Starting phenix.real_space_refine on Wed Mar 4 20:17:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8c_23229/03_2026/7l8c_23229.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9921 2.51 5 N 2654 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 15963 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "D" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3455 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "G" 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: "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: "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: 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "a" 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: "b" 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: "c" 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: 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: "e" 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: "f" 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: "g" 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: "h" 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: "i" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "p" 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: "q" 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: "r" 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: "s" 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: "t" 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: "u" 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: "v" 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: "w" 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: "x" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "F" 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 Time building chain proxies: 3.25, per 1000 atoms: 0.20 Number of scatterers: 15963 At special positions: 0 Unit cell: (128.75, 127.72, 152.44, 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 99 16.00 O 3289 8.00 N 2654 7.00 C 9921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.09 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.09 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.13 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.07 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.01 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA n 3 " - " MAN n 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " 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 p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 355 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 339 " " NAG D 603 " - " ASN D 137 " " NAG E 701 " - " ASN E 637 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 197 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 88 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 133 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 197 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 386 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN C 88 " " NAG f 1 " - " ASN C 160 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 301 " " NAG i 1 " - " ASN E 611 " " NAG j 1 " - " ASN E 618 " " NAG k 1 " - " ASN D 133 " " NAG l 1 " - " ASN D 156 " " NAG m 1 " - " ASN D 197 " " NAG n 1 " - " ASN D 262 " " NAG o 1 " - " ASN D 276 " " NAG p 1 " - " ASN D 295 " " NAG q 1 " - " ASN D 332 " " NAG r 1 " - " ASN D 386 " " NAG s 1 " - " ASN D 392 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN D 88 " " NAG v 1 " - " ASN D 234 " " NAG w 1 " - " ASN D 301 " " NAG x 1 " - " ASN F 611 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 597.1 milliseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3606 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 35 sheets defined 28.5% alpha, 49.