Starting phenix.real_space_refine on Wed Mar 4 20:02:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l89_23226/03_2026/7l89_23226.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 9758 2.51 5 N 2618 2.21 5 O 3204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15679 Number of models: 1 Model: "" Number of chains: 51 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 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: 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: 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: 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: "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: 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: "Y" 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: "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: 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: "l" 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: "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: 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: "E" 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: "F" 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: "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: "C" 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: "B" 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: "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 Time building chain proxies: 3.89, per 1000 atoms: 0.25 Number of scatterers: 15679 At special positions: 0 Unit cell: (128.75, 122.57, 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 3204 8.00 N 2618 7.00 C 9758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.03 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 C 605 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.07 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.07 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA Y 3 " - " MAN Y 5 " " BMA l 3 " - " MAN l 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 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 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 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-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 137 " " NAG B 601 " - " ASN B 133 " " NAG B 602 " - " ASN B 234 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 137 " " NAG C 701 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG G 1 " - " ASN E 156 " " NAG I 1 " - " ASN E 197 " " NAG J 1 " - " ASN E 234 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 295 " " NAG O 1 " - " ASN E 301 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN E 386 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 88 " " NAG U 1 " - " ASN F 611 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 197 " " NAG X 1 " - " ASN A 234 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 332 " " NAG c 1 " - " ASN A 386 " " NAG d 1 " - " ASN A 392 " " NAG e 1 " - " ASN A 448 " " NAG f 1 " - " ASN A 88 " " NAG g 1 " - " ASN C 611 " " NAG h 1 " - " ASN C 618 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 262 " " NAG m 1 " - " ASN B 276 " " NAG n 1 " - " ASN B 295 " " NAG o 1 " - " ASN B 301 " " NAG p 1 " - " ASN B 332 " " NAG q 1 " - " ASN B 386 " " NAG r 1 " - " ASN B 392 " " NAG s 1 " - " ASN B 448 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 497.5 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 41 sheets defined 26.7% alpha, 73.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.176A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.058A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.398A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.511A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.703A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.152A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.039A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.818A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 596 removed outlier: 3.531A pdb=" N LYS C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 661 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.200A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.953A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.995A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.923A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 3.735A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 44 through 45 removed outlier: 6.577A pdb=" N UNK H 34 " --> pdb=" O UNK H 94 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N