Starting phenix.real_space_refine on Wed Jun 25 07:47:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.map" model { file = "/net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8diu_27443/06_2025/8diu_27443.cif" } resolution = 2.61 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15044 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10755 2.51 5 N 2853 2.21 5 O 3539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17228 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3853 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.27, per 1000 atoms: 0.60 Number of scatterers: 17228 At special positions: 0 Unit cell: (128.25, 135.675, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3539 8.00 N 2853 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 492 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 40 " " NAG A 603 " - " ASN A 71 " " NAG A 604 " - " ASN A 142 " " NAG A 605 " - " ASN A 177 " " NAG A 606 " - " ASN A 286 " " NAG A 607 " - " ASN A 498 " " NAG B 601 " - " ASN B 28 " " NAG B 602 " - " ASN B 40 " " NAG B 603 " - " ASN B 71 " " NAG B 604 " - " ASN B 142 " " NAG B 605 " - " ASN B 177 " " NAG B 606 " - " ASN B 286 " " NAG B 607 " - " ASN B 498 " " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 40 " " NAG D 603 " - " ASN D 71 " " NAG D 604 " - " ASN D 142 " " NAG D 605 " - " ASN D 177 " " NAG D 606 " - " ASN D 286 " " NAG D 607 " - " ASN D 498 " " NAG J 1 " - " ASN D 104 " " NAG K 1 " - " ASN D 304 " " NAG L 1 " - " ASN A 104 " " NAG M 1 " - " ASN A 304 " " NAG N 1 " - " ASN B 104 " " NAG O 1 " - " ASN B 304 " Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.2 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 51 sheets defined 18.5% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 81 through 89 removed outlier: 4.057A pdb=" N GLU D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 201 through 210 Processing helix chain 'D' and resid 381 through 403 removed outlier: 3.502A pdb=" N THR D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 471 removed outlier: 3.759A pdb=" N GLU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.647A pdb=" N PHE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.513A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 471 removed outlier: 3.749A pdb=" N GLU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.637A pdb=" N PHE B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 381 through 403 removed outlier: 3.749A pdb=" N MET B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 471 removed outlier: 3.763A pdb=" N GLU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.779A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.861A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.912A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.573A pdb=" N GLU I 84 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 375 through 380 Processing sheet with id=AA2, first strand: chain 'D' and resid 31 through 32 removed outlier: 4.621A pdb=" N ASP D 31 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'D' and resid 57 through 61 removed outlier: 5.166A pdb=" N ARG D 60 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS D 292 " --> pdb=" O ARG D 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.535A pdb=" N LEU D 67 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 132 removed outlier: 7.055A pdb=" N SER D 275 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE D 128 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA D 273 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 130 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 271 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 125 through 132 removed outlier: 7.055A pdb=" N SER D 275 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE D 128 " --> pdb=" O ALA D 273 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA D 273 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 130 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 271 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 155 removed outlier: 4.766A pdb=" N CYS D 153 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 160 " --> pdb=" O CYS D 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 183 removed outlier: 3.510A pdb=" N LEU D 178 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 302 through 303 removed outlier: 3.501A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB4, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.602A pdb=" N ASP A 31 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB6, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'A' and