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.151A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.530A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.354A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.782A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.151A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.552A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.231A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.775A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.094A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.304A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.826A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 98 through 102 removed outlier: 4.307A pdb=" N UNK H 102 " --> pdb=" O UNK H 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.470A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.863A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.213A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.742A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.406A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 10.406A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.543A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.253A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.767A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.007A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.683A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.660A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.382A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.823A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AC7, first strand: chain 'D' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.104A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR D 467 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.511A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.860A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.754A pdb=" N UNK H 73 " --> pdb=" O UNK H 68 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 55 through 57 removed outlier: 5.887A pdb=" N UNK H 45 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N UNK H 37 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N UNK H 91 " --> pdb=" O UNK H 108 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N UNK H 108 " --> pdb=" O UNK H 91 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N UNK H 93 " --> pdb=" O UNK H 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.774A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N UNK L 85 " --> pdb=" O UNK L 38 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1731 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: 2.88 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 2531 1.25 - 1.41: 3781 1.41 - 1.56: 9320 1.56 - 1.72: 472 1.72 - 1.87: 130 Bond restraints: 16234 Sorted by residual: bond pdb=" C TRP A 479 " pdb=" O TRP A 479 " ideal model delta sigma weight residual 1.236 1.095 0.141 1.29e-02 6.01e+03 1.19e+02 bond pdb=" C TRP C 479 " pdb=" O TRP C 479 " ideal model delta sigma weight residual 1.236 1.106 0.131 1.29e-02 6.01e+03 1.02e+02 bond pdb=" C TRP D 479 " pdb=" O TRP D 479 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.19e-02 7.06e+03 9.00e+01 bond pdb=" C LYS A 46 " pdb=" O LYS A 46 " ideal model delta sigma weight residual 1.234 1.120 0.114 1.22e-02 6.72e+03 8.67e+01 bond pdb=" C LYS F 574 " pdb=" O LYS F 574 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.15e-02 7.56e+03 6.99e+01 ... (remaining 16229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 19824 2.77 - 5.54: 2039 5.54 - 8.30: 206 8.30 - 11.07: 19 11.07 - 13.84: 2 Bond angle restraints: 22090 Sorted by residual: angle pdb=" N HIS B 570 " pdb=" CA HIS B 570 " pdb=" C HIS B 570 " ideal model delta sigma weight residual 113.55 103.29 10.26 1.26e+00 6.30e-01 6.63e+01 angle pdb=" N THR D 71 " pdb=" CA THR D 71 " pdb=" C THR D 71 " ideal model delta sigma weight residual 114.56 104.67 9.89 1.27e+00 6.20e-01 6.06e+01 angle pdb=" N LEU B 544 " pdb=" CA LEU B 544 " pdb=" C LEU B 544 " ideal model delta sigma weight residual 110.48 99.23 11.25 1.48e+00 4.57e-01 5.78e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.16 -7.60 1.01e+00 9.80e-01 5.67e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.10 -7.54 1.01e+00 9.80e-01 5.58e+01 ... (remaining 22085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 10824 21.41 - 42.82: 232 42.82 - 64.23: 73 64.23 - 85.64: 44 85.64 - 107.05: 26 Dihedral angle restraints: 11199 sinusoidal: 5657 harmonic: 5542 Sorted by residual: dihedral pdb=" N HIS B 570 " pdb=" C HIS B 570 " pdb=" CA HIS B 570 " pdb=" CB HIS B 570 " ideal model delta harmonic sigma weight residual 122.80 107.74 15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" C HIS B 570 " pdb=" N HIS B 570 " pdb=" CA HIS B 570 " pdb=" CB HIS