Starting phenix.real_space_refine on Fri Mar 6 07:44:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_27443.cif Found real_map, /net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_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 { model { file = "/net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_27443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_27443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_27443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8diu_27443/03_2026/8diu_27443.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.67, per 1000 atoms: 0.21 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: 1.34 Conformation dependent library (CDL) restraints added in 684.5 milliseconds 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: 0.73 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: 2.67 Time building geometry restraints manager: 1.73 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: 0.03 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: 14.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (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 ARG 0.006 0.000 ARG B 325 TYR 0.013 0.001 TYR F 99 PHE 0.016 0.002 PHE B 128 TRP 0.009 0.001 TRP C 92 HIS 0.005 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00423 (17493) covalent geometry : angle 0.69275 (23760) SS BOND : bond 0.00396 ( 23) SS BOND : angle 1.22928 ( 46) hydrogen bonds : bond 0.14809 ( 617) hydrogen bonds : angle 5.73456 ( 1710) link_BETA1-4 : bond 0.00595 ( 9) link_BETA1-4 : angle 2.20504 ( 27) link_NAG-ASN : bond 0.01016 ( 27) link_NAG-ASN : angle 2.96903 ( 81) *********************** 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 : 0.550 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: 0.6121 (m-30) outliers start: 63 outliers final: 55 residues processed: 207 average time/residue: 0.5142 time to fit residues: 120.6304 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 : 0.594 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.140901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102400 restraints weight = 19919.386| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.27 r_work: 0.3148 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17552 Z= 0.136 Angle : 0.636 9.608 23914 Z= 0.319 Chirality : 0.045 0.263 2670 Planarity : 0.005 0.059 3030 Dihedral : 10.653 68.541 3150 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.59 % Favored : 96.99 % Rotamer: Outliers : 5.10 % Allowed : 21.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2127 helix: 2.11 (0.28), residues: 354 sheet: 1.04 (0.21), residues: 615 loop : -1.02 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 30 TYR 0.018 0.001 TYR I 99 PHE 0.016 0.002 PHE D 128 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00293 (17493) covalent geometry : angle 0.61035 (23760) SS BOND : bond 0.00310 ( 23) SS BOND : angle 0.93554 ( 46) hydrogen bonds : bond 0.06604 ( 617) hydrogen bonds : angle 4.55752 ( 1710) link_BETA1-4 : bond 0.00659 ( 9) link_BETA1-4 : angle 2.44187 ( 27) link_NAG-ASN : bond 0.00983 ( 27) link_NAG-ASN : angle 2.79784 ( 81) *********************** 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 249 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 158 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8299 (mp) REVERT: D 187 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: D 371 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7886 (tp40) REVERT: D 502 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7626 (t70) REVERT: A 187 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: A 449 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 465 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7947 (ttmt) REVERT: B 465 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7719 (ttmt) REVERT: G 93 MET cc_start: 0.8505 (tpp) cc_final: 0.8277 (tpp) REVERT: C 68 SER cc_start: 0.7075 (p) cc_final: 0.6527 (m) REVERT: F 68 SER cc_start: 0.7086 (p) cc_final: 0.6628 (m) REVERT: F 71 SER cc_start: 0.7487 (m) cc_final: 0.7090 (p) REVERT: I 68 SER cc_start: 0.7001 (p) cc_final: 0.6497 (m) outliers start: 91 outliers final: 51 residues processed: 218 average time/residue: 0.5317 time to fit residues: 130.7633 Evaluate side-chains 208 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 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 502 ASP 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 202 ILE 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 449 GLU Chi-restraints excluded: chain A residue 465 LYS 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 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 116 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 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 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 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 0.0040 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 B 201 ASN B 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103096 restraints weight = 20157.467| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.28 r_work: 0.3159 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0732 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= 