Starting phenix.real_space_refine on Fri Jul 3 07:19:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.cif Found real_map, /net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7neq_12290/07_2026/7neq_12290.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 68 5.16 5 C 8112 2.51 5 N 2039 2.21 5 O 2309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 2, 'NAG': 1, 'U9N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'CLR': 1, 'NAG': 1, 'R1H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.91, per 1000 atoms: 0.23 Number of scatterers: 12529 At special positions: 0 Unit cell: (102.3, 97.02, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 1 15.00 O 2309 8.00 N 2039 7.00 C 8112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.82 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 596 " " NAG B1102 " - " ASN B 596 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 638.1 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 18 sheets defined 43.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.831A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.841A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.545A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 219 through 233 removed outlier: 4.473A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.601A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.577A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.677A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 removed outlier: 3.596A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.855A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 removed outlier: 4.173A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 441 removed outlier: 3.896A pdb=" N ILE A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.643A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.787A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.506A pdb=" N ILE A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 removed outlier: 3.653A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.413A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 removed outlier: 3.542A pdb=" N PHE A 571 " --> pdb=" O LEU A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.838A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 Processing helix chain 'A' and resid 622 through 650 removed outlier: 4.802A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.719A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 83 " --> pdb=" O THR E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.869A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.592A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 removed outlier: 3.537A pdb=" N GLU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.515A pdb=" N ALA B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.005A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 4.673A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 4.190A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 413 removed outlier: 3.947A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 442 removed outlier: 4.071A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 446 removed outlier: 4.248A pdb=" N GLU B 446 " --> pdb=" O SER B 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 443 through 446' Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 473 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.530A pdb=" N MET B 481 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 482 " --> pdb=" O LEU B 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 482' Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.937A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 removed outlier: 3.538A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 551 removed outlier: 4.035A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.305A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 571 Processing helix chain 'B' and resid 572 through 587 removed outlier: 3.652A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.550A pdb=" N GLN B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.022A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.749A pdb=" N LEU A 37 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.591A pdb=" N GLY A 122 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 255 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 24 removed outlier: 4.103A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.488A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 48 removed outlier: 6.488A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 