resid 57 through 61 removed outlier: 5.117A pdb=" N ARG A 60 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS A 292 " --> pdb=" O ARG A 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.546A pdb=" N LEU A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 125 through 132 removed outlier: 7.066A pdb=" N SER A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 125 through 132 removed outlier: 7.066A pdb=" N SER A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.761A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 160 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 178 through 183 removed outlier: 3.505A pdb=" N ALA A 261 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 302 through 303 removed outlier: 3.633A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC6, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.617A pdb=" N ASP B 31 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AC8, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'B' and resid 57 through 61 removed outlier: 5.207A pdb=" N ARG B 60 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS B 292 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.550A pdb=" N LEU B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 96 " --> pdb=" O ILE B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 125 through 132 removed outlier: 7.063A pdb=" N SER B 275 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B 128 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 273 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG B 130 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 271 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 270 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 193 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 193 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 125 through 132 removed outlier: 7.063A pdb=" N SER B 275 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B 128 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 273 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG B 130 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 271 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR B 270 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 193 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 150 through 155 removed outlier: 4.762A pdb=" N CYS B 153 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 160 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'B' and resid 302 through 303 removed outlier: 3.506A pdb=" N CYS B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.679A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.895A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.910A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.738A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.918A pdb=" N VAL H 110 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.760A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.760A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.749A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.749A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.786A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.786A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 18 through 22 653 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.45 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5478 1.34 - 1.47: 4467 1.47 - 1.59: 7434 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 17493 Sorted by residual: bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.44e+00 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.83e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG B 606 " pdb=" O5 NAG B 606 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 ... (remaining 17488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 23044 1.80 - 3.59: 623 3.59 - 5.39: 74 5.39 - 7.18: 10 7.18 - 8.98: 9 Bond angle restraints: 23760 Sorted by residual: angle pdb=" N ASN D 104 " pdb=" CA ASN D 104 " pdb=" C ASN D 104 " ideal model delta sigma weight residual 108.02 114.86 -6.84 1.75e+00 3.27e-01 1.53e+01 angle pdb=" C ASN A 142 " pdb=" N HIS A 143 " pdb=" CA HIS A 143 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 angle pdb=" C ASN D 142 " pdb=" N HIS D 143 " pdb=" CA HIS D 143 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ASN B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta sigma weight residual 121.54 128.73 -7.19 1.91e+00 2.74e-01 1.42e+01 angle pdb=" C ASP C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.56e+00 ... (remaining 23755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9582 