UNK H 112 " --> pdb=" O UNK H 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.551A pdb=" N UNK H 51 " --> pdb=" O UNK H 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.457A pdb=" N UNK H 66 " --> pdb=" O UNK H 78 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N UNK H 78 " --> pdb=" O UNK H 66 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N UNK H 68 " --> pdb=" O UNK H 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.390A pdb=" N UNK L 36 " --> pdb=" O UNK L 48 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N UNK L 97 " --> pdb=" O UNK L 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.498A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.801A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AB2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.168A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.455A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.658A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.455A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.571A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.716A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.420A pdb=" N VAL C 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N TYR A 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N CYS C 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.699A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AC4, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC5, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.089A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.395A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.502A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.395A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.389A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.787A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.380A pdb=" N VAL D 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR D 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR B 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS D 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.757A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AD7, first strand: chain 'B' and resid 169 through 176 Processing sheet with id=AD8, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.208A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.324A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.620A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.324A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.470A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE B 323 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN B 301 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.788A pdb=" N THR B 450 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1944 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: 3.14 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 2619 1.31 - 1.45: 4815 1.45 - 1.59: 8327 1.59 - 1.73: 59 1.73 - 1.87: 127 Bond restraints: 15947 Sorted by residual: bond pdb=" CB ASN A 195 " pdb=" CG ASN A 195 " ideal model delta sigma weight residual 1.516 1.347 0.169 2.50e-02 1.60e+03 4.57e+01 bond pdb=" CB ASN E 195 " pdb=" CG ASN E 195 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.24e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.87e+01 bond pdb=" C LYS D 655 " pdb=" O LYS D 655 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.19e-02 7.06e+03 3.71e+01 bond pdb=" NE ARG B 503 " pdb=" CZ ARG B 503 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.44e+01 ... (remaining 15942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 20887 4.03 - 8.05: 760 8.05 - 12.08: 36 12.08 - 16.11: 7 16.11 - 20.13: 2 Bond angle restraints: 21692 Sorted by residual: angle pdb=" N ASP A 141 " pdb=" CA ASP A 141 " pdb=" C ASP A 141 " ideal model delta sigma weight residual 113.88 93.75 20.13 1.23e+00 6.61e-01 2.68e+02 angle pdb=" N LEU D 544 " pdb=" CA LEU D 544 " pdb=" C LEU D 544 " ideal model delta sigma weight residual 110.48 98.59 11.89 1.48e+00 4.57e-01 6.46e+01 angle pdb=" C CYS B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 119.56 127.60 -8.04 1.02e+00 9.61e-01 6.22e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 127.22 -7.66 1.02e+00 9.61e-01 5.64e+01 angle pdb=" N SER B 56 " pdb=" CA SER B 56 " pdb=" C SER B 56 " ideal model delta sigma weight residual 113.89 125.65 -11.76 1.58e+00 4.01e-01 5.54e+01 ... (remaining 21687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 