Starting phenix.real_space_refine on Thu Sep 18 23:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuj_45935/09_2025/9cuj_45935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuj_45935/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cuj_45935/09_2025/9cuj_45935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuj_45935/09_2025/9cuj_45935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cuj_45935/09_2025/9cuj_45935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuj_45935/09_2025/9cuj_45935.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} 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-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} 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-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} 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: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1, 'PCW:plan-2': 2} 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: 4.76, per 1000 atoms: 0.22 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: 1.49 Conformation dependent library (CDL) restraints added in 956.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 2.89 Time building geometry restraints manager: 2.04 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 16.570 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 589 TYR 0.027 0.003 TYR A 377 PHE 0.028 0.003 PHE B 169 TRP 0.027 0.003 TRP A 629 HIS 0.012 0.003 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.01125 (21920) covalent geometry : angle 1.39314 (29436) hydrogen bonds : bond 0.33578 ( 1010) hydrogen bonds : angle 9.45382 ( 2922) *********************** 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 : 0.753 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: 0.5623 time to fit residues: 336.2242 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 : 0.599 ------------------------------------------------------------------------------- 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 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.5980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129620 restraints weight = 20943.612| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.82 r_work: 0.3216 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21920 Z= 0.222 Angle : 0.715 7.982 29436 Z= 0.356 Chirality : 0.045 0.294 3204 Planarity : 0.006 0.048 3552 Dihedral : 19.142 179.448 4720 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.07 % Allowed : 7.56 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.15), residues: 2432 helix: -1.54 (0.11), residues: 1460 sheet: -2.14 (0.66), residues: 76 loop : -1.68 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 146 TYR 0.021 0.003 TYR D 377 PHE 0.023 0.002 PHE B 537 TRP 0.014 0.002 TRP D 613 HIS 0.007 0.002 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00545 (21920) covalent geometry : angle 0.71453 (29436) hydrogen bonds : bond 0.06333 ( 1010) hydrogen bonds : angle 4.57348 ( 2922) *********************** 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 468 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 403 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6003 (tm) REVERT: A 96 MET cc_start: 0.5455 (mtm) cc_final: 0.5161 (mtm) REVERT: A 177 GLU cc_start: 0.7149 (mp0) cc_final: 0.6831 (mp0) REVERT: A 375 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 378 MET cc_start: 0.8366 (mtt) cc_final: 0.7986 (mtp) REVERT: A 381 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7172 (mtpt) REVERT: A 458 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 535 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 608 LEU cc_start: 0.7777 (mt) cc_final: 0.7467 (mt) REVERT: A 618 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 637 GLN cc_start: 0.6268 (mp10) cc_final: 0.6024 (mp-120) REVERT: B 51 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5916 (tm) REVERT: B 80 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: B 93 GLU cc_start: 0.7029 (mp0) cc_final: 0.6653 (mp0) REVERT: B 96 MET cc_start: 0.5302 (mtm) cc_final: 0.5001 (mtm) REVERT: B 177 GLU cc_start: 0.7127 (mp0) cc_final: 0.6761 (mp0) REVERT: B 381 LYS cc_start: 0.7331 (mtmt) cc_final: 0.7073 (mtpt) REVERT: B 392 THR cc_start: 0.8362 (t) cc_final: 0.7983 (m) REVERT: B 535 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7759 (mt-10) REVERT: B 590 ASP cc_start: 0.7943 (m-30) cc_final: 0.7714 (m-30) REVERT: B 610 ARG cc_start: 0.6742 (tpm170) cc_final: 0.6433 (tpt170) REVERT: B 618 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7604 (mt) REVERT: B 637 GLN cc_start: 0.6223 (mp10) cc_final: 0.5928 (mp-120) REVERT: C 78 MET cc_start: 0.7606 (mmt) cc_final: 0.7204 (mmp) REVERT: C 80 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: C 93 GLU cc_start: 0.7037 (mp0) cc_final: 0.6646 (mp0) REVERT: C 96 MET cc_start: 0.5384 (mtm) cc_final: 0.5040 (mtm) REVERT: C 177 GLU cc_start: 0.7145 (mp0) cc_final: 0.6802 (mp0) REVERT: C 381 LYS cc_start: 0.7359 (mtmt) cc_final: 0.7118 (mtpt) REVERT: C 392 THR cc_start: 0.8363 (t) cc_final: 0.8005 (m) REVERT: C 535 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 610 ARG cc_start: 0.6724 (tpm170) cc_final: 0.6423 (tpt170) REVERT: C 618 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7612 (mt) REVERT: C 637 GLN cc_start: 0.6182 (mp10) cc_final: 0.5868 (mp-120) REVERT: D 78 MET cc_start: 0.7689 (mmt) cc_final: 0.7265 (mmp) REVERT: D 93 GLU cc_start: 0.7055 (mp0) cc_final: 0.6658 (mp0) REVERT: D 96 MET cc_start: 0.5308 (mtm) cc_final: 0.4929 (mtm) REVERT: D 177 GLU cc_start: 0.7127 (mp0) cc_final: 0.6773 (mp0) REVERT: D 375 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 378 MET cc_start: 0.8381 (mtp) cc_final: 0.7871 (mtt) REVERT: D 381 LYS cc_start: 0.7359 (mtmt) cc_final: 0.7121 (mtpt) REVERT: D 535 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7758 (mt-10) REVERT: D 608 LEU cc_start: 0.7745 (mt) cc_final: 0.7489 (mt) REVERT: D 610 ARG cc_start: 0.6720 (tpm170) cc_final: 0.6422 (tpt170) REVERT: D 618 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 637 GLN cc_start: 0.6225 (mp10) cc_final: 0.5986 (mp-120) outliers start: 65 outliers final: 22 residues processed: 445 average time/residue: 0.5748 time to fit residues: 290.1974 Evaluate side-chains 384 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 80 GLU 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 80 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 97 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 A 582 HIS B 37 ASN B 197 ASN C 37 ASN C 197 ASN D 37 ASN D 174 ASN D 197 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.199777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138283 restraints weight = 20698.002| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.90 r_work: 0.3309 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21920 Z= 0.116 Angle : 0.548 7.837 29436 Z= 0.278 Chirality : 0.040 0.210 3204 Planarity : 0.005 0.039 3552 Dihedral : 17.235 152.998 4718 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.60 % Allowed : 11.20 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2432 helix: 0.04 (0.13), residues: 1460 sheet: -1.91 (0.63), residues: 76 loop : -1.24 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 146 TYR 0.012 0.002 TYR B 467 PHE 0.012 0.001 PHE D 537 TRP 0.009 0.001 TRP C 593 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00250 (21920) covalent geometry : angle 0.54818 (29436) hydrogen bonds : bond 0.04647 ( 1010) hydrogen bonds : angle 4.01900 ( 2922) *********************** 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 436 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 381 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6011 (tm) REVERT: A 93 GLU cc_start: 0.7255 (mp0) cc_final: 0.6481 (mp0) REVERT: A 96 MET cc_start: 0.5361 (mtm) cc_final: 0.4993 (mtm) REVERT: A 131 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6268 (m-40) REVERT: A 177 GLU cc_start: 0.7049 (mp0) cc_final: 0.6819 (mp0) REVERT: A 311 THR cc_start: 0.5272 (OUTLIER) cc_final: 0.4636 (p) REVERT: A 375 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 378 MET cc_start: 0.8366 (mtt) cc_final: 0.8019 (mtm) REVERT: A 535 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 591 GLU cc_start: 0.7927 (pt0) cc_final: 0.7462 (mp0) REVERT: A 608 LEU cc_start: 0.7658 (mt) cc_final: 0.7364 (mt) REVERT: A 618 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7611 (mt) REVERT: A 637 GLN cc_start: 0.6221 (mp10) cc_final: 0.5981 (mp-120) REVERT: B 51 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6007 (tm) REVERT: B 93 GLU cc_start: 0.6978 (mp0) cc_final: 0.6657 (mp0) REVERT: B 96 MET cc_start: 0.5337 (mtm) cc_final: 0.4945 (mtm) REVERT: B 131 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6296 (m-40) REVERT: B 177 GLU cc_start: 0.7091 (mp0) cc_final: 0.6799 (mp0) REVERT: B 311 THR cc_start: 0.5402 (OUTLIER) cc_final: 0.4770 (p) REVERT: B 458 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 535 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 590 ASP cc_start: 0.7837 (m-30) cc_final: 0.7622 (m-30) REVERT: B 591 GLU cc_start: 0.7916 (pt0) cc_final: 0.7474 (mp0) REVERT: B 610 ARG cc_start: 0.6502 (tpm170) cc_final: 0.6274 (tpt170) REVERT: B 618 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7527 (mt) REVERT: C 93 GLU cc_start: 0.6967 (mp0) cc_final: 0.6644 (mp0) REVERT: C 96 MET cc_start: 0.5379 (mtm) cc_final: 0.5002 (mtm) REVERT: C 131 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6288 (m-40) REVERT: C 177 GLU cc_start: 0.7088 (mp0) cc_final: 0.6817 (mp0) REVERT: C 311 THR cc_start: 0.5252 (OUTLIER) cc_final: 0.4625 (p) REVERT: C 458 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 535 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 591 GLU cc_start: 0.7913 (pt0) cc_final: 0.7457 (mp0) REVERT: C 610 ARG cc_start: 0.6513 (tpm170) cc_final: 0.6283 (tpt170) REVERT: C 618 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7579 (mt) REVERT: D 93 GLU cc_start: 0.6981 (mp0) cc_final: 0.6623 (mp0) REVERT: D 96 MET cc_start: 0.5367 (mtm) cc_final: 0.4931 (mtm) REVERT: D 131 ASN cc_start: 0.6855 (OUTLIER) cc_final: 0.6303 (m-40) REVERT: D 177 GLU cc_start: 0.7092 (mp0) cc_final: 0.6798 (mp0) REVERT: D 311 THR cc_start: 0.5302 (OUTLIER) cc_final: 0.4656 (p) REVERT: D 375 