Starting phenix.real_space_refine on Wed Jun 18 00:03:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.map" model { file = "/net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fis_29209/06_2025/8fis_29209.cif" } resolution = 3.18 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= 0.005 sd= 0.053 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 134 5.16 5 C 12660 2.51 5 N 3332 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3562 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3553 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1828 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 10, 'TRANS': 236} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: 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: "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: 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 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: "a" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 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: 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: "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: 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "x" 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: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.33, per 1000 atoms: 0.70 Number of scatterers: 20356 At special positions: 0 Unit cell: (154.869, 134.292, 145.122, 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 134 16.00 O 4230 8.00 N 3332 7.00 C 12660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " 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=2.04 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=2.08 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 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 J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L1023 " - pdb=" SG CYS L1088 " 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA c 3 " - " MAN c 4 " " BMA p 3 " - " MAN p 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA e 3 " - " MAN e 4 " " BMA r 3 " - " MAN r 4 " " BMA w 3 " - " MAN w 5 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 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 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 c 2 " - " BMA c 3 " " 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 339 " " NAG C 602 " - " ASN C 355 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 462 " " NAG D 1 " - " ASN C 197 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG E 703 " - " ASN E 618 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 339 " " NAG F 603 " - " ASN F 355 " " NAG F 604 " - " ASN F 137 " " NAG F 605 " - " ASN F 462 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 339 " " NAG G 605 " - " ASN G 355 " " NAG G 606 " - " ASN G 137 " " NAG G 607 " - " ASN G 462 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 295 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 392 " " NAG S 1 " - " ASN C 160 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 88 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 448 " " NAG Z 1 " - " ASN F 156 " " NAG a 1 " - " ASN F 197 " " NAG b 1 " - " ASN F 234 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN F 295 " " NAG e 1 " - " ASN F 301 " " NAG f 1 " - " ASN F 332 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 392 " " NAG i 1 " - " ASN F 448 " " NAG j 1 " - " ASN F 160 " " NAG k 1 " - " ASN F 363 " " NAG l 1 " - " ASN F 133 " " NAG m 1 " - " ASN F 276 " " NAG n 1 " - " ASN G 197 " " NAG o 1 " - " ASN G 234 " " NAG p 1 " - " ASN G 262 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 301 " " NAG s 1 " - " ASN G 332 " " NAG t 1 " - " ASN G 386 " " NAG u 1 " - " ASN G 392 " " NAG v 1 " - " ASN G 448 " " NAG w 1 " - " ASN G 160 " " NAG x 1 " - " ASN G 363 " " NAG y 1 " - " ASN G 156 " Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4336 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 21.3% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.465A 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 537 through 543 removed outlier: 3.881A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 596 removed outlier: 3.737A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.371A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.935A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.847A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 661 removed outlier: 3.572A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.806A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.639A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.796A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.541A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 116 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.670A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.692A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 removed outlier: 4.195A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 542 Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.648A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.270A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 removed outlier: 3.740A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.661A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 655 removed