cc_start: 0.7517 (t) cc_final: 0.7167 (p) REVERT: A 381 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7566 (mtpt) REVERT: A 589 ARG cc_start: 0.7035 (tmm160) cc_final: 0.6758 (ttm-80) REVERT: A 590 ASP cc_start: 0.7399 (m-30) cc_final: 0.7130 (m-30) REVERT: A 608 LEU cc_start: 0.7416 (mt) cc_final: 0.7174 (mt) REVERT: A 637 GLN cc_start: 0.5700 (mp10) cc_final: 0.5143 (mp-120) REVERT: B 47 SER cc_start: 0.6198 (m) cc_final: 0.5746 (p) REVERT: B 93 GLU cc_start: 0.6723 (mp0) cc_final: 0.6357 (mt-10) REVERT: B 96 MET cc_start: 0.5230 (mtm) cc_final: 0.4907 (mtm) REVERT: B 139 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.6494 (mpt180) REVERT: B 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6683 (mp0) REVERT: B 263 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7323 (mtm-85) REVERT: B 311 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5236 (m) REVERT: B 379 THR cc_start: 0.7899 (t) cc_final: 0.7673 (p) REVERT: B 381 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7746 (mtpt) REVERT: B 392 THR cc_start: 0.8465 (t) cc_final: 0.8205 (m) REVERT: B 458 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (mt) REVERT: B 497 MET cc_start: 0.8172 (mtt) cc_final: 0.7936 (mtm) REVERT: B 524 TYR cc_start: 0.8037 (p90) cc_final: 0.7793 (p90) REVERT: B 535 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 590 ASP cc_start: 0.7573 (m-30) cc_final: 0.7309 (m-30) REVERT: B 637 GLN cc_start: 0.6029 (mp10) cc_final: 0.5400 (mp-120) REVERT: C 78 MET cc_start: 0.7261 (mmt) cc_final: 0.6949 (mmp) REVERT: C 93 GLU cc_start: 0.6660 (mp0) cc_final: 0.6296 (mt-10) REVERT: C 96 MET cc_start: 0.5037 (mtm) cc_final: 0.4706 (mtm) REVERT: C 139 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.6321 (mtm180) REVERT: C 177 GLU cc_start: 0.7106 (mp0) cc_final: 0.6614 (mp0) REVERT: C 263 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7281 (mtm-85) REVERT: C 311 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5111 (m) REVERT: C 375 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 379 THR cc_start: 0.7870 (t) cc_final: 0.7530 (p) REVERT: C 381 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7596 (mtpt) REVERT: C 392 THR cc_start: 0.8431 (t) cc_final: 0.8204 (m) REVERT: C 458 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 497 MET cc_start: 0.8073 (mtt) cc_final: 0.7808 (mtm) REVERT: C 524 TYR cc_start: 0.7991 (p90) cc_final: 0.7682 (p90) REVERT: C 535 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 589 ARG cc_start: 0.7232 (tmm160) cc_final: 0.6930 (ttm-80) REVERT: C 590 ASP cc_start: 0.7567 (m-30) cc_final: 0.7296 (m-30) REVERT: C 637 GLN cc_start: 0.5940 (mp10) cc_final: 0.5294 (mp-120) REVERT: D 78 MET cc_start: 0.7305 (mmt) cc_final: 0.6987 (mmp) REVERT: D 93 GLU cc_start: 0.6671 (mp0) cc_final: 0.6297 (mt-10) REVERT: D 96 MET cc_start: 0.5035 (mtm) cc_final: 0.4663 (mtm) REVERT: D 139 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6309 (mtm180) REVERT: D 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6590 (mp0) REVERT: D 263 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7197 (mtm-85) REVERT: D 311 THR cc_start: 0.6051 (OUTLIER) cc_final: 0.5117 (m) REVERT: D 375 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 379 THR cc_start: 0.7801 (t) cc_final: 0.7372 (p) REVERT: D 381 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7610 (mtpt) REVERT: D 392 THR cc_start: 0.8456 (t) cc_final: 0.8222 (m) REVERT: D 458 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 497 MET cc_start: 0.8075 (mtt) cc_final: 0.7817 (mtm) REVERT: D 535 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 589 ARG cc_start: 0.7207 (tmm160) cc_final: 0.6879 (ttm-80) REVERT: D 590 ASP cc_start: 0.7538 (m-30) cc_final: 0.7243 (m-30) REVERT: D 608 LEU cc_start: 0.7376 (mt) cc_final: 0.7175 (mt) REVERT: D 637 GLN cc_start: 0.5748 (mp10) cc_final: 0.5201 (mp-120) outliers start: 32 outliers final: 5 residues processed: 528 average time/residue: 1.3107 time to fit residues: 785.9198 Evaluate side-chains 378 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 118 GLN A 122 HIS A 174 ASN A 225 HIS A 369 GLN A 370 GLN A 546 ASN A 572 ASN B 37 ASN B 118 GLN B 122 HIS B 174 ASN B 225 HIS B 369 GLN B 370 GLN B 546 ASN B 572 ASN B 582 HIS C 37 ASN C 118 GLN C 122 HIS C 174 ASN C 225 HIS C 369 GLN C 370 GLN C 546 ASN C 572 ASN C 582 HIS D 37 ASN D 118 GLN D 122 HIS D 174 ASN D 225 HIS D 369 GLN D 370 GLN D 546 ASN D 572 ASN D 582 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.196829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131800 restraints weight = 20770.812| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.84 r_work: 0.3225 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21920 Z= 0.194 Angle : 0.687 7.992 29436 Z= 0.344 Chirality : 0.043 0.279 3204 Planarity : 0.006 0.046 3552 Dihedral : 19.029 178.568 4720 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 7.84 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2432 helix: -1.59 (0.11), residues: 1460 sheet: -2.14 (0.66), residues: 76 loop : -1.70 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 613 HIS 0.006 0.001 HIS A 201 PHE 0.023 0.002 PHE B 537 TYR 0.017 0.002 TYR D 377 ARG 0.009 0.001 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.06275 ( 1010) hydrogen bonds : angle 4.56906 ( 2922) covalent geometry : bond 0.00468 (21920) covalent geometry : angle 0.68742 (29436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 408 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5935 (tm) REVERT: A 96 MET cc_start: 0.5439 (mtm) cc_final: 0.5148 (mtm) REVERT: A 177 GLU cc_start: 0.7128 (mp0) cc_final: 0.6804 (mp0) REVERT: A 375 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8009 (mt-10) REVERT: A 378 MET cc_start: 0.8321 (mtt) cc_final: 0.7965 (mtp) REVERT: A 458 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 535 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 608 LEU cc_start: 0.7758 (mt) cc_final: 0.7435 (mt) REVERT: A 618 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 637 GLN cc_start: 0.6265 (mp10) cc_final: 0.6001 (mp-120) REVERT: B 51 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5918 (tm) REVERT: B 93 GLU cc_start: 0.7059 (mp0) cc_final: 0.6690 (mp0) REVERT: B 96 MET cc_start: 0.5258 (mtm) cc_final: 0.4963 (mtm) REVERT: B 177 GLU cc_start: 0.7138 (mp0) cc_final: 0.6770 (mp0) REVERT: B 315 GLU cc_start: 0.8256 (mp0) cc_final: 0.8047 (mp0) REVERT: B 381 LYS cc_start: 0.7362 (mtmt) cc_final: 0.7049 (mtpt) REVERT: B 392 THR cc_start: 0.8307 (t) cc_final: 0.7954 (m) REVERT: B 535 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 590 ASP cc_start: 0.7920 (m-30) cc_final: 0.7690 (m-30) REVERT: B 610 ARG cc_start: 0.6612 (tpm170) cc_final: 0.6250 (tpt170) REVERT: B 618 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7589 (mt) REVERT: B 637 GLN cc_start: 0.6228 (mp10) cc_final: 0.5910 (mp-120) REVERT: C 78 MET cc_start: 0.7608 (mmt) cc_final: 0.7283 (mmp) REVERT: C 93 GLU cc_start: 0.7044 (mp0) cc_final: 0.6661 (mp0) REVERT: C 96 MET cc_start: 0.5380 (mtm) cc_final: 0.5004 (mtm) REVERT: C 177 GLU cc_start: 0.7158 (mp0) cc_final: 0.6826 (mp0) REVERT: C 375 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 378 MET cc_start: 0.8351 (mtp) cc_final: 0.8103 (mtm) REVERT: C 381 LYS cc_start: 0.7322 (mtmt) cc_final: 0.7014 (mtpt) REVERT: C 392 THR cc_start: 0.8325 (t) cc_final: 0.7978 (m) REVERT: C 535 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7601 (mt-10) REVERT: C 610 ARG cc_start: 0.6739 (tpm170) cc_final: 0.6383 (tpt170) REVERT: C 618 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (mt) REVERT: C 637 GLN cc_start: 0.6166 (mp10) cc_final: 0.5912 (mp-120) REVERT: D 37 ASN cc_start: 0.8090 (m110) cc_final: 0.7886 (m110) REVERT: D 78 MET cc_start: 0.7667 (mmt) cc_final: 0.7248 (mmp) REVERT: D 93 GLU cc_start: 0.7064 (mp0) cc_final: 0.6683 (mp0) REVERT: D 96 MET cc_start: 0.5316 (mtm) cc_final: 0.4959 (mtm) REVERT: D 177 GLU cc_start: 0.7125 (mp0) cc_final: 0.6783 (mp0) REVERT: D 375 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 381 LYS cc_start: 0.7382 (mtmt) cc_final: 0.7129 (mtpt) REVERT: D 392 THR cc_start: 0.8316 (t) cc_final: 0.7960 (m) REVERT: D 535 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 608 LEU cc_start: 0.7738 (mt) cc_final: 0.7432 (mt) REVERT: D 610 ARG cc_start: 0.6705 (tpm170) cc_final: 0.6358 (tpt170) REVERT: D 618 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7607 (mt) REVERT: D 637 GLN cc_start: 0.6237 (mp10) cc_final: 0.5983 (mp-120) outliers start: 55 outliers final: 23 residues processed: 440 average time/residue: 1.2986 time to fit residues: 649.9953 Evaluate side-chains 382 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 174 ASN A 197 ASN B 37 ASN B 197 ASN C 37 ASN C 197 ASN D 174 ASN D 197 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.196249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133359 restraints weight = 20681.245| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.92 r_work: 0.3230 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21920 Z= 0.155 Angle : 0.600 7.823 29436 Z= 0.301 Chirality : 0.042 0.253 3204 Planarity : 0.005 0.042 3552 Dihedral : 17.637 157.440 4718 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.79 % Allowed : 10.92 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2432 helix: -0.11 (0.13), residues: 1468 sheet: -1.95 (0.63), residues: 76 loop : -1.35 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 593 HIS 0.004 0.001 HIS B 265 PHE 0.016 0.002 PHE A 537 TYR 0.016 0.002 TYR B 377 ARG 0.009 0.001 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 1010) hydrogen bonds : angle 4.10386 ( 2922) covalent geometry : bond 0.00368 (21920) covalent geometry : angle 0.60003 (29436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 369 time to evaluate : 4.279 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5984 (tm) REVERT: A 93 GLU cc_start: 0.7312 (mp0) cc_final: 0.6525 (mp0) REVERT: A 96 MET cc_start: 0.5329 (mtm) cc_final: 0.4978 (mtm) REVERT: A 146 