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 378 MET cc_start: 0.8295 (mtp) cc_final: 0.8055 (mtp) REVERT: D 458 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8581 (mt) REVERT: D 535 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 591 GLU cc_start: 0.7891 (pt0) cc_final: 0.7439 (mp0) REVERT: D 608 LEU cc_start: 0.7624 (mt) cc_final: 0.7303 (mt) REVERT: D 610 ARG cc_start: 0.6400 (tpm170) cc_final: 0.6196 (tpt170) REVERT: D 618 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7562 (mt) REVERT: D 637 GLN cc_start: 0.6172 (mp10) cc_final: 0.5847 (mp-120) outliers start: 55 outliers final: 12 residues processed: 422 average time/residue: 0.5181 time to fit residues: 250.2819 Evaluate side-chains 372 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 343 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 131 ASN 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 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 131 ASN 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 131 ASN Chi-restraints excluded: chain C residue 294 GLU 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 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 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 14 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.195676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131281 restraints weight = 20863.742| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.86 r_work: 0.3217 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21920 Z= 0.164 Angle : 0.601 7.533 29436 Z= 0.299 Chirality : 0.042 0.194 3204 Planarity : 0.005 0.040 3552 Dihedral : 16.732 151.928 4718 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.69 % Allowed : 12.90 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2432 helix: 0.52 (0.14), residues: 1468 sheet: -1.49 (0.64), residues: 76 loop : -1.15 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 146 TYR 0.014 0.002 TYR A 377 PHE 0.015 0.002 PHE A 537 TRP 0.007 0.001 TRP C 593 HIS 0.005 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00395 (21920) covalent geometry : angle 0.60127 (29436) hydrogen bonds : bond 0.05169 ( 1010) hydrogen bonds : angle 3.99882 ( 2922) *********************** 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 419 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 362 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.5960 (tm) REVERT: A 93 GLU cc_start: 0.7269 (mp0) cc_final: 0.6491 (mp0) REVERT: A 96 MET cc_start: 0.5340 (mtm) cc_final: 0.4939 (mtm) REVERT: A 131 ASN cc_start: 0.6839 (m110) cc_final: 0.6264 (m-40) REVERT: A 177 GLU cc_start: 0.7086 (mp0) cc_final: 0.6865 (mp0) REVERT: A 311 THR cc_start: 0.5471 (OUTLIER) cc_final: 0.4823 (p) REVERT: A 375 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 535 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 608 LEU cc_start: 0.7621 (mt) cc_final: 0.7373 (mt) REVERT: A 618 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 637 GLN cc_start: 0.6368 (mp10) cc_final: 0.6061 (mp-120) REVERT: B 51 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5892 (tm) REVERT: B 93 GLU cc_start: 0.6928 (mp0) cc_final: 0.6578 (mp0) REVERT: B 96 MET cc_start: 0.5344 (mtm) cc_final: 0.4951 (mtm) REVERT: B 131 ASN cc_start: 0.6864 (m110) cc_final: 0.6329 (m-40) REVERT: B 177 GLU cc_start: 0.7144 (mp0) cc_final: 0.6821 (mp0) REVERT: B 215 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: B 535 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7783 (mt-10) REVERT: B 590 ASP cc_start: 0.7959 (m-30) cc_final: 0.7737 (m-30) REVERT: B 618 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7663 (mt) REVERT: C 93 GLU cc_start: 0.6958 (mp0) cc_final: 0.6596 (mp0) REVERT: C 96 MET cc_start: 0.5438 (mtm) cc_final: 0.4997 (mtm) REVERT: C 131 ASN cc_start: 0.6862 (m110) cc_final: 0.6315 (m-40) REVERT: C 177 GLU cc_start: 0.7110 (mp0) cc_final: 0.6822 (mp0) REVERT: C 215 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: C 311 THR cc_start: 0.5600 (OUTLIER) cc_final: 0.4851 (p) REVERT: C 315 GLU cc_start: 0.8079 (mp0) cc_final: 0.7774 (mp0) REVERT: C 535 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7818 (mt-10) REVERT: C 618 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7691 (mt) REVERT: D 93 GLU cc_start: 0.6949 (mp0) cc_final: 0.6633 (mp0) REVERT: D 96 MET cc_start: 0.5579 (mtm) cc_final: 0.5128 (mtm) REVERT: D 131 ASN cc_start: 0.6856 (m110) cc_final: 0.6312 (m-40) REVERT: D 146 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.7297 (mtp-110) REVERT: D 177 GLU cc_start: 0.7135 (mp0) cc_final: 0.6840 (mp0) REVERT: D 311 THR cc_start: 0.5560 (OUTLIER) cc_final: 0.4917 (p) REVERT: D 375 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 378 MET cc_start: 0.8312 (mtp) cc_final: 0.8093 (mtp) REVERT: D 535 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7849 (mt-10) REVERT: D 588 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: D 608 LEU cc_start: 0.7589 (mt) cc_final: 0.7343 (mt) REVERT: D 610 ARG cc_start: 0.6441 (tpm170) cc_final: 0.6234 (tpm170) REVERT: D 618 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7678 (mt) REVERT: D 637 GLN cc_start: 0.6399 (mp10) cc_final: 0.6080 (mp-120) outliers start: 57 outliers final: 24 residues processed: 405 average time/residue: 0.5289 time to fit residues: 244.7989 Evaluate side-chains 379 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 452 VAL 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 215 MET 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 215 MET Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR 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 194 optimal weight: 1.9990 chunk 180 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.5324 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.197102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131971 restraints weight = 20777.605| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.82 r_work: 0.3260 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21920 Z= 0.126 Angle : 0.552 7.707 29436 Z= 0.276 Chirality : 0.040 0.162 3204 Planarity : 0.004 0.040 3552 Dihedral : 15.746 146.354 4718 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.36 % Allowed : 14.08 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.17), residues: 2432 helix: 0.93 (0.14), residues: 1464 sheet: -1.27 (0.65), residues: 76 loop : -1.05 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 146 TYR 0.012 0.002 TYR B 467 PHE 0.011 0.001 PHE D 537 TRP 0.007 0.001 TRP C 593 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00289 (21920) covalent geometry : angle 0.55227 (29436) hydrogen bonds : bond 0.04586 ( 1010) hydrogen bonds : angle 3.86333 ( 2922) *********************** 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 414 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6027 (tm) REVERT: A 93 GLU cc_start: 0.7279 (mp0) cc_final: 0.6517 (mp0) REVERT: A 96 MET cc_start: 0.5278 (mtm) cc_final: 0.4888 (mtm) REVERT: A 131 ASN cc_start: 0.6813 (m110) cc_final: 0.6286 (m-40) REVERT: A 177 GLU cc_start: 0.7070 (mp0) cc_final: 0.6817 (pm20) REVERT: A 379 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6970 (p) REVERT: A 535 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 591 GLU cc_start: 0.7923 (pt0) cc_final: 0.7448 (mp0) REVERT: A 608 LEU cc_start: 0.7571 (mt) cc_final: 0.7334 (mt) REVERT: A 618 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7678 (mt) REVERT: B 51 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5972 (tm) REVERT: B 93 GLU cc_start: 0.6932 (mp0) cc_final: 0.6572 (mp0) REVERT: B 96 MET cc_start: 0.5395 (mtm) cc_final: 0.4970 (mtm) REVERT: B 131 ASN cc_start: 0.6838 (m110) cc_final: 0.6333 (m-40) REVERT: B 177 GLU cc_start: 0.7132 (mp0) cc_final: 0.6799 (mp0) REVERT: B 535 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 591 GLU cc_start: 0.7928 (pt0) cc_final: 0.7450 (mp0) REVERT: B 618 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7632 (mt) REVERT: C 96 MET cc_start: 0.5378 (mtm) cc_final: 0.5001 (mtm) REVERT: C 131 ASN cc_start: 0.6833 (m110) cc_final: 0.6312 (m-40) REVERT: C 177 GLU cc_start: 0.7109 (mp0) cc_final: 0.6781 (mp0) REVERT: C 215 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7730 (mmm) REVERT: C 535 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 591 GLU cc_start: 0.7941 (pt0) cc_final: 0.7466 (mp0) REVERT: C 618 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7633 (mt) REVERT: D 93 GLU cc_start: 0.7017 (mp0) cc_final: 0.6706 (mp0) REVERT: D 96 MET cc_start: 0.5618 (mtm) cc_final: 0.5199 (mtm) REVERT: D 131 ASN cc_start: 0.6805 (m110) cc_final: 0.6289 (m-40) REVERT: D 177 GLU cc_start: 0.7123 (mp0) cc_final: 0.6792 (mp0) REVERT: D 215 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7679 (mmm) REVERT: D 375 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 535 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7737 (mt-10) REVERT: D 591 GLU cc_start: 0.7925 (pt0) cc_final: 0.7453 (mp0) REVERT: D 608 LEU cc_start: 0.7550 (mt) cc_final: 0.7269 (mt) REVERT: D 610 ARG cc_start: 0.6356 (tpm170) cc_final: 0.6079 (tpt170) REVERT: D 618 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7649 (mt) REVERT: D 637 GLN cc_start: 0.6389 (mp10) cc_final: 0.6181 (mp-120) outliers start: 50 outliers final: 19 residues processed: 403 average time/residue: 0.5221 time to fit residues: 242.0932 Evaluate side-chains 371 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 343 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 452 VAL 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 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 215 MET Chi-restraints excluded: chain C residue 294 GLU 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 114 LEU Chi-restraints excluded: chain D residue 215 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 80 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN B 185 HIS D 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.196458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130208 restraints weight = 20343.820| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.90 r_work: 0.3216 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 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 = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3178 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= 