10579 21.24 - 42.47: 210 42.47 - 63.71: 64 63.71 - 84.94: 26 84.94 - 106.18: 12 Dihedral angle restraints: 10891 sinusoidal: 5415 harmonic: 5476 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.56 -63.56 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.28 -60.28 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 147.90 -54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 10888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2121 0.158 - 0.315: 494 0.315 - 0.473: 166 0.473 - 0.631: 8 0.631 - 0.789: 1 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-02 2.50e+03 1.55e+03 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.69e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 ... (remaining 2787 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " 0.342 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG j 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.338 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG h 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " 0.314 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG h 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " 0.200 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 155 2.62 - 3.19: 13566 3.19 - 3.76: 21981 3.76 - 4.33: 33196 4.33 - 4.90: 51310 Nonbonded interactions: 120208 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.051 3.040 nonbonded pdb=" O3 NAG g 2 " pdb=" O7 NAG g 2 " model vdw 2.119 3.040 nonbonded pdb=" O3 NAG g 1 " pdb=" O7 NAG g 1 " model vdw 2.266 3.040 nonbonded pdb=" N ASP A 141 " pdb=" N MET A 150 " model vdw 2.279 2.560 nonbonded pdb=" O UNK H 51 " pdb=" O UNK H 54 " model vdw 2.319 3.040 ... (remaining 120203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 604) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 519 through 701) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' 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' 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 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } ncs_group { reference = (chain 'H' and resid 20 through 116) selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'Y' 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 group one per residue 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: 3.510 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.024 0.169 16080 Z= 1.245 Angle : 1.818 20.134 22058 Z= 1.106 Chirality : 0.153 0.789 2790 Planarity : 0.016 0.294 2646 Dihedral : 10.667 106.178 7226 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1635 helix: -0.04 (0.24), residues: 378 sheet: 1.03 (0.22), residues: 474 loop : 0.70 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.045 0.007 TYR B 486 PHE 0.024 0.007 PHE B 383 TRP 0.043 0.009 TRP E 35 HIS 0.008 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.02323 (15947) covalent geometry : angle 1.76097 (21692) SS BOND : bond 0.01385 ( 33) SS BOND : angle 3.16399 ( 66) hydrogen bonds : bond 0.17231 ( 548) hydrogen bonds : angle 8.04661 ( 1944) link_ALPHA1-3 : bond 0.08162 ( 3) link_ALPHA1-3 : angle 4.26315 ( 9) link_ALPHA1-6 : bond 0.06039 ( 3) link_ALPHA1-6 : angle 3.85801 ( 9) link_BETA1-4 : bond 0.06914 ( 40) link_BETA1-4 : angle 5.13525 ( 120) link_NAG-ASN : bond 0.07068 ( 54) link_NAG-ASN : angle 3.05969 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 579 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8569 (mtm-85) REVERT: A 432 GLN cc_start: 0.8460 (mp10) cc_final: 0.8169 (mp10) REVERT: B 342 LEU cc_start: 0.9450 (tp) cc_final: 0.9208 (tp) REVERT: D 573 ILE cc_start: 0.9047 (tp) cc_final: 0.8769 (tt) REVERT: D 659 ASP cc_start: 0.8383 (m-30) cc_final: 0.7737 (m-30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1683 time to fit residues: 57.3046 Evaluate side-chains 132 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN A 33 ASN A 130 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056826 restraints weight = 47462.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058845 restraints weight = 24027.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.060197 restraints weight = 15978.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.061066 restraints weight = 12319.