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.7109 (mtp-110) REVERT: A 177 GLU cc_start: 0.7078 (mp0) cc_final: 0.6807 (mp0) REVERT: A 315 GLU cc_start: 0.8094 (mp0) cc_final: 0.7807 (mp0) REVERT: A 375 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 378 MET cc_start: 0.8364 (mtt) cc_final: 0.8081 (mtm) REVERT: A 458 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 535 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 608 LEU cc_start: 0.7643 (mt) cc_final: 0.7345 (mt) REVERT: A 618 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 637 GLN cc_start: 0.6333 (mp10) cc_final: 0.6055 (mp-120) REVERT: B 51 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5989 (tm) REVERT: B 93 GLU cc_start: 0.6975 (mp0) cc_final: 0.6633 (mp0) REVERT: B 96 MET cc_start: 0.5319 (mtm) cc_final: 0.4931 (mtm) REVERT: B 131 ASN cc_start: 0.6857 (m110) cc_final: 0.6297 (m-40) REVERT: B 177 GLU cc_start: 0.7121 (mp0) cc_final: 0.6792 (mp0) REVERT: B 311 THR cc_start: 0.5391 (OUTLIER) cc_final: 0.4785 (p) REVERT: B 378 MET cc_start: 0.8297 (mtp) cc_final: 0.7995 (mtp) REVERT: B 535 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 588 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: B 590 ASP cc_start: 0.7934 (m-30) cc_final: 0.7704 (m-30) REVERT: B 610 ARG cc_start: 0.6539 (tpm170) cc_final: 0.6310 (tpt170) REVERT: B 618 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7579 (mt) REVERT: B 637 GLN cc_start: 0.6301 (mp10) cc_final: 0.6083 (mp-120) REVERT: C 93 GLU cc_start: 0.6965 (mp0) cc_final: 0.6605 (mp0) REVERT: C 96 MET cc_start: 0.5339 (mtm) cc_final: 0.4956 (mtm) REVERT: C 131 ASN cc_start: 0.6744 (m110) cc_final: 0.6198 (m-40) REVERT: C 177 GLU cc_start: 0.7066 (mp0) cc_final: 0.6810 (mp0) REVERT: C 311 THR cc_start: 0.5431 (OUTLIER) cc_final: 0.4719 (p) REVERT: C 375 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7960 (mt-10) REVERT: C 535 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7741 (mt-10) REVERT: C 573 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8625 (tt) REVERT: C 610 ARG cc_start: 0.6522 (tpm170) cc_final: 0.6300 (tpt170) REVERT: C 618 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7600 (mt) REVERT: C 637 GLN cc_start: 0.6279 (mp10) cc_final: 0.6062 (mp-120) REVERT: D 93 GLU cc_start: 0.6936 (mp0) cc_final: 0.6616 (mp0) REVERT: D 96 MET cc_start: 0.5364 (mtm) cc_final: 0.4927 (mtm) REVERT: D 131 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6268 (m-40) REVERT: D 146 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7069 (mtp-110) REVERT: D 177 GLU cc_start: 0.7075 (mp0) cc_final: 0.6784 (mp0) REVERT: D 311 THR cc_start: 0.5391 (OUTLIER) cc_final: 0.4852 (p) REVERT: D 375 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 535 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 608 LEU cc_start: 0.7615 (mt) cc_final: 0.7335 (mt) REVERT: D 610 ARG cc_start: 0.6408 (tpm170) cc_final: 0.5995 (tpt170) REVERT: D 618 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7611 (mt) REVERT: D 637 GLN cc_start: 0.6265 (mp10) cc_final: 0.5985 (mp-120) outliers start: 59 outliers final: 21 residues processed: 415 average time/residue: 1.5487 time to fit residues: 739.8126 Evaluate side-chains 375 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 139 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS C 36 GLN D 36 GLN D 37 ASN D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.196091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130758 restraints weight = 20932.924| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.86 r_work: 0.3246 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21920 Z= 0.148 Angle : 0.588 7.539 29436 Z= 0.293 Chirality : 0.042 0.252 3204 Planarity : 0.005 0.041 3552 Dihedral : 16.635 151.248 4718 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.69 % Allowed : 12.57 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2432 helix: 0.56 (0.14), residues: 1464 sheet: -1.43 (0.65), residues: 76 loop : -1.21 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 593 HIS 0.003 0.001 HIS A 201 PHE 0.013 0.002 PHE A 537 TYR 0.013 0.002 TYR B 467 ARG 0.011 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.05006 ( 1010) hydrogen bonds : angle 3.96233 ( 2922) covalent geometry : bond 0.00351 (21920) covalent geometry : angle 0.58830 (29436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 370 time to evaluate : 2.485 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5966 (tm) REVERT: A 93 GLU cc_start: 0.7275 (mp0) cc_final: 0.6511 (mp0) REVERT: A 96 MET cc_start: 0.5332 (mtm) cc_final: 0.4932 (mtm) REVERT: A 131 ASN cc_start: 0.6921 (m110) cc_final: 0.6313 (m-40) REVERT: A 177 GLU cc_start: 0.7138 (mp0) cc_final: 0.6789 (pm20) REVERT: A 311 THR cc_start: 0.5449 (OUTLIER) cc_final: 0.4855 (p) REVERT: A 315 GLU cc_start: 0.8116 (mp0) cc_final: 0.7911 (mp0) REVERT: A 375 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 378 MET cc_start: 0.8346 (mtt) cc_final: 0.8056 (mtm) REVERT: A 458 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 