Starting phenix.real_space_refine on Wed May 21 03:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.map" model { file = "/net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4m_29725/05_2025/8g4m_29725.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 135 5.16 5 C 12837 2.51 5 N 3409 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20584 Number of models: 1 Model: "" Number of chains: 61 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "G" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3521 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 952 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "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: "0" 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: "1" 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: "2" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.18, per 1000 atoms: 0.64 Number of scatterers: 20584 At special positions: 0 Unit cell: (130.31, 132.8, 144.42, 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 135 16.00 O 4203 8.00 N 3409 7.00 C 12837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 99 " - pdb=" SG CYS J 100D" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN e 4 " - " MAN e 5 " " MAN t 4 " - " MAN t 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " " BMA o 3 " - " MAN o 4 " " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 6 " " BMA a 3 " - " MAN a 5 " " BMA o 3 " - " MAN o 5 " " BMA t 3 " - " MAN t 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 e 2 " - " BMA e 3 " " 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 m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " 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 z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN I 392 " " NAG 1 1 " - " ASN I 448 " " NAG 2 1 " - " ASN I 160 " " NAG A 701 " - " ASN A 637 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 355 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 234 " " NAG G 602 " - " ASN G 339 " " NAG G 603 " - " ASN G 355 " " NAG I 601 " - " ASN I 339 " " NAG I 602 " - " ASN I 355 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 276 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN G 88 " " NAG b 1 " - " ASN G 133 " " NAG c 1 " - " ASN G 156 " " NAG d 1 " - " ASN G 197 " " NAG e 1 " - " ASN G 262 " " NAG f 1 " - " ASN G 276 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " " NAG j 1 " - " ASN G 363 " " NAG k 1 " - " ASN G 386 " " NAG l 1 " - " ASN G 392 " " NAG m 1 " - " ASN G 448 " " NAG n 1 " - " ASN G 160 " " NAG o 1 " - " ASN I 88 " " NAG p 1 " - " ASN I 133 " " NAG q 1 " - " ASN I 156 " " NAG r 1 " - " ASN I 197 " " NAG s 1 " - " ASN I 234 " " NAG t 1 " - " ASN I 262 " " NAG u 1 " - " ASN I 276 " " NAG v 1 " - " ASN I 295 " " NAG w 1 " - " ASN I 301 " " NAG x 1 " - " ASN I 332 " " NAG y 1 " - " ASN I 363 " " NAG z 1 " - " ASN I 386 " Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.9 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 45 sheets defined 20.5% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.882A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.542A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.616A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.675A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.771A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.532A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 663 removed outlier: 3.560A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.592A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.839A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.618A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.736A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.713A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.577A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.632A pdb=" N ALA I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.931A pdb=" N ARG I 151 " --> pdb=" O ASP I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 354 removed outlier: 4.030A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.917A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.164A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.471A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.744A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.755A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.513A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.932A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.690A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.248A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.601A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.640A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.297A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.452A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.975A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.586A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.657A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.263A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.470A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.844A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.617A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.340A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR I 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS F 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.544A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.656A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.171A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.508A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.950A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.561A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.041A pdb=" N ARG D 38 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.279A pdb=" N TYR D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.070A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.380A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.438A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.342A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.113A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 4.059A pdb=" N TYR J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.141A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.640A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2046 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: 8.26 Time building geometry restraints manager: 6.