Starting phenix.real_space_refine on Sun Jun 22 12:51:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.map" model { file = "/net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f77_28897/06_2025/8f77_28897.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.059 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 4 5.49 5 S 138 5.16 5 C 16811 2.51 5 N 4191 2.21 5 O 4534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25678 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5916 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5912 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 27, 'TRANS': 688} Chain breaks: 2 Chain: "C" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2560 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 2 Chain: "D" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2637 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 2 Chain: "E" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2652 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 15.04, per 1000 atoms: 0.59 Number of scatterers: 25678 At special positions: 0 Unit cell: (128.904, 126.808, 197.024, 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 138 16.00 P 4 15.00 O 4534 8.00 N 4191 7.00 C 16811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " 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 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 3.2 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 21 sheets defined 59.7% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.098A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.563A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.141A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.019A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 256 removed outlier: 4.172A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.972A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 removed outlier: 3.779A pdb=" N ILE A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 315 through 346 removed outlier: 3.986A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 369 through 383 Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.304A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.637A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.528A pdb=" N ILE A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.888A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.695A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.910A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.954A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.606A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.645A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.549A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.656A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.567A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.789A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.604A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.331A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 343 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.209A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.648A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.877A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 508 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.012A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.513A pdb=" N LEU B 613 " --> pdb=" O ILE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.757A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.718A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.866A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.619A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.637A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.510A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.603A pdb=" N MET C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 4.657A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 167 through 175 removed outlier: 4.151A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.059A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.675A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.282A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 142 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.094A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.664A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 315 through 346 removed outlier: 4.258A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.890A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.670A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.817A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.521A pdb=" N ARG E 117 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 4.643A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.163A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 345 removed outlier: 3.553A pdb=" N LEU E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.051A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.525A pdb=" N ARG F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.027A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 removed outlier: 3.582A pdb=" N PHE F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.338A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 Processing helix chain 'F' and resid 257 through 284 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 312 through 344 removed outlier: 3.907A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 381 through 389 removed outlier: 4.016A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 392 No H-bonds generated for 'chain 'F' and resid 390 through 392' Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.649A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 508 through 513 removed outlier: 3.711A pdb=" N TYR F 511 " --> pdb=" O PRO F 508 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 540 removed outlier: 4.042A pdb=" N ARG F 539 " --> pdb=" O GLU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 3.574A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 610 Processing helix chain 'F' and resid 629 through 636 removed outlier: 4.564A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.797A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 