0.161 Angle : 0.594 7.183 29436 Z= 0.295 Chirality : 0.042 0.200 3204 Planarity : 0.005 0.041 3552 Dihedral : 15.692 151.744 4716 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 14.89 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2432 helix: 1.00 (0.14), residues: 1464 sheet: -1.48 (0.62), residues: 80 loop : -0.94 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 180 TYR 0.013 0.002 TYR B 328 PHE 0.013 0.002 PHE B 537 TRP 0.007 0.001 TRP C 593 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00392 (21920) covalent geometry : angle 0.59370 (29436) hydrogen bonds : bond 0.05074 ( 1010) hydrogen bonds : angle 3.90731 ( 2922) *********************** 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 403 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6069 (tm) REVERT: A 80 GLU cc_start: 0.7926 (pt0) cc_final: 0.7702 (pt0) REVERT: A 93 GLU cc_start: 0.7230 (mp0) cc_final: 0.6462 (mp0) REVERT: A 96 MET cc_start: 0.5405 (mtm) cc_final: 0.5011 (mtm) REVERT: A 131 ASN cc_start: 0.6822 (m110) cc_final: 0.6309 (m-40) REVERT: A 177 GLU cc_start: 0.7044 (mp0) cc_final: 0.6738 (pm20) REVERT: A 379 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6973 (p) REVERT: A 491 MET cc_start: 0.8352 (mmp) cc_final: 0.8110 (mmp) REVERT: A 588 GLU cc_start: 0.8135 (pt0) cc_final: 0.7812 (pt0) REVERT: A 608 LEU cc_start: 0.7570 (mt) cc_final: 0.7322 (mt) REVERT: A 618 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7685 (mt) REVERT: B 51 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6057 (tm) REVERT: B 96 MET cc_start: 0.5325 (mtm) cc_final: 0.4940 (mtm) REVERT: B 131 ASN cc_start: 0.6840 (m110) cc_final: 0.6341 (m-40) REVERT: B 177 GLU cc_start: 0.7120 (mp0) cc_final: 0.6755 (mp0) REVERT: B 491 MET cc_start: 0.8360 (mmp) cc_final: 0.8113 (mmp) REVERT: B 588 GLU cc_start: 0.8123 (pt0) cc_final: 0.7879 (pt0) REVERT: C 93 GLU cc_start: 0.7158 (mp0) cc_final: 0.6413 (mp0) REVERT: C 96 MET cc_start: 0.5335 (mtm) cc_final: 0.4941 (mtm) REVERT: C 131 ASN cc_start: 0.6826 (m110) cc_final: 0.6307 (m-40) REVERT: C 177 GLU cc_start: 0.7065 (mp0) cc_final: 0.6704 (mp0) REVERT: C 588 GLU cc_start: 0.8120 (pt0) cc_final: 0.7792 (pt0) REVERT: D 93 GLU cc_start: 0.6966 (mp0) cc_final: 0.6643 (mp0) REVERT: D 96 MET cc_start: 0.5626 (mtm) cc_final: 0.5213 (mtm) REVERT: D 131 ASN cc_start: 0.6821 (m110) cc_final: 0.6300 (m-40) REVERT: D 177 GLU cc_start: 0.7082 (mp0) cc_final: 0.6731 (mp0) REVERT: D 375 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 588 GLU cc_start: 0.8144 (pt0) cc_final: 0.7821 (pt0) REVERT: D 608 LEU cc_start: 0.7581 (mt) cc_final: 0.7329 (mt) REVERT: D 610 ARG cc_start: 0.6392 (tpm170) cc_final: 0.6082 (tpt170) outliers start: 50 outliers final: 23 residues processed: 387 average time/residue: 0.5008 time to fit residues: 225.0638 Evaluate side-chains 371 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 344 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 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 D residue 114 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.196028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130097 restraints weight = 20457.268| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.79 r_work: 0.3212 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 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 = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3272 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= 0.166 Angle : 0.597 7.172 29436 Z= 0.296 Chirality : 0.042 0.201 3204 Planarity : 0.005 0.042 3552 Dihedral : 15.545 151.229 4714 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.69 % Allowed : 15.03 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2432 helix: 1.00 (0.14), residues: 1464 sheet: -1.37 (0.61), residues: 80 loop : -0.86 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.013 0.002 TYR C 328 PHE 0.012 0.002 PHE D 537 TRP 0.007 0.001 TRP C 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00404 (21920) covalent geometry : angle 0.59722 (29436) hydrogen bonds : bond 0.05114 ( 1010) hydrogen bonds : angle 3.91255 ( 2922) *********************** 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 412 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6197 (tm) REVERT: A 93 GLU cc_start: 0.7226 (mp0) cc_final: 0.6465 (mp0) REVERT: A 96 MET cc_start: 0.5472 (mtm) cc_final: 0.5068 (mtm) REVERT: A 131 ASN cc_start: 0.6832 (m110) cc_final: 0.6330 (m-40) REVERT: A 177 GLU cc_start: 0.7105 (mp0) cc_final: 0.6804 (mp0) REVERT: A 379 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7054 (p) REVERT: A 491 MET cc_start: 0.8390 (mmp) cc_final: 0.8180 (mmp) REVERT: A 588 GLU cc_start: 0.8151 (pt0) cc_final: 0.7829 (pt0) REVERT: A 608 LEU cc_start: 0.7616 (mt) cc_final: 0.7389 (mt) REVERT: B 51 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6170 (tm) REVERT: B 93 GLU cc_start: 0.7214 (mp0) cc_final: 0.6468 (mp0) REVERT: B 96 MET cc_start: 0.5410 (mtm) cc_final: 0.5023 (mtm) REVERT: B 131 ASN cc_start: 0.6890 (m110) cc_final: 0.6364 (m-40) REVERT: B 177 GLU cc_start: 0.7117 (mp0) cc_final: 0.6772 (mp0) REVERT: B 378 MET cc_start: 0.8208 (mtm) cc_final: 