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6415 1.34 - 1.46: 5264 1.46 - 1.58: 9118 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 20977 Sorted by residual: bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" N GLU J 1 " pdb=" CA GLU J 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" C1 NAG p 2 " pdb=" O5 NAG p 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 20972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 27952 2.19 - 4.39: 435 4.39 - 6.58: 71 6.58 - 8.77: 0 8.77 - 10.97: 1 Bond angle restraints: 28459 Sorted by residual: angle pdb=" C2 NAG b 2 " pdb=" N2 NAG b 2 " pdb=" C7 NAG b 2 " ideal model delta sigma weight residual 124.56 135.53 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ILE B 635 " pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " ideal model delta sigma weight residual 110.40 115.22 -4.82 1.70e+00 3.46e-01 8.03e+00 angle pdb=" N GLY I 389 " pdb=" CA GLY I 389 " pdb=" C GLY I 389 " ideal model delta sigma weight residual 114.66 111.25 3.41 1.24e+00 6.50e-01 7.56e+00 angle pdb=" C GLY K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" CB ILE B 635 " pdb=" CG1 ILE B 635 " pdb=" CD1 ILE B 635 " ideal model delta sigma weight residual 113.80 119.50 -5.70 2.10e+00 2.27e-01 7.38e+00 ... (remaining 28454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12568 21.78 - 43.56: 1097 43.56 - 65.34: 302 65.34 - 87.12: 79 87.12 - 108.90: 52 Dihedral angle restraints: 14098 sinusoidal: 7105 harmonic: 6993 Sorted by residual: dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -148.45 62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS D 99 " pdb=" SG CYS D 99 " pdb=" SG CYS D 100D" pdb=" CB CYS D 100D" ideal model delta sinusoidal sigma weight residual 93.00 153.67 -60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -139.44 53.44 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 14095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3030 0.059 - 0.119: 419 0.119 - 0.178: 66 0.178 - 0.238: 6 0.238 - 0.297: 8 Chirality restraints: 3529 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3526 not shown) Planarity restraints: 3521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 18 " -0.176 9.50e-02 1.11e+02 7.93e-02 4.15e+00 pdb=" NE ARG K 18 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG K 18 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K 18 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG K 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 55 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" CG ASP J 55 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP J 55 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP J 55 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 635 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ILE B 635 " -0.018 2.00e-02 2.50e+03 pdb=" O ILE B 635 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 636 " 0.006 2.00e-02 2.50e+03 ... (remaining 3518 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 537 2.69 - 3.24: 19246 3.24 - 3.79: 31779 3.79 - 4.35: 44438 4.35 - 4.90: 74271 Nonbonded interactions: 170271 Sorted by model distance: nonbonded pdb=" N GLU K 81 " pdb=" OE1 GLU K 81 " model vdw 2.132 3.120 nonbonded pdb=" N GLU E 81 " pdb=" OE1 GLU E 81 " model vdw 2.136 3.120 nonbonded pdb=" OE1 GLN I 258 " pdb=" OG1 THR I 387 " model vdw 2.140 3.040 nonbonded pdb=" O SER G 460 " pdb=" OG1 THR G 461 " model vdw 2.161 3.040 nonbonded pdb=" O SER I 460 " pdb=" OG1 THR I 461 " model vdw 2.188 3.040 ... (remaining 170266 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 '0' selection = chain '1' selection = chain '2' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 514 through 664 or resid 701)) selection = chain 'B' selection = (chain 'F' and (resid 514 through 664 or resid 701)) } ncs_group { reference = (chain 'C' and (resid 31 through 505 or resid 601 through 602)) selection = (chain 'G' and (resid 31 through 505 or resid 601 through 602)) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'a' selection = chain 'e' selection = chain 'o' } ncs_group { reference = chain 'Q' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 49.490 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21141 Z= 0.216 Angle : 0.659 10.968 28906 Z= 0.282 Chirality : 0.047 0.297 3529 Planarity : 0.003 0.079 3466 Dihedral : 18.251 108.900 9471 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 21.18 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2384 helix: 1.74 (0.29), residues: 412 sheet: 0.15 (0.19), residues: 771 loop : 0.22 (0.19), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 96 HIS 0.003 0.000 HIS G 105 PHE 0.007 0.001 PHE D 100G TYR 0.012 0.001 TYR D 100E ARG 0.009 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 55) link_NAG-ASN : angle 1.63079 ( 165) link_ALPHA1-6 : bond 0.00391 ( 5) link_ALPHA1-6 : angle 1.75237 ( 15) link_BETA1-4 : bond 0.00357 ( 50) link_BETA1-4 : angle 1.50162 ( 150) link_ALPHA1-2 : bond 0.00595 ( 3) link_ALPHA1-2 : angle 2.70991 ( 9) link_ALPHA1-3 : bond 0.00286 ( 6) link_ALPHA1-3 : angle 1.79232 ( 18) hydrogen bonds : bond 0.20304 ( 744) hydrogen bonds : angle 8.34713 ( 2046) SS BOND : bond 0.00149 ( 45) SS BOND : angle 0.42175 ( 90) covalent geometry : bond 0.00447 (20977) covalent geometry : angle 0.63825 (28459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 259 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 475 MET cc_start: 0.8458 (tpp) cc_final: 