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.061648 restraints weight = 10431.677| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16080 Z= 0.160 Angle : 0.772 14.721 22058 Z= 0.367 Chirality : 0.048 0.400 2790 Planarity : 0.004 0.040 2646 Dihedral : 8.466 84.549 4061 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.74 % Allowed : 5.22 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1635 helix: 1.54 (0.28), residues: 384 sheet: 1.05 (0.24), residues: 408 loop : 0.53 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 178 TYR 0.021 0.001 TYR A 217 PHE 0.015 0.002 PHE A 353 TRP 0.026 0.002 TRP D 571 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00345 (15947) covalent geometry : angle 0.71245 (21692) SS BOND : bond 0.00261 ( 33) SS BOND : angle 0.72999 ( 66) hydrogen bonds : bond 0.06366 ( 548) hydrogen bonds : angle 5.65773 ( 1944) link_ALPHA1-3 : bond 0.01319 ( 3) link_ALPHA1-3 : angle 1.65242 ( 9) link_ALPHA1-6 : bond 0.00515 ( 3) link_ALPHA1-6 : angle 2.05364 ( 9) link_BETA1-4 : bond 0.00820 ( 40) link_BETA1-4 : angle 2.84389 ( 120) link_NAG-ASN : bond 0.00525 ( 54) link_NAG-ASN : angle 2.57235 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: F 588 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8420 (ttm110) REVERT: F 621 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: C 530 MET cc_start: 0.8677 (mtp) cc_final: 0.8257 (mtp) REVERT: C 657 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8036 (pt0) REVERT: D 617 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8824 (mmm-85) REVERT: D 659 ASP cc_start: 0.8491 (m-30) cc_final: 0.8039 (m-30) outliers start: 11 outliers final: 4 residues processed: 182 average time/residue: 0.1275 time to fit residues: 33.8706 Evaluate side-chains 143 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 167 optimal weight: 0.0770 chunk 172 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 99 ASN D 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.056251 restraints weight = 47761.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058262 restraints weight = 24171.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.059619 restraints weight = 16013.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.060516 restraints weight = 12328.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.061119 restraints weight = 10346.543| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16080 Z= 0.137 Angle : 0.627 11.477 22058 Z= 0.298 Chirality : 0.044 0.380 2790 Planarity : 0.004 0.068 2646 Dihedral : 7.401 72.487 4061 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.87 % Allowed : 6.09 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1635 helix: 1.83 (0.28), residues: 384 sheet: 0.75 (0.23), residues: 462 loop : 0.37 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 588 TYR 0.020 0.001 TYR A 217 PHE 0.012 0.001 PHE B 53 TRP 0.015 0.001 TRP D 571 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00305 (15947) covalent geometry : angle 0.58816 (21692) SS BOND : bond 0.00222 ( 33) SS BOND : angle 0.45306 ( 66) hydrogen bonds : bond 0.04587 ( 548) hydrogen bonds : angle 4.79174 ( 1944) link_ALPHA1-3 : bond 0.01216 ( 3) link_ALPHA1-3 : angle 1.43284 ( 9) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 1.84205 ( 9) link_BETA1-4 : bond 0.00544 ( 40) link_BETA1-4 : angle 1.99930 ( 120) link_NAG-ASN : bond 0.00294 ( 54) link_NAG-ASN : angle 1.95227 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: F 588 ARG cc_start: 0.8729 (ttp-110) cc_final: 0.8418 (ttm110) REVERT: F 621 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: A 475 MET cc_start: 0.8965 (mmm) cc_final: 0.8425 (mmm) REVERT: C 530 MET cc_start: 0.8980 (mtp) cc_final: 0.8491 (mtp) REVERT: C 574 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8741 (ttmt) REVERT: C 584 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8490 (mt-10) REVERT: C 622 ILE cc_start: 0.9329 (mt) cc_final: 0.8802 (tp) REVERT: C 654 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7229 (tp30) REVERT: C 657 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8102 (pt0) REVERT: D 659 ASP cc_start: 0.8395 (m-30) cc_final: 0.7938 (m-30) outliers start: 13 outliers final: 6 residues processed: 158 average time/residue: 0.1288 time to fit residues: 30.1549 Evaluate side-chains 136 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 621 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain B residue 434 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN A 33 ASN A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.055899 restraints weight = 47970.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.057920 restraints weight = 24357.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059275 restraints weight = 16137.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060175 restraints weight = 12399.