86 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.823A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.823A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.599A pdb=" N PHE E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.536A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 48 removed outlier: 6.288A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.655A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.584A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 37 " --> pdb=" O MET B 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.475A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1629 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: 2.63 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1940 1.26 - 1.40: 3242 1.40 - 1.54: 7446 1.54 - 1.68: 66 1.68 - 1.83: 106 Bond restraints: 12800 Sorted by residual: bond pdb=" C13 R1H B1101 " pdb=" N08 R1H B1101 " ideal model delta sigma weight residual 1.448 1.148 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C03 R1H B1101 " pdb=" C04 R1H B1101 " ideal model delta sigma weight residual 1.398 1.113 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C10 R1H B1101 " pdb=" C11 R1H B1101 " ideal model delta sigma weight residual 1.505 1.254 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C31 R1H B1101 " pdb=" N30 R1H B1101 " ideal model delta sigma weight residual 1.357 1.514 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C04 R1H B1101 " pdb=" C05 R1H B1101 " ideal model delta sigma weight residual 1.385 1.249 0.136 2.00e-02 2.50e+03 4.60e+01 ... (remaining 12795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 17125 2.79 - 5.57: 184 5.57 - 8.36: 33 8.36 - 11.15: 10 11.15 - 13.93: 3 Bond angle restraints: 17355 Sorted by residual: angle pdb=" N TYR F 95 " pdb=" CA TYR F 95 " pdb=" C TYR F 95 " ideal model delta sigma weight residual 110.80 123.94 -13.14 2.13e+00 2.20e-01 3.80e+01 angle pdb=" N ASN F 36 " pdb=" CA ASN F 36 " pdb=" C ASN F 36 " ideal model delta sigma weight residual 109.81 117.52 -7.71 1.53e+00 4.27e-01 2.54e+01 angle pdb=" N CYS D 96 " pdb=" CA CYS D 96 " pdb=" C CYS D 96 " ideal model delta sigma weight residual 109.59 101.62 7.97 1.61e+00 3.86e-01 2.45e+01 angle pdb=" C10 R1H B1101 " pdb=" C11 R1H B1101 " pdb=" C12 R1H B1101 " ideal model delta sigma weight residual 120.45 134.38 -13.93 3.00e+00 1.11e-01 2.16e+01 angle pdb=" N TYR F 94 " pdb=" CA TYR F 94 " pdb=" C TYR F 94 " ideal model delta sigma weight residual 113.88 119.15 -5.27 1.23e+00 6.61e-01 1.84e+01 ... (remaining 17350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 7077 29.72 - 59.44: 376 59.44 - 89.15: 31 89.15 - 118.87: 3 118.87 - 148.59: 2 Dihedral angle restraints: 7489 sinusoidal: 2953 harmonic: 4536 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 25.18 67.82 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 41.27 51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA ASP D 32 " pdb=" C ASP D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1853 0.088 - 0.175: 114 0.175 - 0.263: 6 0.263 - 0.351: 4 0.351 - 0.438: 2 Chirality restraints: 1979 Sorted by residual: chirality pdb=" CA TYR F 95 " pdb=" N TYR F 95 " pdb=" C TYR F 95 " pdb=" CB TYR F 95 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA TYR F 94 " pdb=" N TYR F 94 " pdb=" C TYR F 94 " pdb=" CB TYR F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C2 U9N A1002 " pdb=" C1 U9N A1002 " pdb=" C3 U9N A1002 " pdb=" O2 U9N A1002 " both_signs ideal model delta sigma weight residual False 2.24 2.53 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1976 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 88 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 95 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C TYR D 95 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR D 95 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS D 96 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO F 88 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.029 5.00e-02 4.00e+02 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 16 2.26 - 2.92: 5373 2.92 - 3.58: 17238 3.58 - 4.24: 28329 4.24 - 4.90: 49687 Nonbonded interactions: 100643 Sorted by model distance: nonbonded pdb=" OD1 ASP B 217 " pdb=" CG2 THR B 220 " model vdw 1.600 3.460 nonbonded pdb=" OD1 ASN B 76 " pdb=" N SER B 255 " model vdw 1.732 3.120 nonbonded pdb=" CE1 TYR B 464 " pdb=" CB TYR B 469 " model vdw 2.051 3.740 nonbonded pdb=" NH1 ARG C 45 " pdb=" CE2 PHE C 58 " model vdw 2.058 3.420 nonbonded pdb=" NH1 ARG C 45 " pdb=" CZ PHE C 58 " model