0.8173 (mpp) REVERT: A 601 LYS cc_start: 0.8922 (mttm) cc_final: 0.8625 (mttp) REVERT: G 475 MET cc_start: 0.8732 (mmm) cc_final: 0.7608 (mpp) REVERT: B 655 LYS cc_start: 0.8419 (tptm) cc_final: 0.8210 (tptp) REVERT: F 599 SER cc_start: 0.9376 (t) cc_final: 0.9055 (m) REVERT: D 3 GLN cc_start: 0.8140 (mm110) cc_final: 0.7566 (mp10) REVERT: D 13 GLN cc_start: 0.8777 (mp10) cc_final: 0.8514 (tp40) REVERT: D 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7307 (t0) REVERT: D 83 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8905 (ptp-170) REVERT: D 100 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8084 (mtp85) REVERT: D 107 THR cc_start: 0.9026 (t) cc_final: 0.8788 (p) REVERT: E 5 THR cc_start: 0.9172 (m) cc_final: 0.8960 (p) REVERT: H 38 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8575 (ptt-90) REVERT: H 72 ASP cc_start: 0.8214 (t0) cc_final: 0.7890 (t0) REVERT: H 85 GLU cc_start: 0.8953 (pm20) cc_final: 0.8688 (pm20) REVERT: H 89 VAL cc_start: 0.8596 (t) cc_final: 0.8225 (p) REVERT: H 107 THR cc_start: 0.8795 (t) cc_final: 0.8449 (p) REVERT: L 24 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: L 70 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8272 (mm-30) REVERT: J 13 GLN cc_start: 0.8563 (mm110) cc_final: 0.8267 (mm110) REVERT: J 43 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8439 (mppt) REVERT: J 72 ASP cc_start: 0.8223 (t0) cc_final: 0.7683 (t70) REVERT: K 79 GLN cc_start: 0.8369 (mt0) cc_final: 0.8148 (mt0) outliers start: 51 outliers final: 39 residues processed: 306 average time/residue: 1.3827 time to fit residues: 475.7202 Evaluate side-chains 258 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 388 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 651 ASN G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051470 restraints weight = 48277.128| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.47 r_work: 0.2513 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21141 Z= 0.227 Angle : 0.636 9.230 28906 Z= 0.305 Chirality : 0.045 0.293 3529 Planarity : 0.003 0.034 3466 Dihedral : 12.677 95.369 5120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 20.56 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2384 helix: 2.33 (0.29), residues: 384 sheet: 0.09 (0.19), residues: 759 loop : 0.19 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.004 0.001 HIS G 330 PHE 0.012 0.001 PHE C 383 TYR 0.019 0.002 TYR E 49 ARG 0.006 0.001 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 55) link_NAG-ASN : angle 1.88382 ( 165) link_ALPHA1-6 : bond 0.00188 ( 5) link_ALPHA1-6 : angle 1.97008 ( 15) link_BETA1-4 : bond 0.00352 ( 50) link_BETA1-4 : angle 1.52908 ( 150) link_ALPHA1-2 : bond 0.01114 ( 3) link_ALPHA1-2 : angle 2.32318 ( 9) link_ALPHA1-3 : bond 0.00972 ( 6) link_ALPHA1-3 : angle 1.99773 ( 18) hydrogen bonds : bond 0.04844 ( 744) hydrogen bonds : angle 5.87359 ( 2046) SS BOND : bond 0.00308 ( 45) SS BOND : angle 0.79706 ( 90) covalent geometry : bond 0.00529 (20977) covalent geometry : angle 0.60758 (28459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9138 (mttm) cc_final: 0.8817 (mtmm) REVERT: G 475 MET cc_start: 0.8824 (mmm) cc_final: 0.7992 (mpp) REVERT: B 632 ASP cc_start: 0.9140 (t0) cc_final: 0.8846 (t0) REVERT: B 655 LYS cc_start: 0.8811 (tptm) cc_final: 0.8515 (tptm) REVERT: I 92 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: I 114 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: F 599 SER cc_start: 0.9501 (t) cc_final: 0.9223 (p) REVERT: F 621 GLU cc_start: 0.9034 (tt0) cc_final: 0.8562 (pt0) REVERT: F 655 LYS cc_start: 0.7916 (tptt) cc_final: 0.7631 (ttmt) REVERT: D 13 GLN cc_start: 0.8837 (mp10) cc_final: 0.8369 (mm-40) REVERT: D 72 ASP cc_start: 0.8233 (t0) cc_final: 0.7506 (t0) REVERT: D 89 VAL cc_start: 0.9016 (t) cc_final: 0.8738 (p) REVERT: D 100 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8180 (mtp85) REVERT: D 107 THR cc_start: 0.9011 (t) cc_final: 0.8808 (p) REVERT: E 79 GLN cc_start: 0.8190 (mt0) cc_final: 0.7910 (mp-120) REVERT: H 85 GLU cc_start: 0.9176 (pm20) cc_final: 0.8921 (pm20) REVERT: H 89 VAL cc_start: 0.8942 (t) cc_final: 0.8586 (p) REVERT: L 24 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7941 (ttp80) REVERT: J 13 GLN cc_start: 0.8702 (mm110) cc_final: 0.8440 (mm110) REVERT: J 72 ASP cc_start: 0.8445 (t0) cc_final: 0.7984 (t70) REVERT: K 17 GLU cc_start: 0.8821 (pt0) cc_final: 0.8608 (pm20) REVERT: K 24 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8136 (ttp80) REVERT: K 79 GLN cc_start: 0.8707 (mt0) cc_final: 0.8198 (mt0) outliers start: 64 outliers final: 24 residues processed: 291 average time/residue: 1.4777 time to fit residues: 480.8589 Evaluate side-chains 243 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 105 HIS G 80 ASN I 67 ASN F 656 ASN D 3 GLN H 13 GLN H 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.051473 restraints weight = 47777.395| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.41 r_work: 0.2527 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21141 Z= 0.192 Angle : 0.604 9.528 28906 Z= 0.287 Chirality : 0.045 0.254 3529 Planarity : 0.003 0.043 3466 Dihedral : 10.981 90.479 5089 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.81 % Allowed : 21.28 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2384 helix: 2.58 (0.29), residues: 376 sheet: 0.11 (0.19), residues: 756 loop : 0.19 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.003 0.001 HIS G 330 PHE 0.011 0.001 PHE C 383 TYR 0.017 0.001 TYR J 100E ARG 0.008 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 55) link_NAG-ASN : angle 1.88395 ( 165) link_ALPHA1-6 : bond 0.00388 ( 5) link_ALPHA1-6 : angle 1.86980 ( 15) link_BETA1-4 : bond 0.00338 ( 50) link_BETA1-4 : angle 1.53812 ( 150) link_ALPHA1-2 : bond 0.01121 ( 3) link_ALPHA1-2 : angle 2.44231 ( 9) link_ALPHA1-3 : bond 0.01094 ( 6) link_ALPHA1-3 : angle 1.59993 ( 18) hydrogen bonds : bond 0.04224 ( 744) hydrogen bonds : angle 5.38304 ( 2046) SS BOND : bond 0.00298 ( 45) SS BOND : angle 0.64007 ( 90) covalent geometry : bond 0.00443 (20977) covalent geometry : angle 0.57558 (28459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9212 (mttm) cc_final: 0.8940 (mttp) REVERT: G 475 MET cc_start: 0.8782 (mmm) cc_final: 0.8031 (mpp) REVERT: B 632 ASP cc_start: 0.9179 (t0) cc_final: 0.8903 (t0) REVERT: B 655 LYS cc_start: 0.8815 (tptm) cc_final: 0.8512 (tptm) REVERT: I 92 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8572 (tp30) REVERT: I 114 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: F 599 SER cc_start: 0.9511 (t) cc_final: 0.9243 (p) REVERT: F 621 GLU cc_start: 0.8996 (tt0) cc_final: 0.8770 (pt0) REVERT: F 655 LYS cc_start: 0.7929 (tptt) cc_final: 0.7574 (ttpt) REVERT: D 13 GLN cc_start: 0.8852 (mp10) cc_final: 0.8355 (mm-40) REVERT: D 34 MET cc_start: 0.9131 (mmt) cc_final: 0.8884 (tpp) REVERT: D 72 ASP cc_start: 0.8235 (t0) cc_final: 0.7520 (t0) REVERT: D 85 GLU cc_start: 0.9269 (pm20) cc_final: 0.9043 (pm20) REVERT: D 86 ASP cc_start: 0.9101 (m-30) cc_final: 0.8550 (m-30) REVERT: D 89 VAL cc_start: 0.9041 (t) cc_final: 0.8787 (p) REVERT: D 100 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8283 (mtp85) REVERT: E 79 GLN cc_start: 0.8292 (mt0) cc_final: 0.8004 (mp-120) REVERT: L 24 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: L 39 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7975 (mmtm) REVERT: L 81 GLU cc_start: 0.8503 (pp20) cc_final: 0.8267 (pp20) REVERT: L 105 GLU cc_start: 0.5392 (tp30) cc_final: 0.5041 (tm-30) REVERT: J 13 GLN cc_start: 0.8725 (mm110) cc_final: 0.8473 (mm110) REVERT: J 43 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8623 (mppt) REVERT: J 72 ASP cc_start: 0.8469 (t0) cc_final: 0.7997 (t70) REVERT: J 105 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8834 (mm-40) REVERT: K 79 GLN cc_start: 0.8515 (mt0) cc_final: 0.8193 (mt0) outliers start: 80 outliers final: 35 residues processed: 289 average time/residue: 1.4187 time to fit residues: 459.8744 Evaluate side-chains 245 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 147 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 GLN G 67 ASN G 80 ASN G 114 GLN F 656 ASN D 13 GLN H 13 GLN H 81 GLN J 39 GLN K 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051432 restraints weight = 48332.836| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.55 r_work: 0.2521 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21141 Z= 0.175 Angle : 0.598 9.570 28906 Z= 0.281 Chirality : 0.045 0.252 3529 Planarity : 0.003 0.043 3466 Dihedral : 9.827 84.539 5089 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.71 % Allowed : 21.70 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2384 helix: 2.94 (0.28), residues: 362 sheet: 0.12 (0.18), residues: 750 loop : 0.15 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 96 HIS 0.003 0.001 HIS G 330 PHE 0.012 0.001 PHE G 383 TYR 0.017 0.001 TYR J 100E ARG 0.008 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 55) link_NAG-ASN : angle 1.87397 ( 165) link_ALPHA1-6 : bond 0.00497 ( 5) link_ALPHA1-6 : angle 1.85378 ( 15) link_BETA1-4 : bond 0.00351 ( 50) link_BETA1-4 : angle 1.55005 ( 150) link_ALPHA1-2 : bond 0.01140 ( 3) link_ALPHA1-2 : angle 2.46562 ( 9) link_ALPHA1-3 : bond 0.01130 ( 6) link_ALPHA1-3 : angle 1.68413 ( 18) hydrogen bonds : bond 0.03890 ( 744) hydrogen bonds : angle 5.13123 ( 2046) SS BOND : bond 0.00243 ( 45) SS BOND : angle 0.60653 ( 90) covalent geometry : bond 0.00402 (20977) covalent geometry : angle 0.56896 (28459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 225 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 601 LYS cc_start: 0.9195 (mttm) cc_final: 0.8899 (mttp) REVERT: G 141 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8519 (p0) REVERT: G 475 MET cc_start: 0.8745 (mmm) cc_final: 0.8006 (mpp) REVERT: B 584 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8573 (mt-10) REVERT: B 632 ASP cc_start: 0.9164 (t0) cc_final: 0.8897 (t0) REVERT: B 655 LYS cc_start: 0.8718 (tptm) cc_final: 0.8425 (tptm) REVERT: I 114 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7995 (mp10) REVERT: F 599 SER cc_start: 0.9485 (t) cc_final: 0.9237 (p) REVERT: F 655 LYS cc_start: 0.7943 (tptt) cc_final: 0.7592 (tppt) REVERT: D 13 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8457 (mm-40) REVERT: D 34 MET cc_start: 0.9126 (mmp) cc_final: 0.8892 (tpp) REVERT: D 72 ASP cc_start: 0.8201 (t0) cc_final: 0.7469 (t0) REVERT: D 86 ASP cc_start: 0.9056 (m-30) cc_final: 0.8545 (m-30) REVERT: D 89 VAL cc_start: 0.9057 (t) cc_final: 0.8819 (p) REVERT: D 100 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8352 (mtp85) REVERT: H 46 GLU cc_start: 0.8696 (tt0) cc_final: 0.8268 (pt0) REVERT: L 24 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: L 39 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7988 (mmtm) REVERT: L 81 GLU cc_start: 0.8483 (pp20) cc_final: 0.8189 (pp20) REVERT: L 105 GLU cc_start: 0.5467 (tp30) cc_final: 0.5231 (tm-30) REVERT: J 13 GLN cc_start: 0.8727 (mm110) cc_final: 0.8459 (mm110) REVERT: J 43 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8587 (mppt) REVERT: J 72 ASP cc_start: 0.8465 (t0) cc_final: 0.7993 (t70) REVERT: J 105 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8868 (mm-40) REVERT: K 17 GLU cc_start: 0.8712 (pm20) cc_final: 0.8393 (pm20) REVERT: K 103 LYS cc_start: 0.8793 (tppp) cc_final: 0.8343 (tppp) outliers start: 78 outliers final: 37 residues processed: 286 average time/residue: 1.3835 time to fit residues: 445.6896 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 203 optimal weight: 0.5980 chunk 229 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 175 optimal weight: 0.0970 chunk 171 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN H 13 GLN H 81 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052376 restraints weight = 48255.177| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.42 r_work: 0.2551 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21141 