535 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 608 LEU cc_start: 0.7581 (mt) cc_final: 0.7328 (mt) REVERT: A 618 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 51 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5904 (tm) REVERT: B 93 GLU cc_start: 0.6926 (mp0) cc_final: 0.6578 (mp0) REVERT: B 96 MET cc_start: 0.5346 (mtm) cc_final: 0.4961 (mtm) REVERT: B 131 ASN cc_start: 0.6848 (m110) cc_final: 0.6308 (m-40) REVERT: B 146 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7183 (mtp-110) REVERT: B 177 GLU cc_start: 0.7118 (mp0) cc_final: 0.6810 (mp0) REVERT: B 311 THR cc_start: 0.5618 (OUTLIER) cc_final: 0.4915 (p) REVERT: B 315 GLU cc_start: 0.8099 (mp0) cc_final: 0.7871 (mp0) REVERT: B 378 MET cc_start: 0.8288 (mtp) cc_final: 0.8066 (mtp) REVERT: B 535 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 590 ASP cc_start: 0.7927 (m-30) cc_final: 0.7712 (m-30) REVERT: B 618 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7645 (mt) REVERT: B 637 GLN cc_start: 0.6369 (mp10) cc_final: 0.6083 (mp-120) REVERT: C 93 GLU cc_start: 0.6955 (mp0) cc_final: 0.6594 (mp0) REVERT: C 96 MET cc_start: 0.5432 (mtm) cc_final: 0.4993 (mtm) REVERT: C 131 ASN cc_start: 0.6815 (m110) cc_final: 0.6257 (m-40) REVERT: C 177 GLU cc_start: 0.7069 (mp0) cc_final: 0.6833 (mp0) REVERT: C 311 THR cc_start: 0.5626 (OUTLIER) cc_final: 0.4992 (p) REVERT: C 375 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 378 MET cc_start: 0.8292 (mtm) cc_final: 0.8040 (mtp) REVERT: C 535 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 618 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (mt) REVERT: C 637 GLN cc_start: 0.6331 (mp10) cc_final: 0.6036 (mp-120) REVERT: D 93 GLU cc_start: 0.6984 (mp0) cc_final: 0.6663 (mp0) REVERT: D 96 MET cc_start: 0.5574 (mtm) cc_final: 0.5116 (mtm) REVERT: D 131 ASN cc_start: 0.6855 (m110) cc_final: 0.6303 (m-40) REVERT: D 146 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.7216 (mtp-110) REVERT: D 177 GLU cc_start: 0.7114 (mp0) cc_final: 0.6798 (mp0) REVERT: D 311 THR cc_start: 0.5458 (OUTLIER) cc_final: 0.4861 (p) REVERT: D 315 GLU cc_start: 0.8111 (mp0) cc_final: 0.7884 (mp0) REVERT: D 375 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8050 (mt-10) REVERT: D 535 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 588 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: D 608 LEU cc_start: 0.7584 (mt) cc_final: 0.7341 (mt) REVERT: D 610 ARG cc_start: 0.6444 (tpm170) cc_final: 0.6225 (tpm170) REVERT: D 618 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7645 (mt) REVERT: D 637 GLN cc_start: 0.6426 (mp10) cc_final: 0.6213 (mp-120) outliers start: 57 outliers final: 22 residues processed: 415 average time/residue: 1.3699 time to fit residues: 653.6407 Evaluate side-chains 384 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 350 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 202 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 200 optimal weight: 40.0000 chunk 63 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS D 91 ASN D 185 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.194784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.131107 restraints weight = 20768.657| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.74 r_work: 0.3238 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21920 Z= 0.178 Angle : 0.618 7.677 29436 Z= 0.305 Chirality : 0.043 0.284 3204 Planarity : 0.005 0.050 3552 Dihedral : 16.318 154.160 4718 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.41 % Allowed : 13.75 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2432 helix: 0.77 (0.14), residues: 1464 sheet: -1.18 (0.64), residues: 76 loop : -1.14 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 593 HIS 0.006 0.001 HIS C 185 PHE 0.014 0.002 PHE A 537 TYR 0.013 0.002 TYR C 467 ARG 0.012 0.001 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 1010) hydrogen bonds : angle 3.97758 ( 2922) covalent geometry : bond 0.00435 (21920) covalent geometry : angle 0.61836 (29436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 355 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5971 (tm) REVERT: A 93 GLU cc_start: 0.7263 (mp0) cc_final: 0.6513 (mp0) REVERT: A 96 MET cc_start: 0.5292 (mtm) cc_final: 0.4921 (mtm) REVERT: A 131 ASN cc_start: 0.6916 (m110) cc_final: 0.6322 (m-40) REVERT: A 177 GLU cc_start: 0.7077 (mp0) cc_final: 0.6746 (pm20) REVERT: A 458 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 588 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: A 608 LEU cc_start: 0.7539 (mt) cc_final: 0.7284 (mt) REVERT: A 618 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7697 (mt) REVERT: B 51 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5979 (tm) REVERT: B 96 MET cc_start: 0.5302 (mtm) cc_final: 0.4921 (mtm) REVERT: B 131 ASN cc_start: 0.6791 (m110) cc_final: 0.6262 (m-40) REVERT: B 177 GLU cc_start: 0.7134 (mp0) cc_final: 0.6817 (mp0) REVERT: B 378 MET cc_start: 0.8292 (mtp) cc_final: 0.8084 (mtp) REVERT: B 588 