vdw 2.070 3.420 ... (remaining 100638 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 35 through 654 or resid 1003)) selection = (chain 'B' and (resid 35 through 654 or resid 1103)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.220 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.010 0.791 12809 Z= 0.506 Angle : 0.827 22.573 17375 Z= 0.410 Chirality : 0.049 0.438 1979 Planarity : 0.004 0.056 2142 Dihedral : 17.382 148.590 4572 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.56 % Allowed : 22.89 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.18), residues: 1558 helix: -1.59 (0.18), residues: 652 sheet: -1.97 (0.28), residues: 286 loop : -3.59 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 160 TYR 0.016 0.002 TYR A 123 PHE 0.024 0.002 PHE F 79 TRP 0.016 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.37 (12800) covalent geometry : angle 0.80568 / 0.40 (17355) SS BOND : bond 0.29913 / 26.47 ( 7) SS BOND : angle 6.13904 / 3.63 ( 14) hydrogen bonds : bond 0.15688 / 10.56 ( 545) hydrogen bonds : angle 6.68323 / 4.75 ( 1629) link_NAG-ASN : bond 0.00275 / 0.13 ( 2) link_NAG-ASN : angle 3.73289 / 2.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 218 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.6881 (t0) cc_final: 0.6677 (t0) REVERT: A 190 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5260 (mm-30) REVERT: A 234 GLN cc_start: 0.6354 (mm-40) cc_final: 0.5977 (mp10) REVERT: A 278 GLU cc_start: 0.4382 (OUTLIER) cc_final: 0.4181 (mt-10) REVERT: A 334 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.5014 (mm-30) REVERT: A 458 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6487 (mm-30) REVERT: A 463 TYR cc_start: 0.7804 (m-80) cc_final: 0.7536 (m-80) REVERT: D 16 GLN cc_start: 0.7250 (tt0) cc_final: 0.6919 (tp40) REVERT: D 18 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7241 (tp) REVERT: E 82 ASP cc_start: 0.7201 (m-30) cc_final: 0.6954 (m-30) REVERT: E 107 ARG cc_start: 0.4954 (mtt90) cc_final: 0.4745 (mmp-170) REVERT: B 66 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6325 (t0) REVERT: B 98 ASP cc_start: 0.6365 (t0) cc_final: 0.5954 (p0) outliers start: 75 outliers final: 54 residues processed: 279 average time/residue: 0.1163 time to fit residues: 46.4296 Evaluate side-chains 227 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0470 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN A 66 ASN A 109 ASN A 299 ASN A 375 HIS A 425 ASN A 436 ASN A 531 GLN A 583 HIS D 36 ASN E 31 ASN E 37 GLN F 36 ASN B 40 HIS B 68 ASN B 243 HIS B 283 HIS B 425 ASN B 436 ASN B 531 GLN B 583 HIS B 601 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137364 restraints weight = 16734.762| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.18 r_work: 0.3311 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12809 Z= 0.217 Angle : 0.700 10.446 17375 Z= 0.353 Chirality : 0.044 0.175 1979 Planarity : 0.005 0.055 2142 Dihedral : 10.778 101.747 1873 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 6.52 % Allowed : 24.81 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.20), residues: 1558 helix: -0.37 (0.20), residues: 654 sheet: -1.31 (0.30), residues: 278 loop : -3.04 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 193 TYR 0.017 0.002 TYR C 91 PHE 0.029 0.002 PHE B 250 TRP 0.014 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (12800) covalent geometry : angle 0.69578 / 0.35 (17355) SS BOND : bond 0.01422 / 1.22 ( 7) SS BOND : angle 1.75996 / 1.33 ( 14) hydrogen bonds : bond 0.04982 / 3.27 ( 545) hydrogen bonds : angle 4.85626 / 3.42 ( 1629) link_NAG-ASN : bond 0.00225 / 0.11 ( 2) link_NAG-ASN : angle 3.16755 / 1.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 178 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5604 (mm-30) REVERT: A 226 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6372 (mm) REVERT: A 234 GLN cc_start: 0.6366 (mm-40) cc_final: 0.5813 (mp10) REVERT: A 458 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6874 (mm-30) REVERT: A 463 TYR cc_start: 0.8201 (m-80) cc_final: 0.7764 (m-80) REVERT: A 587 LEU cc_start: 0.7598 (mt) cc_final: 0.7027 (mt) REVERT: C 82 ASP cc_start: 0.7717 (m-30) cc_final: 0.7513 (m-30) REVERT: D 5 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7515 (tt0) REVERT: D 16 GLN cc_start: 0.7615 (tt0) cc_final: 0.7090 (tp40) REVERT: E 107 ARG cc_start: 0.5077 (mtt90) cc_final: 0.4589 (mmp-170) REVERT: B 64 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6681 (mp) REVERT: B 66 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6730 (t0) REVERT: B 118 