B 570 " ideal model delta harmonic sigma weight residual -122.60 -109.20 -13.40 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -129.54 43.54 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 11196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1754 0.103 - 0.206: 604 0.206 - 0.309: 293 0.309 - 0.412: 143 0.412 - 0.515: 77 Chirality restraints: 2871 Sorted by residual: chirality pdb=" C1 NAG q 2 " pdb=" O4 NAG q 1 " pdb=" C2 NAG q 2 " pdb=" O5 NAG q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.16e+02 chirality pdb=" C1 NAG r 2 " pdb=" O4 NAG r 1 " pdb=" C2 NAG r 2 " pdb=" O5 NAG r 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 2868 not shown) Planarity restraints: 2743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.336 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG C 604 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 2 " 0.260 2.00e-02 2.50e+03 2.19e-01 5.99e+02 pdb=" C7 NAG g 2 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG g 2 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG g 2 " -0.370 2.00e-02 2.50e+03 pdb=" O7 NAG g 2 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 701 " 0.243 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG E 701 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG E 701 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG E 701 " -0.349 2.00e-02 2.50e+03 pdb=" O7 NAG E 701 " 0.182 2.00e-02 2.50e+03 ... (remaining 2740 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 167 2.62 - 3.19: 14014 3.19 - 3.76: 22534 3.76 - 4.33: 33167 4.33 - 4.90: 52037 Nonbonded interactions: 121919 Sorted by model distance: nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.049 3.040 nonbonded pdb=" O HIS B 570 " pdb=" N ILE B 573 " model vdw 2.064 3.120 nonbonded pdb=" O THR F 569 " pdb=" OG1 THR F 569 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN C 234 " pdb=" C1 NAG g 1 " model vdw 2.304 2.776 nonbonded pdb=" N LEU A 179 " pdb=" N ASP A 180 " model vdw 2.405 2.560 ... (remaining 121914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 603) selection = (chain 'C' and resid 33 through 603) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 518 through 663 or resid 702)) selection = (chain 'E' and (resid 518 through 663 or resid 701)) selection = (chain 'F' and (resid 518 through 663 or resid 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain 'H' and resid 8 through 114) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'n' } ncs_group { reference = chain 'O' selection = chain 'Y' selection = chain 'j' selection = chain 'l' } 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.026 0.339 16378 Z= 1.389 Angle : 1.803 25.741 22489 Z= 1.102 Chirality : 0.159 0.515 2871 Planarity : 0.012 0.292 2684 Dihedral : 12.307 107.050 7494 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.28 % 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: 0.69 (0.19), residues: 1655 helix: -0.02 (0.23), residues: 431 sheet: 1.30 (0.24), residues: 405 loop : 0.45 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 166 TYR 0.048 0.007 TYR D 484 PHE 0.034 0.006 PHE D 383 TRP 0.056 0.010 TRP A 35 HIS 0.020 0.003 HIS F 570 Details of bonding type rmsd covalent geometry : bond 0.02564 (16234) covalent geometry : angle 1.74047 (22090) SS BOND : bond 0.03334 ( 33) SS BOND : angle 2.90155 ( 66) hydrogen bonds : bond 0.17689 ( 607) hydrogen bonds : angle 7.35949 ( 1731) link_ALPHA1-3 : bond 0.08037 ( 2) link_ALPHA1-3 : angle 4.31503 ( 6) link_ALPHA1-6 : bond 0.04712 ( 2) link_ALPHA1-6 : angle 3.10052 ( 6) link_BETA1-4 : bond 0.07043 ( 48) link_BETA1-4 : angle 4.86759 ( 144) link_NAG-ASN : bond 0.08563 ( 59) link_NAG-ASN : angle 3.37905 ( 177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7979 (tmtt) REVERT: A 464 THR cc_start: 0.7658 (p) cc_final: 0.7389 (t) REVERT: E 616 ASN cc_start: 0.8606 (t0) cc_final: 0.8219 (t0) REVERT: E 624 ASP cc_start: 0.8500 (m-30) cc_final: 0.8276 (m-30) REVERT: E 632 ASP cc_start: 0.8723 (t70) cc_final: 0.8516 (t0) REVERT: D 102 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8422 (mm-30) REVERT: D 207 LYS cc_start: 0.8717 (pttt) cc_final: 0.8316 (mmtt) REVERT: D 232 LYS cc_start: 0.8603 (mttt) cc_final: 0.8400 (mttp) REVERT: D 462 ASN cc_start: 0.7484 (t0) cc_final: 0.7150 (p0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1470 time to fit residues: 65.8671 Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 590 GLN B 630 GLN B 653 GLN D 114 GLN D 374 HIS F 575 GLN F 607 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096329 restraints weight = 25557.242| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.70 r_work: 0.2952 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16378 Z= 0.170 Angle : 0.760 13.504 22489 Z= 0.367 Chirality : 0.047 0.296 2871 Planarity : 0.004 0.032 2684 Dihedral : 9.262 79.074 4316 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.13 % Allowed : 5.91 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1655 helix: 1.68 (0.27), residues: 413 sheet: 0.84 (0.23), residues: 459 loop : 0.40 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 151 TYR 0.011 0.001 TYR C 191 PHE 0.014 0.002 PHE A 353 TRP 0.026 0.002 TRP B 571 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00380 (16234) covalent geometry : angle 0.69180 (22090) SS BOND : bond 0.00467 ( 33) SS BOND : angle 1.56713 ( 66) hydrogen bonds : bond 0.06182 ( 607) hydrogen bonds : angle 5.61676 ( 1731) link_ALPHA1-3 : bond 0.01026 ( 2) link_ALPHA1-3 : angle 2.78972 ( 6) link_ALPHA1-6 : bond 0.00878 ( 2) link_ALPHA1-6 : angle 1.76091 ( 6) link_BETA1-4 : bond 0.00525 ( 48) link_BETA1-4 : angle 2.63726 ( 144) link_NAG-ASN : bond 0.00437 ( 59) link_NAG-ASN : angle 2.58292 ( 177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7767 (tmtt) REVERT: A 210 PHE cc_start: 0.8871 (m-80) cc_final: 0.8616 (m-80) REVERT: A 484 TYR cc_start: 0.9267 (p90) cc_final: 0.8791 (p90) REVERT: B 620 SER cc_start: 0.9094 (m) cc_final: 0.8827 (t) REVERT: C 82 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7796 (mp10) REVERT: C 246 GLN cc_start: 0.7786 (mt0) cc_final: 0.7408 (mt0) REVERT: C 475 MET cc_start: 0.8877 (mmt) cc_final: 0.8465 (mmt) REVERT: C 503 ARG cc_start: 0.8079 (mmp-170) cc_final: 0.7762 (tpp-160) REVERT: E 545 LEU cc_start: 0.8333 (mt) cc_final: 0.8033 (mt) REVERT: E 616 ASN cc_start: 0.8962 (t0) cc_final: 0.8611 (t0) REVERT: E 624 ASP cc_start: 0.8690 (m-30) cc_final: 0.8460 (m-30) REVERT: D 215 ILE cc_start: 0.8889 (mt) cc_final: 0.8659 (pt) REVERT: D 373 THR cc_start: 0.9258 (m) cc_final: 0.8505 (p) REVERT: D 462 ASN cc_start: 0.7135 (t0) cc_final: 0.6796 (p0) REVERT: F 571 TRP cc_start: 0.5990 (t-100) cc_final: 0.5665 (t60) outliers start: 17 outliers final: 9 residues processed: 254 average time/residue: 0.1197 time to fit residues: 45.9673 Evaluate side-chains 184 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 601 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 540 GLN B 658 GLN C 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.091607 restraints weight = 26268.607| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.69 r_work: 0.2883 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16378 Z= 0.215 Angle : 0.710 10.021 22489 Z= 0.342 Chirality : 0.047 0.252 2871 Planarity : 0.004 0.036 2684 Dihedral : 7.544 70.783 4316 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.06 % Allowed : 7.97 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1655 helix: 1.75 (0.27), residues: 413 sheet: 0.89 (0.24), residues: 429 loop : 0.06 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 151 TYR 0.011 0.001 TYR C 191 PHE 0.020 0.002 PHE F 522 TRP 0.018 0.001 TRP B 571 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00512 (16234) covalent geometry : angle 0.66430 (22090) SS BOND : bond 0.00624 ( 33) SS BOND : angle 1.72485 ( 66) hydrogen bonds : bond 0.05528 ( 607) hydrogen bonds : angle 5.17370 ( 1731) link_ALPHA1-3 : bond 0.01205 ( 2) link_ALPHA1-3 : angle 1.32694 ( 6) link_ALPHA1-6 : bond 0.00925 ( 2) link_ALPHA1-6 : angle 1.72792 ( 6) link_BETA1-4 : bond 0.00633 ( 48) link_BETA1-4 : angle 2.07815 ( 144) link_NAG-ASN : bond 0.00316 ( 59) link_NAG-ASN : angle 2.04533 ( 177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8520 (mmtt) cc_final: 0.7721 (tmtt) REVERT: A 210 PHE cc_start: 0.9021 (m-80) cc_final: 0.8789 (m-80) REVERT: A 484 TYR cc_start: 0.9366 (p90) cc_final: 0.8994 (p90) REVERT: C 82 GLN cc_start: 0.8534 (mm-40) cc_final: 0.6992 (mp10) REVERT: C 153 GLU cc_start: 0.8740 (tp30) cc_final: 0.8427 (mm-30) REVERT: C 161 MET cc_start: 0.9296 (tpp) cc_final: 0.9051 (tpp) REVERT: E 616 ASN cc_start: 0.8947 (t0) cc_final: 0.8487 (t0) REVERT: E 624 ASP cc_start: 0.8683 (m-30) cc_final: 0.8457 (m-30) REVERT: E 648 GLU cc_start: 0.9056 (tt0) cc_final: 0.8824 (tt0) REVERT: D 215 ILE cc_start: 0.8962 (mt) cc_final: 0.8501 (pt) REVERT: D 373 THR cc_start: 0.9288 (m) cc_final: 0.8591 (p) REVERT: D 462 ASN cc_start: 0.7135 (t0) cc_final: 0.6820 (p0) REVERT: F 617 ARG cc_start: 0.8467 (mtt90) cc_final: 0.8261 (mtt90) REVERT: F 634 GLU cc_start: 0.8651 (tt0) cc_final: 0.8219 (tt0) outliers start: 31 outliers final: 18 residues processed: 215 average time/residue: 0.1207 time to fit residues: 38.9772 Evaluate side-chains 187 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092677 restraints weight = 25987.756| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.69 r_work: 0.2903 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16378 Z= 0.151 Angle : 0.616 9.389 22489 Z= 0.297 Chirality : 0.044 0.266 2871 Planarity : 0.003 0.035 2684 Dihedral : 6.559 63.740 4316 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.79 % Allowed : 9.90 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1655 helix: 1.94 (0.27), residues: 413 sheet: 0.82 (0.24), residues: 429 loop : 0.03 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 166 TYR 0.011 0.001 TYR C 191 PHE 0.010 0.002 PHE C 53 TRP 0.014 0.001 TRP B 571 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00353 (16234) covalent geometry : angle 0.57301 (22090) SS BOND : bond 0.00529 ( 33) SS BOND : angle 1.27492 ( 66) hydrogen bonds : bond 0.04700 ( 607) hydrogen bonds : angle 4.90971 ( 1731) link_ALPHA1-3 : bond 0.01099 ( 2) link_ALPHA1-3 : angle 2.01904 ( 6) link_ALPHA1-6 : bond 0.00959 ( 2) link_ALPHA1-6 : angle 1.79761 ( 6) link_BETA1-4 : bond 0.00486 ( 48) link_BETA1-4 : angle 1.79241 ( 144) link_NAG-ASN : bond 0.00230 ( 59) link_NAG-ASN : angle 1.94040 ( 177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 207 LYS cc_start: 0.8442 (mmtt) cc_final: 0.7635 (tmtt) REVERT: A 381 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8147 (mt-10) REVERT: A 484 TYR cc_start: 0.9358 (p90) cc_final: 0.9022 (p90) REVERT: C 246 GLN cc_start: 0.7680 (pm20) cc_final: 0.7278 (tp-100) REVERT: E 616 ASN cc_start: 0.8904 (t0) cc_final: 0.8453 (t0) REVERT: E 624 ASP cc_start: 0.8668 (m-30) cc_final: 0.8434 (m-30) REVERT: E 648 GLU cc_start: 0.9032 (tt0) cc_final: 0.8806 (tt0) REVERT: D 215 ILE cc_start: 0.8965 (mt) cc_final: 0.8463 (pt) REVERT: D 347 LYS cc_start: 0.8880 (tttt) cc_final: 0.8568 (ttpp) REVERT: D 373 THR cc_start: 0.9296 (m) cc_final: 0.8636 (p) REVERT: F 655 LYS cc_start: 0.8446 (tptm) cc_final: 0.8204 (tptt) outliers start: 27 outliers final: 22 residues processed: 199 average time/residue: 0.1183 time to fit residues: 35.8772 Evaluate side-chains 185 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 43 optimal weight: 0.0020 chunk 103 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091903 restraints weight = 26438.781| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.84 r_work: 0.2883 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16378 Z= 0.159 Angle : 0.605 9.395 22489 Z= 0.290 Chirality : 0.044 0.253 2871 Planarity : 0.003 0.037 2684 Dihedral : 6.232 59.515 4316 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.99 % Allowed : 10.50 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.95 (0.21), residues: 1655 helix: 1.98 (0.27), residues: 413 sheet: 0.64 (0.24), residues: 465 loop : -0.04 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.009 0.001 TYR C 191 PHE 0.010 0.002 PHE C 353 TRP 0.013 0.001 TRP B 571 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00375 (16234) covalent geometry : angle 0.56784 (22090) SS BOND : bond 0.00441 ( 33) SS BOND : angle 1.11303 ( 66) hydrogen bonds : bond 0.04632 ( 607) hydrogen bonds : angle 4.84825 ( 1731) link_ALPHA1-3 : bond 0.01163 ( 2) link_ALPHA1-3 : angle 1.68363 ( 6) link_ALPHA1-6 : bond 0.01012 ( 2) link_ALPHA1-6 : angle 1.77196 ( 6) link_BETA1-4 : bond 0.00501 ( 48) link_BETA1-4 : angle 1.68021 ( 144) link_NAG-ASN : bond 0.00244 ( 59) link_NAG-ASN : angle 1.82334 ( 177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9351 (m) cc_final: 0.9139 (t) REVERT: A 207 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7620 (tmtt) REVERT: A 381 