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: C 96 MET cc_start: 0.5276 (mtm) cc_final: 0.4887 (mtm) REVERT: C 131 ASN cc_start: 0.6789 (m110) cc_final: 0.6248 (m-40) REVERT: C 177 GLU cc_start: 0.7067 (mp0) cc_final: 0.6743 (pm20) REVERT: C 375 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8059 (mt-10) REVERT: C 378 MET cc_start: 0.8247 (mtm) cc_final: 0.8037 (mtp) REVERT: C 588 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: C 637 GLN cc_start: 0.6305 (mp10) cc_final: 0.6072 (mp-120) REVERT: D 93 GLU cc_start: 0.6984 (mp0) cc_final: 0.6647 (mp0) REVERT: D 96 MET cc_start: 0.5614 (mtm) cc_final: 0.5197 (mtm) REVERT: D 131 ASN cc_start: 0.6839 (m110) cc_final: 0.6306 (m-40) REVERT: D 146 ARG cc_start: 0.7388 (mtp-110) cc_final: 0.7119 (mtp-110) REVERT: D 177 GLU cc_start: 0.7100 (mp0) cc_final: 0.6754 (mp0) REVERT: D 375 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8059 (mt-10) REVERT: D 588 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: D 608 LEU cc_start: 0.7527 (mt) cc_final: 0.7307 (mt) REVERT: D 610 ARG cc_start: 0.6396 (tpm170) cc_final: 0.6113 (tpt170) REVERT: D 637 GLN cc_start: 0.6355 (mp10) cc_final: 0.6152 (mp-120) outliers start: 51 outliers final: 25 residues processed: 395 average time/residue: 1.1741 time to fit residues: 534.6575 Evaluate side-chains 373 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 340 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.198850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.135061 restraints weight = 20390.560| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.86 r_work: 0.3259 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21920 Z= 0.111 Angle : 0.525 7.281 29436 Z= 0.264 Chirality : 0.040 0.213 3204 Planarity : 0.004 0.053 3552 Dihedral : 15.141 143.703 4715 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.98 % Allowed : 15.17 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2432 helix: 1.13 (0.14), residues: 1456 sheet: -1.24 (0.62), residues: 80 loop : -0.88 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 593 HIS 0.003 0.001 HIS D 265 PHE 0.009 0.001 PHE C 537 TYR 0.011 0.001 TYR B 467 ARG 0.012 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 1010) hydrogen bonds : angle 3.78878 ( 2922) covalent geometry : bond 0.00247 (21920) covalent geometry : angle 0.52500 (29436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 374 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6108 (tm) REVERT: A 93 GLU cc_start: 0.7253 (mp0) cc_final: 0.6495 (mp0) REVERT: A 96 MET cc_start: 0.5342 (mtm) cc_final: 0.4955 (mtm) REVERT: A 131 ASN cc_start: 0.6945 (m110) cc_final: 0.6386 (m-40) REVERT: A 177 GLU cc_start: 0.7143 (mp0) cc_final: 0.6802 (pm20) REVERT: A 379 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6886 (p) REVERT: A 458 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 491 MET cc_start: 0.8254 (mmp) cc_final: 0.8012 (mmp) REVERT: A 535 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 591 GLU cc_start: 0.7943 (pt0) cc_final: 0.7526 (mp0) REVERT: A 608 LEU cc_start: 0.7553 (mt) cc_final: 0.7311 (mt) REVERT: A 618 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7711 (mt) REVERT: B 51 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6082 (tm) REVERT: B 93 GLU cc_start: 0.7159 (mp0) cc_final: 0.6397 (mp0) REVERT: B 96 MET cc_start: 0.5326 (mtm) cc_final: 0.4883 (mtm) REVERT: B 131 ASN cc_start: 0.6860 (m110) cc_final: 0.6357 (m-40) REVERT: B 177 GLU cc_start: 0.7170 (mp0) cc_final: 0.6827 (mp0) REVERT: B 190 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6836 (mtp-110) REVERT: B 535 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 591 GLU cc_start: 0.7961 (pt0) cc_final: 0.7558 (mp0) REVERT: C 93 GLU cc_start: 0.7161 (mp0) cc_final: 0.6390 (mp0) REVERT: C 96 MET cc_start: 0.5364 (mtm) cc_final: 0.4933 (mtm) REVERT: C 131 ASN cc_start: 0.6833 (m110) cc_final: 0.6347 (m-40) REVERT: C 177 GLU cc_start: 0.7158 (mp0) cc_final: 0.6814 (pm20) REVERT: C 375 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 535 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7740 (mt-10) REVERT: C 591 GLU cc_start: 0.7954 (pt0) cc_final: 0.7529 (mp0) REVERT: D 93 GLU cc_start: 0.6996 (mp0) cc_final: 0.6665 (mp0) REVERT: D 96 MET cc_start: 0.5635 (mtm) cc_final: 0.5212 (mtm) REVERT: D 131 ASN cc_start: 0.6828 (m110) cc_final: 0.6329 (m-40) REVERT: D 146 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.7202 (mtp-110) REVERT: D 177 GLU cc_start: 0.7113 (mp0) cc_final: 0.6744 (mp0) REVERT: D 315 GLU cc_start: 0.8046 (mp0) cc_final: 0.7659 (mp0) REVERT: D 375 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 535 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 591 GLU cc_start: 0.7936 (pt0) cc_final: 0.7529 (mp0) REVERT: D 608 LEU cc_start: 0.7560 (mt) cc_final: 0.7310 (mt) REVERT: D 610 ARG cc_start: 0.6270 (tpm170) cc_final: 0.5958 (tpt170) REVERT: D 618 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7625 (mt) REVERT: D 637 GLN cc_start: 0.6333 (mp10) cc_final: 0.6131 (mp-120) outliers