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.060729 restraints weight = 10415.212| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16080 Z= 0.125 Angle : 0.584 10.210 22058 Z= 0.275 Chirality : 0.044 0.317 2790 Planarity : 0.004 0.047 2646 Dihedral : 6.708 63.993 4061 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.87 % Allowed : 7.30 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1635 helix: 2.00 (0.28), residues: 384 sheet: 0.92 (0.24), residues: 441 loop : 0.31 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.020 0.001 TYR D 586 PHE 0.010 0.001 PHE B 53 TRP 0.014 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (15947) covalent geometry : angle 0.54842 (21692) SS BOND : bond 0.00199 ( 33) SS BOND : angle 0.40189 ( 66) hydrogen bonds : bond 0.04153 ( 548) hydrogen bonds : angle 4.39405 ( 1944) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.62497 ( 9) link_ALPHA1-6 : bond 0.00888 ( 3) link_ALPHA1-6 : angle 1.86884 ( 9) link_BETA1-4 : bond 0.00531 ( 40) link_BETA1-4 : angle 1.83135 ( 120) link_NAG-ASN : bond 0.00226 ( 54) link_NAG-ASN : angle 1.79572 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 588 ARG cc_start: 0.8745 (ttp-110) cc_final: 0.8408 (ttm110) REVERT: A 195 ASN cc_start: 0.7983 (p0) cc_final: 0.7723 (p0) REVERT: C 530 MET cc_start: 0.9066 (mtp) cc_final: 0.8586 (mtp) REVERT: C 574 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8713 (ttmt) REVERT: C 584 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8428 (mt-10) REVERT: C 622 ILE cc_start: 0.9347 (mt) cc_final: 0.9036 (tp) REVERT: D 584 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8490 (mt-10) REVERT: D 618 ASN cc_start: 0.7598 (m-40) cc_final: 0.7257 (m-40) REVERT: D 621 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8212 (pm20) REVERT: D 633 LYS cc_start: 0.9404 (mptt) cc_final: 0.9180 (mmtm) REVERT: D 659 ASP cc_start: 0.8347 (m-30) cc_final: 0.7856 (m-30) outliers start: 13 outliers final: 9 residues processed: 150 average time/residue: 0.1263 time to fit residues: 28.2833 Evaluate side-chains 139 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 112 optimal weight: 0.0050 chunk 129 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN F 540 GLN A 33 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.056237 restraints weight = 47897.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.058261 restraints weight = 24418.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.059624 restraints weight = 16193.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.060472 restraints weight = 12434.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.061066 restraints weight = 10509.722| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16080 Z= 0.106 Angle : 0.552 10.138 22058 Z= 0.259 Chirality : 0.043 0.312 2790 Planarity : 0.003 0.053 2646 Dihedral : 6.216 58.902 4061 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.27 % Allowed : 7.50 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.21), residues: 1635 helix: 2.26 (0.28), residues: 366 sheet: 0.89 (0.24), residues: 447 loop : 0.34 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 588 TYR 0.009 0.001 TYR D 586 PHE 0.010 0.001 PHE B 53 TRP 0.011 0.001 TRP D 571 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00231 (15947) covalent geometry : angle 0.52079 (21692) SS BOND : bond 0.00170 ( 33) SS BOND : angle 0.38979 ( 66) hydrogen bonds : bond 0.03743 ( 548) hydrogen bonds : angle 4.11294 ( 1944) link_ALPHA1-3 : bond 0.01212 ( 3) link_ALPHA1-3 : angle 1.48662 ( 9) link_ALPHA1-6 : bond 0.00997 ( 3) link_ALPHA1-6 : angle 1.75055 ( 9) link_BETA1-4 : bond 0.00537 ( 40) link_BETA1-4 : angle 1.69324 ( 120) link_NAG-ASN : bond 0.00219 ( 54) link_NAG-ASN : angle 1.64907 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8606 (mt-10) REVERT: F 588 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8409 (ttm110) REVERT: F 621 GLU cc_start: 0.8618 (pt0) cc_final: 0.8070 (pt0) REVERT: A 195 ASN cc_start: 0.8011 (p0) cc_final: 0.7729 (p0) REVERT: C 530 MET cc_start: 0.9097 (mtp) cc_final: 0.8600 (mtp) REVERT: C 574 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8742 (ttmt) REVERT: D 618 ASN cc_start: 0.7601 (m-40) cc_final: 0.7154 (m-40) REVERT: D 621 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8328 (pm20) REVERT: D 633 LYS cc_start: 0.9434 (mptt) cc_final: 0.9167 (mmmm) REVERT: D 659 ASP cc_start: 0.8279 (m-30) cc_final: 0.8040 (m-30) outliers start: 19 outliers final: 13 residues processed: 156 average time/residue: 0.1233 time to fit residues: 29.1772 Evaluate side-chains 138 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053414 restraints weight = 48764.