3.939A pdb=" N PHE F 680 " --> pdb=" O PRO F 676 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS F 682 " --> pdb=" O HIS F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.537A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY F 703 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 728 Processing helix chain 'F' and resid 768 through 774 removed outlier: 3.696A pdb=" N CYS F 774 " --> pdb=" O LEU F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.838A pdb=" N MET F 800 " --> pdb=" O VAL F 796 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.828A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.378A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.352A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.660A pdb=" N ASP A 691 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.342A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.557A pdb=" N ILE B 53 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.517A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 501 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AB2, first strand: chain 'B' and resid 712 through 714 removed outlier: 7.029A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.503A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.749A pdb=" N ILE E 53 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 removed outlier: 3.602A pdb=" N TYR E 351 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 368 " --> pdb=" O TYR E 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC1, first strand: chain 'F' and resid 348 through 349 removed outlier: 3.668A pdb=" N VAL F 366 " --> pdb=" O TYR F 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 419 through 420 removed outlier: 6.080A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 735 " --> pdb=" O PHE F 711 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 758 " --> pdb=" O LEU F 734 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 457 through 459 removed outlier: 5.735A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 1325 hydrogen bonds defined for protein. 3708 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: 9.29 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4354 1.32 - 1.45: 6837 1.45 - 1.57: 14878 1.57 - 1.69: 6 1.69 - 1.81: 199 Bond restraints: 26274 Sorted by residual: bond pdb=" C10 PEE D 901 " pdb=" O4 PEE D 901 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C10 PEE B 903 " pdb=" O4 PEE B 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " ideal model delta sigma weight residual 1.653 1.779 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" O4P PEE C 901 " pdb=" P PEE C 901 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O4P PEE B 901 " pdb=" P PEE B 901 " ideal model delta sigma weight residual 1.653 1.775 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 26269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 35081 2.76 - 5.52: 351 5.52 - 8.28: 61 8.28 - 11.04: 10 11.04 - 13.81: 5 Bond angle restraints: 35508 Sorted by residual: angle pdb=" N ARG B 685 " pdb=" CA ARG B 685 " pdb=" C ARG B 685 " ideal model delta sigma weight residual 113.16 122.65 -9.49 1.24e+00 6.50e-01 5.86e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE B 901 " pdb=" P PEE B 901 " pdb=" O2P PEE B 901 " ideal model delta sigma weight residual 119.43 133.13 -13.70 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CA LYS F 555 " pdb=" CB LYS F 555 " pdb=" CG LYS F 555 " ideal model delta sigma weight residual 114.10 122.85 -8.75 2.00e+00 2.50e-01 1.91e+01 ... (remaining 35503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 15328 34.77 - 69.54: 479 69.54 - 104.31: 28 104.31 - 139.08: 2 139.08 - 173.86: 5 Dihedral angle restraints: 15842 sinusoidal: 6664 harmonic: 9178 Sorted by residual: dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 295 " pdb=" CB CYS C 295 " ideal model delta sinusoidal sigma weight residual 93.00 43.52 49.48 1 1.00e+01 1.00e-02 3.36e+01 dihedral pdb=" N PEE C 901 " pdb=" C4 PEE C 901 " pdb=" C5 PEE C 901 " pdb=" O4P PEE C 901 " ideal model delta sinusoidal sigma weight residual 303.03 129.17 173.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C2 PEE C 901 " pdb=" O3P PEE C 901 " ideal model delta sinusoidal sigma weight residual -59.96 111.18 -171.14 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 15839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3279 0.056 - 0.112: 646 0.112 - 0.168: 58 0.168 - 0.224: 6 0.224 - 0.280: 7 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CB VAL E 283 " pdb=" CA VAL E 283 " pdb=" CG1 VAL E 283 " pdb=" CG2 VAL E 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2 PEE F 901 " pdb=" C1 PEE F 901 " pdb=" C3 PEE F 901 " pdb=" O2 PEE F 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.61 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3993 not shown) Planarity restraints: 4352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 23 " -0.021 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP F 23 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP F 23 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 23 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 23 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 23 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 23 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 795 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A 796 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 796 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 796 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.017 2.00e-02 2.50e+03 1.67e-02 6.94e+00 pdb=" CG TRP C 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 ... (remaining 4349 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2120 2.74 - 3.28: 25690 3.28 - 3.82: 44795 3.82 - 4.36: 53560 4.36 - 4.90: 89751 Nonbonded interactions: 215916 Sorted by model distance: nonbonded pdb=" NE2 GLN A 46 " pdb=" O LYS A 123 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR B 351 " pdb=" OD2 ASP B 380 " model vdw 2.249 3.040 nonbonded pdb=" O ILE F 556 " pdb=" ND2 ASN F 584 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR E 303 " pdb=" OH TYR E 308 " model vdw 2.269 3.040 nonbonded pdb=" O PRO D 167 " pdb=" OG1 THR D 170 " model vdw 2.272 3.040 ... (remaining 