21.78 - 43.57: 864 43.57 - 65.35: 284 65.35 - 87.14: 46 87.14 - 108.92: 12 Dihedral angle restraints: 10788 sinusoidal: 4641 harmonic: 6147 Sorted by residual: dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual -86.00 -19.35 -66.65 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 292 " pdb=" CB CYS D 292 " ideal model delta sinusoidal sigma weight residual -86.00 -21.43 -64.57 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CA ILE D 303 " pdb=" C ILE D 303 " pdb=" N ASN D 304 " pdb=" CA ASN D 304 " ideal model delta harmonic sigma weight residual 180.00 147.60 32.40 0 5.00e+00 4.00e-02 4.20e+01 ... (remaining 10785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2170 0.059 - 0.119: 462 0.119 - 0.178: 31 0.178 - 0.237: 2 0.237 - 0.297: 5 Chirality restraints: 2670 Sorted by residual: chirality pdb=" CA ASN D 104 " pdb=" N ASN D 104 " pdb=" C ASN D 104 " pdb=" CB ASN D 104 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D 104 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2667 not shown) Planarity restraints: 3057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 503 " 0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 504 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 104 " -0.027 2.00e-02 2.50e+03 2.53e-02 8.01e+00 pdb=" CG ASN B 104 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 104 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 104 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 177 " 0.021 2.00e-02 2.50e+03 1.91e-02 4.54e+00 pdb=" CG ASN A 177 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 177 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 177 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 605 " 0.020 2.00e-02 2.50e+03 ... (remaining 3054 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3398 2.78 - 3.31: 13857 3.31 - 3.84: 27069 3.84 - 4.37: 33657 4.37 - 4.90: 58903 Nonbonded interactions: 136884 Sorted by model distance: nonbonded pdb=" OD1 ASN B 472 " pdb=" OH TYR B 503 " model vdw 2.248 3.040 nonbonded pdb=" OD1 ASN D 472 " pdb=" OH TYR D 503 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASN B 71 " pdb=" N2 NAG B 603 " model vdw 2.252 3.120 nonbonded pdb=" O LYS G 13 " pdb=" OG SER G 16 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP A 453 " pdb=" O HOH A 701 " model vdw 2.259 3.040 ... (remaining 136879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 44.620 Find NCS groups from input model: 0.720 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 : 0.004 0.047 17552 Z= 0.197 Angle : 0.718 10.017 23914 Z= 0.364 Chirality : 0.048 0.297 2670 Planarity : 0.005 0.086 3030 Dihedral : 18.251 108.920 6819 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.15 % Favored : 96.43 % Rotamer: Outliers : 3.53 % Allowed : 24.03 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2127 helix: 2.04 (0.29), residues: 345 sheet: 0.91 (0.21), residues: 615 loop : -1.17 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.005 0.001 HIS A 25 PHE 0.016 0.002 PHE B 128 TYR 0.013 0.001 TYR F 99 ARG 0.006 0.000 ARG B 325 Details of bonding type rmsd link_NAG-ASN : bond 0.01016 ( 27) link_NAG-ASN : angle 2.96903 ( 81) link_BETA1-4 : bond 0.00595 ( 9) link_BETA1-4 : angle 2.20504 ( 27) hydrogen bonds : bond 0.14809 ( 617) hydrogen bonds : angle 5.73456 ( 1710) SS BOND : bond 0.00396 ( 23) SS BOND : angle 1.22928 ( 46) covalent geometry : bond 0.00423 (17493) covalent geometry : angle 0.69275 (23760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: B 295 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7977 (ptmt) REVERT: C 32 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6246 (m-30) REVERT: F 32 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6138 (m-30) REVERT: I 32 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6120 (m-30) outliers start: 63 outliers final: 55 residues processed: 207 average time/residue: 1.0724 time to fit residues: 253.1496 Evaluate side-chains 199 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 140 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 492 CYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 0.0030 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 ASN D 404 ASN D 469 GLN A 201 ASN A 469 GLN B 201 ASN B 469 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103007 restraints weight = 19982.502| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.27 r_work: 0.3158 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17552 Z= 0.125 Angle : 0.617 9.491 23914 Z= 0.310 Chirality : 0.044 0.240 2670 Planarity : 0.004 0.061 3030 Dihedral : 11.154 75.863 