Starting phenix.real_space_refine on Thu Feb 5 12:37:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.map" model { file = "/net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9omg_70613/02_2026/9omg_70613.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 100 5.16 5 C 10542 2.51 5 N 2751 2.21 5 O 3475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16868 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3505 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 4 Chain: "B" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 962 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "C" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3505 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 4 Chain: "E" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3505 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 4 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 962 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "G" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 962 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "H" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 793 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "D" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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: 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: "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: 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: "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: 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: 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: "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: 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: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Time building chain proxies: 4.40, per 1000 atoms: 0.26 Number of scatterers: 16868 At special positions: 0 Unit cell: (130.54, 130.54, 158.36, 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 100 16.00 O 3475 8.00 N 2751 7.00 C 10542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 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 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA V 3 " - " MAN V 4 " " BMA j 3 " - " MAN j 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 Y 1 " - " NAG Y 2 " " 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 d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG 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 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 u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 339 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 448 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 339 " " NAG D 1 " - " ASN A 156 " " NAG E 601 " - " ASN E 339 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 625 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 625 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 465 " " NAG O 1 " - " ASN A 392 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 133 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 160 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 241 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 276 " " NAG c 1 " - " ASN C 465 " " NAG d 1 " - " ASN C 392 " " NAG e 1 " - " ASN C 363 " " NAG f 1 " - " ASN C 332 " " NAG g 1 " - " ASN C 301 " " NAG h 1 " - " ASN C 262 " " NAG i 1 " - " ASN C 197 " " NAG j 1 " - " ASN C 160 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 241 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 392 " " NAG q 1 " - " ASN E 363 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 133 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 197 " " NAG w 1 " - " ASN E 160 " " NAG x 1 " - " ASN E 465 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 665.1 milliseconds 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 33 sheets defined 24.4% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.542A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.614A pdb=" N GLY A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.693A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.219A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.474A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.585A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.205A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.679A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.073A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 4.175A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.262A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.644A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.827A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 479 removed outlier: 4.084A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.743A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.948A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 4.184A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 475 through 481' Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.697A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.643A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.888A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.979A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 4.067A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 595 removed outlier: 3.682A pdb=" N ASP G 589 " --> pdb=" O HIS G 585 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G 592 " --> pdb=" O ARG G 588 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 625 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 639 through 661 removed outlier: 3.753A pdb=" N TYR G 643 " --> pdb=" O THR G 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.890A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.478A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.361A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.962A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 