outlier: 3.542A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 660 removed outlier: 3.763A pdb=" N ASP E 659 " --> pdb=" O ASN E 656 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU E 660 " --> pdb=" O GLU E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 660' Processing helix chain 'F' and resid 58 through 65 removed outlier: 4.375A pdb=" N GLU F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 115 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.543A pdb=" N ARG F 151 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.021A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.791A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 61 removed outlier: 3.919A pdb=" N ALA G 60 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 117 removed outlier: 3.673A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.817A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.679A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.790A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.509A pdb=" N GLN J 31 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS J 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100C through 100E No H-bonds generated for 'chain 'J' and resid 100C through 100E' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.904A pdb=" N GLN I 31 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.673A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100E No H-bonds generated for 'chain 'I' and resid 100C through 100E' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.655A pdb=" N GLN L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing helix chain 'L' and resid 83 through 87 removed outlier: 4.002A pdb=" N THR L 87 " --> pdb=" O PRO L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1079 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.833A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.716A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.778A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.796A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.832A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.205A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 17.654A pdb=" N PHE C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 17.775A pdb=" N THR C 455 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 17.430A pdb=" N THR C 290 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 13.365A pdb=" N ILE C 453 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY C 451 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE C 294 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 449 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N CYS C 296 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER C 447 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 603 through 604 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.907A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.719A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'F' and resid 271 through 274 removed outlier: 7.343A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 271 through 274 removed outlier: 11.480A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N PHE F 288 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 12.119A pdb=" N ILE F 453 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 301 through 312 removed outlier: 6.558A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.164A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 86 " --> pdb=" O VAL G 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.726A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.249A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 181 through 183 removed outlier: 4.623A pdb=" N LYS G 171 " --> pdb=" O GLU H 100B" (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLU H 100B" --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 100A" --> pdb=" O SER H 100T" (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER H 100T" --> pdb=" O CYS H 100A" (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU H 100C" --> pdb=" O ALA H 100R" (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.566A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 315 through 323 removed outlier: 6.692A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.131A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.640A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 423 through 425 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.645A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 34 " --> pdb=" O MET J 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.645A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 34 " --> pdb=" O MET J 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.640A pdb=" N ILE I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.718A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.513A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL L 5 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 57 through 59 removed outlier: 5.599A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR L 102 " --> pdb=" O ARG L 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 57 through 59 removed outlier: 5.599A pdb=" N PHE L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG L 38 " --> pdb=" O PHE L 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 1009 through 1013 removed outlier: 3.659A pdb=" N ALA L1013 " --> pdb=" O ILE L1105 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP L1035 " --> pdb=" O LEU L1047 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 1009 through 1013 removed outlier: 3.659A pdb=" N ALA L1013 " --> pdb=" O ILE L1105 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L1097 " --> pdb=" O THR L1090 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 1019 through 1024 666 hydrogen bonds defined for protein. 