3150 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.68 % Favored : 96.90 % Rotamer: Outliers : 4.59 % Allowed : 21.51 % Favored : 73.89 % 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: 0.26 (0.18), residues: 2127 helix: 2.24 (0.28), residues: 351 sheet: 1.05 (0.21), residues: 615 loop : -1.02 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.018 0.001 TYR I 99 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00936 ( 27) link_NAG-ASN : angle 2.77718 ( 81) link_BETA1-4 : bond 0.00721 ( 9) link_BETA1-4 : angle 2.57135 ( 27) hydrogen bonds : bond 0.06513 ( 617) hydrogen bonds : angle 4.60866 ( 1710) SS BOND : bond 0.00276 ( 23) SS BOND : angle 0.87650 ( 46) covalent geometry : bond 0.00255 (17493) covalent geometry : angle 0.58928 (23760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8283 (mp) REVERT: D 293 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: A 187 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: B 465 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7683 (ttmt) REVERT: F 68 SER cc_start: 0.7080 (p) cc_final: 0.6611 (m) REVERT: F 71 SER cc_start: 0.7490 (m) cc_final: 0.7097 (p) REVERT: I 68 SER cc_start: 0.7010 (p) cc_final: 0.6498 (m) outliers start: 82 outliers final: 52 residues processed: 214 average time/residue: 2.0081 time to fit residues: 496.2458 Evaluate side-chains 205 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 4.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 131 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN B 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099838 restraints weight = 19884.738| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.27 r_work: 0.3113 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17552 Z= 0.182 Angle : 0.698 8.804 23914 Z= 0.353 Chirality : 0.048 0.391 2670 Planarity : 0.005 0.047 3030 Dihedral : 9.432 59.065 3114 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.96 % Favored : 96.61 % Rotamer: Outliers : 5.49 % Allowed : 20.67 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2127 helix: 2.04 (0.29), residues: 354 sheet: 1.13 (0.20), residues: 603 loop : -1.08 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.018 0.002 TYR I 99 ARG 0.004 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 27) link_NAG-ASN : angle 2.91457 ( 81) link_BETA1-4 : bond 0.00504 ( 9) link_BETA1-4 : angle 2.32787 ( 27) hydrogen bonds : bond 0.07558 ( 617) hydrogen bonds : angle 4.50513 ( 1710) SS BOND : bond 0.00433 ( 23) SS BOND : angle 1.13741 ( 46) covalent geometry : bond 0.00422 (17493) covalent geometry : angle 0.67241 (23760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 156 time to evaluate : 2.088 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8376 (mp) REVERT: D 187 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: D 293 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: D 371 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7961 (tp40) REVERT: D 449 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 187 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: A 449 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: B 187 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: B 465 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7908 (ttmt) REVERT: G 93 MET cc_start: 0.8586 (tpp) cc_final: 0.8238 (tpp) REVERT: C 68 SER cc_start: 0.7043 (p) cc_final: 0.6494 (m) REVERT: C 111 LEU cc_start: 0.4027 (OUTLIER) cc_final: 0.3525 (pp) REVERT: F 32 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.5869 (m-30) REVERT: F 68 SER cc_start: 0.7066 (p) cc_final: 0.6602 (m) REVERT: F 71 SER cc_start: 0.7531 (m) cc_final: 0.7140 (p) REVERT: I 32 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.5948 (m-30) REVERT: I 68 SER cc_start: 0.6983 (p) cc_final: 0.6470 (m) REVERT: I 107 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7050 (tttp) outliers start: 98 outliers final: 52 residues processed: 218 average time/residue: 1.1346 time to fit residues: 281.1305 Evaluate side-chains 215 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 150 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 465 LYS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 107 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 30 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099558 restraints weight = 20552.640| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.20 r_work: 0.3170 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17552 Z= 0.114 Angle : 0.576 10.263 23914 Z= 0.290 Chirality : 0.044 0.354 2670 Planarity : 0.004 0.043 3030 Dihedral : 7.957 59.054 3103 