215911 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 15 through 175 or resid 231 through 808 or resid 901 or (r \ esid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name O2 or name O4 )) or (resid 903 an \ d (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name \ C16 or name C17 or name O2 or name O4 )))) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 15 through 402 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name O2 or name O4 ) \ ))) selection = (chain 'D' and (resid 15 through 175 or resid 235 through 402 or resid 902)) selection = (chain 'E' and (resid 15 through 175 or resid 235 through 402 or resid 903)) } 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: 0.010 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 55.110 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 : 0.005 0.150 26291 Z= 0.241 Angle : 0.754 13.805 35542 Z= 0.412 Chirality : 0.044 0.280 3996 Planarity : 0.005 0.072 4352 Dihedral : 16.495 173.856 9821 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.28 % Allowed : 18.72 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3036 helix: 0.29 (0.12), residues: 1636 sheet: -1.73 (0.30), residues: 289 loop : -1.05 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 23 HIS 0.021 0.001 HIS D 155 PHE 0.034 0.002 PHE C 142 TYR 0.030 0.002 TYR E 281 ARG 0.009 0.001 ARG C 389 Details of bonding type rmsd hydrogen bonds : bond 0.15011 ( 1325) hydrogen bonds : angle 6.19983 ( 3708) SS BOND : bond 0.00287 ( 17) SS BOND : angle 1.09901 ( 34) covalent geometry : bond 0.00455 (26274) covalent geometry : angle 0.75338 (35508) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 533 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7284 (tp30) cc_final: 0.7041 (tp30) REVERT: A 233 ASP cc_start: 0.7744 (t0) cc_final: 0.7068 (t0) REVERT: A 343 MET cc_start: 0.8756 (ttm) cc_final: 0.8215 (ttm) REVERT: A 414 ASP cc_start: 0.9059 (m-30) cc_final: 0.8810 (t0) REVERT: A 478 HIS cc_start: 0.7250 (m170) cc_final: 0.6807 (m-70) REVERT: A 533 ARG cc_start: 0.6007 (ttt180) cc_final: 0.5123 (ptm160) REVERT: A 596 LEU cc_start: 0.6763 (tp) cc_final: 0.6312 (mt) REVERT: A 646 LEU cc_start: 0.9164 (mt) cc_final: 0.8907 (mm) REVERT: A 667 LEU cc_start: 0.8389 (tp) cc_final: 0.8188 (tt) REVERT: B 66 ASN cc_start: 0.5083 (t0) cc_final: 0.4880 (t0) REVERT: B 590 MET cc_start: 0.0815 (tpt) cc_final: 0.0520 (mmt) REVERT: B 687 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5694 (mt) REVERT: C 33 ILE cc_start: 0.8710 (tp) cc_final: 0.8473 (tt) REVERT: C 35 MET cc_start: 0.8212 (mtt) cc_final: 0.7978 (mtm) REVERT: C 59 TRP cc_start: 0.7967 (m100) cc_final: 0.7687 (m100) REVERT: C 286 VAL cc_start: 0.8530 (p) cc_final: 0.8295 (t) REVERT: C 337 MET cc_start: 0.6594 (tmm) cc_final: 0.6297 (tmm) REVERT: C 359 GLU cc_start: 0.5319 (tm-30) cc_final: 0.4938 (mt-10) REVERT: C 375 MET cc_start: 0.6787 (mtm) cc_final: 0.6559 (mtm) REVERT: C 385 LEU cc_start: 0.8123 (tp) cc_final: 0.7819 (tt) REVERT: D 46 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7131 (tt0) REVERT: D 127 TYR cc_start: 0.8621 (m-80) cc_final: 0.8380 (m-80) REVERT: E 265 MET cc_start: 0.7406 (ttp) cc_final: 0.7129 (tmm) REVERT: E 354 GLU cc_start: 0.7199 (pt0) cc_final: 0.6775 (mm-30) REVERT: F 96 MET cc_start: 0.7488 (mmm) cc_final: 0.7075 (mtt) REVERT: F 147 LYS cc_start: 0.4716 (mmmt) cc_final: 0.4481 (ptmt) REVERT: F 166 PHE cc_start: 0.6826 (t80) cc_final: 0.6620 (t80) REVERT: F 323 TYR cc_start: 0.8313 (t80) cc_final: 0.7796 (t80) outliers start: 8 outliers final: 2 residues processed: 540 average time/residue: 0.4924 time to fit residues: 393.9969 Evaluate side-chains 311 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain F residue 366 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 288 ASN D 400 ASN E 141 ASN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN F 406 ASN F 558 GLN F 635 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.197262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.142428 restraints weight = 41186.908| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.01 r_work: 0.3478 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26291 Z= 0.224 Angle : 0.662 15.623 35542 Z= 0.335 Chirality : 0.043 0.161 3996 Planarity : 0.005 0.082 4352 Dihedral : 8.732 163.098 3538 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.87 % Allowed : 20.12 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3036 helix: 0.56 (0.13), residues: 1685 sheet: -2.03 (0.29), residues: 302 loop : -1.18 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 168 HIS 0.011 0.001 HIS A 499 PHE 0.027 0.002 PHE E 324 TYR 0.020 0.002 TYR C 382 ARG 0.013 0.001 ARG B 417 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 1325) hydrogen bonds : angle 4.88700 ( 3708) SS BOND : bond 0.00521 ( 17) SS BOND : angle 1.47656 ( 34) covalent geometry : bond 0.00516 (26274) covalent geometry : angle 0.66032 (35508) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 338 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8057 (m-30) cc_final: 0.7848 (m-30) REVERT: A 434 MET cc_start: 0.8432 (mmm) cc_final: 0.8153 (mmm) REVERT: A 440 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: A 478 HIS cc_start: 0.6845 (m170) cc_final: 0.6560 (m90) REVERT: A 522 HIS cc_start: 0.7915 (m90) cc_final: 0.7549 (m90) REVERT: A 533 ARG cc_start: 0.5874 (ttt180) cc_final: 0.5075 (ptm160) REVERT: A 646 LEU cc_start: 0.9012 (mt) cc_final: 0.8750 (mm) REVERT: B 161 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8495 (mm) REVERT: B 590 MET cc_start: 0.2108 (tpt) cc_final: 0.1244 (mmt) REVERT: C 59 TRP cc_start: 0.8245 (m100) cc_final: 0.7975 (m100) REVERT: C 266 ARG cc_start: 0.6955 (mtt180) cc_final: 0.6198 (mtm-85) REVERT: C 337 MET cc_start: 0.6500 (tmm) cc_final: 0.6156 (tmm) REVERT: C 375 MET cc_start: 0.7035 (mtm) cc_final: 0.6689 (mtm) REVERT: D 46 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7527 (tt0) REVERT: D 143 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.7135 (t60) REVERT: D 250 PHE cc_start: 0.6626 (t80) cc_final: 0.6121 (t80) REVERT: D 375 MET cc_start: 0.7793 (mtm) cc_final: 0.7455 (mtm) REVERT: E 265 MET cc_start: 0.7780 (ttp) cc_final: 0.7384 (tmm) REVERT: E 354 GLU cc_start: 0.7029 (pt0) cc_final: 0.6606 (pm20) REVERT: E 375 