start: 42 outliers final: 21 residues processed: 408 average time/residue: 1.1782 time to fit residues: 556.9867 Evaluate side-chains 376 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 348 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.195573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131389 restraints weight = 20380.610| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.95 r_work: 0.3190 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21920 Z= 0.181 Angle : 0.609 6.972 29436 Z= 0.300 Chirality : 0.043 0.291 3204 Planarity : 0.005 0.042 3552 Dihedral : 15.572 152.156 4715 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.65 % Allowed : 15.50 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2432 helix: 1.04 (0.14), residues: 1464 sheet: -1.04 (0.63), residues: 76 loop : -0.95 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 495 HIS 0.004 0.001 HIS A 201 PHE 0.013 0.002 PHE C 537 TYR 0.013 0.002 TYR B 328 ARG 0.008 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.05210 ( 1010) hydrogen bonds : angle 3.92059 ( 2922) covalent geometry : bond 0.00446 (21920) covalent geometry : angle 0.60862 (29436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 2.212 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6157 (tm) REVERT: A 93 GLU cc_start: 0.7215 (mp0) cc_final: 0.6450 (mp0) REVERT: A 96 MET cc_start: 0.5374 (mtm) cc_final: 0.4976 (mtm) REVERT: A 131 ASN cc_start: 0.6930 (m110) cc_final: 0.6367 (m-40) REVERT: A 177 GLU cc_start: 0.7114 (mp0) cc_final: 0.6781 (pm20) REVERT: A 379 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6985 (p) REVERT: A 458 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 588 GLU cc_start: 0.8178 (pt0) cc_final: 0.7866 (pt0) REVERT: A 608 LEU cc_start: 0.7592 (mt) cc_final: 0.7360 (mt) REVERT: B 51 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6137 (tm) REVERT: B 93 GLU cc_start: 0.7162 (mp0) cc_final: 0.6394 (mp0) REVERT: B 96 MET cc_start: 0.5422 (mtm) cc_final: 0.4985 (mtm) REVERT: B 131 ASN cc_start: 0.6844 (m110) cc_final: 0.6322 (m-40) REVERT: B 177 GLU cc_start: 0.7179 (mp0) cc_final: 0.6832 (mp0) REVERT: B 573 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8480 (tt) REVERT: B 588 GLU cc_start: 0.8150 (pt0) cc_final: 0.7913 (pt0) REVERT: B 618 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7647 (mt) REVERT: C 93 GLU cc_start: 0.7176 (mp0) cc_final: 0.6403 (mp0) REVERT: C 96 MET cc_start: 0.5428 (mtm) cc_final: 0.4990 (mtm) REVERT: C 131 ASN cc_start: 0.6810 (m110) cc_final: 0.6284 (m-40) REVERT: C 177 GLU cc_start: 0.7104 (mp0) cc_final: 0.6772 (pm20) REVERT: C 375 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 588 GLU cc_start: 0.8161 (pt0) cc_final: 0.7843 (pt0) REVERT: C 618 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7680 (mt) REVERT: D 93 GLU cc_start: 0.6925 (mp0) cc_final: 0.6570 (mp0) REVERT: D 96 MET cc_start: 0.5554 (mtm) cc_final: 0.5133 (mtm) REVERT: D 131 ASN cc_start: 0.6836 (m110) cc_final: 0.6320 (m-40) REVERT: D 177 GLU cc_start: 0.7063 (mp0) cc_final: 0.6703 (mp0) REVERT: D 608 LEU cc_start: 0.7579 (mt) cc_final: 0.7336 (mt) REVERT: D 618 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7681 (mt) outliers start: 56 outliers final: 23 residues processed: 388 average time/residue: 1.1122 time to fit residues: 501.2573 Evaluate side-chains 369 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 91 ASN C 91 ASN C 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.200081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134669 restraints weight = 20506.227| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.87 r_work: 0.3293 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 21920 Z= 0.104 Angle : 0.517 7.846 29436 Z= 0.259 Chirality : 0.039 0.190 3204 Planarity : 0.004 0.040 3552 Dihedral : 14.558 139.052 4714 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.08 % Allowed : 16.16 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2432 helix: 1.36 (0.14), residues: 1452 sheet: -0.72 (0.63), residues: 76 loop : -0.70 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 593 HIS 0.002 0.001 HIS A 122 PHE 0.009 0.001 PHE B 493 TYR 0.011 0.001 TYR C 467 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1010) hydrogen bonds : angle 3.73033 ( 2922) covalent geometry : bond 0.00227 (21920) covalent geometry : angle 0.51713 (29436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 373 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6196 (tm) REVERT: A 78 MET cc_start: 0.7131 (mmp) cc_final: 0.6500 (mmt) REVERT: A 93 GLU cc_start: 0.7275 (mp0) cc_final: 0.6510 (mp0) REVERT: A 96 MET cc_start: 0.5491 (mtm) cc_final: 0.5051 (mtm) REVERT: A 131 ASN cc_start: 0.6850 (m110) cc_final: 0.6400 (m-40) REVERT: A 177 GLU cc_start: 0.7137 (mp0) cc_final: 0.6807 (pm20) REVERT: A 458 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8648 (mt) REVERT: A 535 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 588 GLU cc_start: 0.8001 (pt0) cc_final: 0.7763 (pt0) REVERT: A 591 GLU