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5494 (mmmt) REVERT: B 514 MET cc_start: 0.8005 (ttm) cc_final: 0.7743 (mtp) outliers start: 88 outliers final: 62 residues processed: 250 average time/residue: 0.0987 time to fit residues: 37.2655 Evaluate side-chains 229 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN B 40 HIS B 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.166653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138833 restraints weight = 16781.479| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.06 r_work: 0.3350 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12809 Z= 0.165 Angle : 0.631 9.681 17375 Z= 0.319 Chirality : 0.042 0.170 1979 Planarity : 0.004 0.057 2142 Dihedral : 9.357 97.823 1819 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.22 % Allowed : 25.48 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1558 helix: 0.16 (0.21), residues: 654 sheet: -1.00 (0.31), residues: 278 loop : -2.69 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.022 0.002 TYR B 342 PHE 0.017 0.001 PHE F 99 TRP 0.014 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (12800) covalent geometry : angle 0.62770 / 0.32 (17355) SS BOND : bond 0.00725 / 0.56 ( 7) SS BOND : angle 1.37547 / 1.00 ( 14) hydrogen bonds : bond 0.04430 / 2.91 ( 545) hydrogen bonds : angle 4.50919 / 3.16 ( 1629) link_NAG-ASN : bond 0.00132 / 0.06 ( 2) link_NAG-ASN : angle 2.74725 / 1.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 0.484 Fit side-chains REVERT: A 173 VAL cc_start: 0.6771 (OUTLIER) cc_final: 0.6338 (p) REVERT: A 190 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5527 (mm-30) REVERT: A 226 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6356 (mm) REVERT: A 234 GLN cc_start: 0.6399 (mm-40) cc_final: 0.5840 (mp10) REVERT: A 343 LYS cc_start: 0.6329 (mmtt) cc_final: 0.5798 (mttm) REVERT: A 458 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6954 (mm-30) REVERT: D 5 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7530 (tt0) REVERT: D 16 GLN cc_start: 0.7576 (tt0) cc_final: 0.7110 (tp40) REVERT: D 18 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7341 (tp) REVERT: E 107 ARG cc_start: 0.5046 (mtt90) cc_final: 0.4594 (mmp-170) REVERT: B 64 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6672 (mp) REVERT: B 66 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.6796 (t0) REVERT: B 98 ASP cc_start: 0.6813 (t0) cc_final: 0.5877 (p0) REVERT: B 118 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5517 (mmmt) REVERT: B 272 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: B 514 MET cc_start: 0.7964 (ttm) cc_final: 0.7721 (mtp) outliers start: 84 outliers final: 64 residues processed: 238 average time/residue: 0.0927 time to fit residues: 33.3475 Evaluate side-chains 234 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 103 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 66 ASN F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140984 restraints weight = 16810.979| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.10 r_work: 0.3398 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.118 Angle : 0.560 8.618 17375 Z= 0.286 Chirality : 0.040 0.200 1979 Planarity : 0.004 0.053 2142 Dihedral : 8.591 94.455 1810 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 5.41 % Allowed : 26.22 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1558 helix: 0.76 (0.21), residues: 640 sheet: -0.73 (0.31), residues: 278 loop : -2.36 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.016 0.001 TYR B 463 PHE 0.016 0.001 PHE F 79 TRP 0.013 0.001 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12800) covalent geometry : angle 0.55714 / 0.29 (17355) SS BOND : bond 0.00559 / 0.43 ( 7) SS BOND : angle 1.33728 / 0.87 ( 14) hydrogen bonds : bond 0.03749 / 2.47 ( 545) hydrogen bonds : angle 4.16908 / 2.91 ( 1629) link_NAG-ASN : bond 0.00106 / 0.06 ( 2) link_NAG-ASN : angle 2.37895 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 181 time to evaluate : 0.456 Fit side-chains REVERT: A 173 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.6330 (p) REVERT: A 190 GLU cc_start: 0.6228 (mm-30) cc_final: 0.5703 (mm-30) REVERT: A 226 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6365 (mm) REVERT: A 234 GLN cc_start: 0.6403 (mm-40) cc_final: 0.5842 (mp10) REVERT: A 343 LYS cc_start: 0.6398 (mmtt) cc_final: 0.5883 (mttm) REVERT: A 458 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6867 (mm-30) REVERT: C 11 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.5765 (m-80) REVERT: D 5 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7666 (tt0) REVERT: D 16 GLN cc_start: 0.7676 (tt0) cc_final: 0.7202 (tp40) REVERT: D 18 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7340 (tp) REVERT: D 65 ARG cc_start: 0.7336 (tpm170) cc_final: 0.7028 (mmp80) REVERT: E 107 ARG cc_start: 0.5058 (mtt90) cc_final: 0.4560 (mmp-170) REVERT: B 64 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6701 (mp) REVERT: B 66 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6903 (t0) REVERT: B 98 ASP cc_start: 0.6938 (t0) cc_final: 0.6001 (p0) REVERT: B 198 MET cc_start: 0.7669 (ttm) cc_final: 0.7420 (ttt) REVERT: B 207 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7129 (mp) REVERT: B 272 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7207 (mm-30) outliers start: 73 outliers final: 54 residues processed: 239 average time/residue: 0.0957 time to fit residues: 34.6034 Evaluate side-chains 231 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 37 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 134 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 457 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.168623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141217 restraints weight = 16865.084| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.14 r_work: 0.3361 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.133 Angle : 0.566 8.533 17375 Z= 0.289 Chirality : 0.041 0.215 1979 Planarity : 0.004 0.052 2142 Dihedral : 8.378 94.075 1801 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.89 % Allowed : 24.89 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1558 helix: 0.90 (0.21), residues: 640 sheet: -0.60 (0.31), residues: 278 loop : -2.26 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.024 0.001 TYR B 342 PHE 0.027 0.001 PHE B 250 TRP 0.013 0.001 TRP D 35 HIS 0.002 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12800) covalent geometry : angle 0.56305 / 0.29 (17355) SS BOND : bond 0.00558 / 0.41 ( 7) SS BOND : angle 1.27603 / 0.94 ( 14) hydrogen bonds : bond 0.03804 / 2.50 ( 545) hydrogen bonds : angle 4.10314 / 2.87 ( 1629) link_NAG-ASN : bond 0.00137 / 0.07 ( 2) link_NAG-ASN : angle 2.36310 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 176 time to evaluate : 0.383 Fit side-chains REVERT: A 118 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.6803 (mmmt) REVERT: A 173 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6302 (p) REVERT: A 190 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5635 (mm-30) REVERT: A 226 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6269 (mm) REVERT: A 234 GLN cc_start: 0.6433 (mm-40) cc_final: 0.5893 (mp10) REVERT: A 343 LYS cc_start: 0.6399 (mmtt) cc_final: 0.5914 (mttm) REVERT: A 458 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6971 (mm-30) REVERT: C 11 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: D 16 GLN cc_start: 0.7550 (tt0) cc_final: 0.7092 (tp40) REVERT: D 18 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7284 (tp) REVERT: D 65 ARG cc_start: 0.7200 (tpm170) cc_final: 0.6919 (mmp80) REVERT: E 107 ARG cc_start: 0.4984 (mtt90) cc_final: 0.4572 (mmp-170) REVERT: B 64 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6527 (mp) REVERT: B 66 ASN cc_start: 0.7230 (OUTLIER) cc_final: 0.6797 (t0) REVERT: B 198 MET cc_start: 0.7654 (ttm) cc_final: 0.7389 (ttt) REVERT: B 207 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7090 (mp) REVERT: B 272 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6466 (mm-30) outliers start: 93 outliers final: 69 residues processed: 248 average time/residue: 0.0951 time to fit residues: 36.0272 Evaluate side-chains 250 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN F 36 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140457 restraints weight = 16699.767| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.06 r_work: 0.3386 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.127 Angle : 0.555 8.530 17375 Z= 0.283 Chirality : 0.041 0.209 1979 Planarity : 0.003 0.042 2142 Dihedral : 8.129 92.820 1799 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.44 % Allowed : 25.85 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1558 helix: 1.03 (0.21), residues: 640 sheet: -0.53 (0.31), residues: 278 loop : -2.16 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.016 0.001 TYR B 463 PHE 0.016 0.001 PHE F 79 TRP 0.013 0.001 TRP D 35 HIS 0.002 0.000 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12800) covalent geometry : angle 0.55303 / 0.28 (17355) SS BOND : bond 0.00538 / 0.40 ( 7) SS BOND : angle 1.14386 / 0.83 ( 14) hydrogen bonds : bond 0.03710 / 2.43 ( 545) hydrogen bonds : angle 4.02058 / 2.81 ( 1629) link_NAG-ASN : bond 0.00149 / 0.08 ( 2) link_NAG-ASN : angle 2.28770 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 178 time to evaluate : 0.450 Fit side-chains REVERT: A 118 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6881 (mmmt) REVERT: A 173 VAL cc_start: 0.6709 (OUTLIER) cc_final: 0.6233 (p) REVERT: A 190 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5775 (mm-30) REVERT: A 226 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6254 (mm) REVERT: A 234 GLN cc_start: 0.6447 (mm-40) cc_final: 0.5873 (mp10) REVERT: A 288 ASN cc_start: 0.6439 (t0) cc_final: 0.5112 (p0) REVERT: A 343 LYS cc_start: 0.6328 (mmtt) cc_final: 0.5805 (mttm) REVERT: A 458 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 11 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5814 (m-80) REVERT: D 16 GLN cc_start: 0.7671 (tt0) cc_final: 0.7175 (tp40) REVERT: D 18 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (tp) REVERT: D 65 ARG cc_start: 0.7339 (tpm170) cc_final: 0.7068 (mmp80) REVERT: E 107 ARG cc_start: 0.5031 (mtt90) cc_final: 0.4533 (mmp-170) REVERT: B 64 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6644 (mp) REVERT: B 66 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6867 (t0) REVERT: B 198 MET cc_start: 0.7760 (ttm) cc_final: 0.7506 (ttt) REVERT: B 207 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7133 (mp) REVERT: B 272 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6534 (mm-30) outliers start: 87 outliers final: 68 residues processed: 246 average time/residue: 0.0993 time to fit residues: 36.7056 Evaluate side-chains 247 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 66 ASN A 158 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142460 restraints weight = 16648.122| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.86 r_work: 0.3410 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12809 Z= 0.111 Angle : 0.542 7.994 17375 Z= 0.277 Chirality : 0.040 0.206 1979 Planarity : 0.003 0.042 2142 Dihedral : 7.905 91.316 1796 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.07 % Allowed : 26.44 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1558 helix: 1.14 (0.21), residues: 642 sheet: -0.49 (0.32), residues: 278 loop : -2.03 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 61 TYR 0.017 0.001 TYR B 463 PHE 0.015 0.001 PHE F 79 TRP 0.013 0.001 TRP D 35 HIS 0.001 0.000 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (12800) covalent geometry : angle 0.53959 / 0.28 (17355) SS BOND : bond 0.00462 / 0.34 ( 7) SS BOND : angle 0.99595 / 0.71 ( 14) hydrogen bonds : bond 0.03509 / 2.31 ( 545) hydrogen bonds : angle 3.94002 / 2.75 ( 1629) link_NAG-ASN : bond 0.00171 / 0.09 ( 2) link_NAG-ASN : angle 2.20885 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.492 Fit side-chains REVERT: A 118 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6875 (mmmt) REVERT: A 173 VAL cc_start: 0.6731 (OUTLIER) cc_final: 0.6264 (p) REVERT: A 190 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5782 (mm-30) REVERT: A 226 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6248 (mm) REVERT: A 234 GLN cc_start: 0.6445 (mm-40) cc_final: 0.5852 (mp10) REVERT: A 343 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5829 (mttm) REVERT: A 458 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7146 (mm-30) REVERT: C 11 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.5829 (m-80) REVERT: D 16 GLN cc_start: 0.7632 (tt0) cc_final: 0.7154 (tp40) REVERT: D 18 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7269 (tp) REVERT: D 65 ARG cc_start: 0.7263 (tpm170) cc_final: 0.7004 (mmp80) REVERT: E 107 ARG cc_start: 0.5031 (mtt90) cc_final: 0.4548 (mmp-170) REVERT: B 64 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6626 (mp) REVERT: B 66 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6815 (t0) REVERT: B 198 MET cc_start: 0.7709 (ttm) cc_final: 0.7452 (ttt) REVERT: B 207 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7124 (mp) REVERT: B 272 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6562 (mm-30) outliers start: 82 outliers final: 67 residues processed: 240 average time/residue: 0.1035 time to fit residues: 37.6282 Evaluate side-chains 248 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 172 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 6 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN F 36 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.169473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140459 restraints weight = 