MET cc_start: 0.7497 (mtm) cc_final: 0.7274 (mtt) REVERT: F 140 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7409 (mt) REVERT: F 147 LYS cc_start: 0.6089 (mmmt) cc_final: 0.4930 (ptmt) REVERT: F 242 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5758 (t80) REVERT: F 279 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (p90) REVERT: F 370 PHE cc_start: 0.7129 (t80) cc_final: 0.6734 (t80) REVERT: F 391 PHE cc_start: 0.4273 (m-10) cc_final: 0.3624 (m-80) REVERT: F 458 MET cc_start: 0.7987 (tpt) cc_final: 0.7724 (tpt) REVERT: F 687 TYR cc_start: 0.5410 (t80) cc_final: 0.4922 (t80) outliers start: 82 outliers final: 41 residues processed: 404 average time/residue: 0.3863 time to fit residues: 245.2229 Evaluate side-chains 332 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 679 LEU Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 9.9990 chunk 141 optimal weight: 0.0970 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A 755 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 HIS E 155 HIS E 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.196273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131994 restraints weight = 41041.127| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 4.76 r_work: 0.3409 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26291 Z= 0.209 Angle : 0.618 12.651 35542 Z= 0.316 Chirality : 0.043 0.325 3996 Planarity : 0.004 0.046 4352 Dihedral : 7.817 172.818 3534 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.39 % Allowed : 20.22 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3036 helix: 0.63 (0.13), residues: 1685 sheet: -1.97 (0.29), residues: 310 loop : -1.10 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 411 HIS 0.006 0.001 HIS F 475 PHE 0.029 0.002 PHE E 324 TYR 0.020 0.002 TYR F 323 ARG 0.006 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1325) hydrogen bonds : angle 4.71374 ( 3708) SS BOND : bond 0.00401 ( 17) SS BOND : angle 1.28391 ( 34) covalent geometry : bond 0.00486 (26274) covalent geometry : angle 0.61709 (35508) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 306 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8468 (mmm) cc_final: 0.8179 (mmm) REVERT: A 478 HIS cc_start: 0.7081 (m170) cc_final: 0.6799 (m170) REVERT: A 515 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7050 (mm) REVERT: A 522 HIS cc_start: 0.8145 (m90) cc_final: 0.7709 (m90) REVERT: A 533 ARG cc_start: 0.5918 (ttt180) cc_final: 0.5110 (ptm160) REVERT: A 555 LEU cc_start: 0.6672 (mp) cc_final: 0.6299 (mp) REVERT: A 646 LEU cc_start: 0.9007 (mt) cc_final: 0.8711 (mm) REVERT: B 17 TYR cc_start: 0.8635 (m-10) cc_final: 0.8358 (m-10) REVERT: B 396 GLU cc_start: 0.8069 (pp20) cc_final: 0.7867 (pp20) REVERT: B 590 MET cc_start: 0.2197 (tpt) cc_final: 0.1395 (mmt) REVERT: B 667 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7812 (tp) REVERT: B 749 ARG cc_start: 0.4948 (OUTLIER) cc_final: 0.4651 (tmm160) REVERT: C 59 TRP cc_start: 0.8286 (m100) cc_final: 0.7942 (m100) REVERT: C 266 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6227 (mtm-85) REVERT: C 375 MET cc_start: 0.7072 (mtm) cc_final: 0.6819 (mtm) REVERT: D 143 TRP cc_start: 0.7502 (OUTLIER) cc_final: 0.7297 (t60) REVERT: D 250 PHE cc_start: 0.6484 (t80) cc_final: 0.6126 (t80) REVERT: D 353 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6044 (m-80) REVERT: E 143 TRP cc_start: 0.7179 (t60) cc_final: 0.6887 (t60) REVERT: E 245 GLU cc_start: 0.8420 (tp30) cc_final: 0.7855 (tp30) REVERT: E 265 MET cc_start: 0.7843 (ttp) cc_final: 0.7390 (tmm) REVERT: E 354 GLU cc_start: 0.7058 (pt0) cc_final: 0.6583 (pm20) REVERT: E 375 MET cc_start: 0.7667 (mtm) cc_final: 0.7358 (mtm) REVERT: F 48 MET cc_start: 0.6987 (ptm) cc_final: 0.6695 (mtp) REVERT: F 140 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7478 (mt) REVERT: F 242 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5821 (t80) REVERT: F 279 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8392 (p90) REVERT: F 370 PHE cc_start: 0.7056 (t80) cc_final: 0.6761 (t80) REVERT: F 391 PHE cc_start: 0.4093 (m-10) cc_final: 0.3437 (m-80) REVERT: F 458 MET cc_start: 0.8099 (tpt) cc_final: 0.7850 (tpt) REVERT: F 472 LEU cc_start: 0.7723 (tt) cc_final: 0.6666 (mt) REVERT: F 616 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: F 800 MET cc_start: 0.4034 (mmt) cc_final: 0.3740 (mmt) outliers start: 97 outliers final: 54 residues processed: 375 average time/residue: 0.3644 time to fit residues: 216.9445 Evaluate side-chains 337 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 274 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 297 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 232 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 300 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 467 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 377 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.197244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.143492 restraints weight = 41234.044| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.96 r_work: 0.3512 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26291 Z= 0.135 Angle : 0.570 10.803 35542 Z= 0.289 Chirality : 0.041 0.284 3996 Planarity : 0.004 0.036 4352 Dihedral : 7.215 169.449 3534 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.11 % Allowed : 20.85 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3036 helix: 0.81 (0.13), residues: 1689 sheet: -1.82 (0.30), residues: 305 loop : -1.01 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 411 HIS 0.005 0.001 HIS E 253 PHE 0.029 0.001 PHE E 324 TYR 0.023 0.001 TYR F 323 ARG 0.010 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 1325) hydrogen bonds : angle 4.50826 ( 3708) SS BOND : bond 0.00296 ( 17) SS BOND : angle 1.04294 ( 34) covalent geometry : bond 0.00305 (26274) covalent geometry : angle 0.56911 (35508) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 295 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8192 (m-30) cc_final: 0.7985 (m-30) REVERT: A 512 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7936 (pt) REVERT: A 522 HIS cc_start: 0.7991 (m90) cc_final: 0.7527 (m90) REVERT: A 533 ARG cc_start: 0.5669 (ttt180) cc_final: 0.4821 (ptm160) REVERT: A 544 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.4286 (ptpp) REVERT: B 590 MET cc_start: 0.2127 (tpt) cc_final: 0.1543 (mmt) REVERT: B 667 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7880 (tp) REVERT: B 779 LEU cc_start: 0.2736 (OUTLIER) cc_final: 0.2136 (tp) REVERT: C 59 TRP cc_start: 0.8278 (m100) cc_final: 0.7947 (m100) REVERT: C 266 ARG cc_start: 0.7007 (mtt180) cc_final: 0.4982 (ttp80) REVERT: D 46 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D 143 TRP cc_start: 0.7410 (OUTLIER) cc_final: 0.7104 (t60) REVERT: D 250 PHE cc_start: 0.6369 (t80) cc_final: 0.6121 (t80) REVERT: D 375 MET cc_start: 0.7671 (mtm) cc_final: 0.7287 (mtm) REVERT: D 404 GLN cc_start: 0.7221 (tm-30) cc_final: 0.7005 (tp40) REVERT: E 265 MET cc_start: 0.7731 (ttp) cc_final: 0.7513 (tmm) REVERT: E 354 GLU cc_start: 0.7036 (pt0) cc_final: 0.6623 (pm20) REVERT: F 140 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7568 (mt) REVERT: F 170 TRP cc_start: 0.6878 (t-100) cc_final: 0.6420 (t-100) REVERT: F 242 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.5825 (t80) REVERT: F 261 MET cc_start: 0.7381 (ttp) cc_final: 0.7179 (ttp) REVERT: F 279 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8353 (p90) REVERT: F 370 PHE cc_start: 0.7084 (t80) cc_final: 0.6729 (t80) REVERT: F 458 MET cc_start: 0.7977 (tpt) cc_final: 0.7719 (tpt) REVERT: F 472 LEU cc_start: 0.7559 (tt) cc_final: 0.6565 (mt) REVERT: F 475 HIS cc_start: 0.5626 (m90) cc_final: 0.5411 (m90) REVERT: F 616 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: F 654 GLU cc_start: 0.4579 (tp30) cc_final: 0.3461 (tp30) REVERT: F 800 MET cc_start: 0.3847 (mmt) cc_final: 0.3473 (mmt) outliers start: 89 outliers final: 49 residues processed: 361 average time/residue: 0.3630 time to fit residues: 210.9617 Evaluate side-chains 329 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 287 optimal weight: 0.0060 chunk 95 optimal weight: 0.5980 chunk 201 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.197386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.143848 restraints weight = 41337.342| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.29 r_work: 0.3469 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26291 Z= 0.132 Angle : 0.580 15.135 35542 Z= 0.290 Chirality : 0.041 0.276 3996 Planarity : 0.004 0.079 4352 Dihedral : 6.860 170.019 3534 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.57 % Allowed : 20.75 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3036 helix: 0.84 (0.13), residues: 1695 sheet: -1.77 (0.30), residues: 304 loop : -0.93 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 411 HIS 0.005 0.001 HIS E 253 PHE 0.029 0.001 PHE E 324 TYR 0.023 0.001 TYR A 689 ARG 0.012 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 1325) hydrogen bonds : angle 4.43201 ( 3708) SS BOND : bond 0.00283 ( 17) SS BOND : angle 1.01218 ( 34) covalent geometry : bond 0.00297 (26274) covalent geometry : angle 0.57969 (35508) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 290 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8267 (mmm) cc_final: 0.8012 (mmm) REVERT: A 506 LYS cc_start: 0.7663 (tptp) cc_final: 0.7106 (pttp) REVERT: A 512 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7907 (pt) REVERT: A 515 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6767 (mm) REVERT: A 522 HIS cc_start: 0.8148 (m90) cc_final: 0.7584 (m90) REVERT: A 533 ARG cc_start: 0.5798 (ttt180) cc_final: 0.4923 (ptm160) REVERT: A 544 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.4636 (ptpp) REVERT: A 646 LEU cc_start: 0.8647 (mm) cc_final: 0.8193 (mm) REVERT: B 286 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8488 (t) REVERT: B 590 MET cc_start: 0.2338 (tpt) cc_final: 0.1641 (mmt) REVERT: B 614 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5826 (m-70) REVERT: B 667 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8102 (tp) REVERT: C 59 TRP cc_start: 0.8240 (m100) cc_final: 0.7927 (m100) REVERT: C 266 ARG cc_start: 0.7031 (mtt180) cc_final: 0.4997 (ttp80) REVERT: C 319 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7912 (tttt) REVERT: D 143 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.7098 (t60) REVERT: D 250 PHE cc_start: 0.6392 (t80) cc_final: 0.6127 (t80) REVERT: E 265 MET cc_start: 0.7769 (ttp) cc_final: 0.7412 (tmm) REVERT: E 354 GLU cc_start: 0.7079 (pt0) cc_final: 0.6615 (pm20) REVERT: F 140 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7536 (mt) REVERT: F 145 TRP cc_start: 0.5682 (OUTLIER) cc_final: 0.4497 (t60) REVERT: F 242 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5733 (t80) REVERT: F 261 MET cc_start: 0.7347 (ttp) cc_final: 0.7070 (ttt) REVERT: F 370 PHE cc_start: 0.7049 (t80) cc_final: 0.6698 (t80) REVERT: F 458 MET cc_start: 0.8049 (tpt) cc_final: 0.7798 (tpt) REVERT: F 472 LEU cc_start: 0.7562 (tt) cc_final: 0.6610 (mt) REVERT: F 616 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: F 654 GLU cc_start: 0.4588 (tp30) cc_final: 0.3663 (tp30) REVERT: F 800 MET cc_start: 0.4052 (mmt) cc_final: 0.3735 (mmt) outliers start: 102 outliers final: 58 residues processed: 364 average time/residue: 0.3557 time to fit residues: 208.8027 Evaluate side-chains 334 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 264 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 199 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 300 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 135 optimal weight: 0.0670 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS ** F 670 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 = 0.4550 r_free = 0.4550 target = 0.195991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.129994 restraints weight = 40977.370| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.37 r_work: 0.3393 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26291 Z= 0.172 Angle : 0.598 14.559 35542 Z= 0.301 Chirality : 0.042 0.276 3996 Planarity : 0.004 0.053 4352 Dihedral : 6.814 171.173 3534 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.02 % Allowed : 20.29 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3036 helix: 0.85 (0.13), residues: 1679 sheet: -1.84 (0.30), residues: 311 loop : -0.92 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 411 HIS 0.005 0.001 HIS E 253 PHE 0.032 0.001 PHE E 324 TYR 0.024 0.002 TYR A 648 