Z= 0.128 Angle : 0.578 9.537 28906 Z= 0.271 Chirality : 0.044 0.260 3529 Planarity : 0.003 0.034 3466 Dihedral : 9.180 79.947 5086 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.09 % Allowed : 22.99 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2384 helix: 3.06 (0.28), residues: 356 sheet: 0.15 (0.18), residues: 753 loop : 0.15 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 96 HIS 0.002 0.000 HIS G 105 PHE 0.011 0.001 PHE G 383 TYR 0.014 0.001 TYR J 100E ARG 0.008 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 55) link_NAG-ASN : angle 1.81572 ( 165) link_ALPHA1-6 : bond 0.00612 ( 5) link_ALPHA1-6 : angle 1.83315 ( 15) link_BETA1-4 : bond 0.00380 ( 50) link_BETA1-4 : angle 1.54027 ( 150) link_ALPHA1-2 : bond 0.01020 ( 3) link_ALPHA1-2 : angle 2.47648 ( 9) link_ALPHA1-3 : bond 0.01205 ( 6) link_ALPHA1-3 : angle 1.60267 ( 18) hydrogen bonds : bond 0.03613 ( 744) hydrogen bonds : angle 4.96666 ( 2046) SS BOND : bond 0.00201 ( 45) SS BOND : angle 0.57529 ( 90) covalent geometry : bond 0.00290 (20977) covalent geometry : angle 0.54945 (28459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: C 189 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7549 (pttm) REVERT: C 348 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: A 601 LYS cc_start: 0.9197 (mttm) cc_final: 0.8888 (mtmm) REVERT: G 475 MET cc_start: 0.8671 (mmm) cc_final: 0.7967 (mpp) REVERT: B 632 ASP cc_start: 0.9154 (t0) cc_final: 0.8831 (t0) REVERT: B 655 LYS cc_start: 0.8728 (tptm) cc_final: 0.8440 (tptm) REVERT: F 599 SER cc_start: 0.9482 (t) cc_final: 0.9250 (p) REVERT: F 621 GLU cc_start: 0.9018 (pt0) cc_final: 0.8720 (pt0) REVERT: F 655 LYS cc_start: 0.8003 (tptt) cc_final: 0.7696 (tppt) REVERT: D 6 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: D 13 GLN cc_start: 0.9026 (mp10) cc_final: 0.8728 (tp40) REVERT: D 34 MET cc_start: 0.9137 (mmp) cc_final: 0.8902 (tpp) REVERT: D 72 ASP cc_start: 0.8236 (t0) cc_final: 0.7475 (t0) REVERT: D 86 ASP cc_start: 0.9013 (m-30) cc_final: 0.8444 (m-30) REVERT: D 89 VAL cc_start: 0.9088 (t) cc_final: 0.8842 (p) REVERT: D 100 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8357 (mtp85) REVERT: D 100 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8761 (p90) REVERT: E 54 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8218 (ttm-80) REVERT: H 46 GLU cc_start: 0.8720 (tt0) cc_final: 0.8335 (pt0) REVERT: L 105 GLU cc_start: 0.5442 (tp30) cc_final: 0.5130 (tm-30) REVERT: J 13 GLN cc_start: 0.8735 (mm110) cc_final: 0.8470 (mm110) REVERT: J 72 ASP cc_start: 0.8476 (t0) cc_final: 0.8002 (t70) REVERT: J 100 SER cc_start: 0.9326 (OUTLIER) cc_final: 0.8933 (p) REVERT: J 105 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8870 (mm-40) REVERT: K 24 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8021 (mtm-85) REVERT: K 79 GLN cc_start: 0.8737 (mt0) cc_final: 0.8415 (mt0) REVERT: K 103 LYS cc_start: 0.8806 (tppp) cc_final: 0.8357 (tppp) outliers start: 65 outliers final: 27 residues processed: 281 average time/residue: 1.4435 time to fit residues: 457.7404 Evaluate side-chains 248 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 TYR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 153 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN H 13 GLN H 81 GLN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.051649 restraints weight = 48161.159| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.53 r_work: 0.2526 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21141 Z= 0.170 Angle : 0.598 9.596 28906 Z= 0.279 Chirality : 0.044 0.269 3529 Planarity : 0.003 0.034 3466 Dihedral : 8.676 74.929 5082 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.19 % Allowed : 23.18 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2384 helix: 2.85 (0.28), residues: 369 sheet: 0.17 (0.19), residues: 753 loop : 0.16 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 103 HIS 0.002 0.001 HIS G 330 PHE 0.012 0.001 PHE G 383 TYR 0.015 0.001 TYR J 100E ARG 0.009 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 55) link_NAG-ASN : angle 1.86248 ( 165) link_ALPHA1-6 : bond 0.00644 ( 5) link_ALPHA1-6 : angle 1.80615 ( 15) link_BETA1-4 : bond 0.00371 ( 50) link_BETA1-4 : angle 1.56544 ( 150) link_ALPHA1-2 : bond 0.00963 ( 3) link_ALPHA1-2 : angle 2.48315 ( 9) link_ALPHA1-3 : bond 0.01119 ( 6) link_ALPHA1-3 : angle 1.61812 ( 18) hydrogen bonds : bond 0.03719 ( 744) hydrogen bonds : angle 4.92057 ( 2046) SS BOND : bond 0.00268 ( 45) SS BOND : angle 0.61448 ( 90) covalent geometry : bond 0.00394 (20977) covalent geometry : angle 0.56886 (28459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: C 138 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8886 (pp) REVERT: C 348 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: A 601 LYS cc_start: 0.9205 (mttm) cc_final: 0.8891 (mtmm) REVERT: G 141 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8512 (p0) REVERT: G 475 MET cc_start: 0.8711 (mmm) cc_final: 0.7971 (mpp) REVERT: B 584 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8595 (mt-10) REVERT: B 632 ASP cc_start: 0.9158 (t0) cc_final: 0.8827 (t0) REVERT: B 655 LYS cc_start: 0.8708 (tptm) cc_final: 0.8417 (tptm) REVERT: I 114 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: I 231 LYS cc_start: 0.9454 (mttt) cc_final: 0.9204 (mttm) REVERT: F 599 SER cc_start: 0.9488 (t) cc_final: 0.9229 (p) REVERT: F 621 GLU cc_start: 0.9010 (pt0) cc_final: 0.8676 (pt0) REVERT: F 655 LYS cc_start: 0.8037 (tptt) cc_final: 0.7735 (ttpt) REVERT: D 12 VAL cc_start: 0.9634 (t) cc_final: 0.9388 (p) REVERT: D 13 GLN cc_start: 0.9091 (mp10) cc_final: 0.8626 (mm-40) REVERT: D 34 MET cc_start: 0.9148 (mmp) cc_final: 0.8909 (tpp) REVERT: D 72 ASP cc_start: 0.8212 (t0) cc_final: 0.7456 (t0) REVERT: D 86 ASP cc_start: 0.9055 (m-30) cc_final: 0.8510 (m-30) REVERT: D 89 VAL cc_start: 0.9069 (t) cc_final: 0.8811 (p) REVERT: D 100 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8349 (mtp85) REVERT: E 32 