330 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.859A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLN A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ASN A 448 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N VAL A 292 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.626A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 307 removed outlier: 6.439A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.043A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.553A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.618A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.822A pdb=" N GLY C 451 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N GLN C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR C 293 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N THR C 334 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS C 330 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.312A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N GLN C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY C 451 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AC1, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.004A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.014A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.615A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR E 293 " --> pdb=" O THR E 334 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR E 334 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 419 " --> pdb=" O TYR E 384 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 384 " --> pdb=" O ARG E 419 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLN E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N ASN E 448 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N VAL E 292 " --> pdb=" O GLU E 446 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE E 361 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.653A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.914A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.802A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.517A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.601A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5072 1.34 - 1.47: 4474 1.47 - 1.59: 7514 1.59 - 1.71: 0 1.71 - 1.83: 130 Bond restraints: 17190 Sorted by residual: bond pdb=" N ILE E 371 " pdb=" CA ILE E 371 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.98e+00 bond pdb=" N GLN L 89 " pdb=" CA GLN L 89 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.43e+00 bond pdb=" N ASP E 368 " pdb=" CA ASP E 368 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.82e+00 bond pdb=" N PHE L 98 " pdb=" CA PHE L 98 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.30e-02 5.92e+03 6.12e+00 bond pdb=" N TYR L 91 " pdb=" CA TYR L 91 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.14e-02 7.69e+03 5.82e+00 ... (remaining 17185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 22496 2.02 - 4.05: 713 4.05 - 6.07: 94 6.07 - 8.10: 23 8.10 - 10.12: 9 Bond angle restraints: 23335 Sorted by residual: angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 112.12 116.11 -3.99 8.40e-01 1.42e+00 2.25e+01 angle pdb=" C ILE C 358 " pdb=" N ILE C 359 " pdb=" CA ILE C 359 " ideal model delta sigma weight residual 122.77 117.94 4.83 1.05e+00 9.07e-01 2.12e+01 angle pdb=" N LYS E 117 " pdb=" CA LYS E 117 " pdb=" C LYS E 117 " ideal model delta sigma weight residual 109.81 119.44 -9.63 2.21e+00 2.05e-01 1.90e+01 angle pdb=" C CYS E 385 " pdb=" N ASN E 386 " pdb=" CA ASN E 386 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" N ILE C 358 " pdb=" CA ILE C 358 " pdb=" C ILE C 358 " ideal model delta sigma weight residual 109.21 103.83 5.38 1.36e+00 5.41e-01 1.57e+01 ... (remaining 23330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10952 17.95 - 35.91: 676 35.91 - 53.86: 186 53.86 - 71.82: 46 71.82 - 89.77: 22 Dihedral angle restraints: 11882 sinusoidal: 6320 harmonic: 5562 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 163.57 -70.57 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.79 -64.79 1 1.00e+01 1.00e-02 5.51e+01 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 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 11879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2633 0.082 - 0.163: 308 0.163 - 0.245: 27 0.245 - 0.326: 1 0.326 - 0.408: 2 Chirality restraints: 2971 Sorted by residual: chirality pdb=" C4 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" C5 NAG I 1 " pdb=" O4 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.12 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" C4 NAG l 1 " pdb=" C3 NAG l 1 " pdb=" C5 NAG l 1 " pdb=" O4 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN E 88 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2968 not shown) Planarity restraints: 2851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 298 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 299 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO C 43 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 492 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO C 493 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 493 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 493 " 0.028 5.00e-02 4.00e+02 ... (remaining 2848 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4369 2.81 - 3.33: 15665 3.33 - 3.85: 26516 3.85 - 4.38: 29276 4.38 - 4.90: 51806 Nonbonded interactions: 127632 Sorted by model distance: nonbonded pdb=" OH TYR H 100N" pdb=" OE1 GLU L 55 " model vdw 2.286 3.040 nonbonded pdb=" O6 NAG h 1 " pdb=" O6 NAG C 602 " model vdw 2.296 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" O ALA E 497 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG C 503 " pdb=" OE1 GLN F 650 " model vdw 2.314 3.120 nonbonded pdb=" N GLU H 85 " pdb=" OE1 GLU H 85 " model