Starting phenix.real_space_refine on Sat Mar 16 23:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_23229_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_23229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_23229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_23229_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8c_23229/03_2024/7l8c_23229_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 8.74, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 41 helices and 32 sheets defined 25.5% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.627A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 335 through 353 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 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.915A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 543 removed outlier: 5.228A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 662 removed outlier: 5.050A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 650 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 661 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.586A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 335 through 353 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 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.515A pdb=" N TRP C 479 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 543 removed outlier: 4.333A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL E 539 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 619 through 625 Processing helix chain 'E' and resid 628 through 634 Processing helix chain 'E' and resid 636 through 662 removed outlier: 4.384A pdb=" N GLN E 640 " --> pdb=" O ASN E 637 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 643 " --> pdb=" O GLN E 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.632A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 140 through 150 No H-bonds generated for 'chain 'D' and resid 140 through 150' Processing helix chain 'D' and resid 335 through 352 removed outlier: 4.034A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'F' and resid 530 through 543 removed outlier: 5.008A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 619 through 625 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 663 removed outlier: 5.007A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'A' and resid 200 through 203 Processing sheet with id= G, first strand: chain 'A' and resid 271 through 274 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) removed outlier: 8.454A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.866A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 302 through 308 removed outlier: 6.017A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= K, 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= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= N, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= P, first strand: chain 'C' and resid 271 through 274 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) removed outlier: 8.540A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.999A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.917A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= T, 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= U, first strand: chain 'D' and resid 53 through 55 Processing sheet with id= V, first strand: chain 'D' and resid 130 through 133 Processing sheet with id= W, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= X, first strand: chain 'D' and resid 200 through 203 Processing sheet with id= Y, first strand: chain 'D' and resid 271 through 274 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) removed outlier: 8.580A pdb=" N ALA D 362 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.006A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 301 through 308 removed outlier: 3.895A pdb=" N ASN D 301 " --> pdb=" O ILE D 323A" (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id= AB, 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= AC, first strand: chain 'H' and resid 55 through 57 removed outlier: 6.847A pdb=" N UNK H 35 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N UNK H 48 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N UNK H 33 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= AE, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.181A pdb=" N UNK L 103 " --> pdb=" O UNK L 11 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N UNK L 13 " --> pdb=" O UNK L 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N UNK L 105 " --> pdb=" O UNK L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'L' and resid 87 through 90 removed outlier: 5.607A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1257 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: 5.48 Time building geometry restraints manager: 7.78 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: 99.23 - 106.40: 571 106.40 - 113.57: 9299 113.57 - 120.74: 7111 120.74 - 127.91: 4934 127.91 - 135.07: 175 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: 14124 3.19 - 3.76: 22487 3.76 - 4.33: 33357 4.33 - 4.90: 52044 Nonbonded interactions: 122179 Sorted by model distance: nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.049 2.440 nonbonded pdb=" O HIS B 570 " pdb=" N ILE B 573 " model