0.7991 (mtp) REVERT: B 491 MET cc_start: 0.8385 (mmp) cc_final: 0.8169 (mmp) REVERT: B 588 GLU cc_start: 0.8129 (pt0) cc_final: 0.7880 (pt0) REVERT: B 618 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7656 (mt) REVERT: C 93 GLU cc_start: 0.7215 (mp0) cc_final: 0.6464 (mp0) REVERT: C 96 MET cc_start: 0.5451 (mtm) cc_final: 0.5066 (mtm) REVERT: C 131 ASN cc_start: 0.6885 (m110) cc_final: 0.6369 (m-40) REVERT: C 177 GLU cc_start: 0.7057 (mp0) cc_final: 0.6659 (mp0) REVERT: C 491 MET cc_start: 0.8368 (mmp) cc_final: 0.8143 (mmp) REVERT: C 588 GLU cc_start: 0.8136 (pt0) cc_final: 0.7860 (pt0) REVERT: C 591 GLU cc_start: 0.8057 (pt0) cc_final: 0.7548 (mp0) REVERT: C 618 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7677 (mt) REVERT: D 93 GLU cc_start: 0.6949 (mp0) cc_final: 0.6603 (mp0) REVERT: D 96 MET cc_start: 0.5604 (mtm) cc_final: 0.5188 (mtm) REVERT: D 131 ASN cc_start: 0.6843 (m110) cc_final: 0.6330 (m-40) REVERT: D 177 GLU cc_start: 0.7129 (mp0) cc_final: 0.6776 (mp0) REVERT: D 491 MET cc_start: 0.8369 (mmp) cc_final: 0.8155 (mmp) REVERT: D 591 GLU cc_start: 0.8042 (pt0) cc_final: 0.7535 (mp0) REVERT: D 608 LEU cc_start: 0.7540 (mt) cc_final: 0.7293 (mt) REVERT: D 618 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7678 (mt) outliers start: 57 outliers final: 31 residues processed: 399 average time/residue: 0.4696 time to fit residues: 216.8571 Evaluate side-chains 381 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL 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 520 LEU 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 520 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 114 LEU 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 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 171 optimal weight: 0.9980 chunk 126 optimal weight: 0.0070 chunk 162 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 174 optimal weight: 0.0770 chunk 187 optimal weight: 30.0000 chunk 141 optimal weight: 5.9990 chunk 190 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 174 ASN B 637 GLN C 637 GLN D 91 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.201012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138258 restraints weight = 20449.119| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.01 r_work: 0.3290 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21920 Z= 0.100 Angle : 0.509 7.275 29436 Z= 0.257 Chirality : 0.039 0.152 3204 Planarity : 0.004 0.040 3552 Dihedral : 14.456 137.540 4714 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.84 % Allowed : 16.45 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2432 helix: 1.28 (0.14), residues: 1452 sheet: -1.06 (0.62), residues: 80 loop : -0.63 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.009 0.001 TYR B 467 PHE 0.009 0.001 PHE C 493 TRP 0.007 0.001 TRP C 593 HIS 0.002 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00214 (21920) covalent geometry : angle 0.50917 (29436) hydrogen bonds : bond 0.04008 ( 1010) hydrogen bonds : angle 3.73136 ( 2922) *********************** 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 422 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6190 (tm) REVERT: A 93 GLU cc_start: 0.7246 (mp0) cc_final: 0.6472 (mp0) REVERT: A 96 MET cc_start: 0.5454 (mtm) cc_final: 0.4998 (mtm) REVERT: A 110 MET cc_start: 0.7095 (mtt) cc_final: 0.6724 (mtt) REVERT: A 131 ASN cc_start: 0.6809 (m110) cc_final: 0.6367 (m-40) REVERT: A 177 GLU cc_start: 0.7119 (mp0) cc_final: 0.6807 (mp0) REVERT: A 535 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 588 GLU cc_start: 0.7993 (pt0) cc_final: 0.7753 (pt0) REVERT: A 591 GLU cc_start: 0.7928 (pt0) cc_final: 0.7573 (mp0) REVERT: A 608 LEU cc_start: 0.7565 (mt) cc_final: 0.7314 (mt) REVERT: A 618 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7549 (mt) REVERT: B 51 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6196 (tm) REVERT: B 93 GLU cc_start: 0.7160 (mp0) cc_final: 0.6407 (mp0) REVERT: B 96 MET cc_start: 0.5442 (mtm) cc_final: 0.4994 (mtm) REVERT: B 131 ASN cc_start: 0.6805 (m110) cc_final: 0.6392 (m-40) REVERT: B 177 GLU cc_start: 0.7150 (mp0) cc_final: 0.6769 (mp0) REVERT: B 458 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8570 (mt) REVERT: B 535 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 591 GLU cc_start: 0.7922 (pt0) cc_final: 0.7558 (mp0) REVERT: C 93 GLU cc_start: 0.7167 (mp0) cc_final: 0.6418 (mp0) REVERT: C 96 MET cc_start: 0.5453 (mtm) cc_final: 0.5003 (mtm) REVERT: C 131 ASN cc_start: 0.6797 (m110) cc_final: 0.6374 (m-40) REVERT: C 177 GLU cc_start: 0.7063 (mp0) cc_final: 0.6689 (mp0) REVERT: C 458 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 535 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7668 (mt-10) REVERT: C 588 GLU cc_start: 0.7967 (pt0) cc_final: 0.7726 (pt0) REVERT: C 591 GLU cc_start: 0.7918 (pt0) cc_final: 0.7559 (mp0) REVERT: C 618 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7660 (mt) REVERT: D 93 GLU cc_start: 0.6985 (mp0) cc_final: 0.6636 (mp0) REVERT: D 96 MET cc_start: 0.5460 (mtm) cc_final: 0.5023 (mtm) REVERT: D 131 ASN cc_start: 0.6765 (m110) cc_final: 0.6359 (m-40) REVERT: D 177 GLU cc_start: 