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.35 % Favored : 97.23 % Rotamer: Outliers : 4.26 % Allowed : 21.96 % Favored : 73.78 % 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: 0.37 (0.18), residues: 2127 helix: 2.34 (0.28), residues: 351 sheet: 1.21 (0.20), residues: 600 loop : -1.00 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.001 PHE D 128 TYR 0.012 0.001 TYR G 95 ARG 0.002 0.000 ARG B 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 27) link_NAG-ASN : angle 2.65786 ( 81) link_BETA1-4 : bond 0.00586 ( 9) link_BETA1-4 : angle 1.81315 ( 27) hydrogen bonds : bond 0.06007 ( 617) hydrogen bonds : angle 4.22345 ( 1710) SS BOND : bond 0.00269 ( 23) SS BOND : angle 0.79075 ( 46) covalent geometry : bond 0.00234 (17493) covalent geometry : angle 0.55165 (23760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 187 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: D 371 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7870 (tp40) REVERT: D 502 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7566 (t70) REVERT: A 187 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: A 325 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8455 (mtt90) REVERT: B 465 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: G 93 MET cc_start: 0.8478 (tpp) cc_final: 0.8108 (tpp) REVERT: C 64 SER cc_start: 0.7285 (m) cc_final: 0.6813 (t) REVERT: C 68 SER cc_start: 0.7037 (p) cc_final: 0.6631 (m) REVERT: C 71 SER cc_start: 0.7477 (m) cc_final: 0.7090 (p) REVERT: C 111 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3777 (pp) REVERT: F 32 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5831 (m-30) REVERT: F 64 SER cc_start: 0.7449 (m) cc_final: 0.6954 (t) REVERT: F 68 SER cc_start: 0.7044 (p) cc_final: 0.6605 (m) REVERT: F 71 SER cc_start: 0.7474 (m) cc_final: 0.7102 (p) REVERT: I 32 ASP cc_start: 0.6432 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: I 64 SER cc_start: 0.7304 (m) cc_final: 0.6808 (t) REVERT: I 68 SER cc_start: 0.6949 (p) cc_final: 0.6490 (m) REVERT: I 71 SER cc_start: 0.7456 (m) cc_final: 0.7059 (p) outliers start: 76 outliers final: 39 residues processed: 222 average time/residue: 1.0689 time to fit residues: 270.6287 Evaluate side-chains 213 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 198 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 110 optimal weight: 0.0170 chunk 132 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 190 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102362 restraints weight = 20158.671| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.37 r_work: 0.3155 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17552 Z= 0.134 Angle : 0.602 10.233 23914 Z= 0.305 Chirality : 0.045 0.332 2670 Planarity : 0.004 0.044 3030 Dihedral : 7.007 57.775 3091 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.96 % Favored : 96.61 % Rotamer: Outliers : 4.99 % Allowed : 21.29 % Favored : 73.73 % 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: 0.43 (0.18), residues: 2127 helix: 2.22 (0.28), residues: 357 sheet: 1.27 (0.20), residues: 600 loop : -0.93 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.013 0.001 TYR G 95 ARG 0.003 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 27) link_NAG-ASN : angle 2.72145 ( 81) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 1.60418 ( 27) hydrogen bonds : bond 0.06501 ( 617) hydrogen bonds : angle 4.22354 ( 1710) SS BOND : bond 0.00375 ( 23) SS BOND : angle 0.97298 ( 46) covalent geometry : bond 0.00295 (17493) covalent geometry : angle 0.57827 (23760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 171 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8301 (mp) REVERT: D 187 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: D 371 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7885 (tp40) REVERT: A 22 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 187 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 187 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: B 465 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7726 (ttmt) REVERT: G 93 MET cc_start: 0.8527 (tpp) cc_final: 0.8232 (tpp) REVERT: C 64 SER cc_start: 0.7224 (m) cc_final: 0.6795 (t) REVERT: C 68 SER cc_start: 0.7036 (p) cc_final: 0.6610 (m) REVERT: C 71 SER cc_start: 0.7431 (m) cc_final: 0.7227 (t) REVERT: C 111 LEU cc_start: 0.4389 (OUTLIER) cc_final: 0.3949 (pp) REVERT: F 64 SER cc_start: 0.7430 (m) cc_final: 0.6916 (t) REVERT: F 68 SER cc_start: 0.7017 (p) cc_final: 0.6588 (m) REVERT: F 71 SER cc_start: 0.7472 (m) cc_final: 0.7079 (p) REVERT: I 64 SER cc_start: 0.7179 (m) cc_final: 0.6781 (t) REVERT: I 68 SER