ARG 0.008 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 1325) hydrogen bonds : angle 4.45377 ( 3708) SS BOND : bond 0.00357 ( 17) SS BOND : angle 1.10183 ( 34) covalent geometry : bond 0.00401 (26274) covalent geometry : angle 0.59737 (35508) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 292 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8301 (mmm) cc_final: 0.8055 (mmm) REVERT: A 506 LYS cc_start: 0.7703 (tptp) cc_final: 0.7299 (pttp) REVERT: A 512 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7937 (pt) REVERT: A 522 HIS cc_start: 0.8230 (m90) cc_final: 0.7661 (m90) REVERT: A 533 ARG cc_start: 0.5878 (ttt180) cc_final: 0.4951 (ptm160) REVERT: A 590 MET cc_start: 0.4798 (mmm) cc_final: 0.4581 (mmm) REVERT: A 646 LEU cc_start: 0.8689 (mm) cc_final: 0.8374 (mm) REVERT: A 712 ASN cc_start: 0.8970 (m-40) cc_final: 0.8042 (p0) REVERT: B 454 GLU cc_start: 0.8427 (tt0) cc_final: 0.7727 (tp30) REVERT: B 456 ILE cc_start: 0.7971 (mm) cc_final: 0.7461 (tt) REVERT: B 590 MET cc_start: 0.2975 (tpt) cc_final: 0.2158 (mmt) REVERT: C 30 TYR cc_start: 0.7058 (m-10) cc_final: 0.6635 (t80) REVERT: C 59 TRP cc_start: 0.8193 (m100) cc_final: 0.7853 (m100) REVERT: C 168 TRP cc_start: 0.6320 (t-100) cc_final: 0.6087 (t-100) REVERT: C 266 ARG cc_start: 0.6859 (mtt180) cc_final: 0.4881 (ttp80) REVERT: C 319 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7862 (tttt) REVERT: D 143 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (t60) REVERT: D 250 PHE cc_start: 0.6423 (t80) cc_final: 0.6193 (t80) REVERT: D 325 TYR cc_start: 0.8255 (t80) cc_final: 0.8012 (t80) REVERT: D 353 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: E 265 MET cc_start: 0.7596 (ttp) cc_final: 0.7234 (tmm) REVERT: E 354 GLU cc_start: 0.7084 (pt0) cc_final: 0.6614 (pm20) REVERT: F 140 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7473 (mt) REVERT: F 170 TRP cc_start: 0.7198 (t-100) cc_final: 0.6816 (t-100) REVERT: F 242 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5823 (t80) REVERT: F 370 PHE cc_start: 0.7079 (t80) cc_final: 0.6701 (t80) REVERT: F 458 MET cc_start: 0.8201 (tpt) cc_final: 0.7992 (tpt) REVERT: F 472 LEU cc_start: 0.7602 (tt) cc_final: 0.6708 (mt) REVERT: F 616 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: F 654 GLU cc_start: 0.4986 (tp30) cc_final: 0.4150 (tp30) REVERT: F 800 MET cc_start: 0.4186 (mmt) cc_final: 0.3962 (mmt) outliers start: 115 outliers final: 77 residues processed: 382 average time/residue: 0.3473 time to fit residues: 216.5528 Evaluate side-chains 359 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 275 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 568 HIS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 652 ILE Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 766 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 292 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 277 optimal weight: 20.0000 chunk 236 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 GLN E 155 HIS F 606 HIS F 670 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.196131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.141346 restraints weight = 41056.584| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.93 r_work: 0.3484 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26291 Z= 0.161 Angle : 0.592 15.710 35542 Z= 0.295 Chirality : 0.041 0.275 3996 Planarity : 0.004 0.037 4352 Dihedral : 6.712 171.027 3534 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.53 % Allowed : 20.99 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3036 helix: 0.92 (0.13), residues: 1661 sheet: -1.73 (0.30), residues: 316 loop : -0.84 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 411 HIS 0.006 0.001 HIS A 431 PHE 0.038 0.001 PHE A 443 TYR 0.029 0.001 TYR F 323 ARG 0.010 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 1325) hydrogen bonds : angle 4.42031 ( 3708) SS BOND : bond 0.00324 ( 17) SS BOND : angle 1.05015 ( 34) covalent geometry : bond 0.00375 (26274) covalent geometry : angle 0.59156 (35508) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 288 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4868 (tp) REVERT: A 448 LEU cc_start: 0.7864 (mt) cc_final: 0.7426 (mt) REVERT: A 506 LYS cc_start: 0.7669 (tptp) cc_final: 0.7402 (pttp) REVERT: A 511 TRP cc_start: 0.6632 (m100) cc_final: 0.6277 (m-90) REVERT: A 522 HIS cc_start: 0.8191 (m90) cc_final: 0.7606 (m90) REVERT: A 533 ARG cc_start: 0.5739 (ttt180) cc_final: 0.4894 (ptm160) REVERT: A 544 LYS cc_start: 0.5525 (OUTLIER) cc_final: 0.4855 (mmtt) REVERT: A 646 LEU cc_start: 0.8583 (mm) cc_final: 0.8269 (mm) REVERT: A 712 ASN cc_start: 0.8692 (m-40) cc_final: 0.7550 (p0) REVERT: B 286 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8405 (t) REVERT: B 454 GLU cc_start: 0.8249 (tt0) cc_final: 0.7686 (tp30) REVERT: B 455 LEU cc_start: 0.8592 (pp) cc_final: 0.7989 (pp) REVERT: B 456 ILE cc_start: 0.7873 (mm) cc_final: 0.7351 (tt) REVERT: B 590 MET cc_start: 0.2604 (tpt) cc_final: 0.2257 (mmm) REVERT: B 614 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.5731 (m-70) REVERT: C 59 TRP cc_start: 0.8196 (m100) cc_final: 0.7845 (m100) REVERT: C 266 ARG cc_start: 0.7019 (mtt180) cc_final: 0.5000 (ttp80) REVERT: C 319 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7868 (tttt) REVERT: D 143 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.7064 (t60) REVERT: E 265 MET cc_start: 0.7748 (ttp) cc_final: 0.7250 (tmm) REVERT: F 140 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7518 (mt) REVERT: F 145 TRP cc_start: 0.5749 (OUTLIER) cc_final: 0.4547 (t60) REVERT: F 170 TRP cc_start: 0.7233 (t-100) cc_final: 0.7002 (t-100) REVERT: F 242 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.5965 (t80) REVERT: F 370 PHE cc_start: 0.7124 (t80) cc_final: 0.6662 (t80) REVERT: F 458 MET cc_start: 0.7993 (tpt) cc_final: 0.7741 (tpt) REVERT: F 472 LEU cc_start: 0.7574 (tt) cc_final: 0.6630 (mt) REVERT: F 616 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: F 800 MET cc_start: 0.4392 (mmt) cc_final: 0.4072 (mmt) outliers start: 101 outliers final: 72 residues processed: 363 average time/residue: 0.3452 time to fit residues: 205.0973 Evaluate side-chains 351 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 456 ASN Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 