0.7114 (mp0) cc_final: 0.6776 (mp0) REVERT: D 458 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8573 (mt) REVERT: D 535 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 591 GLU cc_start: 0.7900 (pt0) cc_final: 0.7545 (mp0) REVERT: D 608 LEU cc_start: 0.7518 (mt) cc_final: 0.7262 (mt) REVERT: D 610 ARG cc_start: 0.6141 (tpm170) cc_final: 0.5755 (tpt170) REVERT: D 618 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7644 (mt) outliers start: 39 outliers final: 14 residues processed: 417 average time/residue: 0.4935 time to fit residues: 237.7863 Evaluate side-chains 376 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 354 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 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 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 618 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 179 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 242 optimal weight: 20.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 174 ASN A 637 GLN B 91 ASN B 122 HIS B 185 HIS C 122 HIS D 122 HIS D 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.200750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138154 restraints weight = 20518.587| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.11 r_work: 0.3270 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 21920 Z= 0.106 Angle : 0.522 8.753 29436 Z= 0.264 Chirality : 0.039 0.189 3204 Planarity : 0.004 0.039 3552 Dihedral : 14.162 134.999 4714 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.56 % Allowed : 16.92 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.17), residues: 2432 helix: 1.35 (0.14), residues: 1456 sheet: -0.86 (0.61), residues: 80 loop : -0.63 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.010 0.001 TYR D 328 PHE 0.008 0.001 PHE D 537 TRP 0.007 0.001 TRP C 593 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00231 (21920) covalent geometry : angle 0.52172 (29436) hydrogen bonds : bond 0.04102 ( 1010) hydrogen bonds : angle 3.75806 ( 2922) *********************** 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 400 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6180 (tm) REVERT: A 78 MET cc_start: 0.7110 (mmp) cc_final: 0.6447 (mmt) REVERT: A 93 GLU cc_start: 0.7250 (mp0) cc_final: 0.6461 (mp0) REVERT: A 96 MET cc_start: 0.5489 (mtm) cc_final: 0.5047 (mtm) REVERT: A 131 ASN cc_start: 0.6807 (m110) cc_final: 0.6406 (m-40) REVERT: A 177 GLU cc_start: 0.7120 (mp0) cc_final: 0.6801 (mp0) REVERT: A 378 MET cc_start: 0.8290 (mtp) cc_final: 0.8060 (mmm) REVERT: A 535 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 591 GLU cc_start: 0.7966 (pt0) cc_final: 0.7551 (mp0) REVERT: A 608 LEU cc_start: 0.7468 (mt) cc_final: 0.7159 (mt) REVERT: A 612 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6776 (mp) REVERT: A 618 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7515 (mt) REVERT: B 51 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6216 (tm) REVERT: B 93 GLU cc_start: 0.7186 (mp0) cc_final: 0.6426 (mp0) REVERT: B 96 MET cc_start: 0.5424 (mtm) cc_final: 0.4988 (mtm) REVERT: B 131 ASN cc_start: 0.6761 (m110) cc_final: 0.6397 (m-40) REVERT: B 177 GLU cc_start: 0.7150 (mp0) cc_final: 0.6764 (mp0) REVERT: B 458 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 535 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 591 GLU cc_start: 0.7945 (pt0) cc_final: 0.7566 (mp0) REVERT: C 78 MET cc_start: 0.7122 (mmp) cc_final: 0.6590 (mmt) REVERT: C 93 GLU cc_start: 0.7206 (mp0) cc_final: 0.6437 (mp0) REVERT: C 96 MET cc_start: 0.5462 (mtm) cc_final: 0.5015 (mtm) REVERT: C 131 ASN cc_start: 0.6784 (m110) cc_final: 0.6433 (m-40) REVERT: C 177 GLU cc_start: 0.7099 (mp0) cc_final: 0.6707 (mp0) REVERT: C 458 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (mt) REVERT: C 535 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 591 GLU cc_start: 0.7945 (pt0) cc_final: 0.7531 (mp0) REVERT: C 618 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7560 (mt) REVERT: D 93 GLU cc_start: 0.7005 (mp0) cc_final: 0.6649 (mp0) REVERT: D 96 MET cc_start: 0.5484 (mtm) cc_final: 0.5045 (mtm) REVERT: D 131 ASN cc_start: 0.6815 (m110) cc_final: 0.6455 (m-40) REVERT: D 177 GLU cc_start: 0.7121 (mp0) cc_final: 0.6766 (mp0) REVERT: D 458 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8554 (mt) REVERT: D 535 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7777 (mt-10) REVERT: D 591 GLU cc_start: 0.7930 (pt0) cc_final: 0.7518 (mp0) REVERT: D 608 LEU cc_start: 0.7433 (mt) cc_final: 0.7197 (mt) REVERT: D 618 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7577 (mt) outliers start: 33 outliers final: 15 residues processed: 396 average time/residue: 0.4909 time to fit residues: 224.9231 Evaluate side-chains 383 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 359 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 372 LEU 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 C residue 311 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 205 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 180 optimal weight: 0.0030 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 122 HIS A 637 GLN B 91 ASN B 122 HIS B 174 ASN C 91 ASN C 122 HIS C 174 ASN D 91 ASN D 122 HIS D 637 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.199530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.134085 restraints weight = 20640.147| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.89 r_work: 0.3274 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21920 Z= 0.117 Angle : 0.539 8.250 29436 Z= 0.272 Chirality : 0.040 0.206 3204 Planarity : 0.004 0.038 3552 Dihedral : 14.130 133.955 4714 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.37 % Allowed : 17.