cc_start: 0.6962 (p) cc_final: 0.6524 (m) REVERT: I 71 SER cc_start: 0.7523 (m) cc_final: 0.7077 (p) outliers start: 89 outliers final: 51 residues processed: 229 average time/residue: 1.1019 time to fit residues: 287.5697 Evaluate side-chains 226 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 142 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 469 GLN B 469 GLN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093535 restraints weight = 20699.448| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.20 r_work: 0.3085 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 17552 Z= 0.302 Angle : 0.822 9.602 23914 Z= 0.419 Chirality : 0.054 0.489 2670 Planarity : 0.006 0.052 3030 Dihedral : 7.702 59.969 3091 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 2.96 % Favored : 96.47 % Rotamer: Outliers : 5.94 % Allowed : 20.06 % Favored : 74.01 % 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: 0.12 (0.17), residues: 2127 helix: 1.73 (0.28), residues: 354 sheet: 1.22 (0.20), residues: 600 loop : -1.12 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 93 HIS 0.010 0.002 HIS D 25 PHE 0.018 0.003 PHE A 128 TYR 0.021 0.002 TYR D 215 ARG 0.004 0.001 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 27) link_NAG-ASN : angle 3.40180 ( 81) link_BETA1-4 : bond 0.00562 ( 9) link_BETA1-4 : angle 2.18177 ( 27) hydrogen bonds : bond 0.08943 ( 617) hydrogen bonds : angle 4.63670 ( 1710) SS BOND : bond 0.00703 ( 23) SS BOND : angle 1.59717 ( 46) covalent geometry : bond 0.00746 (17493) covalent geometry : angle 0.79424 (23760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 176 time to evaluate : 1.978 Fit side-chains REVERT: D 37 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8347 (mp) REVERT: D 187 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: D 266 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8331 (mt) REVERT: D 371 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8076 (tp40) REVERT: A 22 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8761 (mt) REVERT: A 187 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: B 22 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8754 (mt) REVERT: B 37 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 187 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 465 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: G 93 MET cc_start: 0.8562 (tpp) cc_final: 0.8267 (tpp) REVERT: C 64 SER cc_start: 0.7322 (m) cc_final: 0.6894 (t) REVERT: C 68 SER cc_start: 0.7031 (p) cc_final: 0.6579 (m) REVERT: C 71 SER cc_start: 0.7437 (m) cc_final: 0.7225 (t) REVERT: C 111 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4017 (pp) REVERT: F 64 SER cc_start: 0.7465 (m) cc_final: 0.6990 (t) REVERT: F 68 SER cc_start: 0.7017 (p) cc_final: 0.6547 (m) REVERT: F 71 SER cc_start: 0.7461 (m) cc_final: 0.7219 (t) REVERT: F 74 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5638 (tm) REVERT: I 64 SER cc_start: 0.7352 (m) cc_final: 0.6897 (t) REVERT: I 68 SER cc_start: 0.6974 (p) cc_final: 0.6473 (m) REVERT: I 71 SER cc_start: 0.7499 (m) cc_final: 0.7260 (t) outliers start: 106 outliers final: 57 residues processed: 247 average time/residue: 1.0513 time to fit residues: 298.9353 Evaluate side-chains 239 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 170 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 492 CYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110968 restraints weight = 20141.818| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.20 r_work: 0.3267 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17552 Z= 0.124 Angle : 0.601 9.587 23914 Z= 0.304 Chirality : 0.045 0.378 2670 Planarity : 0.004 0.046 3030 Dihedral : 6.941 54.092 3091 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.54 % Favored : 97.18 % Rotamer: Outliers : 4.31 % Allowed : 21.90 % Favored : 73.78 % 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: 0.31 (0.18), residues: 2127 helix: 2.20 (0.28), residues: 348 sheet: 1.25 (0.20), residues: 603 loop : -1.04 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.001 PHE D 128 TYR 0.012 0.001 TYR G 95 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 27) link_NAG-ASN : angle 2.97970 ( 81) link_BETA1-4 : bond 0.00578 ( 9) link_BETA1-4 : angle 1.59466 ( 27) hydrogen bonds : bond 0.06452 ( 617) hydrogen bonds : angle 4.27906 ( 1710) SS BOND : bond 0.00293 ( 23) SS BOND : angle 0.93132 ( 46) covalent geometry : bond 0.00259 (17493) covalent geometry : angle 0.57335 (23760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 174 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 187 