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.055354 restraints weight = 25328.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056658 restraints weight = 17055.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.057516 restraints weight = 13261.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058085 restraints weight = 11255.147| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16080 Z= 0.214 Angle : 0.634 10.984 22058 Z= 0.298 Chirality : 0.045 0.301 2790 Planarity : 0.004 0.049 2646 Dihedral : 6.299 59.392 4061 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.07 % Allowed : 7.97 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1635 helix: 2.52 (0.29), residues: 348 sheet: 1.21 (0.26), residues: 384 loop : 0.06 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 579 TYR 0.010 0.001 TYR E 486 PHE 0.014 0.002 PHE A 361 TRP 0.013 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00491 (15947) covalent geometry : angle 0.60460 (21692) SS BOND : bond 0.00273 ( 33) SS BOND : angle 0.48704 ( 66) hydrogen bonds : bond 0.04328 ( 548) hydrogen bonds : angle 4.24971 ( 1944) link_ALPHA1-3 : bond 0.01129 ( 3) link_ALPHA1-3 : angle 1.59864 ( 9) link_ALPHA1-6 : bond 0.00888 ( 3) link_ALPHA1-6 : angle 1.76479 ( 9) link_BETA1-4 : bond 0.00445 ( 40) link_BETA1-4 : angle 1.78218 ( 120) link_NAG-ASN : bond 0.00313 ( 54) link_NAG-ASN : angle 1.75444 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8573 (mt-10) REVERT: F 621 GLU cc_start: 0.8609 (pt0) cc_final: 0.7972 (pt0) REVERT: C 574 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8814 (ttmt) REVERT: D 530 MET cc_start: 0.8968 (mmm) cc_final: 0.8539 (mtp) REVERT: D 621 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8147 (mp0) REVERT: D 633 LYS cc_start: 0.9448 (mptt) cc_final: 0.9223 (mmmm) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 0.1181 time to fit residues: 24.4478 Evaluate side-chains 134 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 540 GLN C 543 ASN D 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.053447 restraints weight = 48653.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.055369 restraints weight = 25302.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.056669 restraints weight = 17020.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057482 restraints weight = 13216.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058068 restraints weight = 11253.394| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16080 Z= 0.207 Angle : 0.625 11.899 22058 Z= 0.295 Chirality : 0.044 0.299 2790 Planarity : 0.004 0.047 2646 Dihedral : 6.247 58.425 4061 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.07 % Allowed : 8.23 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1635 helix: 2.30 (0.28), residues: 366 sheet: 1.13 (0.26), residues: 384 loop : -0.03 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 588 TYR 0.012 0.001 TYR A 217 PHE 0.013 0.002 PHE A 361 TRP 0.014 0.001 TRP D 571 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00474 (15947) covalent geometry : angle 0.59650 (21692) SS BOND : bond 0.00278 ( 33) SS BOND : angle 0.45759 ( 66) hydrogen bonds : bond 0.04282 ( 548) hydrogen bonds : angle 4.21540 ( 1944) link_ALPHA1-3 : bond 0.01124 ( 3) link_ALPHA1-3 : angle 1.54254 ( 9) link_ALPHA1-6 : bond 0.00879 ( 3) link_ALPHA1-6 : angle 1.68758 ( 9) link_BETA1-4 : bond 0.00459 ( 40) link_BETA1-4 : angle 1.70834 ( 120) link_NAG-ASN : bond 0.00289 ( 54) link_NAG-ASN : angle 1.71099 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8596 (mt-10) REVERT: F 621 GLU cc_start: 0.8560 (pt0) cc_final: 0.7916 (pt0) REVERT: C 530 MET cc_start: 0.9092 (mtp) cc_final: 0.8649 (mtp) REVERT: D 530 MET cc_start: 0.8970 (mmm) cc_final: 0.8628 (mtp) REVERT: D 621 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8165 (mp0) REVERT: D 633 LYS cc_start: 0.9464 (mptt) cc_final: 0.9212 (mmmm) REVERT: D 655 LYS cc_start: 0.8847 (tptp) cc_final: 0.8519 (tptp) outliers start: 16 outliers final: 14 residues processed: 138 average time/residue: 0.1262 time to fit residues: 26.3030 Evaluate side-chains 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 576 LEU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 647 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 74 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.0060 chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 126 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.055265 restraints weight = 47947.