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.6097 (mmtm) REVERT: E 54 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8223 (ttm-80) REVERT: H 46 GLU cc_start: 0.8755 (tt0) cc_final: 0.8347 (pt0) REVERT: H 105 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8544 (mm-40) REVERT: L 24 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7824 (ttm-80) REVERT: L 105 GLU cc_start: 0.5487 (tp30) cc_final: 0.5195 (tm-30) REVERT: J 13 GLN cc_start: 0.8748 (mm110) cc_final: 0.8487 (mm110) REVERT: J 43 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8511 (mppt) REVERT: J 72 ASP cc_start: 0.8479 (t0) cc_final: 0.8000 (t70) REVERT: J 100 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.8938 (p) REVERT: J 105 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8924 (mm-40) REVERT: K 103 LYS cc_start: 0.8771 (tppp) cc_final: 0.8260 (tppp) outliers start: 67 outliers final: 39 residues processed: 276 average time/residue: 1.4451 time to fit residues: 447.4043 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 210 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN B 651 ASN F 656 ASN D 105 GLN H 13 GLN H 81 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.070933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.049970 restraints weight = 48491.111| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.54 r_work: 0.2484 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 21141 Z= 0.298 Angle : 0.665 9.796 28906 Z= 0.312 Chirality : 0.046 0.265 3529 Planarity : 0.003 0.031 3466 Dihedral : 8.520 70.039 5080 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.90 % Allowed : 23.04 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2384 helix: 2.64 (0.29), residues: 371 sheet: 0.15 (0.19), residues: 738 loop : 0.06 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 69 HIS 0.004 0.001 HIS C 105 PHE 0.015 0.002 PHE C 383 TYR 0.020 0.002 TYR D 100E ARG 0.010 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 55) link_NAG-ASN : angle 2.08093 ( 165) link_ALPHA1-6 : bond 0.00607 ( 5) link_ALPHA1-6 : angle 1.73648 ( 15) link_BETA1-4 : bond 0.00343 ( 50) link_BETA1-4 : angle 1.67631 ( 150) link_ALPHA1-2 : bond 0.00708 ( 3) link_ALPHA1-2 : angle 2.55015 ( 9) link_ALPHA1-3 : bond 0.00958 ( 6) link_ALPHA1-3 : angle 1.76112 ( 18) hydrogen bonds : bond 0.04261 ( 744) hydrogen bonds : angle 5.10278 ( 2046) SS BOND : bond 0.00352 ( 45) SS BOND : angle 0.77849 ( 90) covalent geometry : bond 0.00701 (20977) covalent geometry : angle 0.63389 (28459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 2.312 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9204 (mttm) cc_final: 0.8924 (mttp) REVERT: G 141 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8494 (p0) REVERT: G 475 MET cc_start: 0.8763 (mmm) cc_final: 0.7988 (mpp) REVERT: B 632 ASP cc_start: 0.9183 (t0) cc_final: 0.8862 (t0) REVERT: B 633 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8833 (mtpt) REVERT: B 655 LYS cc_start: 0.8734 (tptm) cc_final: 0.8440 (tptm) REVERT: I 114 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: F 599 SER cc_start: 0.9486 (t) cc_final: 0.9212 (p) REVERT: F 621 GLU cc_start: 0.8997 (pt0) cc_final: 0.8638 (pt0) REVERT: F 655 LYS cc_start: 0.7992 (tptt) cc_final: 0.7665 (ttpt) REVERT: D 12 VAL cc_start: 0.9601 (t) cc_final: 0.9356 (p) REVERT: D 72 ASP cc_start: 0.8206 (t0) cc_final: 0.7494 (t0) REVERT: D 100 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8397 (mtp85) REVERT: E 32 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6135 (mmtm) REVERT: E 54 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8279 (ttm-80) REVERT: H 46 GLU cc_start: 0.8820 (tt0) cc_final: 0.8391 (pt0) REVERT: H 105 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8574 (mm-40) REVERT: L 24 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7856 (ttm-80) REVERT: L 105 GLU cc_start: 0.5410 (tp30) cc_final: 0.5120 (tm-30) REVERT: J 13 GLN cc_start: 0.8728 (mm110) cc_final: 0.8463 (mm110) REVERT: J 72 ASP cc_start: 0.8500 (t0) cc_final: 0.8029 (t70) REVERT: J 100 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.8949 (p) REVERT: J 105 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8936 (mm-40) REVERT: K 24 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7875 (mtm-85) REVERT: K 103 LYS cc_start: 0.8740 (tppp) cc_final: 0.8193 (tppp) outliers start: 82 outliers final: 42 residues processed: 273 average time/residue: 1.3957 time to fit residues: 428.3963 Evaluate side-chains 253 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 17 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 196 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.051705 restraints weight = 48241.658| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.52 r_work: 0.2532 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21141 Z= 0.141 Angle : 0.607 9.683 28906 Z= 0.284 Chirality : 0.044 0.274 3529 Planarity : 0.003 0.050 3466 Dihedral : 7.915 61.361 5080 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.95 % Allowed : 24.32 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2384 helix: 2.82 (0.28), residues: 369 sheet: 0.15 (0.19), residues: 744 loop : 0.10 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.002 0.000 HIS G 105 PHE 0.012 0.001 PHE G 383 TYR 0.014 0.001 TYR J 100E ARG 0.013 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 55) link_NAG-ASN : angle 1.83183 ( 165) link_ALPHA1-6 : bond 0.00780 ( 5) link_ALPHA1-6 : angle 1.62914 ( 15) link_BETA1-4 : bond 0.00382 ( 50) link_BETA1-4 : angle 1.58777 ( 150) link_ALPHA1-2 : bond 0.00925 ( 3) link_ALPHA1-2 : angle 2.59094 ( 9) link_ALPHA1-3 : bond 0.01159 ( 6) link_ALPHA1-3 : angle 1.44941 ( 18) hydrogen bonds : bond 0.03624 ( 744) hydrogen bonds : angle 4.87603 ( 2046) SS BOND : bond 0.00207 ( 45) SS BOND : angle 0.59734 ( 90) covalent geometry : bond 0.00323 (20977) covalent geometry : angle 0.57875 (28459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 2.134 Fit side-chains revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9186 (mttm) cc_final: 0.8908 (mttp) REVERT: G 141 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8440 (p0) REVERT: G 475 MET cc_start: 0.8668 (mmm) cc_final: 0.7984 (mpp) REVERT: B 584 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 632 ASP cc_start: 0.9081 (t70) cc_final: 0.8792 (t0) REVERT: B 655 LYS cc_start: 0.8697 (tptm) cc_final: 0.8389 (tptm) REVERT: I 114 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: F 599 SER cc_start: 0.9456 (t) cc_final: 0.9208 (p) REVERT: F 621 GLU cc_start: 0.9000 (pt0) cc_final: 0.8666 (pt0) REVERT: F 655 LYS cc_start: 0.8008 (tptt) cc_final: 0.7690 (ttpt) REVERT: D 12 VAL cc_start: 0.9589 (t) cc_final: 0.9339 (p) REVERT: D 13 GLN cc_start: 0.8999 (mp10) cc_final: 0.8444 (mm-40) REVERT: D 18 LEU cc_start: 0.8833 (tp) cc_final: 0.8530 (mt) REVERT: D 34 MET cc_start: 0.9122 (mmp) cc_final: 0.8907 (tpp) REVERT: D 72 ASP cc_start: 0.8187 (t0) cc_final: 0.7435 (t0) REVERT: D 86 ASP cc_start: 0.9015 (m-30) cc_final: 0.8480 (m-30) REVERT: D 100 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8374 (mtp85) REVERT: E 32 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.6087 (mmtm) REVERT: E 54 ARG cc_start: 0.8679 (ttm110) cc_final: 0.8226 (ttm-80) REVERT: H 46 GLU cc_start: 0.8790 (tt0) cc_final: 0.8398 (pt0) REVERT: H 105 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8575 (mm-40) REVERT: L 24 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7811 (ttm-80) REVERT: J 13 GLN cc_start: 0.8749 (mm110) cc_final: 0.8480 (mm110) REVERT: J 43 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8460 (mppt) REVERT: J 72 ASP cc_start: 0.8475 (t0) cc_final: 0.8031 (t70) REVERT: J 100 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8926 (p) REVERT: J 105 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8941 (mm-40) REVERT: K 24 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7744 (mtm-85) REVERT: K 74 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8366 (p) REVERT: K 103 LYS cc_start: 0.8759 (tppp) cc_final: 0.8198 (tppp) outliers start: 62 outliers final: 43 residues processed: 267 average time/residue: 1.4059 time to fit residues: 424.0736 Evaluate side-chains 262 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 66 HIS Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 172 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 3 GLN D 13 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.051517 restraints weight = 48358.656| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.54 r_work: 0.2525 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21141 Z= 0.170 Angle : 0.620 11.244 28906 Z= 0.288 Chirality : 0.044 0.273 3529 Planarity : 0.003 0.050 3466 Dihedral : 7.353 56.826 5080 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.76 % Allowed : 24.46 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2384 helix: 2.83 (0.28), residues: 369 sheet: 0.14 (0.19), residues: 744 loop : 0.11 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 103 HIS 0.002 0.001 HIS G 330 PHE 0.013 0.001 PHE G 383 TYR 0.014 0.001 TYR J 100E ARG 0.012 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 55) link_NAG-ASN : angle 1.86887 ( 165) link_ALPHA1-6 : bond 0.00784 ( 5) link_ALPHA1-6 : angle 1.53295 ( 15) link_BETA1-4 : bond 0.00387 ( 50) link_BETA1-4 : angle 1.62838 ( 150) link_ALPHA1-2 : bond 0.00857 ( 3) link_ALPHA1-2 : angle 2.48973 ( 9) link_ALPHA1-3 : bond 0.01063 ( 6) link_ALPHA1-3 : angle 1.48041 ( 18) hydrogen bonds : bond 0.03674 ( 744) hydrogen bonds : angle 4.83950 ( 2046) SS BOND : bond 0.00244 ( 45) SS BOND : angle 0.63342 ( 90) covalent geometry : bond 0.00396 (20977) covalent geometry : angle 0.59227 (28459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8360 (mp10) REVERT: A 601 LYS cc_start: 0.9198 (mttm) cc_final: 0.8925 (mttp) REVERT: G 141 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8566 (p0) REVERT: G 475 MET cc_start: 0.8721 (mmm) cc_final: 0.7990 (mpp) REVERT: B 584 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 632 ASP cc_start: 0.9040 (t70) cc_final: 0.8779 (t0) REVERT: B 655 LYS cc_start: 0.8674 (tptm) cc_final: 0.8399 (tptm) REVERT: I 114 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: I 231 LYS cc_start: 0.9461 (mttt) cc_final: 0.9211 (mttm) REVERT: F 599 SER cc_start: 0.9465 (t) cc_final: 0.9233 (p) REVERT: F 621 GLU cc_start: 0.8994 (pt0) cc_final: 0.8661 (pt0) REVERT: F 655 LYS cc_start: 0.8014 (tptt) cc_final: 0.7703 (ttmt) REVERT: D 12 VAL cc_start: 0.9574 (t) cc_final: 0.9321 (p) REVERT: D 13 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8572 (mm-40) REVERT: D 34 MET cc_start: 0.9143 (mmp) cc_final: 0.8926 (tpp) REVERT: D 72 ASP cc_start: 0.8208 (t0) cc_final: 0.7474 (t0) REVERT: D 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8471 (m-30) REVERT: D 100 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8347 (mtp85) REVERT: E 32 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.6112 (mmtm) REVERT: E 54 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8268 (ttm-80) REVERT: H 46 GLU cc_start: 0.8793 (tt0) cc_final: 0.8408 (pt0) REVERT: H 105 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8678 (mm-40) REVERT: L 24 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7859 (ttm-80) REVERT: L 39 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8137 (mmtm) REVERT: L 81 GLU cc_start: 0.8510 (pp20) cc_final: 0.8308 (pp20) REVERT: J 13 GLN cc_start: 0.8766 (mm110) cc_final: 0.8502 (mm110) REVERT: J 43 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8472 (mppt) REVERT: J 72 ASP cc_start: 0.8496 (t0) cc_final: 0.8033 (t70) REVERT: J 100 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8979 (p) REVERT: J 105 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8944 (mm-40) REVERT: K 17 GLU cc_start: 0.8686 (pm20) cc_final: 0.8349 (pm20) REVERT: K 24 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7781 (mtm-85) REVERT: K 74 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8382 (p) REVERT: K 103 LYS cc_start: 0.8756 (tppp) cc_final: 0.8194 (tppp) outliers start: 58 outliers final: 42 residues processed: 261 average time/residue: 1.4240 time to fit residues: 416.0637 Evaluate side-chains 264 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 47 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 206 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN D 13 GLN H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051424 restraints weight = 48310.388| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.54 r_work: 0.2524 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21141 Z= 0.193 Angle : 0.774 59.196 28906 Z= 0.405 Chirality : 0.044 0.273 3529 Planarity : 0.003 0.048 3466 Dihedral : 7.349 56.820 5080 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 24.61 % Favored : 72.