cc_start: 0.7944 (pt0) cc_final: 0.7577 (mp0) REVERT: A 608 LEU cc_start: 0.7565 (mt) cc_final: 0.7280 (mt) REVERT: A 612 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6689 (mp) REVERT: A 618 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7668 (mt) REVERT: B 51 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6210 (tm) REVERT: B 93 GLU cc_start: 0.7205 (mp0) cc_final: 0.6470 (mp0) REVERT: B 96 MET cc_start: 0.5506 (mtm) cc_final: 0.5060 (mtm) REVERT: B 131 ASN cc_start: 0.6812 (m110) cc_final: 0.6389 (m-40) REVERT: B 177 GLU cc_start: 0.7176 (mp0) cc_final: 0.6856 (mp0) REVERT: B 458 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8574 (mt) REVERT: B 535 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 591 GLU cc_start: 0.7941 (pt0) cc_final: 0.7597 (mp0) REVERT: C 93 GLU cc_start: 0.7191 (mp0) cc_final: 0.6446 (mp0) REVERT: C 96 MET cc_start: 0.5488 (mtm) cc_final: 0.5056 (mtm) REVERT: C 131 ASN cc_start: 0.6811 (m110) cc_final: 0.6400 (m-40) REVERT: C 177 GLU cc_start: 0.7115 (mp0) cc_final: 0.6775 (pm20) REVERT: C 458 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 535 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7652 (mt-10) REVERT: C 588 GLU cc_start: 0.7962 (pt0) cc_final: 0.7724 (pt0) REVERT: C 591 GLU cc_start: 0.7937 (pt0) cc_final: 0.7566 (mp0) REVERT: D 80 GLU cc_start: 0.7805 (pt0) cc_final: 0.7030 (pm20) REVERT: D 93 GLU cc_start: 0.7020 (mp0) cc_final: 0.6671 (mp0) REVERT: D 96 MET cc_start: 0.5511 (mtm) cc_final: 0.5077 (mtm) REVERT: D 110 MET cc_start: 0.7108 (mtt) cc_final: 0.6807 (mtt) REVERT: D 131 ASN cc_start: 0.6767 (m110) cc_final: 0.6344 (m-40) REVERT: D 177 GLU cc_start: 0.7130 (mp0) cc_final: 0.6768 (mp0) REVERT: D 315 GLU cc_start: 0.8075 (mp0) cc_final: 0.7812 (mp0) REVERT: D 458 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8578 (mt) REVERT: D 535 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7755 (mt-10) REVERT: D 591 GLU cc_start: 0.7888 (pt0) cc_final: 0.7521 (mp0) REVERT: D 608 LEU cc_start: 0.7549 (mt) cc_final: 0.7292 (mt) REVERT: D 610 ARG cc_start: 0.6446 (tpt170) cc_final: 0.6195 (tpt170) outliers start: 44 outliers final: 17 residues processed: 410 average time/residue: 1.1369 time to fit residues: 539.3858 Evaluate side-chains 373 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 126 optimal weight: 0.0870 chunk 128 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 GLN C 174 ASN C 185 HIS D 91 ASN D 122 HIS D 185 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.195259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130624 restraints weight = 20387.790| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21920 Z= 0.187 Angle : 0.623 8.507 29436 Z= 0.308 Chirality : 0.044 0.301 3204 Planarity : 0.005 0.041 3552 Dihedral : 15.289 151.667 4714 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.89 % Allowed : 16.87 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2432 helix: 1.15 (0.14), residues: 1464 sheet: -1.18 (0.57), residues: 84 loop : -0.79 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 495 HIS 0.005 0.001 HIS C 185 PHE 0.013 0.002 PHE B 537 TYR 0.015 0.002 TYR D 328 ARG 0.008 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 1010) hydrogen bonds : angle 3.92994 ( 2922) covalent geometry : bond 0.00460 (21920) covalent geometry : angle 0.62323 (29436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 341 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6195 (tm) REVERT: A 78 MET cc_start: 0.7249 (mmp) cc_final: 0.6644 (mmt) REVERT: A 93 GLU cc_start: 0.7206 (mp0) cc_final: 0.6450 (mp0) REVERT: A 96 MET cc_start: 0.5443 (mtm) cc_final: 0.5061 (mtm) REVERT: A 131 ASN cc_start: 0.6886 (m110) cc_final: 0.6407 (m-40) REVERT: A 177 GLU cc_start: 0.7132 (mp0) cc_final: 0.6758 (pm20) REVERT: A 379 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7120 (p) REVERT: A 573 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 588 GLU cc_start: 0.8177 (pt0) cc_final: 0.7933 (pt0) REVERT: A 608 LEU cc_start: 0.7566 (mt) cc_final: 0.7332 (mt) REVERT: B 51 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6204 (tm) REVERT: B 93 GLU cc_start: 0.7164 (mp0) cc_final: 0.6418 (mp0) REVERT: B 96 MET cc_start: 0.5444 (mtm) cc_final: 0.4999 (mtm) REVERT: B 131 ASN cc_start: 0.6877 (m110) cc_final: 0.6426 (m-40) REVERT: B 177 GLU cc_start: 0.7054 (mp0) cc_final: 0.6706 (mp0) REVERT: B 618 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 93 GLU cc_start: 0.7205 (mp0) cc_final: 0.6450 (mp0) REVERT: C 96 MET cc_start: 0.5459 (mtm) cc_final: 0.5018 (mtm) REVERT: C 110 MET cc_start: 0.6410 (mmm) cc_final: 0.6131 (mtp) REVERT: C 131 ASN cc_start: 0.6778 (m110) cc_final: 0.6325 (m-40) REVERT: C 177 GLU cc_start: 0.7168 (mp0) cc_final: 0.6780 (pm20) REVERT: C 588 GLU cc_start: 0.8141 (pt0) cc_final: 0.7889 (pt0) REVERT: C 618 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7677 (mt) REVERT: D 93 GLU cc_start: 0.6986 (mp0) cc_final: 0.6604 (mp0) REVERT: D 96 MET cc_start: 0.5541 (mtm) cc_final: 0.5050 (mtm) REVERT: D 131 ASN cc_start: 0.6808 (m110) cc_final: 0.6358 (m-40) REVERT: D 177 GLU cc_start: 0.7071 (mp0) cc_final: 0.6683 (mp0) REVERT: D 608 LEU cc_start: 0.7566 (mt) cc_final: 0.7322 (mt) outliers start: 40 outliers final: 29 residues processed: 373 average time/residue: 1.2467 time to fit residues: 541.6388 Evaluate side-chains 375 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 340 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 GLN C 174 ASN D 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.197238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134717 restraints weight = 20431.937| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.00 r_work: 0.3221 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21920 Z= 0.132 Angle : 0.561 8.002 29436 Z= 0.280 Chirality : 0.041 0.243 3204 Planarity : 0.004 0.041 3552 Dihedral : 14.847 145.628 4714 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.51 % Allowed : 17.25 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2432 helix: 1.24 (0.14), residues: 1464 sheet: -0.63 (0.60), residues: 76 loop : -0.73 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 593 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE B 537 TYR 0.012 0.002 TYR B 467 ARG 0.008 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 1010) hydrogen bonds : angle 3.85981 ( 2922) covalent geometry : bond 0.00311 (21920) covalent geometry : angle 0.56101 (29436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 4.048 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6179 (tm) REVERT: A 93 GLU cc_start: 0.7250 (mp0) cc_final: 0.6503 (mp0) REVERT: A 96 MET cc_start: 0.5371 (mtm) cc_final: 0.4930 (mtm) REVERT: A 131 ASN cc_start: 0.6807 (m110) cc_final: 0.6379 (m-40) REVERT: A 177 GLU cc_start: 0.7137 (mp0) cc_final: 0.6787 (pm20) REVERT: A 315 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 379 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6972 (p) REVERT: A 458 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 588 GLU cc_start: 0.8074 (pt0) cc_final: 0.7817 (pt0) REVERT: A 591 GLU cc_start: 0.8044 (pt0) cc_final: 0.7579 (mp0) REVERT: A 608 LEU cc_start: 0.7532 (mt) cc_final: 0.7232 (mt) REVERT: A 612 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6629 (mp) REVERT: B 51 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6216 (tm) REVERT: B 93 GLU cc_start: 0.7193 (mp0) cc_final: 0.6451 (mp0) REVERT: B 96 MET cc_start: 0.5451 (mtm) cc_final: 0.5022 (mtm) REVERT: B 131 ASN cc_start: 0.6827 (m110) cc_final: 0.6405 (m-40) REVERT: B 177 GLU cc_start: 0.7115 (mp0) cc_final: 0.6746 (mp0) REVERT: B 591 GLU cc_start: 0.8054 (pt0) cc_final: 0.7549 (mp0) REVERT: C 93 GLU cc_start: 0.7207 (mp0) cc_final: 0.6467 (mp0) REVERT: C 96 MET cc_start: 0.5457 (mtm) cc_final: 0.5022 (mtm) REVERT: C 110 MET cc_start: 0.6334 (mmm) cc_final: 0.6111 (mtp) REVERT: C 131 ASN cc_start: 0.6809 (m110) cc_final: 0.6418 (m-40) REVERT: C 177 GLU cc_start: 0.7180 (mp0) cc_final: 0.6789 (pm20) REVERT: C 591 GLU cc_start: 0.8019 (pt0) cc_final: 0.7553 (mp0) REVERT: C 618 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7655 (mt) REVERT: D 80 GLU cc_start: 0.7772 (pt0) cc_final: 0.6979 (pm20) REVERT: D 93 GLU cc_start: 0.7019 (mp0) cc_final: 0.6626 (mp0) REVERT: D 96 MET cc_start: 0.5498 (mtm) cc_final: 0.5010 (mtm) REVERT: D 131 ASN cc_start: 0.6757 (m110) cc_final: 0.6348 (m-40) REVERT: D 177 GLU cc_start: 0.7081 (mp0) cc_final: 0.6696 (mp0) REVERT: D 591 GLU cc_start: 0.7971 (pt0) cc_final: 0.7470 (mp0) REVERT: D 608 LEU cc_start: 0.7574 (mt) cc_final: 0.7348 (mt) outliers start: 32 outliers final: 19 residues processed: 374 average time/residue: 1.2781 time to fit residues: 555.0248 Evaluate side-chains 365 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 339 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 234 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 181 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN C 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.200691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138189 restraints weight = 20524.630| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.86 r_work: 0.3304 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21920 Z= 0.101 Angle : 0.512 8.449 29436 Z= 0.258 Chirality : 0.039 0.192 3204 Planarity : 0.004 0.040 3552 Dihedral : 14.104 135.190 4714 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.47 % Allowed : 17.53 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2432 helix: 1.49 (0.14), residues: 1452 sheet: -0.58 (0.59), residues: 80 loop : -0.53 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 593 HIS 0.003 0.001 HIS A 582 PHE 0.010 0.001 PHE D 493 TYR 0.009 0.001 TYR B 467 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 1010) hydrogen bonds : angle 3.74032 ( 2922) covalent geometry : bond 0.00216 (21920) covalent geometry : angle 0.51179 (29436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21372.97 seconds wall clock time: 369 minutes 21.41 seconds (22161.41 seconds total)