vdw 2.064 2.520 nonbonded pdb=" O THR F 569 " pdb=" OG1 THR F 569 " model vdw 2.220 2.440 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 122174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 503 or resid 601 through 603)) selection = (chain 'C' and (resid 33 through 503 or resid 601 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.900 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 44.640 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.500 ------------------------------------------------------------------------------- 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 0.220 16234 Z= 1.609 Angle : 1.740 13.838 22090 Z= 1.096 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (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 TRP 0.056 0.010 TRP A 35 HIS 0.020 0.003 HIS F 570 PHE 0.034 0.006 PHE D 383 TYR 0.048 0.007 TYR D 484 ARG 0.011 0.001 ARG D 166 *********************** 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 fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7977 (tmtt) REVERT: A 464 THR cc_start: 0.7658 (p) cc_final: 0.7388 (t) REVERT: E 616 ASN cc_start: 0.8606 (t0) cc_final: 0.8224 (t0) REVERT: E 624 ASP cc_start: 0.8500 (m-30) cc_final: 0.8277 (m-30) REVERT: E 632 ASP cc_start: 0.8723 (t70) cc_final: 0.8513 (t0) REVERT: D 102 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8423 (mm-30) REVERT: D 207 LYS cc_start: 0.8717 (pttt) cc_final: 0.8314 (mmtt) REVERT: D 462 ASN cc_start: 0.7484 (t0) cc_final: 0.7152 (p0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3289 time to fit residues: 146.7858 Evaluate side-chains 164 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 302 ASN D 374 HIS F 575 GLN F 607 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16234 Z= 0.233 Angle : 0.678 12.661 22090 Z= 0.346 Chirality : 0.046 0.305 2871 Planarity : 0.005 0.028 2684 Dihedral : 9.420 79.619 4316 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.33 % Allowed : 5.85 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1655 helix: 0.76 (0.25), residues: 413 sheet: 0.72 (0.22), residues: 501 loop : 0.38 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 571 HIS 0.003 0.001 HIS A 105 PHE 0.015 0.002 PHE C 53 TYR 0.012 0.001 TYR C 191 ARG 0.006 0.001 ARG D 151 *********************** 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 246 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7798 (tmtt) REVERT: A 484 TYR cc_start: 0.9175 (p90) cc_final: 0.8860 (p90) REVERT: B 660 LEU cc_start: 0.9151 (tt) cc_final: 0.8906 (mt) REVERT: C 503 ARG cc_start: 0.7956 (tpm170) cc_final: 0.7554 (tpp-160) REVERT: E 545 LEU cc_start: 0.8234 (mt) cc_final: 0.7916 (mt) REVERT: E 616 ASN cc_start: 0.8515 (t0) cc_final: 0.8272 (t0) REVERT: E 632 ASP cc_start: 0.8556 (t70) cc_final: 0.8307 (t0) REVERT: D 462 ASN cc_start: 0.7233 (t0) cc_final: 0.6996 (p0) outliers start: 20 outliers final: 9 residues processed: 235 average time/residue: 0.2637 time to fit residues: 92.2317 Evaluate side-chains 180 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 93 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 652 GLN B 658 GLN C 85 HIS C 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 16234 Z= 0.525 Angle : 0.777 11.783 22090 Z= 0.383 Chirality : 0.051 0.270 2871 Planarity : 0.005 0.046 2684 Dihedral : 8.259 70.076 4316 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.26 % Allowed : 9.10 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1655 helix: 0.13 (0.25), residues: 416 sheet: 0.47 (0.23), residues: 471 loop : -0.27 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 45 HIS 0.007 0.002 HIS D 105 PHE 0.022 0.003 PHE A 53 TYR 0.013 0.002 TYR C 191 ARG 0.006 0.001 ARG D 192 *********************** 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 211 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7733 (tmtt) REVERT: B 660 LEU cc_start: 0.9196 (tt) cc_final: 0.8911 (mt) REVERT: C 42 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8863 (m) REVERT: C 161 MET cc_start: 0.8902 (tpp) cc_final: 0.8687 (tpp) REVERT: C 207 LYS cc_start: 0.8532 (pttt) cc_final: 0.8192 (ptpp) REVERT: C 373 THR cc_start: 0.9320 (m) cc_final: 0.8977 (p) REVERT: E 616 ASN cc_start: 0.8567 (t0) cc_final: 0.8120 (t0) REVERT: E 632 ASP cc_start: 0.8901 (t70) cc_final: 0.8559 (t0) REVERT: E 648 GLU cc_start: 0.8513 (tt0) cc_final: 0.8308 (tt0) REVERT: D 161 MET cc_start: 0.8860 (tpt) cc_final: 0.8512 (tpt) REVERT: D 217 TYR cc_start: 0.8738 (m-80) cc_final: 0.8471 (m-80) REVERT: D 462 ASN cc_start: 0.7324 (t0) cc_final: 0.7068 (p0) outliers start: 34 outliers final: 25 residues processed: 203 average time/residue: 0.2615 time to fit residues: 80.4790 Evaluate side-chains 185 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 A residue 198 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 569 THR 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 42 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 634 GLU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16234 Z= 0.189 Angle : 0.577 9.385 22090 Z= 0.290 Chirality : 0.044 0.275 2871 Planarity : 0.004 0.033 2684 Dihedral : 7.082 65.853 4316 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 10.10 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1655 helix: 0.25 (0.26), residues: 416 sheet: 0.53 (0.24), residues: 465 loop : -0.22 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 571 HIS 0.003 0.001 HIS A 105 PHE 0.010 0.001 PHE C 353 TYR 0.012 0.001 TYR C 191 ARG 0.003 0.000 ARG A 166 *********************** 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 214 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7693 (tmtt) REVERT: B 648 GLU cc_start: 0.8594 (tp30) cc_final: 0.8111 (tt0) REVERT: B 660 LEU cc_start: 0.9153 (tt) cc_final: 0.8875 (mt) REVERT: C 246 GLN cc_start: 0.7731 (pm20) cc_final: 0.7326 (tp-100) REVERT: C 373 THR cc_start: 0.9266 (m) cc_final: 0.8912 (p) REVERT: E 616 ASN cc_start: 0.8453 (t0) cc_final: 0.8096 (t0) REVERT: E 632 ASP cc_start: 0.8773 (t70) cc_final: 0.8385 (t0) REVERT: D 161 MET cc_start: 0.8838 (tpt) cc_final: 0.8539 (tpt) REVERT: D 462 ASN cc_start: 0.7321 (t0) cc_final: 0.7092 (p0) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 0.2770 time to fit residues: 83.5524 Evaluate side-chains 189 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 569 THR Chi-restraints excluded: chain F residue 601 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 0.0770 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16234 Z= 0.268 Angle : 0.578 9.354 22090 Z= 0.289 Chirality : 0.044 0.267 2871 Planarity : 0.004 0.037 2684 Dihedral : 6.653 60.714 4316 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.93 % Allowed : 10.83 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1655 helix: 0.22 (0.26), residues: 416 sheet: 0.43 (0.24), residues: 465 loop : -0.29 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 571 HIS 0.003 0.001 HIS D 374 PHE 0.011 0.002 PHE C 353 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.000 ARG D 166 *********************** 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 203 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7743 (tmtt) REVERT: B 648 GLU cc_start: 0.8508 (tp30) cc_final: 0.8251 (tt0) REVERT: B 660 LEU cc_start: 0.9165 (tt) cc_final: 0.8875 (mt) REVERT: C 111 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9094 (mp) REVERT: C 246 GLN cc_start: 0.7878 (pm20) cc_final: 0.7475 (tp40) REVERT: E 616 ASN cc_start: 0.8442 (t0) cc_final: 0.8129 (t0) REVERT: E 632 ASP cc_start: 0.8838 (t70) cc_final: 0.8494 (t0) REVERT: D 161 MET cc_start: 0.8821 (tpt) cc_final: 0.8567 (tpt) REVERT: D 205 CYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6545 (m) REVERT: D 347 LYS cc_start: 0.8818 (tttt) cc_final: 0.8573 (ttpp) REVERT: D 462 ASN cc_start: 0.7321 (t0) cc_final: 0.7118 (p0) outliers start: 29 outliers final: 25 residues processed: 194 average time/residue: 0.2764 time to fit residues: 79.8072 Evaluate side-chains 194 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER 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 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 84 ILE 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 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16234 Z= 0.332 Angle : 0.604 9.444 22090 Z= 0.299 Chirality : 0.045 0.272 2871 Planarity : 0.004 0.038 2684 Dihedral : 6.606 58.116 4316 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.19 % Allowed : 10.90 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1655 helix: 0.14 (0.26), residues: 416 sheet: 0.37 (0.24), residues: 465 loop : -0.42 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 571 HIS 0.004 0.001 HIS D 374 PHE 0.011 0.002 PHE C 353 TYR 0.011 0.001 TYR A 173 ARG 0.003 0.001 ARG F 617 *********************** 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 199 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8680 (tpt) cc_final: 0.8388 (tpt) REVERT: B 648 GLU cc_start: 0.8547 (tp30) cc_final: 0.8290 (tt0) REVERT: B 660 LEU cc_start: 0.9174 (tt) cc_final: 0.8872 (mt) REVERT: C 111 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9108 (mp) REVERT: C 207 LYS cc_start: 0.8500 (pttt) cc_final: 0.8226 (ptpp) REVERT: C 246 GLN cc_start: 0.7931 (pm20) cc_final: 0.7489 (tp40) REVERT: E 616 ASN cc_start: 0.8468 (t0) cc_final: 0.8200 (t0) REVERT: E 632 ASP cc_start: 0.8878 (t70) cc_final: 0.8522 (t0) REVERT: D 161 MET cc_start: 0.8835 (tpt) cc_final: 0.8600 (tpt) outliers start: 33 outliers final: 27 residues processed: 189 average time/residue: 0.2726 time to fit residues: 77.5590 Evaluate side-chains 188 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER 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 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16234 Z= 0.201 Angle : 0.532 9.413 22090 Z= 0.267 Chirality : 0.043 0.264 2871 Planarity : 0.004 0.033 2684 Dihedral : 6.120 59.090 4316 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.66 % Allowed : 11.