1779 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: 8.00 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3406 1.32 - 1.45: 5958 1.45 - 1.58: 11196 1.58 - 1.71: 2 1.71 - 1.83: 180 Bond restraints: 20742 Sorted by residual: bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.634 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.534 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" CA SER G 199 " pdb=" CB SER G 199 " ideal model delta sigma weight residual 1.537 1.452 0.084 1.45e-02 4.76e+03 3.38e+01 ... (remaining 20737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 26938 1.86 - 3.72: 911 3.72 - 5.58: 226 5.58 - 7.45: 53 7.45 - 9.31: 5 Bond angle restraints: 28133 Sorted by residual: angle pdb=" N MET C 150 " pdb=" CA MET C 150 " pdb=" C MET C 150 " ideal model delta sigma weight residual 112.92 103.97 8.95 1.23e+00 6.61e-01 5.30e+01 angle pdb=" N ILE A 641 " pdb=" CA ILE A 641 " pdb=" C ILE A 641 " ideal model delta sigma weight residual 112.96 106.20 6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" C PRO G 118 " pdb=" CA PRO G 118 " pdb=" CB PRO G 118 " ideal model delta sigma weight residual 111.56 102.93 8.63 1.65e+00 3.67e-01 2.74e+01 angle pdb=" CA THR C 139 " pdb=" C THR C 139 " pdb=" O THR C 139 " ideal model delta sigma weight residual 122.01 116.96 5.05 1.05e+00 9.07e-01 2.31e+01 angle pdb=" N ASP C 141 " pdb=" CA ASP C 141 " pdb=" C ASP C 141 " ideal model delta sigma weight residual 113.97 107.90 6.07 1.28e+00 6.10e-01 2.25e+01 ... (remaining 28128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12816 22.64 - 45.28: 967 45.28 - 67.91: 223 67.91 - 90.55: 140 90.55 - 113.19: 76 Dihedral angle restraints: 14222 sinusoidal: 7470 harmonic: 6752 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -170.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.46 61.46 1 1.00e+01 1.00e-02 5.01e+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 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 14219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3485 0.143 - 0.286: 42 0.286 - 0.429: 1 0.429 - 0.573: 0 0.573 - 0.716: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C1 NAG j 1 " pdb=" ND2 ASN F 160 " pdb=" C2 NAG j 1 " pdb=" O5 NAG j 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG G 606 " pdb=" ND2 ASN G 137 " pdb=" C2 NAG G 606 " pdb=" O5 NAG G 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 3527 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 151 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.59e+00 pdb=" NE ARG C 151 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 151 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 151 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 151 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO C 206 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 173 " -0.013 2.00e-02 2.50e+03 1.45e-02 4.20e+00 pdb=" CG TYR F 173 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 173 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 173 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR F 173 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 173 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 173 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 173 " -0.001 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 432 2.67 - 3.23: 18730 3.23 - 3.78: 29220 3.78 - 4.34: 41923 4.34 - 4.90: 68342 Nonbonded interactions: 158647 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.110 3.040 nonbonded pdb=" O ASN G 355 " pdb=" OG SER G 397 " model vdw 2.117 3.040 nonbonded pdb=" O ASN F 478 " pdb=" OG SER F 481 " model vdw 2.179 3.040 nonbonded pdb=" O LEU B 629 " pdb=" NZ LYS B 633 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR E 606 " pdb=" O VAL F 36 " model vdw 2.213 3.040 ... (remaining 158642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = (chain 'B' and (resid 520 through 546 or resid 569 through 664 or resid 701 thro \ ugh 703)) selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 32 through 185 or resid 188 through 505 or resid 601 throu \ gh 604)) selection = (chain 'F' and (resid 32 through 505 or resid 601 through 604)) selection = (chain 'G' and (resid 32 through 505 or resid 601 through 604)) } ncs_group { reference = chain 'D' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'c' selection = chain 'e' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'w' selection = chain 'y' } 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: 4.180 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 52.070 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.006 0.176 20924 Z= 0.286 Angle : 0.864 14.520 28639 Z= 0.394 Chirality : 0.055 0.716 3530 Planarity : 0.004 0.111 3407 Dihedral : 19.549 113.189 9766 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.25 % Allowed : 9.68 % Favored : 90.