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7861 (mt-10) REVERT: A 484 TYR cc_start: 0.9316 (p90) cc_final: 0.8988 (p90) REVERT: C 111 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8943 (mp) REVERT: C 246 GLN cc_start: 0.7791 (pm20) cc_final: 0.7546 (tp40) REVERT: E 616 ASN cc_start: 0.8752 (t0) cc_final: 0.8306 (t0) REVERT: E 624 ASP cc_start: 0.8508 (m-30) cc_final: 0.8253 (m-30) REVERT: E 648 GLU cc_start: 0.8795 (tt0) cc_final: 0.8561 (tt0) REVERT: D 46 LYS cc_start: 0.9034 (ptmt) cc_final: 0.8819 (ptmt) REVERT: D 215 ILE cc_start: 0.8896 (mt) cc_final: 0.8409 (pt) REVERT: D 347 LYS cc_start: 0.8815 (tttt) cc_final: 0.8543 (ttpp) REVERT: D 373 THR cc_start: 0.9289 (m) cc_final: 0.8619 (p) outliers start: 30 outliers final: 25 residues processed: 191 average time/residue: 0.1156 time to fit residues: 33.6880 Evaluate side-chains 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 3.9990 chunk 158 optimal weight: 0.3980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092789 restraints weight = 26275.569| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.83 r_work: 0.2895 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16378 Z= 0.136 Angle : 0.573 9.437 22489 Z= 0.276 Chirality : 0.043 0.248 2871 Planarity : 0.003 0.033 2684 Dihedral : 5.949 59.037 4316 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.93 % Allowed : 10.90 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1655 helix: 2.08 (0.27), residues: 413 sheet: 0.69 (0.24), residues: 465 loop : -0.07 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.010 0.001 TYR C 191 PHE 0.008 0.001 PHE C 233 TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (16234) covalent geometry : angle 0.53715 (22090) SS BOND : bond 0.00367 ( 33) SS BOND : angle 1.18513 ( 66) hydrogen bonds : bond 0.04311 ( 607) hydrogen bonds : angle 4.73636 ( 1731) link_ALPHA1-3 : bond 0.01159 ( 2) link_ALPHA1-3 : angle 1.74198 ( 6) link_ALPHA1-6 : bond 0.01031 ( 2) link_ALPHA1-6 : angle 1.75759 ( 6) link_BETA1-4 : bond 0.00474 ( 48) link_BETA1-4 : angle 1.55796 ( 144) link_NAG-ASN : bond 0.00227 ( 59) link_NAG-ASN : angle 1.74799 ( 177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8537 (mmtt) cc_final: 0.7669 (tmtt) REVERT: A 484 TYR cc_start: 0.9314 (p90) cc_final: 0.8983 (p90) REVERT: C 111 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8940 (mp) REVERT: E 616 ASN cc_start: 0.8738 (t0) cc_final: 0.8307 (t0) REVERT: E 624 ASP cc_start: 0.8485 (m-30) cc_final: 0.8224 (m-30) REVERT: E 648 GLU cc_start: 0.8784 (tt0) cc_final: 0.8540 (tt0) REVERT: D 215 ILE cc_start: 0.8888 (mt) cc_final: 0.8423 (pt) REVERT: D 347 LYS cc_start: 0.8830 (tttt) cc_final: 0.8544 (ttpp) REVERT: D 373 THR cc_start: 0.9268 (m) cc_final: 0.8599 (p) REVERT: F 616 ASN cc_start: 0.8401 (t0) cc_final: 0.8195 (p0) outliers start: 29 outliers final: 24 residues processed: 194 average time/residue: 0.1192 time to fit residues: 34.9131 Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 143 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093423 restraints weight = 26082.819| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.82 r_work: 0.2906 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16378 Z= 0.120 Angle : 0.552 9.437 22489 Z= 0.266 Chirality : 0.043 0.248 2871 Planarity : 0.003 0.031 2684 Dihedral : 5.642 59.528 4316 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.19 % Allowed : 11.10 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1655 helix: 2.19 (0.27), residues: 413 sheet: 0.72 (0.24), residues: 465 loop : -0.08 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.009 0.001 TYR A 486 PHE 0.009 0.001 PHE C 233 TRP 0.012 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00274 (16234) covalent geometry : angle 0.51916 (22090) SS BOND : bond 0.00442 ( 33) SS BOND : angle 1.00384 ( 66) hydrogen bonds : bond 0.04047 ( 607) hydrogen bonds : angle 4.63362 ( 1731) link_ALPHA1-3 : bond 0.01194 ( 2) link_ALPHA1-3 : angle 1.63885 ( 6) link_ALPHA1-6 : bond 0.01059 ( 2) link_ALPHA1-6 : angle 1.66047 ( 6) link_BETA1-4 : bond 0.00475 ( 48) link_BETA1-4 : angle 1.47636 ( 144) link_NAG-ASN : bond 0.00213 ( 59) link_NAG-ASN : angle 1.65235 ( 177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8557 (mmtt) cc_final: 0.7705 (tmtt) REVERT: A 484 TYR cc_start: 