0.120 Angle : 0.585 8.929 23914 Z= 0.295 Chirality : 0.044 0.286 2670 Planarity : 0.004 0.042 3030 Dihedral : 8.893 58.025 3110 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.59 % Favored : 96.99 % Rotamer: Outliers : 4.59 % Allowed : 21.74 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2127 helix: 2.32 (0.28), residues: 354 sheet: 1.11 (0.20), residues: 615 loop : -0.95 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.013 0.001 TYR I 99 PHE 0.016 0.001 PHE D 128 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00252 (17493) covalent geometry : angle 0.56281 (23760) SS BOND : bond 0.00267 ( 23) SS BOND : angle 0.85158 ( 46) hydrogen bonds : bond 0.06155 ( 617) hydrogen bonds : angle 4.29709 ( 1710) link_BETA1-4 : bond 0.00466 ( 9) link_BETA1-4 : angle 2.01019 ( 27) link_NAG-ASN : bond 0.00558 ( 27) link_NAG-ASN : angle 2.55337 ( 81) *********************** 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 239 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 293 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: A 37 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 187 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: A 465 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7894 (ttmt) REVERT: B 187 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 465 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7670 (ttmt) REVERT: G 93 MET cc_start: 0.8515 (tpp) cc_final: 0.8150 (tpp) REVERT: C 68 SER cc_start: 0.7057 (p) cc_final: 0.6536 (m) REVERT: C 111 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3570 (pp) REVERT: F 32 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.5919 (m-30) REVERT: F 64 SER cc_start: 0.7323 (m) cc_final: 0.6783 (t) REVERT: F 68 SER cc_start: 0.7044 (p) cc_final: 0.6593 (m) REVERT: F 71 SER cc_start: 0.7518 (m) cc_final: 0.7173 (p) REVERT: I 32 ASP cc_start: 0.6453 (OUTLIER) cc_final: 0.5966 (m-30) REVERT: I 68 SER cc_start: 0.7016 (p) cc_final: 0.6512 (m) outliers start: 82 outliers final: 40 residues processed: 210 average time/residue: 0.5356 time to fit residues: 126.4867 Evaluate side-chains 198 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 128 PHE 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 477 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 37 LEU 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 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 LYS 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 187 GLU 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 H residue 100 MET Chi-restraints excluded: chain H residue 108 MET 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 73 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094222 restraints weight = 20690.346| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.21 r_work: 0.3099 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17552 Z= 0.249 Angle : 0.773 9.386 23914 Z= 0.394 Chirality : 0.051 0.415 2670 Planarity : 0.005 0.051 3030 Dihedral : 8.299 59.738 3091 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 2.87 % Favored : 96.66 % Rotamer: Outliers : 5.55 % Allowed : 20.84 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2127 helix: 1.89 (0.28), residues: 354 sheet: 1.15 (0.20), residues: 600 loop : -1.11 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 30 TYR 0.017 0.002 TYR A 215 PHE 0.017 0.003 PHE D 128 TRP 0.009 0.002 TRP B 93 HIS 0.008 0.002 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00606 (17493) covalent geometry : angle 0.74614 (23760) SS BOND : bond 0.00568 ( 23) SS BOND : angle 1.43143 ( 46) hydrogen bonds : bond 0.08499 ( 617) hydrogen bonds : angle 4.60844 ( 1710) link_BETA1-4 : bond 0.00553 ( 9) link_BETA1-4 : angle 2.23911 ( 27) link_NAG-ASN : bond 0.00720 ( 27) link_NAG-ASN : angle 3.21528 ( 81) *********************** 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 252 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 153 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8352 (mp) REVERT: D 187 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: D 266 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8341 (mt) REVERT: D 371 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7859 (tp40) REVERT: A 187 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: A 465 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7987 (ttmt) REVERT: B 22 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8791 (mt) REVERT: B 37 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8506 (mp) REVERT: B 187 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 465 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7981 (ttmt) REVERT: G 93 MET cc_start: 0.8564 (tpp) cc_final: 0.8205 (tpp) REVERT: C 68 SER cc_start: 0.6995 (p) cc_final: 0.6484 (m) REVERT: C 111 LEU cc_start: 0.4283 (OUTLIER) cc_final: 0.3764 (pp) REVERT: F 64 SER cc_start: 0.7519 (m) cc_final: 0.6980 (t) REVERT: F 68 SER cc_start: 0.7019 (p) cc_final: 0.6569 (m) REVERT: F 71 SER cc_start: 0.7530 (m) cc_final: 0.7105 (p) REVERT: I 32 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.5898 (m-30) REVERT: I 68 SER cc_start: 0.6946 (p) cc_final: 0.6443 (m) REVERT: I 107 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7087 (tttp) outliers start: 99 outliers final: 53 residues processed: 221 average time/residue: 0.5051 time to fit residues: 127.0826 Evaluate side-chains 209 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 465 LYS 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 204 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 256 THR 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 465 LYS 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 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 32 ASP Chi-restraints excluded: chain C residue 73 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 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 180 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 201 ASN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111755 restraints weight = 20163.387| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.08 r_work: 0.3285 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0941 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= 0.118 Angle : 0.579 9.832 23914 Z= 0.293 Chirality : 0.044 0.291 2670 Planarity : 0.004 0.044 3030 Dihedral : 7.208 55.885 3091 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.16 % Favored : 97.41 % Rotamer: Outliers : 4.59 % Allowed : 21.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2127 helix: 2.27 (0.28), residues: 351 sheet: 1.23 (0.20), residues: 600 loop : -0.99 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.012 0.001 TYR H 95 PHE 0.016 0.001 PHE A 128 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00247 (17493) covalent geometry : angle 0.55403 (23760) SS BOND : bond 0.00293 ( 23) SS BOND : angle 0.83913 ( 46) hydrogen bonds : bond 0.06138 ( 617) hydrogen bonds : angle 4.23832 ( 1710) link_BETA1-4 : bond 0.00501 ( 9) link_BETA1-4 : angle 1.61565 ( 27) link_NAG-ASN : bond 0.00640 ( 27) link_NAG-ASN : angle 2.75512 ( 81) *********************** 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 252 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 170 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8441 (mp) REVERT: D 187 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: D 502 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7742 (t70) REVERT: A 187 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: A 325 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8409 (mtt90) REVERT: A 465 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7903 (ttmt) REVERT: B 187 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 465 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7676 (ttmt) REVERT: G 93 MET cc_start: 0.8561 (tpp) cc_final: 0.8193 (tpp) REVERT: C 64 SER cc_start: 0.7297 (m) cc_final: 0.6882 (t) REVERT: C 68 SER cc_start: 0.7054 (p) cc_final: 0.6599 (m) REVERT: C 71 SER cc_start: 0.7534 (m) cc_final: 0.7280 (t) REVERT: C 111 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.3963 (pp) REVERT: F 64 SER cc_start: 0.7498 (m) cc_final: 0.6970 (t) REVERT: F 68 SER cc_start: 0.7057 (p) cc_final: 0.6616 (m) REVERT: F 71 SER cc_start: 0.7487 (m) cc_final: 0.7095 (p) REVERT: I 64 SER cc_start: 0.7318 (m) cc_final: 0.6848 (t) REVERT: I 68 SER cc_start: 0.7024 (p) cc_final: 0.6556 (m) REVERT: I 71 SER cc_start: 0.7579 (m) cc_final: 0.7313 (t) outliers start: 82 outliers final: 44 residues processed: 221 average time/residue: 0.5139 time to fit residues: 128.8015 Evaluate side-chains 220 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 404 ASN 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 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 465 LYS 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 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 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 108 MET Chi-restraints excluded: chain C residue 18 VAL 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 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 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 205 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 201 ASN 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 = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110793 restraints weight = 20045.454| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.20 r_work: 0.3286 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17552 Z= 0.137 Angle : 0.605 9.708 23914 Z= 0.306 Chirality : 0.045 0.385 2670 Planarity : 0.004 0.045 3030 Dihedral : 6.901 52.751 3091 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.61 % Rotamer: Outliers : 4.71 % Allowed : 21.68 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2127 helix: 2.24 (0.28), residues: 354 sheet: 1.27 (0.20), residues: 600 loop : -0.94 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.013 0.001 TYR G 95 PHE 0.016 0.002 PHE D 128 TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00304 (17493) covalent geometry : angle 0.58010 (23760) SS BOND : bond 0.00340 ( 23) SS BOND : angle 0.99024 ( 46) hydrogen bonds : bond 0.06526 ( 617) hydrogen bonds : angle 4.23725 ( 1710) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 1.60537 ( 27) link_NAG-ASN : bond 0.00604 ( 27) link_NAG-ASN : angle 2.79659 ( 81) *********************** 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 252 