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.17), residues: 2432 helix: 1.36 (0.14), residues: 1456 sheet: -0.52 (0.62), residues: 76 loop : -0.62 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.011 0.001 TYR C 328 PHE 0.010 0.001 PHE B 537 TRP 0.007 0.001 TRP D 495 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00265 (21920) covalent geometry : angle 0.53851 (29436) hydrogen bonds : bond 0.04393 ( 1010) hydrogen bonds : angle 3.80468 ( 2922) ********************** 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 385 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 356 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6233 (tm) REVERT: A 78 MET cc_start: 0.7030 (mmp) cc_final: 0.6456 (mmt) REVERT: A 93 GLU cc_start: 0.7249 (mp0) cc_final: 0.6472 (mp0) REVERT: A 96 MET cc_start: 0.5514 (mtm) cc_final: 0.5070 (mtm) REVERT: A 131 ASN cc_start: 0.6787 (m110) cc_final: 0.6417 (m-40) REVERT: A 177 GLU cc_start: 0.7106 (mp0) cc_final: 0.6787 (mp0) REVERT: A 221 SER cc_start: 0.8007 (m) cc_final: 0.7743 (p) REVERT: A 591 GLU cc_start: 0.7951 (pt0) cc_final: 0.7536 (mp0) REVERT: A 608 LEU cc_start: 0.7440 (mt) cc_final: 0.7170 (mt) REVERT: A 612 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6693 (mp) REVERT: A 618 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7617 (mt) REVERT: B 51 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6251 (tm) REVERT: B 93 GLU cc_start: 0.7241 (mp0) cc_final: 0.6458 (mp0) REVERT: B 96 MET cc_start: 0.5483 (mtm) cc_final: 0.5035 (mtm) REVERT: B 131 ASN cc_start: 0.6847 (m110) cc_final: 0.6532 (m-40) REVERT: B 177 GLU cc_start: 0.7163 (mp0) cc_final: 0.6789 (mp0) REVERT: B 458 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 591 GLU cc_start: 0.7960 (pt0) cc_final: 0.7555 (mp0) REVERT: C 51 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6168 (tm) REVERT: C 93 GLU cc_start: 0.7235 (mp0) cc_final: 0.6476 (mp0) REVERT: C 96 MET cc_start: 0.5480 (mtm) cc_final: 0.5030 (mtm) REVERT: C 131 ASN cc_start: 0.6843 (m110) cc_final: 0.6505 (m-40) REVERT: C 177 GLU cc_start: 0.7110 (mp0) cc_final: 0.6717 (mp0) REVERT: C 458 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8563 (mt) REVERT: C 591 GLU cc_start: 0.7968 (pt0) cc_final: 0.7549 (mp0) REVERT: D 96 MET cc_start: 0.5570 (mtm) cc_final: 0.5227 (mtm) REVERT: D 131 ASN cc_start: 0.6861 (m110) cc_final: 0.6536 (m-40) REVERT: D 177 GLU cc_start: 0.7114 (mp0) cc_final: 0.6743 (mp0) REVERT: D 458 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8576 (mt) REVERT: D 591 GLU cc_start: 0.7947 (pt0) cc_final: 0.7528 (mp0) REVERT: D 608 LEU cc_start: 0.7467 (mt) cc_final: 0.7231 (mt) REVERT: D 610 ARG cc_start: 0.6415 (tpt170) cc_final: 0.6101 (tpt170) outliers start: 29 outliers final: 17 residues processed: 378 average time/residue: 0.5412 time to fit residues: 235.8347 Evaluate side-chains 377 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 352 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL 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 114 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 372 LEU 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 C residue 51 LEU Chi-restraints excluded: chain C residue 311 THR 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 D residue 311 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 32 optimal weight: 7.9990 chunk 148 optimal weight: 0.0570 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 637 GLN B 122 HIS B 174 ASN C 122 HIS D 122 HIS D 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.201492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137167 restraints weight = 20607.528| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.85 r_work: 0.3314 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21920 Z= 0.105 Angle : 0.524 8.374 29436 Z= 0.265 Chirality : 0.039 0.226 3204 Planarity : 0.004 0.037 3552 Dihedral : 13.768 125.076 4714 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.13 % Allowed : 17.82 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.17), residues: 2432 helix: 1.48 (0.14), residues: 1456 sheet: -0.29 (0.62), residues: 76 loop : -0.54 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.009 0.001 TYR A 555 PHE 0.009 0.001 PHE B 493 TRP 0.006 0.001 TRP D 593 HIS 0.002 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00227 (21920) covalent geometry : angle 0.52424 (29436) hydrogen bonds : bond 0.04088 ( 1010) hydrogen bonds : angle 3.77386 ( 2922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8990.18 seconds wall clock time: 153 minutes 10.18 seconds (9190.18 seconds total)