0.9282 (p90) cc_final: 0.8964 (p90) REVERT: B 660 LEU cc_start: 0.9269 (tt) cc_final: 0.8475 (mt) REVERT: C 111 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (mp) REVERT: E 616 ASN cc_start: 0.8731 (t0) cc_final: 0.8314 (t0) REVERT: E 624 ASP cc_start: 0.8459 (m-30) cc_final: 0.8192 (m-30) REVERT: E 648 GLU cc_start: 0.8781 (tt0) cc_final: 0.8538 (tt0) REVERT: D 161 MET cc_start: 0.8893 (tpt) cc_final: 0.8523 (tpt) REVERT: D 215 ILE cc_start: 0.8911 (mt) cc_final: 0.8463 (pt) REVERT: D 347 LYS cc_start: 0.8808 (tttt) cc_final: 0.8528 (ttpp) REVERT: D 373 THR cc_start: 0.9230 (m) cc_final: 0.8580 (p) REVERT: F 655 LYS cc_start: 0.8340 (tptp) cc_final: 0.7891 (mtpt) outliers start: 33 outliers final: 27 residues processed: 195 average time/residue: 0.1192 time to fit residues: 34.7123 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092590 restraints weight = 26392.499| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.83 r_work: 0.2891 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16378 Z= 0.141 Angle : 0.569 9.465 22489 Z= 0.274 Chirality : 0.043 0.247 2871 Planarity : 0.003 0.037 2684 Dihedral : 5.598 59.972 4316 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.19 % Allowed : 10.96 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.21), residues: 1655 helix: 2.10 (0.27), residues: 416 sheet: 0.72 (0.24), residues: 465 loop : -0.17 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.007 0.001 TYR A 173 PHE 0.010 0.001 PHE C 53 TRP 0.010 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00330 (16234) covalent geometry : angle 0.53725 (22090) SS BOND : bond 0.00425 ( 33) SS BOND : angle 1.01719 ( 66) hydrogen bonds : bond 0.04235 ( 607) hydrogen bonds : angle 4.66437 ( 1731) link_ALPHA1-3 : bond 0.01145 ( 2) link_ALPHA1-3 : angle 1.65981 ( 6) link_ALPHA1-6 : bond 0.01058 ( 2) link_ALPHA1-6 : angle 1.62977 ( 6) link_BETA1-4 : bond 0.00459 ( 48) link_BETA1-4 : angle 1.47796 ( 144) link_NAG-ASN : bond 0.00221 ( 59) link_NAG-ASN : angle 1.66380 ( 177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8566 (mmtt) cc_final: 0.7684 (tmtt) REVERT: A 484 TYR cc_start: 0.9284 (p90) cc_final: 0.8956 (p90) REVERT: C 111 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8939 (mp) REVERT: E 616 ASN cc_start: 0.8734 (t0) cc_final: 0.8330 (t0) REVERT: E 624 ASP cc_start: 0.8455 (m-30) cc_final: 0.8154 (m-30) REVERT: E 648 GLU cc_start: 0.8783 (tt0) cc_final: 0.8539 (tt0) REVERT: D 215 ILE cc_start: 0.8927 (mt) cc_final: 0.8483 (pt) REVERT: D 347 LYS cc_start: 0.8810 (tttt) cc_final: 0.8529 (ttpp) REVERT: D 373 THR cc_start: 0.9247 (m) cc_final: 0.8612 (p) REVERT: F 546 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8105 (m) REVERT: F 655 LYS cc_start: 0.8313 (tptp) cc_final: 0.7869 (mtpt) outliers start: 33 outliers final: 30 residues processed: 188 average time/residue: 0.1258 time to fit residues: 35.6510 Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091502 restraints weight = 26423.162| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.83 r_work: 0.2874 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16378 Z= 0.171 Angle : 0.597 9.468 22489 Z= 0.288 Chirality : 0.044 0.247 2871 Planarity : 0.003 0.040 2684 Dihedral : 5.716 59.123 4316 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.06 % Allowed : 11.16 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.91 (0.21), residues: 1655 helix: 2.01 (0.27), residues: 416 sheet: 0.85 (0.24), residues: 459 loop : -0.28 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.014 0.001 TYR A 173 PHE 0.010 0.002 PHE C 317 TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00406 (16234) covalent geometry : angle 0.56630 (22090) SS BOND : bond 0.00609 ( 33) SS BOND : angle 1.15495 ( 66) hydrogen bonds : bond 0.04498 ( 607) hydrogen bonds : angle 4.76115 ( 1731) link_ALPHA1-3 : bond 0.01160 ( 2) link_ALPHA1-3 : angle 1.61032 ( 6) link_ALPHA1-6 : bond 0.01039 ( 2) link_ALPHA1-6 : angle 1.61937 ( 6) link_BETA1-4 : bond 0.00461 ( 48) link_BETA1-4 : angle 1.48407 ( 144) link_NAG-ASN : bond 0.00241 ( 59) link_NAG-ASN : angle 1.68574 ( 177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8547 (mmtt) cc_final: 0.7684 (tmtt) REVERT: A 484 TYR cc_start: 0.9284 (p90) cc_final: 0.8932 (p90) REVERT: B 590 GLN cc_start: 0.8972 (mm110) cc_final: 