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2384 helix: 2.82 (0.28), residues: 369 sheet: 0.14 (0.19), residues: 744 loop : 0.10 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 103 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.001 PHE G 383 TYR 0.014 0.001 TYR D 100E ARG 0.007 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 55) link_NAG-ASN : angle 1.86387 ( 165) link_ALPHA1-6 : bond 0.00787 ( 5) link_ALPHA1-6 : angle 1.53142 ( 15) link_BETA1-4 : bond 0.00387 ( 50) link_BETA1-4 : angle 1.62900 ( 150) link_ALPHA1-2 : bond 0.00864 ( 3) link_ALPHA1-2 : angle 2.50808 ( 9) link_ALPHA1-3 : bond 0.01059 ( 6) link_ALPHA1-3 : angle 1.47424 ( 18) hydrogen bonds : bond 0.03682 ( 744) hydrogen bonds : angle 4.83941 ( 2046) SS BOND : bond 0.00406 ( 45) SS BOND : angle 1.06068 ( 90) covalent geometry : bond 0.00441 (20977) covalent geometry : angle 0.75243 (28459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: C 348 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: A 601 LYS cc_start: 0.9193 (mttm) cc_final: 0.8919 (mttp) REVERT: G 141 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8563 (p0) REVERT: G 475 MET cc_start: 0.8725 (mmm) cc_final: 0.7985 (mpp) REVERT: B 584 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 632 ASP cc_start: 0.9037 (t70) cc_final: 0.8752 (t0) REVERT: B 655 LYS cc_start: 0.8670 (tptm) cc_final: 0.8393 (tptm) REVERT: I 114 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: I 231 LYS cc_start: 0.9458 (mttt) cc_final: 0.9205 (mttm) REVERT: F 599 SER cc_start: 0.9459 (t) cc_final: 0.9224 (p) REVERT: F 621 GLU cc_start: 0.8994 (pt0) cc_final: 0.8657 (pt0) REVERT: F 655 LYS cc_start: 0.7989 (tptt) cc_final: 0.7681 (tppt) REVERT: D 12 VAL cc_start: 0.9481 (t) cc_final: 0.9273 (p) REVERT: D 34 MET cc_start: 0.9140 (mmp) cc_final: 0.8923 (tpp) REVERT: D 72 ASP cc_start: 0.8205 (t0) cc_final: 0.7470 (t0) REVERT: D 86 ASP cc_start: 0.9004 (m-30) cc_final: 0.8494 (m-30) REVERT: D 100 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8349 (mtp85) REVERT: E 32 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.6104 (mmtm) REVERT: E 54 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8251 (ttm-80) REVERT: H 46 GLU cc_start: 0.8802 (tt0) cc_final: 0.8414 (pt0) REVERT: H 105 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8679 (mm-40) REVERT: L 24 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7852 (ttm-80) REVERT: L 39 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8128 (mmtm) REVERT: L 81 GLU cc_start: 0.8501 (pp20) cc_final: 0.8293 (pp20) REVERT: J 13 GLN cc_start: 0.8762 (mm110) cc_final: 0.8497 (mm110) REVERT: J 43 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8467 (mppt) REVERT: J 72 ASP cc_start: 0.8489 (t0) cc_final: 0.8024 (t70) REVERT: J 100 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8976 (p) REVERT: J 105 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8945 (mm-40) REVERT: K 17 GLU cc_start: 0.8682 (pm20) cc_final: 0.8347 (pm20) REVERT: K 24 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7777 (mtm-85) REVERT: K 74 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 103 LYS cc_start: 0.8750 (tppp) cc_final: 0.8189 (tppp) outliers start: 55 outliers final: 46 residues processed: 257 average time/residue: 1.4489 time to fit residues: 415.9768 Evaluate side-chains 267 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 478 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 142 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 216 optimal weight: 0.0770 chunk 179 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN F 656 ASN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN L 79 GLN K 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.050871 restraints weight = 47755.186| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.39 r_work: 0.2484 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 21141 Z= 0.215 Angle : 0.781 59.196 28906 Z= 0.408 Chirality : 0.044 0.273 3529 Planarity : 0.003 0.048 3466 Dihedral : 7.349 56.820 5080 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.62 % Allowed : 24.65 % Favored : 72.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2384 helix: 2.82 (0.28), residues: 369 sheet: 0.14 (0.19), residues: 744 loop : 0.10 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 103 HIS 0.004 0.001 HIS C 105 PHE 0.013 0.001 PHE G 383 TYR 0.014 0.001 TYR D 100E ARG 0.007 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 55) link_NAG-ASN : angle 1.86387 ( 165) link_ALPHA1-6 : bond 0.00787 ( 5) link_ALPHA1-6 : angle 1.53142 ( 15) link_BETA1-4 : bond 0.00387 ( 50) link_BETA1-4 : angle 1.62900 ( 150) link_ALPHA1-2 : bond 0.00864 ( 3) link_ALPHA1-2 : angle 2.50808 ( 9) link_ALPHA1-3 : bond 0.01059 ( 6) link_ALPHA1-3 : angle 1.47424 ( 18) hydrogen bonds : bond 0.03682 ( 744) hydrogen bonds : angle 4.83941 ( 2046) SS BOND : bond 0.04091 ( 45) SS BOND : angle 2.11472 ( 90) covalent geometry : bond 0.00441 (20977) covalent geometry : angle 0.75243 (28459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11957.30 seconds wall clock time: 208 minutes 14.48 seconds (12494.48 seconds total)