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2315 helix: -0.93 (0.26), residues: 377 sheet: 0.39 (0.22), residues: 597 loop : -0.98 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 69 HIS 0.011 0.001 HIS F 374 PHE 0.014 0.001 PHE G 288 TYR 0.035 0.001 TYR F 173 ARG 0.011 0.000 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 66) link_NAG-ASN : angle 2.32774 ( 198) link_ALPHA1-6 : bond 0.00371 ( 8) link_ALPHA1-6 : angle 1.60669 ( 24) link_BETA1-4 : bond 0.00484 ( 60) link_BETA1-4 : angle 1.78453 ( 180) link_ALPHA1-3 : bond 0.00382 ( 8) link_ALPHA1-3 : angle 1.69118 ( 24) hydrogen bonds : bond 0.26261 ( 628) hydrogen bonds : angle 9.05600 ( 1779) SS BOND : bond 0.00864 ( 40) SS BOND : angle 2.20587 ( 80) covalent geometry : bond 0.00567 (20742) covalent geometry : angle 0.82685 (28133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 364 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.3714 time to fit residues: 200.6001 Evaluate side-chains 223 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 50.0000 chunk 176 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN A 630 GLN C 80 ASN C 103 GLN C 195 ASN E 575 GLN E 630 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 432 GLN G 33 ASN G 66 HIS G 80 ASN G 478 ASN J 3 GLN I 73 ASN H 39 GLN H 52AHIS L1037 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.120166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.081213 restraints weight = 36970.537| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.91 r_work: 0.2991 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20924 Z= 0.165 Angle : 0.768 16.611 28639 Z= 0.361 Chirality : 0.048 0.407 3530 Planarity : 0.004 0.050 3407 Dihedral : 14.487 81.741 5442 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 13.37 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2315 helix: 0.04 (0.26), residues: 373 sheet: 0.63 (0.22), residues: 566 loop : -1.05 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 69 HIS 0.005 0.001 HIS G 105 PHE 0.018 0.002 PHE G 288 TYR 0.023 0.001 TYR B 638 ARG 0.006 0.001 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 66) link_NAG-ASN : angle 2.74067 ( 198) link_ALPHA1-6 : bond 0.00688 ( 8) link_ALPHA1-6 : angle 1.56797 ( 24) link_BETA1-4 : bond 0.00491 ( 60) link_BETA1-4 : angle 2.11473 ( 180) link_ALPHA1-3 : bond 0.00901 ( 8) link_ALPHA1-3 : angle 2.63947 ( 24) hydrogen bonds : bond 0.05018 ( 628) hydrogen bonds : angle 5.81869 ( 1779) SS BOND : bond 0.00443 ( 40) SS BOND : angle 1.47996 ( 80) covalent geometry : bond 0.00378 (20742) covalent geometry : angle 0.71013 (28133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.9110 (m110) cc_final: 0.8904 (m110) REVERT: B 530 MET cc_start: 0.7698 (mtp) cc_final: 0.7275 (mtp) REVERT: B 624 ASP cc_start: 0.8601 (t0) cc_final: 0.8245 (t0) REVERT: C 100 MET cc_start: 0.9043 (ptm) cc_final: 0.8804 (ptm) REVERT: C 217 TYR cc_start: 0.8252 (m-80) cc_final: 0.7483 (m-80) REVERT: E 588 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7348 (tpp-160) REVERT: E 647 GLU cc_start: 0.8247 (tp30) cc_final: 0.7808 (tp30) REVERT: F 82 GLN cc_start: 0.8259 (mp10) cc_final: 0.7985 (mp10) REVERT: F 217 TYR cc_start: 0.8363 (m-80) cc_final: 0.8003 (m-80) REVERT: G 33 ASN cc_start: 0.6425 (t0) cc_final: 0.6167 (t0) REVERT: G 292 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8153 (m) REVERT: J 25 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8743 (mmt90) REVERT: J 82 MET cc_start: 0.7572 (mmm) cc_final: 0.7036 (tpp) REVERT: I 24 LEU cc_start: 0.8417 (tt) cc_final: 0.8184 (tp) REVERT: I 46 GLU cc_start: 0.7893 (pt0) cc_final: 0.7394 (pt0) REVERT: I 105 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8771 (mt0) REVERT: H 100 GLU cc_start: 0.8104 (pm20) cc_final: 0.7897 (pm20) outliers start: 47 outliers final: 20 residues processed: 281 average time/residue: 0.3078 time to fit residues: 134.9270 Evaluate side-chains 230 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 220 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079536 restraints weight = 37964.225| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.30 r_work: 0.2985 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20924 Z= 0.187 Angle : 0.723 11.531 28639 Z= 0.338 Chirality : 0.048 0.401 3530 Planarity : 0.004 0.051 3407 Dihedral : 11.797 71.536 5441 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 2.95 % Allowed : 14.30 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2315 helix: 0.31 (0.27), residues: 384 sheet: 0.45 (0.21), residues: 616 loop : -1.04 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 69 HIS 0.006 0.001 HIS H 35 PHE 0.023 0.002 PHE F 288 TYR 0.023 0.001 TYR B 638 ARG 0.004 0.000 ARG L1096 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 66) link_NAG-ASN : angle 2.70691 ( 198) link_ALPHA1-6 : bond 0.00752 ( 8) link_ALPHA1-6 : angle 1.71141 ( 24) link_BETA1-4 : bond 0.00506 ( 60) link_BETA1-4 : angle 1.91410 ( 180) link_ALPHA1-3 : bond 0.01014 ( 8) link_ALPHA1-3 : angle 1.93895 ( 24) hydrogen bonds : bond 0.04682 ( 628) hydrogen bonds : angle 5.39164 ( 1779) SS BOND : bond 0.00330 ( 40) SS BOND : angle 1.47853 ( 80) covalent geometry : bond 0.00442 (20742) covalent geometry : angle 0.66707 (28133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7980 (mtp) cc_final: 0.7754 (mtp) REVERT: B 624 ASP cc_start: 0.8449 (t0) cc_final: 0.7966 (t0) REVERT: C 63 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.5060 (p) REVERT: C 100 MET cc_start: 0.9010 (ptm) cc_final: 0.8716 (ptm) REVERT: C 150 MET cc_start: 0.8524 (mmm) cc_final: 0.7631 (mmm) REVERT: C 217 TYR cc_start: 0.8640 (m-80) cc_final: 0.8024 (m-80) REVERT: C 374 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.6919 (p-80) REVERT: C 434 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8779 (ptm) REVERT: E 588 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7860 (tpp-160) REVERT: F 271 MET cc_start: 0.8603 (mmm) cc_final: 0.8360 (mmp) REVERT: F 374 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6898 (p-80) REVERT: J 82 MET cc_start: 0.8101 (mmm) cc_final: 0.7766 (mtp) REVERT: J 85 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: I 46 GLU cc_start: 0.8390 (pt0) cc_final: 0.7877 (pt0) REVERT: I 105 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8613 (mt0) REVERT: H 95 ASP cc_start: 0.7449 (m-30) cc_final: 0.7000 (m-30) REVERT: H 100 GLU cc_start: 0.8267 (pm20) cc_final: 0.8038 (pm20) REVERT: H 100 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8118 (ttpp) outliers start: 60 outliers final: 28 residues processed: 267 average time/residue: 0.3226 time to fit residues: 134.0354 Evaluate side-chains 233 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 258 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 226 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 118 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 33 ASN J 3 GLN I 100CASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078800 restraints weight = 38412.138| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.39 r_work: 0.2973 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20924 Z= 0.177 Angle : 0.705 12.313 28639 Z= 0.329 Chirality : 0.048 0.403 3530 Planarity : 0.003 0.051 3407 Dihedral : 9.475 61.778 5441 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 3.10 % Allowed : 14.69 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2315 helix: 0.23 (0.26), residues: 398 sheet: 0.41 (0.21), residues: 621 loop : -1.12 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 96 HIS 0.008 0.001 HIS H 52A PHE 0.021 0.002 PHE F 288 TYR 0.026 0.001 TYR B 638 ARG 0.006 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 66) link_NAG-ASN : angle 2.75941 ( 198) link_ALPHA1-6 : bond 0.00958 ( 8) link_ALPHA1-6 : angle 1.88470 ( 24) link_BETA1-4 : bond 0.00463 ( 60) link_BETA1-4 : angle 1.83575 ( 180) link_ALPHA1-3 : bond 0.00997 ( 8) link_ALPHA1-3 : angle 2.34658 ( 24) hydrogen bonds : bond 0.04036 ( 628) hydrogen bonds : angle 5.16640 ( 1779) SS BOND : bond 0.00370 ( 40) SS BOND : angle 1.48936 ( 80) covalent geometry : bond 0.00417 (20742) covalent geometry : angle 0.64583 (28133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5609 (tp) REVERT: B 588 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: B 624 ASP cc_start: 0.8480 (t0) cc_final: 0.7904 (t0) REVERT: C 63 THR cc_start: 0.5427 (OUTLIER) cc_final: 0.5103 (p) REVERT: C 100 MET cc_start: 0.8995 (ptm) cc_final: 0.8655 (ptm) REVERT: C 217 TYR cc_start: 0.8657 (m-80) cc_final: 0.8067 (m-80) REVERT: C 374 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.6755 (p-80) REVERT: E 588 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7868 (tpp-160) REVERT: F 374 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.6632 (p-80) REVERT: G 302 ASN cc_start: 0.8303 (m-40) cc_final: 0.8091 (m-40) REVERT: J 85 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: I 46 GLU cc_start: 0.8443 (pt0) cc_final: 0.8187 (pt0) REVERT: I 105 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8647 (mt0) REVERT: H 100 GLU cc_start: 0.8274 (pm20) cc_final: 0.7977 (pm20) REVERT: H 100 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8013 (ttpp) outliers start: 63 outliers final: 37 residues processed: 263 average time/residue: 0.3062 time to fit residues: 126.5851 Evaluate side-chains 243 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 258 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN H 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078575 restraints weight = 38358.667| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.37 r_work: 0.2968 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20924 Z= 0.180 Angle : 0.693 11.462 28639 Z= 0.326 Chirality : 0.046 0.398 3530 Planarity : 0.003 0.050 3407 Dihedral : 8.511 58.972 5441 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.40 % Favored : 94.56 % Rotamer: Outliers : 3.44 % Allowed : 15.23 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.17), residues: 2315 helix: 0.38 (0.27), residues: 396 sheet: 0.39 (0.21), residues: 623 loop : -1.14 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 36 HIS 0.004 0.001 HIS G 105 PHE 0.018 0.002 PHE G 288 TYR 0.023 0.001 TYR B 638 ARG 0.003 0.000 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 66) link_NAG-ASN : angle 2.73359 ( 198) link_ALPHA1-6 : bond 0.00836 ( 8) link_ALPHA1-6 : angle 1.54402 ( 24) link_BETA1-4 : bond 0.00471 ( 60) link_BETA1-4 : angle 1.68470 ( 180) link_ALPHA1-3 : bond 0.01009 ( 