16752.071| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.41 r_work: 0.3357 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.142 Angle : 0.569 8.521 17375 Z= 0.289 Chirality : 0.041 0.204 1979 Planarity : 0.004 0.042 2142 Dihedral : 8.004 92.593 1796 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.74 % Allowed : 25.56 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.22), residues: 1558 helix: 1.15 (0.21), residues: 640 sheet: -0.43 (0.32), residues: 278 loop : -2.05 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.026 0.001 TYR B 342 PHE 0.023 0.001 PHE B 250 TRP 0.012 0.001 TRP D 35 HIS 0.002 0.001 HIS B 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12800) covalent geometry : angle 0.56654 / 0.29 (17355) SS BOND : bond 0.00575 / 0.43 ( 7) SS BOND : angle 1.18995 / 0.90 ( 14) hydrogen bonds : bond 0.03767 / 2.47 ( 545) hydrogen bonds : angle 3.97769 / 2.78 ( 1629) link_NAG-ASN : bond 0.00144 / 0.08 ( 2) link_NAG-ASN : angle 2.26532 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 0.554 Fit side-chains REVERT: A 118 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6767 (mmmt) REVERT: A 163 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7641 (mtp180) REVERT: A 173 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6251 (p) REVERT: A 190 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5758 (mm-30) REVERT: A 198 MET cc_start: 0.8162 (ttm) cc_final: 0.7945 (mtp) REVERT: A 226 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6230 (mm) REVERT: A 234 GLN cc_start: 0.6434 (mm-40) cc_final: 0.5840 (mp10) REVERT: A 343 LYS cc_start: 0.6408 (mmtt) cc_final: 0.5899 (mttm) REVERT: C 11 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: C 81 GLU cc_start: 0.7647 (pp20) cc_final: 0.7411 (pp20) REVERT: D 16 GLN cc_start: 0.7510 (tt0) cc_final: 0.7088 (tp40) REVERT: D 18 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7225 (tp) REVERT: D 65 ARG cc_start: 0.7172 (tpm170) cc_final: 0.6907 (mmp80) REVERT: E 107 ARG cc_start: 0.4967 (mtt90) cc_final: 0.4573 (mmp-170) REVERT: B 64 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6576 (mp) REVERT: B 66 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6738 (t0) REVERT: B 198 MET cc_start: 0.7678 (ttm) cc_final: 0.7404 (ttt) REVERT: B 207 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7093 (mp) REVERT: B 272 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6485 (mm-30) outliers start: 91 outliers final: 73 residues processed: 245 average time/residue: 0.0991 time to fit residues: 36.8144 Evaluate side-chains 252 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 170 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 74 optimal weight: 0.0670 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.0520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 36 ASN B 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140632 restraints weight = 16792.692| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.17 r_work: 0.3343 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.136 Angle : 0.568 8.543 17375 Z= 0.289 Chirality : 0.041 0.210 1979 Planarity : 0.004 0.042 2142 Dihedral : 7.980 92.448 1796 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.59 % Allowed : 25.56 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1558 helix: 1.19 (0.21), residues: 638 sheet: -0.42 (0.32), residues: 278 loop : -1.97 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.025 0.001 TYR B 342 PHE 0.017 0.001 PHE F 79 TRP 0.013 0.001 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12800) covalent geometry : angle 0.56549 / 0.29 (17355) SS BOND : bond 0.00553 / 0.41 ( 7) SS BOND : angle 1.14214 / 0.85 ( 14) hydrogen bonds : bond 0.03748 / 2.45 ( 545) hydrogen bonds : angle 3.96448 / 2.77 ( 1629) link_NAG-ASN : bond 0.00148 / 0.08 ( 2) link_NAG-ASN : angle 2.25405 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 173 time to evaluate : 0.490 Fit side-chains REVERT: A 118 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.6771 (mmmt) REVERT: A 173 VAL cc_start: 0.6717 (OUTLIER) cc_final: 0.6211 (p) REVERT: A 190 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5755 (mm-30) REVERT: A 198 MET cc_start: 0.8153 (ttm) cc_final: 0.7898 (mtp) REVERT: A 226 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6222 (mm) REVERT: A 234 GLN cc_start: 0.6424 (mm-40) cc_final: 0.5818 (mp10) REVERT: A 343 LYS cc_start: 0.6415 (mmtt) cc_final: 0.5887 (mttm) REVERT: A 385 PHE cc_start: 0.6643 (t80) cc_final: 0.6355 (t80) REVERT: C 11 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: C 81 GLU cc_start: 0.7614 (pp20) cc_final: 