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 168 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8510 (mp) REVERT: D 187 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 502 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (t70) REVERT: A 22 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8696 (mt) REVERT: A 187 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: A 325 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8486 (mtt90) REVERT: A 465 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: B 187 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: B 465 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7827 (ttmt) REVERT: G 93 MET cc_start: 0.8694 (tpp) cc_final: 0.8439 (tpp) REVERT: C 64 SER cc_start: 0.7339 (m) cc_final: 0.6917 (t) REVERT: C 68 SER cc_start: 0.7060 (p) cc_final: 0.6623 (m) REVERT: C 71 SER cc_start: 0.7460 (m) cc_final: 0.7257 (t) REVERT: C 111 LEU cc_start: 0.4404 (OUTLIER) cc_final: 0.3926 (pp) REVERT: F 64 SER cc_start: 0.7484 (m) cc_final: 0.6942 (t) REVERT: F 68 SER cc_start: 0.7073 (p) cc_final: 0.6639 (m) REVERT: F 71 SER cc_start: 0.7527 (m) cc_final: 0.7276 (t) REVERT: I 64 SER cc_start: 0.7231 (m) cc_final: 0.6838 (t) REVERT: I 68 SER cc_start: 0.7062 (p) cc_final: 0.6596 (m) REVERT: I 71 SER cc_start: 0.7598 (m) cc_final: 0.7331 (t) outliers start: 84 outliers final: 55 residues processed: 225 average time/residue: 0.5068 time to fit residues: 129.2633 Evaluate side-chains 230 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 D residue 502 ASP 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 144 THR 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 465 LYS 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 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU 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 196 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 39 optimal weight: 0.0000 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 177 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6864 ------------------------------------------------------------------------------- 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 201 ASN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112621 restraints weight = 20119.298| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.12 r_work: 0.3292 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1077 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= 0.113 Angle : 0.559 9.968 23914 Z= 0.283 Chirality : 0.044 0.303 2670 Planarity : 0.004 0.043 3030 Dihedral : 6.493 54.210 3091 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.35 % Favored : 97.37 % Rotamer: Outliers : 4.26 % Allowed : 22.07 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2127 helix: 2.42 (0.28), residues: 351 sheet: 1.40 (0.20), residues: 594 loop : -0.90 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.012 0.001 TYR H 95 PHE 0.016 0.001 PHE D 128 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00238 (17493) covalent geometry : angle 0.53545 (23760) SS BOND : bond 0.00256 ( 23) SS BOND : angle 0.85088 ( 46) hydrogen bonds : bond 0.05935 ( 617) hydrogen bonds : angle 4.12727 ( 1710) link_BETA1-4 : bond 0.00500 ( 9) link_BETA1-4 : angle 1.49475 ( 27) link_NAG-ASN : bond 0.00565 ( 27) link_NAG-ASN : angle 2.66830 ( 81) *********************** 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 249 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8396 (mp) REVERT: D 187 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: D 502 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7777 (t70) REVERT: A 187 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: A 325 ARG cc_start: 0.8702 (mtt-85) cc_final: 0.8375 (mtt90) REVERT: A 465 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7924 (ttmt) REVERT: B 187 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 465 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7689 (ttmt) REVERT: G 93 MET cc_start: 0.8568 (tpp) cc_final: 0.8279 (tpp) REVERT: C 68 SER cc_start: 0.7026 (p) cc_final: 0.6594 (m) REVERT: C 111 LEU cc_start: 0.4497 (OUTLIER) cc_final: 0.4055 (pp) REVERT: F 64 SER cc_start: 0.7415 (m) cc_final: 0.6916 (t) REVERT: F 68 SER cc_start: 0.7067 (p) cc_final: 0.6647 (m) REVERT: F 71 SER cc_start: 0.7462 (m) cc_final: 0.7247 (t) REVERT: I 64 SER cc_start: 0.7167 (m) cc_final: 0.6804 (t) REVERT: I 68 SER cc_start: 0.6997 (p) cc_final: 0.6557 (m) REVERT: I 71 SER cc_start: 0.7623 (m) cc_final: 0.7355 (t) outliers start: 76 outliers final: 45 residues processed: 222 average time/residue: 0.4999 time to fit residues: 125.9733 Evaluate side-chains 221 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 502 ASP 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 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 465 LYS 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 249 THR 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 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 32 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain I residue 32 ASP 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 42 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 50 optimal weight: 0.0040 overall best weight: 0.5252 ------------------------------------------------------------------------------- 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 201 ASN B 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112792 restraints weight = 20261.461| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.10 r_work: 0.3303 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17552 Z= 0.105 Angle : 0.542 10.144 23914 Z= 0.274 Chirality : 0.043 0.269 2670 Planarity : 0.004 0.041 3030 Dihedral : 6.162 55.304 3085 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.63 % Favored : 97.09 % Rotamer: Outliers : 4.03 % Allowed : 22.75 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2127 helix: 2.50 (0.28), residues: 351 sheet: 1.40 (0.20), residues: 600 loop : -0.83 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.012 0.001 TYR H 95 PHE 0.015 0.001 PHE D 128 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00212 (17493) covalent geometry : angle 0.51849 (23760) SS BOND : bond 0.00250 ( 23) SS BOND : angle 0.84727 ( 46) hydrogen bonds : bond 0.05637 ( 617) hydrogen bonds : angle 4.06427 ( 1710) link_BETA1-4 : bond 0.00504 ( 9) link_BETA1-4 : angle 1.47531 ( 27) link_NAG-ASN : bond 0.00551 ( 27) link_NAG-ASN : angle 2.61030 ( 81) *********************** 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 242 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 187 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: D 293 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: D 502 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7712 (t70) REVERT: A 187 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: A 325 ARG cc_start: 0.8670 (mtt-85) cc_final: 0.8341 (mtt90) REVERT: B 187 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: B 465 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7627 (ttmt) REVERT: G 93 MET cc_start: 0.8516 (tpp) cc_final: 0.8226 (tpp) REVERT: E 93 MET cc_start: 0.8507 (tpp) cc_final: 0.8189 (tpp) REVERT: C 68 SER cc_start: 0.7017 (p) cc_final: 0.6576 (m) REVERT: C 111 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4108 (pp) REVERT: F 64 SER cc_start: 0.7326 (m) cc_final: 0.6837 (t) REVERT: F 68 SER cc_start: 0.7079 (p) cc_final: 0.6668 (m) REVERT: F 71 SER cc_start: 0.7399 (m) cc_final: 0.7188 (t) REVERT: I 64 SER cc_start: 0.7149 (m) cc_final: 0.6775 (t) REVERT: I 68 SER cc_start: 0.6984 (p) cc_final: 0.6555 (m) REVERT: I 71 SER cc_start: 0.7597 (m) cc_final: 0.7328 (t) outliers start: 72 outliers final: 47 residues processed: 217 average time/residue: 0.5070 time to fit residues: 124.7322 Evaluate side-chains 221 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 502 ASP 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 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 502 ASP 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 202 ILE Chi-restraints excluded: chain B residue 249 THR 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 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 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 32 ASP 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 77 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 192 optimal weight: 6.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.149093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113297 restraints weight = 20228.983| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.11 r_work: 0.3326 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17552 Z= 0.103 Angle : 0.548 11.321 23914 Z= 0.273 Chirality : 0.044 0.393 2670 Planarity : 0.004 0.041 3030 Dihedral : 5.967 55.873 3084 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.35 % Favored : 97.37 % Rotamer: Outliers : 3.81 % Allowed : 23.25 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.18), residues: 2127 helix: 2.56 (0.28), residues: 351 sheet: 1.43 (0.20), residues: 600 loop : -0.80 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 30 TYR 0.012 0.001 TYR E 95 PHE 0.015 0.001 PHE D 128 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00204 (17493) covalent geometry : angle 0.51516 (23760) SS BOND : bond 0.00265 ( 23) SS BOND : angle 0.84171 ( 46) hydrogen bonds : bond 0.05482 ( 617) hydrogen bonds : angle 4.01893 ( 1710) link_BETA1-4 : bond 0.00610 ( 9) link_BETA1-4 : angle 1.83451 ( 27) link_NAG-ASN : bond 0.00871 ( 27) link_NAG-ASN : angle 3.02855 ( 81) *********************** 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 243 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 187 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: D 293 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: D 502 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7882 (t70) REVERT: A 187 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 187 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: G 93 MET cc_start: 0.8704 (tpp) cc_final: 0.8487 (tpp) REVERT: E 93 MET cc_start: 0.8653 (tpp) cc_final: 0.8411 (tpp) REVERT: C 68 SER cc_start: 0.7066 (p) cc_final: 0.6622 (m) REVERT: C 111 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.4006 (pp) REVERT: F 64 SER cc_start: 0.7375 (m) cc_final: 0.6865 (t) REVERT: F 68 SER cc_start: 0.7144 (p) cc_final: 0.6732 (m) REVERT: F 71 SER cc_start: 0.7458 (m) cc_final: 0.7234 (t) REVERT: I 64 SER cc_start: 0.7216 (m) cc_final: 0.6838 (t) REVERT: I 68 SER cc_start: 0.7056 (p) cc_final: 0.6628 (m) REVERT: I 71 SER cc_start: 0.7623 (m) cc_final: 0.7349 (t) outliers start: 68 outliers final: 42 residues processed: 222 average time/residue: 0.5119 time to fit residues: 128.6520 Evaluate side-chains 211 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 502 ASP Chi-restraints excluded: chain A residue 29 SER 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 335 LEU Chi-restraints excluded: chain A residue 449 GLU 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 249 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 91 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 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 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 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 8 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 GLN B 469 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094894 restraints weight = 20425.835| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.20 r_work: 0.3110 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17552 Z= 0.246 Angle : 0.769 10.473 23914 Z= 0.389 Chirality : 0.052 0.445 2670 Planarity : 0.005 0.047 3030 Dihedral : 6.755 53.722 3082 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.91 % Favored : 96.71 % Rotamer: Outliers : 3.42 % Allowed : 23.42 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2127 helix: 2.01 (0.29), residues: 354 sheet: 1.36 (0.20), residues: 603 loop : -0.99 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 206 TYR 0.018 0.002 TYR A 215 PHE 0.031 0.003 PHE A 128 TRP 0.010 0.002 TRP H 36 HIS 0.008 0.002 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00595 (17493) covalent geometry : angle 0.73626 (23760) SS BOND : bond 0.00606 ( 23) SS BOND : angle 1.63529 ( 46) hydrogen bonds : bond 0.08197 ( 617) hydrogen bonds : angle 4.43641 ( 1710) link_BETA1-4 : bond 0.00548 ( 9) link_BETA1-4 : angle 2.07683 ( 27) link_NAG-ASN : bond 0.00966 ( 27) link_NAG-ASN : angle 3.56640 ( 81) ********************** 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 : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8360 (mp) REVERT: D 187 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: D 293 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: A 187 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: A 325 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.8434 (mtt90) REVERT: B 187 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 421 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: G 93 MET cc_start: 0.8578 (tpp) cc_final: 0.8306 (tpp) REVERT: C 68 SER cc_start: 0.7025 (p) cc_final: 0.6584 (m) REVERT: C 111 LEU cc_start: 0.4651 (OUTLIER) cc_final: 0.4157 (pp) REVERT: F 64 SER cc_start: 0.7343 (m) cc_final: 0.6853 (t) REVERT: F 68 SER cc_start: 0.7080 (p) cc_final: 0.6657 (m) REVERT: F 71 SER cc_start: 0.7407 (m) cc_final: 0.7188 (t) REVERT: I 64 SER cc_start: 0.7131 (m) cc_final: 0.6775 (t) REVERT: I 68 SER cc_start: 0.6936 (p) cc_final: 0.6492 (m) REVERT: I 71 SER cc_start: 0.7541 (m) cc_final: 0.7277 (t) REVERT: I 107 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6993 (tttp) outliers start: 61 outliers final: 40 residues processed: 215 average time/residue: 0.4976 time to fit residues: 121.1702 Evaluate side-chains 217 residues out of total 1827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 A residue 29 SER 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 335 LEU Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 449 GLU 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 249 THR 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 133 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 45 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 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 = 0.146480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110565 restraints weight = 20176.397| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.09 r_work: 0.3289 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1170 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= 0.131 Angle : 0.613 11.595 23914 Z= 0.307 Chirality : 0.046 0.434 2670 Planarity : 0.004 0.043 3030 Dihedral : 6.398 52.494 3082 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.49 % Favored : 97.23 % Rotamer: Outliers : 3.53 % Allowed : 23.08 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2127 helix: 2.25 (0.28), residues: 351 sheet: 1.42 (0.21), residues: 600 loop : -0.95 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 238 TYR 0.012 0.001 TYR G 95 PHE 0.019 0.002 PHE A 128 TRP 0.007 0.001 TRP H 47 HIS 0.005 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00285 (17493) covalent geometry : angle 0.57602 (23760) SS BOND : bond 0.00309 ( 23) SS BOND : angle 1.13978 ( 46) hydrogen bonds : bond 0.06411 ( 617) hydrogen bonds : angle 4.19473 ( 1710) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 1.74888 ( 27) link_NAG-ASN : bond 0.00795 ( 27) link_NAG-ASN : angle 3.41910 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.93 seconds wall clock time: 115 minutes 31.71 seconds (6931.71 seconds total)