8) link_ALPHA1-3 : angle 2.11558 ( 24) hydrogen bonds : bond 0.03989 ( 628) hydrogen bonds : angle 5.08081 ( 1779) SS BOND : bond 0.00360 ( 40) SS BOND : angle 1.57396 ( 80) covalent geometry : bond 0.00430 (20742) covalent geometry : angle 0.63670 (28133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7983 (mtp) cc_final: 0.7744 (mtp) REVERT: B 588 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7920 (ttm-80) REVERT: B 626 MET cc_start: 0.7600 (ttm) cc_final: 0.6768 (ttm) REVERT: C 63 THR cc_start: 0.5469 (OUTLIER) cc_final: 0.5138 (p) REVERT: C 100 MET cc_start: 0.8992 (ptm) cc_final: 0.8555 (ttp) REVERT: C 150 MET cc_start: 0.8733 (mmm) cc_final: 0.8170 (tpt) REVERT: C 217 TYR cc_start: 0.8624 (m-80) cc_final: 0.8043 (m-80) REVERT: C 374 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.6683 (p-80) REVERT: F 217 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.6809 (t80) REVERT: F 374 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.6447 (p-80) REVERT: G 302 ASN cc_start: 0.8326 (m-40) cc_final: 0.8104 (m-40) REVERT: J 85 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: I 46 GLU cc_start: 0.8452 (pt0) cc_final: 0.8163 (pt0) REVERT: I 105 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8638 (mt0) REVERT: H 95 ASP cc_start: 0.7653 (m-30) cc_final: 0.7418 (m-30) REVERT: H 100 GLU cc_start: 0.8279 (pm20) cc_final: 0.7938 (pm20) outliers start: 70 outliers final: 47 residues processed: 269 average time/residue: 0.3004 time to fit residues: 127.3540 Evaluate side-chains 251 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 258 GLN Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 100 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 4 optimal weight: 0.2980 chunk 160 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS J 3 GLN I 100CASN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.115969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079550 restraints weight = 38154.045| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.37 r_work: 0.2991 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20924 Z= 0.129 Angle : 0.653 11.443 28639 Z= 0.307 Chirality : 0.045 0.397 3530 Planarity : 0.003 0.049 3407 Dihedral : 7.740 59.563 5441 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 3.19 % Allowed : 16.12 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2315 helix: 0.57 (0.27), residues: 394 sheet: 0.50 (0.21), residues: 615 loop : -1.09 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.003 0.001 HIS C 72 PHE 0.013 0.001 PHE G 288 TYR 0.023 0.001 TYR B 638 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 66) link_NAG-ASN : angle 2.70219 ( 198) link_ALPHA1-6 : bond 0.00835 ( 8) link_ALPHA1-6 : angle 1.46531 ( 24) link_BETA1-4 : bond 0.00461 ( 60) link_BETA1-4 : angle 1.56032 ( 180) link_ALPHA1-3 : bond 0.01009 ( 8) link_ALPHA1-3 : angle 1.98558 ( 24) hydrogen bonds : bond 0.03568 ( 628) hydrogen bonds : angle 4.93990 ( 1779) SS BOND : bond 0.00300 ( 40) SS BOND : angle 1.42704 ( 80) covalent geometry : bond 0.00298 (20742) covalent geometry : angle 0.59723 (28133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5715 (tp) REVERT: A 654 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 588 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: C 63 THR cc_start: 0.5399 (OUTLIER) cc_final: 0.5067 (p) REVERT: C 100 MET cc_start: 0.8857 (ptm) cc_final: 0.8559 (ttp) REVERT: C 150 MET cc_start: 0.8690 (mmm) cc_final: 0.8119 (tpt) REVERT: C 217 TYR cc_start: 0.8614 (m-80) cc_final: 0.8074 (m-80) REVERT: C 374 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.6637 (p-80) REVERT: F 217 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.6857 (t80) REVERT: F 374 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.6218 (p-80) REVERT: J 82 MET cc_start: 0.8103 (mtp) cc_final: 0.7581 (mtp) REVERT: J 85 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: I 46 GLU cc_start: 0.8485 (pt0) cc_final: 0.8198 (pt0) REVERT: I 105 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8667 (mt0) REVERT: H 52 HIS cc_start: 0.6364 (p-80) cc_final: 0.5961 (p-80) REVERT: H 100 GLU cc_start: 0.8332 (pm20) cc_final: 0.7978 (pm20) outliers start: 65 outliers final: 42 residues processed: 257 average time/residue: 0.3763 time to fit residues: 154.2172 Evaluate side-chains 249 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 135 optimal weight: 0.0010 chunk 182 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.114873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078424 restraints weight = 38205.895| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.37 r_work: 0.2972 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20924 Z= 0.170 Angle : 0.673 13.345 28639 Z= 0.317 Chirality : 0.045 0.391 3530 Planarity : 0.003 0.048 3407 Dihedral : 7.365 59.780 5441 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 3.39 % Allowed : 15.97 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2315 helix: 0.63 (0.27), residues: 395 sheet: 0.53 (0.21), residues: 584 loop : -1.13 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.004 0.001 HIS G 105 PHE 0.023 0.002 PHE I 67 TYR 0.022 0.001 TYR B 638 ARG 0.007 0.000 ARG J 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 66) link_NAG-ASN : angle 2.81468 ( 198) link_ALPHA1-6 : bond 0.00786 ( 