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: D 371 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: A 187 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 187 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 465 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7725 (ttmt) REVERT: G 93 MET cc_start: 0.8572 (tpp) cc_final: 0.8273 (tpp) REVERT: C 64 SER cc_start: 0.7354 (m) cc_final: 0.6918 (t) REVERT: C 68 SER cc_start: 0.7043 (p) cc_final: 0.6594 (m) REVERT: C 71 SER cc_start: 0.7446 (m) cc_final: 0.7224 (t) REVERT: C 111 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.4035 (pp) REVERT: F 64 SER cc_start: 0.7462 (m) cc_final: 0.6934 (t) REVERT: F 68 SER cc_start: 0.7122 (p) cc_final: 0.6689 (m) REVERT: F 71 SER cc_start: 0.7513 (m) cc_final: 0.7286 (t) REVERT: I 64 SER cc_start: 0.7211 (m) cc_final: 0.6820 (t) REVERT: I 68 SER cc_start: 0.7025 (p) cc_final: 0.6570 (m) REVERT: I 71 SER cc_start: 0.7626 (m) cc_final: 0.7347 (t) outliers start: 77 outliers final: 52 residues processed: 220 average time/residue: 1.0790 time to fit residues: 270.9067 Evaluate side-chains 227 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 GLN Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111260 restraints weight = 20210.601| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.19 r_work: 0.3273 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17552 Z= 0.126 Angle : 0.587 9.467 23914 Z= 0.297 Chirality : 0.045 0.346 2670 Planarity : 0.004 0.044 3030 Dihedral : 6.579 52.561 3091 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.10 % Favored : 96.61 % Rotamer: Outliers : 4.37 % Allowed : 21.68 % Favored : 73.95 % 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: 0.46 (0.18), residues: 2127 helix: 2.31 (0.28), residues: 351 sheet: 1.34 (0.20), residues: 600 loop : -0.94 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 27) link_NAG-ASN : angle 2.75968 ( 81) link_BETA1-4 : bond 0.00501 ( 9) link_BETA1-4 : angle 1.55904 ( 27) hydrogen bonds : bond 0.06322 ( 617) hydrogen bonds : angle 4.18891 ( 1710) SS BOND : bond 0.00321 ( 23) SS BOND : angle 0.93496 ( 46) covalent geometry : bond 0.00274 (17493) covalent geometry : angle 0.56263 (23760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 1.778 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8431 (mp) REVERT: D 187 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 37 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 187 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 22 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 187 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 465 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7746 (ttmt) REVERT: G 93 MET cc_start: 0.8556 (tpp) cc_final: 0.8270 (tpp) REVERT: C 68 SER cc_start: 0.7033 (p) cc_final: 0.6596 (m) REVERT: C 111 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.4128 (pp) REVERT: F 64 SER cc_start: 0.7360 (m) cc_final: 0.6869 (t) REVERT: F 68 SER cc_start: 0.7099 (p) cc_final: 0.6675 (m) REVERT: F 71 SER cc_start: 0.7445 (m) cc_final: 0.7216 (t) REVERT: I 64 SER cc_start: 0.7212 (m) cc_final: 0.6819 (t) REVERT: I 68 SER cc_start: 0.7008 (p) cc_final: 0.6559 (m) REVERT: I 71 SER cc_start: 0.7597 (m) cc_final: 0.7327 (t) outliers start: 78 outliers final: 49 residues processed: 221 average time/residue: 1.0014 time to fit residues: 254.0798 Evaluate side-chains 226 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 74 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 162 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111195 restraints weight = 20312.115| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.13 r_work: 0.3297 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17552 Z= 0.124 Angle : 0.590 11.359 23914 Z= 0.297 Chirality : 0.045 0.422 2670 Planarity : 0.004 0.044 3030 Dihedral : 6.432 51.925 3089 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.73 % Favored : 96.99 % Rotamer: Outliers : 3.92 % Allowed : 22.30 % Favored : 73.78 % 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: 0.50 (0.18), residues: 2127 helix: 2.36 (0.28), residues: 351 sheet: 1.36 (0.20), residues: 600 loop : -0.91 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.012 0.001 TYR H 95 ARG 0.002 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 27) link_NAG-ASN : angle 3.13641 ( 81) link_BETA1-4 : bond 0.00562 ( 9) link_BETA1-4 : angle 1.85722 ( 27) hydrogen bonds : bond 0.06198 ( 617) hydrogen bonds : angle 4.15473 ( 1710) SS BOND : bond 0.00324 ( 23) SS BOND : angle 0.96055 ( 46) covalent geometry : bond 0.00264 (17493) covalent geometry : angle 0.55754 (23760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 171 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 187 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 187 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: B 187 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: B 465 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7820 (ttmt) REVERT: G 93 MET cc_start: 0.8670 (tpp) cc_final: 0.8431 (tpp) REVERT: E 93 MET cc_start: 0.8664 (tpp) cc_final: 0.8418 (tpp) REVERT: C 68 SER cc_start: 0.7124 (p) cc_final: 0.6670 (m) REVERT: C 111 LEU cc_start: 0.4558 (OUTLIER) cc_final: 0.4051 (pp) REVERT: F 64 SER cc_start: 0.7367 (m) cc_final: 0.6873 (t) REVERT: F 68 SER cc_start: 0.7147 (p) cc_final: 0.6720 (m) REVERT: F 71 SER cc_start: 0.7478 (m) cc_final: 0.7245 (t) REVERT: I 64 SER cc_start: 0.7230 (m) cc_final: 0.6830 (t) REVERT: I 68 SER cc_start: 0.7055 (p) cc_final: 0.6610 (m) REVERT: I 71 SER cc_start: 0.7634 (m) cc_final: 0.7361 (t) outliers start: 70 outliers final: 49 residues processed: 215 average time/residue: 1.1867 time to fit residues: 292.1160 Evaluate side-chains 226 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110937 restraints weight = 20141.293| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.07 r_work: 0.3295 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17552 Z= 0.132 Angle : 0.607 11.556 23914 Z= 0.305 Chirality : 0.046 0.429 2670 Planarity : 0.004 0.044 3030 Dihedral : 6.390 51.699 3085 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.06 % Favored : 96.66 % Rotamer: Outliers : 3.42 % Allowed : 22.97 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2127 helix: 2.36 (0.28), residues: 351 sheet: 1.39 (0.20), residues: 600 loop : -0.90 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.002 PHE D 128 TYR 0.013 0.001 TYR G 95 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 27) link_NAG-ASN : angle 3.35274 ( 81) link_BETA1-4 : bond 0.00564 ( 9) link_BETA1-4 : angle 1.79099 ( 27) hydrogen bonds : bond 0.06330 ( 617) hydrogen bonds : angle 4.15800 ( 1710) SS BOND : bond 0.00338 ( 23) SS BOND : angle 0.99927 ( 46) covalent geometry : bond 0.00288 (17493) covalent geometry : angle 0.57145 (23760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 187 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: A 187 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: B 187 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: B 465 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7842 (ttmt) REVERT: G 93 MET cc_start: 0.8685 (tpp) cc_final: 0.8458 (tpp) REVERT: E 93 MET cc_start: 0.8679 (tpp) cc_final: 0.8441 (tpp) REVERT: C 68 SER cc_start: 0.7142 (p) cc_final: 0.6697 (m) REVERT: C 111 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4006 (pp) REVERT: F 64 SER cc_start: 0.7404 (m) cc_final: 0.6902 (t) REVERT: F 68 SER cc_start: 0.7153 (p) cc_final: 0.6728 (m) REVERT: F 71 SER cc_start: 0.7500 (m) cc_final: 0.7262 (t) REVERT: I 64 SER cc_start: 0.7240 (m) cc_final: 0.6839 (t) REVERT: I 68 SER cc_start: 0.7079 (p) cc_final: 0.6639 (m) REVERT: I 71 SER cc_start: 0.7647 (m) cc_final: 0.7367 (t) outliers start: 61 outliers final: 48 residues processed: 212 average time/residue: 1.5690 time to fit residues: 379.0582 Evaluate side-chains 225 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 421 MET Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN A 469 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111865 restraints weight = 20191.308| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.09 r_work: 0.3310 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17552 Z= 0.116 Angle : 0.572 11.691 23914 Z= 0.287 Chirality : 0.045 0.425 2670 Planarity : 0.004 0.043 3030 Dihedral : 6.239 52.782 3085 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.49 % Favored : 97.23 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.61 (0.18), residues: 2127 helix: 2.44 (0.28), residues: 351 sheet: 1.51 (0.21), residues: 594 loop : -0.88 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS D 25 PHE 0.016 0.001 PHE D 128 TYR 0.012 0.001 TYR G 95 ARG 0.002 0.000 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 27) link_NAG-ASN : angle 3.25566 ( 81) link_BETA1-4 : bond 0.00519 ( 9) link_BETA1-4 : angle 1.58164 ( 27) hydrogen bonds : bond 0.05935 ( 617) hydrogen bonds : angle 4.08069 ( 1710) SS BOND : bond 0.00288 ( 23) SS BOND : angle 0.90060 ( 46) covalent geometry : bond 0.00244 (17493) covalent geometry : angle 0.53716 (23760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15247.47 seconds wall clock time: 265 minutes 34.11 seconds (15934.11 seconds total)