0.7366 (pp20) REVERT: D 16 GLN cc_start: 0.7526 (tt0) cc_final: 0.7093 (tp40) REVERT: D 18 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7233 (tp) REVERT: D 65 ARG cc_start: 0.7181 (tpm170) cc_final: 0.6923 (mmp80) REVERT: E 107 ARG cc_start: 0.4956 (mtt90) cc_final: 0.4547 (mmp-170) REVERT: B 64 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6633 (mp) REVERT: B 66 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6724 (t0) REVERT: B 198 MET cc_start: 0.7674 (ttm) cc_final: 0.7399 (ttt) REVERT: B 207 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 272 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6487 (mm-30) outliers start: 89 outliers final: 77 residues processed: 242 average time/residue: 0.0999 time to fit residues: 36.6143 Evaluate side-chains 257 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.167724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139229 restraints weight = 16878.208| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.20 r_work: 0.3321 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12809 Z= 0.191 Angle : 0.629 9.682 17375 Z= 0.319 Chirality : 0.043 0.211 1979 Planarity : 0.004 0.043 2142 Dihedral : 8.277 95.191 1796 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.44 % Allowed : 25.56 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1558 helix: 1.04 (0.21), residues: 640 sheet: -0.42 (0.32), residues: 278 loop : -2.10 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.022 0.002 TYR B 463 PHE 0.025 0.002 PHE B 250 TRP 0.012 0.002 TRP D 35 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (12800) covalent geometry : angle 0.62665 / 0.32 (17355) SS BOND : bond 0.00719 / 0.54 ( 7) SS BOND : angle 1.42478 / 1.12 ( 14) hydrogen bonds : bond 0.04240 / 2.77 ( 545) hydrogen bonds : angle 4.11439 / 2.87 ( 1629) link_NAG-ASN : bond 0.00144 / 0.07 ( 2) link_NAG-ASN : angle 2.38416 / 1.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 172 time to evaluate : 0.507 Fit side-chains REVERT: A 118 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6772 (mmmt) REVERT: A 173 VAL cc_start: 0.6717 (OUTLIER) cc_final: 0.6219 (p) REVERT: A 190 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5808 (mm-30) REVERT: A 226 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6238 (mm) REVERT: A 234 GLN cc_start: 0.6430 (mm-40) cc_final: 0.5839 (mp10) REVERT: A 343 LYS cc_start: 0.6453 (mmtt) cc_final: 0.5876 (mttm) REVERT: A 385 PHE cc_start: 0.6634 (t80) cc_final: 0.6328 (t80) REVERT: C 11 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.5808 (m-80) REVERT: C 81 GLU cc_start: 0.7551 (pp20) cc_final: 0.7319 (pp20) REVERT: D 16 GLN cc_start: 0.7516 (tt0) cc_final: 0.7086 (tp40) REVERT: D 18 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7260 (tp) REVERT: E 107 ARG cc_start: 0.4990 (mtt90) cc_final: 0.4571 (mmp-170) REVERT: B 66 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6771 (t0) REVERT: B 207 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7145 (mp) REVERT: B 272 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6510 (mm-30) outliers start: 87 outliers final: 77 residues processed: 238 average time/residue: 0.1028 time to fit residues: 37.1454 Evaluate side-chains 255 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 170 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 89 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN F 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139348 restraints weight = 16666.658| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.98 r_work: 0.3378 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12809 Z= 0.142 Angle : 0.584 8.736 17375 Z= 0.297 Chirality : 0.041 0.201 1979 Planarity : 0.004 0.042 2142 Dihedral : 8.019 93.082 1794 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.15 % Allowed : 26.00 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.22), residues: 1558 helix: 1.18 (0.21), residues: 638 sheet: -0.40 (0.32), residues: 278 loop : -1.97 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.025 0.001 TYR B 463 PHE 0.023 0.001 PHE B 250 TRP 0.012 0.001 TRP D 35 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12800) covalent geometry : angle 0.58155 / 0.30 (17355) SS BOND : bond 0.00575 / 0.43 ( 7) SS BOND : angle 1.15064 / 0.84 ( 14) hydrogen bonds : bond 0.03836 / 2.52 ( 545) hydrogen bonds : angle 3.98962 / 2.79 ( 1629) link_NAG-ASN : bond 0.00128 / 0.07 ( 2) link_NAG-ASN : angle 2.25968 / 1.45 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.50 seconds wall clock time: 53 minutes 9.79 seconds (3189.79 seconds total)