8) link_ALPHA1-6 : angle 1.52629 ( 24) link_BETA1-4 : bond 0.00474 ( 60) link_BETA1-4 : angle 1.53713 ( 180) link_ALPHA1-3 : bond 0.00927 ( 8) link_ALPHA1-3 : angle 1.91380 ( 24) hydrogen bonds : bond 0.03756 ( 628) hydrogen bonds : angle 4.93308 ( 1779) SS BOND : bond 0.00329 ( 40) SS BOND : angle 1.49018 ( 80) covalent geometry : bond 0.00407 (20742) covalent geometry : angle 0.61525 (28133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5831 (tp) REVERT: A 654 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 63 THR cc_start: 0.5307 (OUTLIER) cc_final: 0.4996 (p) REVERT: C 150 MET cc_start: 0.8680 (mmm) cc_final: 0.8312 (tpp) REVERT: C 217 TYR cc_start: 0.8578 (m-80) cc_final: 0.8018 (m-80) REVERT: C 374 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.6636 (p-80) REVERT: F 217 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.6900 (t80) REVERT: F 374 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.6292 (p-80) REVERT: J 85 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: I 46 GLU cc_start: 0.8480 (pt0) cc_final: 0.8172 (pt0) REVERT: I 105 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8687 (mt0) REVERT: H 52 HIS cc_start: 0.6406 (p-80) cc_final: 0.6057 (p-80) REVERT: H 100 GLU cc_start: 0.8379 (pm20) cc_final: 0.8006 (pm20) outliers start: 69 outliers final: 51 residues processed: 256 average time/residue: 0.4020 time to fit residues: 168.9201 Evaluate side-chains 252 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078898 restraints weight = 38533.705| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.37 r_work: 0.2984 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20924 Z= 0.143 Angle : 0.657 14.593 28639 Z= 0.309 Chirality : 0.044 0.389 3530 Planarity : 0.003 0.048 3407 Dihedral : 7.085 59.796 5441 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 3.19 % Allowed : 16.66 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2315 helix: 0.68 (0.27), residues: 396 sheet: 0.56 (0.21), residues: 586 loop : -1.10 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.003 0.001 HIS C 72 PHE 0.017 0.001 PHE I 17 TYR 0.022 0.001 TYR B 638 ARG 0.006 0.000 ARG J 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 66) link_NAG-ASN : angle 2.80297 ( 198) link_ALPHA1-6 : bond 0.00760 ( 8) link_ALPHA1-6 : angle 1.50383 ( 24) link_BETA1-4 : bond 0.00467 ( 60) link_BETA1-4 : angle 1.47127 ( 180) link_ALPHA1-3 : bond 0.00886 ( 8) link_ALPHA1-3 : angle 1.79009 ( 24) hydrogen bonds : bond 0.03548 ( 628) hydrogen bonds : angle 4.86595 ( 1779) SS BOND : bond 0.00319 ( 40) SS BOND : angle 1.35397 ( 80) covalent geometry : bond 0.00337 (20742) covalent geometry : angle 0.60019 (28133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.5882 (tp) REVERT: A 654 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7900 (mm-30) REVERT: C 63 THR cc_start: 0.5336 (OUTLIER) cc_final: 0.5002 (p) REVERT: C 150 MET cc_start: 0.8650 (mmm) cc_final: 0.8276 (tpp) REVERT: C 217 TYR cc_start: 0.8571 (m-80) cc_final: 0.8030 (m-80) REVERT: C 374 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.6576 (p-80) REVERT: E 624 ASP cc_start: 0.7523 (m-30) cc_final: 0.7261 (p0) REVERT: F 217 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.6956 (t80) REVERT: F 374 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.6279 (p-80) REVERT: J 82 MET cc_start: 0.7955 (mtp) cc_final: 0.7024 (mtp) REVERT: J 85 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: I 46 GLU cc_start: 0.8495 (pt0) cc_final: 0.8196 (pt0) REVERT: I 105 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8629 (mt0) REVERT: H 100 GLU cc_start: 0.8382 (pm20) cc_final: 0.8002 (pm20) outliers start: 65 outliers final: 51 residues processed: 254 average time/residue: 0.3835 time to fit residues: 153.4164 Evaluate side-chains 256 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 199 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 116 optimal weight: 0.9990 chunk 232 optimal weight: 20.0000 chunk 71 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079756 restraints weight = 38219.179| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.36 r_work: 0.3003 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20924 Z= 0.122 Angle : 0.635 13.197 28639 Z= 0.299 Chirality : 0.044 0.383 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.786 59.526 5441 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 3.05 % Allowed : 16.61 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2315 helix: 0.98 (0.28), residues: 378 sheet: 0.63 (0.21), residues: 570 loop : -1.07 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 36 HIS 0.003 0.001 HIS C 72 PHE 0.018 0.001 PHE I 17 TYR 0.022 0.001 TYR B 638 ARG 0.006 0.000 ARG J 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 66) link_NAG-ASN : angle 2.63778 ( 198) link_ALPHA1-6 : bond 0.00735 ( 8) link_ALPHA1-6 : angle 1.48287 ( 24) link_BETA1-4 : bond 0.00469 ( 60) link_BETA1-4 : angle 1.43056 ( 180) link_ALPHA1-3 : bond 0.00827 ( 8) link_ALPHA1-3 : angle 1.63930 ( 24) hydrogen bonds : bond 0.03319 ( 628) hydrogen bonds : angle 4.79381 ( 1779) SS BOND : bond 0.00310 ( 40) SS BOND : angle 1.27229 ( 80) covalent geometry : bond 0.00281 (20742) covalent geometry : angle 0.58318 (28133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5898 (tp) REVERT: B 530 