0.8745 (mm-40) REVERT: C 111 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8960 (mp) REVERT: E 616 ASN cc_start: 0.8738 (t0) cc_final: 0.8386 (t0) REVERT: E 624 ASP cc_start: 0.8476 (m-30) cc_final: 0.8187 (m-30) REVERT: E 648 GLU cc_start: 0.8773 (tt0) cc_final: 0.8528 (tt0) REVERT: D 161 MET cc_start: 0.8932 (tpt) cc_final: 0.8568 (tpt) REVERT: D 215 ILE cc_start: 0.8932 (mt) cc_final: 0.8481 (pt) REVERT: D 347 LYS cc_start: 0.8812 (tttt) cc_final: 0.8539 (ttpp) REVERT: D 373 THR cc_start: 0.9270 (m) cc_final: 0.8638 (p) REVERT: F 546 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8124 (m) REVERT: F 655 LYS cc_start: 0.8320 (tptp) cc_final: 0.7871 (mtpt) outliers start: 31 outliers final: 28 residues processed: 189 average time/residue: 0.1152 time to fit residues: 33.0365 Evaluate side-chains 195 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093202 restraints weight = 26244.186| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.82 r_work: 0.2903 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16378 Z= 0.121 Angle : 0.551 9.425 22489 Z= 0.267 Chirality : 0.043 0.247 2871 Planarity : 0.003 0.034 2684 Dihedral : 5.466 59.222 4316 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.06 % Allowed : 11.36 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.21), residues: 1655 helix: 2.18 (0.27), residues: 413 sheet: 0.91 (0.24), residues: 459 loop : -0.17 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.015 0.001 TYR A 173 PHE 0.009 0.001 PHE C 233 TRP 0.010 0.001 TRP B 571 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00279 (16234) covalent geometry : angle 0.52119 (22090) SS BOND : bond 0.00422 ( 33) SS BOND : angle 1.05800 ( 66) hydrogen bonds : bond 0.04031 ( 607) hydrogen bonds : angle 4.62195 ( 1731) link_ALPHA1-3 : bond 0.01183 ( 2) link_ALPHA1-3 : angle 1.47928 ( 6) link_ALPHA1-6 : bond 0.01064 ( 2) link_ALPHA1-6 : angle 1.48655 ( 6) link_BETA1-4 : bond 0.00461 ( 48) link_BETA1-4 : angle 1.39037 ( 144) link_NAG-ASN : bond 0.00213 ( 59) link_NAG-ASN : angle 1.60813 ( 177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8555 (mmtt) cc_final: 0.7705 (tmtt) REVERT: A 484 TYR cc_start: 0.9235 (p90) cc_final: 0.8902 (p90) REVERT: B 660 LEU cc_start: 0.9272 (tt) cc_final: 0.8434 (mt) REVERT: E 616 ASN cc_start: 0.8716 (t0) cc_final: 0.8356 (t0) REVERT: E 624 ASP cc_start: 0.8456 (m-30) cc_final: 0.8147 (m-30) REVERT: E 648 GLU cc_start: 0.8750 (tt0) cc_final: 0.8503 (tt0) REVERT: D 215 ILE cc_start: 0.8932 (mt) cc_final: 0.8468 (pt) REVERT: D 347 LYS cc_start: 0.8810 (tttt) cc_final: 0.8519 (ttpp) REVERT: D 373 THR cc_start: 0.9238 (m) cc_final: 0.8611 (p) REVERT: F 546 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8106 (m) REVERT: F 655 LYS cc_start: 0.8292 (tptp) cc_final: 0.7848 (mtpt) outliers start: 31 outliers final: 28 residues processed: 194 average time/residue: 0.1214 time to fit residues: 35.6864 Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.090433 restraints weight = 26247.896| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.81 r_work: 0.2858 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16378 Z= 0.207 Angle : 0.636 9.497 22489 Z= 0.305 Chirality : 0.045 0.251 2871 Planarity : 0.004 0.047 2684 Dihedral : 5.851 59.768 4316 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 11.43 % Favored : 86.64 % 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: 0.77 (0.21), residues: 1655 helix: 1.83 (0.27), residues: 416 sheet: 1.13 (0.26), residues: 387 loop : -0.43 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 542 TYR 0.015 0.001 TYR A 173 PHE 0.012 0.002 PHE C 317 TRP 0.013 0.001 TRP C 96 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00499 (16234) covalent geometry : angle 0.60543 (22090) SS BOND : bond 0.00466 ( 33) SS BOND : angle 1.18242 ( 66) hydrogen bonds : bond 0.04828 ( 607) hydrogen bonds : angle 4.88085 ( 1731) link_ALPHA1-3 : bond 0.01118 ( 2) link_ALPHA1-3 : angle 1.62626 ( 6) link_ALPHA1-6 : bond 0.01023 ( 2) link_ALPHA1-6 : angle 1.59765 ( 6) link_BETA1-4 : bond 0.00458 ( 48) link_BETA1-4 : angle 1.52769 ( 144) link_NAG-ASN : bond 0.00291 ( 59) link_NAG-ASN : angle 1.73487 ( 177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.75 seconds wall clock time: 54 minutes 12.25 seconds (3252.25 seconds total)