766 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 103 optimal weight: 6.9990 chunk 267 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 272 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN E 155 HIS E 381 GLN F 402 GLN F 456 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.196065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131605 restraints weight = 40780.468| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.08 r_work: 0.3384 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26291 Z= 0.164 Angle : 0.614 19.762 35542 Z= 0.302 Chirality : 0.042 0.283 3996 Planarity : 0.004 0.039 4352 Dihedral : 6.641 170.979 3534 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.36 % Allowed : 21.59 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3036 helix: 0.87 (0.13), residues: 1670 sheet: -1.67 (0.30), residues: 315 loop : -0.78 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 168 HIS 0.005 0.001 HIS B 499 PHE 0.043 0.001 PHE A 443 TYR 0.031 0.002 TYR F 323 ARG 0.008 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1325) hydrogen bonds : angle 4.40150 ( 3708) SS BOND : bond 0.00329 ( 17) SS BOND : angle 1.04551 ( 34) covalent geometry : bond 0.00384 (26274) covalent geometry : angle 0.61303 (35508) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 284 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7998 (mt) cc_final: 0.7466 (mt) REVERT: A 506 LYS cc_start: 0.7946 (tptp) cc_final: 0.7542 (pttp) REVERT: A 511 TRP cc_start: 0.6896 (m100) cc_final: 0.6513 (m-90) REVERT: A 522 HIS cc_start: 0.8306 (m90) cc_final: 0.7700 (m90) REVERT: A 533 ARG cc_start: 0.5835 (ttt180) cc_final: 0.4989 (ptm160) REVERT: A 544 LYS cc_start: 0.5681 (OUTLIER) cc_final: 0.5008 (mmtt) REVERT: A 646 LEU cc_start: 0.8613 (mm) cc_final: 0.8352 (mm) REVERT: B 286 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8511 (t) REVERT: B 454 GLU cc_start: 0.8420 (tt0) cc_final: 0.7768 (tp30) REVERT: B 455 LEU cc_start: 0.8714 (pp) cc_final: 0.8105 (pp) REVERT: B 456 ILE cc_start: 0.8006 (mm) cc_final: 0.7591 (tt) REVERT: B 590 MET cc_start: 0.2800 (tpt) cc_final: 0.2302 (mmm) REVERT: B 614 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.5889 (m-70) REVERT: C 59 TRP cc_start: 0.8220 (m100) cc_final: 0.7899 (m100) REVERT: C 266 ARG cc_start: 0.7026 (mtt180) cc_final: 0.4930 (ttp80) REVERT: C 319 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7883 (tttt) REVERT: D 143 TRP cc_start: 0.7575 (OUTLIER) cc_final: 0.7240 (t60) REVERT: D 353 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: D 375 MET cc_start: 0.7780 (mtm) cc_final: 0.7124 (mtm) REVERT: E 265 MET cc_start: 0.7866 (ttp) cc_final: 0.7359 (tmm) REVERT: E 375 MET cc_start: 0.7594 (mtm) cc_final: 0.7337 (ptp) REVERT: F 140 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7488 (mt) REVERT: F 145 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.4817 (t60) REVERT: F 170 TRP cc_start: 0.7491 (t-100) cc_final: 0.7214 (t-100) REVERT: F 242 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5901 (t80) REVERT: F 370 PHE cc_start: 0.7070 (t80) cc_final: 0.6596 (t80) REVERT: F 458 MET cc_start: 0.8162 (tpt) cc_final: 0.7942 (tpt) REVERT: F 472 LEU cc_start: 0.7721 (tt) cc_final: 0.6912 (mt) REVERT: F 616 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: F 654 GLU cc_start: 0.4596 (tp30) cc_final: 0.3461 (tp30) REVERT: F 800 MET cc_start: 0.4508 (mmt) cc_final: 0.4235 (mmt) outliers start: 96 outliers final: 76 residues processed: 356 average time/residue: 0.3392 time to fit residues: 197.3437 Evaluate side-chains 365 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 279 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 573 HIS Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 766 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 267 optimal weight: 0.0970 chunk 236 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 129 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN E 155 HIS ** F 113 GLN ** 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 = 0.4563 r_free = 0.4563 target = 0.197203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141983 restraints weight = 41010.728| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.02 r_work: 0.3495 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26291 Z= 0.122 Angle : 0.580 14.853 35542 Z= 0.286 Chirality : 0.041 0.241 3996 Planarity : 0.004 0.038 4352 Dihedral : 6.424 170.566 3534 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.76 % Allowed : 22.29 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 3036 helix: 0.97 (0.13), residues: 1671 sheet: -1.50 (0.31), residues: 310 loop : -0.73 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 168 HIS 0.005 0.001 HIS A 431 PHE 0.031 0.001 PHE E 324 TYR 0.033 0.001 TYR F 323 ARG 0.007 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 1325) hydrogen bonds : angle 4.28967 ( 3708) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.93346 ( 34) covalent geometry : bond 0.00276 (26274) covalent geometry : angle 0.57942 (35508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 298 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7838 (mt) cc_final: 0.7366 (mt) REVERT: A 511 TRP cc_start: 0.6759 (m100) cc_final: 0.6367 (m-90) REVERT: A 515 LEU cc_start: 0.7404 (mm) cc_final: 0.7092 (mm) REVERT: A 522 HIS cc_start: 0.8244 (m90) cc_final: 0.7666 (m90) REVERT: A 527 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6710 (mp) REVERT: A 533 ARG cc_start: 0.5766 (ttt180) cc_final: 0.4889 (ptm160) REVERT: A 544 LYS cc_start: 0.5465 (OUTLIER) cc_final: 0.4861 (mmtt) REVERT: A 646 LEU cc_start: 0.8533 (mm) cc_final: 0.8258 (mm) REVERT: A 749 ARG cc_start: 0.6267 (mtp180) cc_final: 0.6020 (mtp85) REVERT: B 286 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8396 (t) REVERT: B 454 GLU cc_start: 0.8303 (tt0) cc_final: 0.7802 (tp30) REVERT: B 455 LEU cc_start: 0.8647 (pp) cc_final: 0.8396 (pp) REVERT: B 456 ILE cc_start: 0.7860 (mm) cc_final: 0.7348 (tt) REVERT: B 590 MET cc_start: 0.3052 (tpt) cc_final: 0.2546 (mmm) REVERT: B 614 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.5745 (m-70) REVERT: C 59 TRP cc_start: 0.8222 (m100) cc_final: 0.7907 (m100) REVERT: C 266 ARG cc_start: 0.7082 (mtt180) cc_final: 0.5038 (ttp80) REVERT: C 319 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7861 (tttt) REVERT: D 143 TRP cc_start: 0.7442 (OUTLIER) cc_final: 0.7048 (t60) REVERT: D 250 PHE cc_start: 0.6617 (t80) cc_final: 0.6336 (t80) REVERT: E 265 MET cc_start: 0.7718 (ttp) cc_final: 0.7294 (tmm) REVERT: F 140 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7620 (mt) REVERT: F 145 TRP cc_start: 0.5617 (OUTLIER) cc_final: 0.4845 (t60) REVERT: F 170 TRP cc_start: 0.7386 (t-100) cc_final: 0.7159 (t-100) REVERT: F 242 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6003 (t80) REVERT: F 370 PHE cc_start: 0.7132 (t80) cc_final: 0.6619 (t80) REVERT: F 458 MET cc_start: 0.7963 (tpt) cc_final: 0.7745 (tpt) REVERT: F 472 LEU cc_start: 0.7586 (tt) cc_final: 0.6675 (mt) REVERT: F 616 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: F 654 GLU cc_start: 0.4264 (tp30) cc_final: 0.3073 (tp30) REVERT: F 800 MET cc_start: 0.4349 (mmt) cc_final: 0.4049 (mmt) outliers start: 79 outliers final: 57 residues processed: 358 average time/residue: 0.3503 time to fit residues: 203.7736 Evaluate side-chains 343 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 753 PHE Chi-restraints excluded: chain F residue 766 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 chunk 286 optimal weight: 0.4980 chunk 157 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS A 532 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 ASN E 155 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.196824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132595 restraints weight = 40799.171| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 4.38 r_work: 0.3406 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26291 Z= 0.135 Angle : 0.592 14.476 35542 Z= 0.294 Chirality : 0.041 0.244 3996 Planarity : 0.004 0.042 4352 Dihedral : 6.355 170.540 3534 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.45 % Allowed : 22.99 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 3036 helix: 0.94 (0.13), residues: 1669 sheet: -1.44 (0.31), residues: 313 loop : -0.68 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 411 HIS 0.005 0.001 HIS B 499 PHE 0.036 0.001 PHE F 166 TYR 0.031 0.001 TYR F 323 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 1325) hydrogen bonds : angle 4.27271 ( 3708) SS BOND : bond 0.00284 ( 17) SS BOND : angle 0.99073 ( 34) covalent geometry : bond 0.00310 (26274) covalent geometry : angle 0.59111 (35508) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.7767 (mt) cc_final: 0.7300 (mt) REVERT: A 511 TRP cc_start: 0.7030 (m100) cc_final: 0.6563 (m-90) REVERT: A 515 LEU cc_start: 0.7634 (mm) cc_final: 0.7301 (mm) REVERT: A 522 HIS cc_start: 0.8297 (m90) cc_final: 0.7703 (m90) REVERT: A 533 ARG cc_start: 0.5776 (ttt180) cc_final: 0.4886 (ptm160) REVERT: A 544 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.4927 (mmtt) REVERT: A 646 LEU cc_start: 0.8569 (mm) cc_final: 0.8322 (mm) REVERT: A 749 ARG cc_start: 0.6547 (mtp180) cc_final: 0.6297 (mtp85) REVERT: B 286 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8459 (t) REVERT: B 456 ILE cc_start: 0.8035 (mm) cc_final: 0.7642 (tt) REVERT: B 590 MET cc_start: 0.3369 (tpt) cc_final: 0.2768 (mmm) REVERT: B 614 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5900 (m-70) REVERT: C 59 TRP cc_start: 0.8236 (m100) cc_final: 0.7916 (m100) REVERT: C 241 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7244 (mmtm) REVERT: C 266 ARG cc_start: 0.7129 (mtt180) cc_final: 0.5037 (ttp80) REVERT: C 319 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7916 (tttt) REVERT: D 143 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.7114 (t60) REVERT: D 250 PHE cc_start: 0.6557 (t80) cc_final: 0.6317 (t80) REVERT: D 375 MET cc_start: 0.7781 (mtm) cc_final: 0.7447 (mtm) REVERT: E 265 MET cc_start: 0.7827 (ttp) cc_final: 0.7347 (tmm) REVERT: E 375 MET cc_start: 0.7665 (mtm) cc_final: 0.7217 (ptp) REVERT: F 140 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7599 (mt) REVERT: F 145 TRP cc_start: 0.5842 (OUTLIER) cc_final: 0.4929 (t60) REVERT: F 170 TRP cc_start: 0.7663 (t-100) cc_final: 0.7442 (t-100) REVERT: F 242 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5994 (t80) REVERT: F 370 PHE cc_start: 0.7122 (t80) cc_final: 0.6596 (t80) REVERT: F 472 LEU cc_start: 0.7767 (tt) cc_final: 0.6882 (mt) REVERT: F 616 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: F 654 GLU cc_start: 0.4574 (tp30) cc_final: 0.3417 (mm-30) REVERT: F 800 MET cc_start: 0.4464 (mmt) cc_final: 0.4195 (mmt) outliers start: 70 outliers final: 56 residues processed: 336 average time/residue: 0.3448 time to fit residues: 189.5501 Evaluate side-chains 341 residues out of total 2858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 143 TRP Chi-restraints excluded: chain E residue 144 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 644 LEU Chi-restraints excluded: chain F residue 645 TRP Chi-restraints excluded: chain F residue 766 VAL Chi-restraints excluded: chain F residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS E 155 HIS ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 GLN F 598 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.196683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.140431 restraints weight = 40903.267| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.14 r_work: 0.3469 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26291 Z= 0.138 Angle : 0.599 14.790 35542 Z= 0.297 Chirality : 0.041 0.244 3996 Planarity : 0.004 0.044 4352 Dihedral : 6.318 170.627 3534 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.62 % Allowed : 22.99 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 3036 helix: 0.92 (0.13), residues: 1665 sheet: -1.51 (0.30), residues: 323 loop : -0.62 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 411 HIS 0.006 0.001 HIS B 499 PHE 0.056 0.001 PHE A 443 TYR 0.039 0.001 TYR D 325 ARG 0.006 0.000 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1325) hydrogen bonds : angle 4.24697 ( 3708) SS BOND : bond 0.00286 ( 17) SS BOND : angle 0.99295 ( 34) covalent geometry : bond 0.00320 (26274) covalent geometry : angle 0.59831 (35508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20788.66 seconds wall clock time: 358 minutes 23.52 seconds (21503.52 seconds total)