MET cc_start: 0.7854 (mtp) cc_final: 0.7475 (mtp) REVERT: C 63 THR cc_start: 0.5023 (OUTLIER) cc_final: 0.4732 (p) REVERT: C 150 MET cc_start: 0.8623 (mmm) cc_final: 0.8266 (tpp) REVERT: C 217 TYR cc_start: 0.8543 (m-80) cc_final: 0.8016 (m-80) REVERT: C 374 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.6369 (p-80) REVERT: F 374 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.6052 (p-80) REVERT: J 85 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: I 46 GLU cc_start: 0.8489 (pt0) cc_final: 0.8164 (pt0) REVERT: I 105 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8719 (mt0) REVERT: H 52 HIS cc_start: 0.6543 (p-80) cc_final: 0.6128 (p-80) REVERT: H 100 GLU cc_start: 0.8345 (pm20) cc_final: 0.7965 (pm20) outliers start: 62 outliers final: 49 residues processed: 260 average time/residue: 0.5906 time to fit residues: 249.8131 Evaluate side-chains 257 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 54 CYS Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.6980 chunk 188 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 135 optimal weight: 0.0070 chunk 171 optimal weight: 0.1980 chunk 151 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081587 restraints weight = 38150.872| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.35 r_work: 0.3034 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20924 Z= 0.102 Angle : 0.617 12.862 28639 Z= 0.294 Chirality : 0.043 0.382 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.470 58.490 5441 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 2.36 % Allowed : 17.44 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2315 helix: 1.06 (0.28), residues: 378 sheet: 0.73 (0.21), residues: 583 loop : -1.00 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 36 HIS 0.003 0.001 HIS C 72 PHE 0.019 0.001 PHE I 17 TYR 0.022 0.001 TYR B 638 ARG 0.005 0.000 ARG J 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 66) link_NAG-ASN : angle 2.49543 ( 198) link_ALPHA1-6 : bond 0.00741 ( 8) link_ALPHA1-6 : angle 1.45558 ( 24) link_BETA1-4 : bond 0.00480 ( 60) link_BETA1-4 : angle 1.41192 ( 180) link_ALPHA1-3 : bond 0.00795 ( 8) link_ALPHA1-3 : angle 1.53116 ( 24) hydrogen bonds : bond 0.03012 ( 628) hydrogen bonds : angle 4.68770 ( 1779) SS BOND : bond 0.00259 ( 40) SS BOND : angle 1.13096 ( 80) covalent geometry : bond 0.00225 (20742) covalent geometry : angle 0.56870 (28133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5697 (tp) REVERT: B 584 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8346 (tt0) REVERT: B 624 ASP cc_start: 0.8521 (t0) cc_final: 0.8142 (m-30) REVERT: C 63 THR cc_start: 0.4952 (OUTLIER) cc_final: 0.4670 (p) REVERT: C 150 MET cc_start: 0.8594 (mmm) cc_final: 0.8131 (tpt) REVERT: C 217 TYR cc_start: 0.8532 (m-80) cc_final: 0.8046 (m-80) REVERT: C 374 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.6442 (p-80) REVERT: F 374 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.5961 (p-80) REVERT: J 85 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: I 46 GLU cc_start: 0.8442 (pt0) cc_final: 0.8124 (pt0) REVERT: I 105 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8682 (mt0) outliers start: 48 outliers final: 38 residues processed: 258 average time/residue: 0.5124 time to fit residues: 212.7290 Evaluate side-chains 254 residues out of total 2035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 288 PHE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 69 TRP Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 374 HIS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 64 TRP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 1069 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 132 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 227 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 chunk 149 optimal weight: 0.4980 chunk 141 optimal weight: 0.3980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN J 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.081296 restraints weight = 38386.270| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.36 r_work: 0.3028 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20924 Z= 0.107 Angle : 0.613 12.053 28639 Z= 0.291 Chirality : 0.043 0.371 3530 Planarity : 0.003 0.047 3407 Dihedral : 6.385 59.234 5441 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 2.21 % Allowed : 17.74 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2315 helix: 1.12 (0.28), residues: 378 sheet: 0.74 (0.21), residues: 587 loop : -0.97 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 36 HIS 0.003 0.001 HIS C 72 PHE 0.018 0.001 PHE I 17 TYR 0.022 0.001 TYR B 638 ARG 0.005 0.000 ARG J 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 66) link_NAG-ASN : angle 2.44109 ( 198) link_ALPHA1-6 : bond 0.00726 ( 8) link_ALPHA1-6 : angle 1.46285 ( 24) link_BETA1-4 : bond 0.00470 ( 60) link_BETA1-4 : angle 1.38765 ( 180) link_ALPHA1-3 : bond 0.00754 ( 8) link_ALPHA1-3 : angle 1.52121 ( 24) hydrogen bonds : bond 0.03029 ( 628) hydrogen bonds : angle 4.65222 ( 1779) SS BOND : bond 0.00254 ( 40) SS BOND : angle 1.13095 ( 80) covalent geometry : bond 0.00243 (20742) covalent geometry : angle 0.56622 (28133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11490.90 seconds wall clock time: 207 minutes 3.83 seconds (12423.83 seconds total)