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.057251 restraints weight = 24405.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.058578 restraints weight = 16177.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.059485 restraints weight = 12451.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060073 restraints weight = 10433.900| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16080 Z= 0.101 Angle : 0.554 11.771 22058 Z= 0.262 Chirality : 0.043 0.299 2790 Planarity : 0.003 0.047 2646 Dihedral : 5.817 58.640 4061 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.94 % Allowed : 8.57 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1635 helix: 2.67 (0.28), residues: 348 sheet: 0.85 (0.24), residues: 435 loop : 0.12 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 588 TYR 0.011 0.001 TYR A 217 PHE 0.011 0.001 PHE A 53 TRP 0.026 0.001 TRP A 479 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00217 (15947) covalent geometry : angle 0.52796 (21692) SS BOND : bond 0.00163 ( 33) SS BOND : angle 0.36478 ( 66) hydrogen bonds : bond 0.03778 ( 548) hydrogen bonds : angle 3.96855 ( 1944) link_ALPHA1-3 : bond 0.01161 ( 3) link_ALPHA1-3 : angle 1.33246 ( 9) link_ALPHA1-6 : bond 0.01057 ( 3) link_ALPHA1-6 : angle 1.66887 ( 9) link_BETA1-4 : bond 0.00548 ( 40) link_BETA1-4 : angle 1.58138 ( 120) link_NAG-ASN : bond 0.00228 ( 54) link_NAG-ASN : angle 1.53344 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8538 (mt-10) REVERT: F 621 GLU cc_start: 0.8516 (pt0) cc_final: 0.7840 (pt0) REVERT: A 50 THR cc_start: 0.9150 (t) cc_final: 0.8930 (m) REVERT: C 530 MET cc_start: 0.9125 (mtp) cc_final: 0.8740 (mtp) REVERT: C 586 TYR cc_start: 0.9416 (t80) cc_final: 0.9090 (t80) REVERT: D 530 MET cc_start: 0.8913 (mmm) cc_final: 0.8527 (mtp) REVERT: D 621 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8330 (pm20) REVERT: D 633 LYS cc_start: 0.9432 (mptt) cc_final: 0.9205 (mmmm) REVERT: D 647 GLU cc_start: 0.8858 (pt0) cc_final: 0.8654 (tt0) REVERT: D 655 LYS cc_start: 0.8963 (tptp) cc_final: 0.8626 (tptp) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.1209 time to fit residues: 26.3585 Evaluate side-chains 136 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 0.0010 chunk 100 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.069189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.054008 restraints weight = 48659.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.055971 restraints weight = 25192.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.057290 restraints weight = 16894.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.058150 restraints weight = 13095.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.058628 restraints weight = 11082.172| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16080 Z= 0.191 Angle : 0.613 12.211 22058 Z= 0.288 Chirality : 0.044 0.296 2790 Planarity : 0.004 0.047 2646 Dihedral : 5.960 59.282 4061 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.87 % Allowed : 8.90 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1635 helix: 2.40 (0.28), residues: 366 sheet: 1.09 (0.26), residues: 384 loop : -0.06 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 588 TYR 0.012 0.001 TYR A 217 PHE 0.013 0.002 PHE A 361 TRP 0.012 0.001 TRP A 96 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00438 (15947) covalent geometry : angle 0.58669 (21692) SS BOND : bond 0.00248 ( 33) SS BOND : angle 0.44492 ( 66) hydrogen bonds : bond 0.04117 ( 548) hydrogen bonds : angle 4.10629 ( 1944) link_ALPHA1-3 : bond 0.01054 ( 3) link_ALPHA1-3 : angle 1.44325 ( 9) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.59351 ( 9) link_BETA1-4 : bond 0.00428 ( 40) link_BETA1-4 : angle 1.67081 ( 120) link_NAG-ASN : bond 0.00299 ( 54) link_NAG-ASN : angle 1.64845 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 621 GLU cc_start: 0.8503 (pt0) cc_final: 0.7861 (pt0) REVERT: A 195 ASN cc_start: 0.7988 (p0) cc_final: 0.7651 (p0) REVERT: C 530 MET cc_start: 0.9083 (mtp) cc_final: 0.8626 (mtp) REVERT: C 574 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8775 (ttmt) REVERT: C 586 TYR cc_start: 0.9468 (t80) cc_final: 0.9195 (t80) REVERT: B 202 THR cc_start: 0.9583 (m) cc_final: 0.9353 (p) REVERT: D 530 MET cc_start: 0.8963 (mmm) cc_final: 0.8560 (mtp) REVERT: D 633 LYS cc_start: 0.9403 (mptt) cc_final: 0.9190 (mmmm) REVERT: D 655 LYS cc_start: 0.8998 (tptp) cc_final: 0.8653 (tptp) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.1230 time to fit residues: 25.0300 Evaluate side-chains 133 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 123 optimal weight: 0.0170 chunk 160 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.071045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055913 restraints weight = 47942.