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1655 helix: 0.32 (0.27), residues: 416 sheet: 0.65 (0.24), residues: 465 loop : -0.39 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.003 0.001 HIS A 105 PHE 0.009 0.001 PHE D 53 TYR 0.011 0.001 TYR C 191 ARG 0.002 0.000 ARG A 166 *********************** 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 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8669 (tpt) cc_final: 0.8392 (tpt) REVERT: B 633 LYS cc_start: 0.9213 (mttm) cc_final: 0.8966 (mmtm) REVERT: B 660 LEU cc_start: 0.9145 (tt) cc_final: 0.8857 (mt) REVERT: C 246 GLN cc_start: 0.7858 (pm20) cc_final: 0.7382 (tp40) REVERT: E 616 ASN cc_start: 0.8335 (t0) cc_final: 0.8131 (t0) REVERT: E 632 ASP cc_start: 0.8850 (t70) cc_final: 0.8454 (t0) REVERT: D 161 MET cc_start: 0.8777 (tpt) cc_final: 0.8560 (tpt) outliers start: 25 outliers final: 20 residues processed: 187 average time/residue: 0.2694 time to fit residues: 75.1140 Evaluate side-chains 183 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16234 Z= 0.313 Angle : 0.585 9.468 22090 Z= 0.289 Chirality : 0.045 0.260 2871 Planarity : 0.004 0.038 2684 Dihedral : 6.238 59.960 4316 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 11.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1655 helix: 0.23 (0.26), residues: 416 sheet: 0.60 (0.24), residues: 459 loop : -0.53 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 96 HIS 0.003 0.001 HIS D 374 PHE 0.011 0.002 PHE C 53 TYR 0.012 0.001 TYR A 173 ARG 0.004 0.000 ARG E 542 *********************** 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 194 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8703 (tpt) cc_final: 0.8398 (tpt) REVERT: B 660 LEU cc_start: 0.9166 (tt) cc_final: 0.8865 (mt) REVERT: C 246 GLN cc_start: 0.7822 (pm20) cc_final: 0.7267 (tp40) REVERT: E 616 ASN cc_start: 0.8406 (t0) cc_final: 0.8193 (t0) REVERT: E 632 ASP cc_start: 0.8871 (t70) cc_final: 0.8458 (t0) REVERT: D 161 MET cc_start: 0.8785 (tpt) cc_final: 0.8576 (tpt) outliers start: 28 outliers final: 26 residues processed: 184 average time/residue: 0.2784 time to fit residues: 76.2396 Evaluate side-chains 188 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER 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 C residue 248 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 166 optimal weight: 20.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16234 Z= 0.225 Angle : 0.540 9.411 22090 Z= 0.269 Chirality : 0.043 0.262 2871 Planarity : 0.004 0.033 2684 Dihedral : 5.979 59.165 4316 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.66 % Allowed : 11.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1655 helix: 0.32 (0.27), residues: 416 sheet: 0.44 (0.26), residues: 405 loop : -0.46 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.003 0.001 HIS A 105 PHE 0.009 0.001 PHE C 233 TYR 0.014 0.001 TYR A 173 ARG 0.003 0.000 ARG E 542 *********************** 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 194 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8682 (tpt) cc_final: 0.8387 (tpt) REVERT: B 660 LEU cc_start: 0.9150 (tt) cc_final: 0.8867 (mt) REVERT: C 161 MET cc_start: 0.8808 (tpp) cc_final: 0.8576 (tpp) REVERT: C 246 GLN cc_start: 0.7778 (pm20) cc_final: 0.7333 (tp40) REVERT: E 632 ASP cc_start: 0.8825 (t70) cc_final: 0.8411 (t0) outliers start: 25 outliers final: 22 residues processed: 187 average time/residue: 0.2742 time to fit residues: 76.5050 Evaluate side-chains 186 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 303 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 chunk 113 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16234 Z= 0.299 Angle : 0.582 9.428 22090 Z= 0.289 Chirality : 0.044 0.259 2871 Planarity : 0.004 0.039 2684 Dihedral : 6.109 59.640 4316 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.46 % Allowed : 11.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1655 helix: 0.26 (0.26), residues: 416 sheet: 0.37 (0.26), residues: 405 loop : -0.54 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.003 0.001 HIS D 374 PHE 0.010 0.002 PHE C 353 TYR 0.014 0.001 TYR A 173 ARG 0.005 0.000 ARG E 542 ********************** 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 194 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8706 (tpt) cc_final: 0.8408 (tpt) REVERT: B 660 LEU cc_start: 0.9166 (tt) cc_final: 0.8871 (mt) REVERT: C 246 GLN cc_start: 0.7883 (pm20) cc_final: 0.7287 (tp40) REVERT: E 632 ASP cc_start: 0.8888 (t70) cc_final: 0.8459 (t0) REVERT: D 161 MET cc_start: 0.8482 (tpt) cc_final: 0.8018 (tpt) REVERT: F 574 LYS cc_start: 0.8214 (tppt) cc_final: 0.7894 (ttmt) outliers start: 22 outliers final: 20 residues processed: 189 average time/residue: 0.2765 time to fit residues: 78.2373 Evaluate side-chains 186 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS 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 303 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 356 ASN 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 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.092448 restraints weight = 26455.573| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.82 r_work: 0.2893 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16234 Z= 0.160 Angle : 0.508 9.402 22090 Z= 0.256 Chirality : 0.042 0.263 2871 Planarity : 0.004 0.031 2684 Dihedral : 5.616 58.666 4316 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.20 % Allowed : 12.29 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1655 helix: 0.55 (0.27), residues: 410 sheet: 0.54 (0.26), residues: 405 loop : -0.41 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 69 HIS 0.003 0.000 HIS A 105 PHE 0.010 0.001 PHE C 233 TYR 0.016 0.001 TYR A 173 ARG 0.003 0.000 ARG E 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.85 seconds wall clock time: 54 minutes 6.10 seconds (3246.10 seconds total)