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.057943 restraints weight = 24627.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.059283 restraints weight = 16372.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.060171 restraints weight = 12632.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.060747 restraints weight = 10632.611| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16080 Z= 0.103 Angle : 0.548 12.201 22058 Z= 0.259 Chirality : 0.042 0.289 2790 Planarity : 0.003 0.048 2646 Dihedral : 5.529 56.630 4061 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.60 % Allowed : 9.44 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1635 helix: 2.71 (0.28), residues: 348 sheet: 1.07 (0.26), residues: 393 loop : -0.01 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 588 TYR 0.007 0.001 TYR A 384 PHE 0.011 0.001 PHE A 53 TRP 0.018 0.001 TRP A 479 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00227 (15947) covalent geometry : angle 0.52437 (21692) SS BOND : bond 0.00178 ( 33) SS BOND : angle 0.37451 ( 66) hydrogen bonds : bond 0.03649 ( 548) hydrogen bonds : angle 3.89805 ( 1944) link_ALPHA1-3 : bond 0.01108 ( 3) link_ALPHA1-3 : angle 1.24234 ( 9) link_ALPHA1-6 : bond 0.00917 ( 3) link_ALPHA1-6 : angle 1.35720 ( 9) link_BETA1-4 : bond 0.00531 ( 40) link_BETA1-4 : angle 1.51362 ( 120) link_NAG-ASN : bond 0.00219 ( 54) link_NAG-ASN : angle 1.47708 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: F 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8548 (mt-10) REVERT: F 621 GLU cc_start: 0.8477 (pt0) cc_final: 0.7884 (pt0) REVERT: F 654 GLU cc_start: 0.8599 (tt0) cc_final: 0.8388 (tt0) REVERT: A 50 THR cc_start: 0.9143 (t) cc_final: 0.8887 (m) REVERT: C 530 MET cc_start: 0.9103 (mtp) cc_final: 0.8650 (mtp) REVERT: C 574 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8742 (ttmt) REVERT: C 586 TYR cc_start: 0.9411 (t80) cc_final: 0.9094 (t80) REVERT: D 530 MET cc_start: 0.8883 (mmm) cc_final: 0.8477 (mtp) REVERT: D 621 GLU cc_start: 0.8777 (pt0) cc_final: 0.8421 (pm20) REVERT: D 633 LYS cc_start: 0.9381 (mptt) cc_final: 0.9150 (mmmm) REVERT: D 655 LYS cc_start: 0.9002 (tptp) cc_final: 0.8654 (tptp) outliers start: 9 outliers final: 9 residues processed: 141 average time/residue: 0.1288 time to fit residues: 26.7868 Evaluate side-chains 137 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 89 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3112 r_free = 0.3112 target = 0.069982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.054879 restraints weight = 47981.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.056850 restraints weight = 24915.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058167 restraints weight = 16706.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.059045 restraints weight = 12943.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.059579 restraints weight = 10921.075| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16080 Z= 0.146 Angle : 0.568 12.619 22058 Z= 0.268 Chirality : 0.043 0.284 2790 Planarity : 0.003 0.054 2646 Dihedral : 5.372 56.658 4061 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.80 % Allowed : 9.44 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1635 helix: 2.75 (0.28), residues: 348 sheet: 1.00 (0.25), residues: 411 loop : 0.02 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 588 TYR 0.011 0.001 TYR A 217 PHE 0.010 0.001 PHE A 361 TRP 0.009 0.001 TRP D 571 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00333 (15947) covalent geometry : angle 0.54322 (21692) SS BOND : bond 0.00206 ( 33) SS BOND : angle 0.40163 ( 66) hydrogen bonds : bond 0.03805 ( 548) hydrogen bonds : angle 3.93702 ( 1944) link_ALPHA1-3 : bond 0.00967 ( 3) link_ALPHA1-3 : angle 1.32810 ( 9) link_ALPHA1-6 : bond 0.00715 ( 3) link_ALPHA1-6 : angle 1.38847 ( 9) link_BETA1-4 : bond 0.00461 ( 40) link_BETA1-4 : angle 1.57967 ( 120) link_NAG-ASN : bond 0.00223 ( 54) link_NAG-ASN : angle 1.52894 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.00 seconds wall clock time: 36 minutes 13.92 seconds (2173.92 seconds total)