vdw 2.333 3.120 ... (remaining 127627 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' selection = (chain 'C' and resid 33 through 603) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'a' selection = chain 'f' selection = chain 'h' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'r' selection = chain 'u' } 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=0.09 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.400 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.046 17343 Z= 0.179 Angle : 0.891 18.735 23760 Z= 0.452 Chirality : 0.051 0.408 2971 Planarity : 0.005 0.064 2795 Dihedral : 12.685 89.773 8186 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.06 % Allowed : 9.10 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1877 helix: 0.94 (0.28), residues: 342 sheet: -0.81 (0.23), residues: 469 loop : -1.17 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 166 TYR 0.021 0.001 TYR L 91 PHE 0.014 0.001 PHE E 383 TRP 0.022 0.002 TRP C 479 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00343 (17190) covalent geometry : angle 0.84335 (23335) SS BOND : bond 0.00313 ( 34) SS BOND : angle 0.87413 ( 68) hydrogen bonds : bond 0.22928 ( 541) hydrogen bonds : angle 8.32404 ( 1515) link_ALPHA1-3 : bond 0.00971 ( 2) link_ALPHA1-3 : angle 1.37272 ( 6) link_ALPHA1-6 : bond 0.00674 ( 2) link_ALPHA1-6 : angle 1.71515 ( 6) link_BETA1-4 : bond 0.01057 ( 59) link_BETA1-4 : angle 2.93564 ( 177) link_NAG-ASN : bond 0.00306 ( 56) link_NAG-ASN : angle 1.99909 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7155 (tpt) cc_final: 0.6506 (tpt) REVERT: A 207 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8654 (tptt) REVERT: A 377 ASN cc_start: 0.8226 (t0) cc_final: 0.7514 (t0) REVERT: B 530 MET cc_start: 0.8615 (mmm) cc_final: 0.7859 (tpp) REVERT: B 626 MET cc_start: 0.8782 (ptp) cc_final: 0.8259 (ptp) REVERT: C 479 TRP cc_start: 0.8873 (m-10) cc_final: 0.8439 (m-10) REVERT: E 473 SER cc_start: 0.8426 (m) cc_final: 0.8004 (p) REVERT: F 543 ASN cc_start: 0.8205 (t0) cc_final: 0.7716 (m110) REVERT: F 595 ILE cc_start: 0.9118 (tp) cc_final: 0.8719 (tt) REVERT: F 648 GLU cc_start: 0.9146 (tp30) cc_final: 0.8945 (tp30) REVERT: G 569 THR cc_start: 0.6903 (p) cc_final: 0.6679 (t) REVERT: G 607 ASN cc_start: 0.9561 (t0) cc_final: 0.9206 (m-40) REVERT: G 647 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8502 (mt-10) REVERT: G 653 GLN cc_start: 0.9106 (mt0) cc_final: 0.8729 (mt0) REVERT: H 64 LYS cc_start: 0.9118 (tttp) cc_final: 0.8778 (tptp) REVERT: H 75 LYS cc_start: 0.9711 (mptt) cc_final: 0.8946 (mptt) REVERT: H 83 ARG cc_start: 0.9438 (ptp-170) cc_final: 0.9163 (ptp-170) REVERT: H 96 ASP cc_start: 0.8168 (t0) cc_final: 0.7714 (t0) REVERT: L 21 ILE cc_start: 0.8456 (mm) cc_final: 0.8216 (tp) REVERT: L 47 LEU cc_start: 0.9194 (tp) cc_final: 0.8641 (mt) REVERT: L 73 LEU cc_start: 0.8953 (tp) cc_final: 0.7842 (tp) REVERT: L 92 ASN cc_start: 0.7834 (t0) cc_final: 0.7601 (t0) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.1402 time to fit residues: 40.3015 Evaluate side-chains 133 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 432 GLN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 HIS L 90 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.070659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054523 restraints weight = 62941.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056628 restraints weight = 32752.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.058002 restraints weight = 22626.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058891 restraints weight = 18102.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059463 restraints weight = 15697.648| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17343 Z= 0.159 Angle : 0.705 16.983 23760 Z= 0.326 Chirality : 0.046 0.383 2971 Planarity : 0.004 0.052 2795 Dihedral : 8.287 59.558 4575 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.41 % Allowed : 10.68 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1877 helix: 1.12 (0.28), residues: 372 sheet: -0.75 (0.23), residues: 469 loop : -1.00 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.015 0.001 TYR H 100D PHE 0.020 0.002 PHE C 376 TRP 0.021 0.001 TRP G 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00352 (17190) covalent geometry : angle 0.64838 (23335) SS BOND : bond 0.00274 ( 34) SS BOND : angle 0.82543 ( 68) hydrogen bonds : bond 0.04576 ( 541) hydrogen bonds : angle 5.86012 ( 1515) link_ALPHA1-3 : bond 0.00880 ( 2) link_ALPHA1-3 : angle 1.38463 ( 6) link_ALPHA1-6 : bond 0.00674 ( 2) link_ALPHA1-6 : angle 1.82048 ( 6) link_BETA1-4 : bond 0.00888 ( 59) link_BETA1-4 : angle 2.69927 ( 177) link_NAG-ASN : bond 0.00267 ( 56) link_NAG-ASN : angle 1.94582 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7421 (tpt) cc_final: 0.6916 (tpt) REVERT: A 377 ASN cc_start: 0.8340 (t0) cc_final: 0.7717 (t0) REVERT: A 464 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9157 (p) REVERT: B 654 GLU cc_start: 0.9330 (tp30) cc_final: 0.8958 (tp30) REVERT: C 99 ASN cc_start: 0.7523 (t0) cc_final: 0.7031 (t0) REVERT: C 161 MET cc_start: 0.8538 (tpt) cc_final: 0.8024 (tpt) REVERT: C 195 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7396 (t0) REVERT: C 432 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: E 161 MET cc_start: 0.8088 (mmm) cc_final: 0.7571 (tpt) REVERT: F 595 ILE cc_start: 0.9227 (tp) cc_final: 0.8914 (tt) REVERT: F 644 ARG cc_start: 0.9022 (tpp80) cc_final: 0.8790 (mmp80) REVERT: G 575 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 607 ASN cc_start: 0.9528 (t0) cc_final: 0.9239 (m-40) REVERT: G 626 MET cc_start: 0.8147 (tpt) cc_final: 0.7817 (tpt) REVERT: G 633 LYS cc_start: 0.9526 (tttt) cc_final: 0.9297 (ttpp) REVERT: G 647 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8383 (mt-10) REVERT: G 653 GLN cc_start: 0.9042 (mt0) cc_final: 0.8685 (mt0) REVERT: H 11 LEU cc_start: 0.9367 (mt) cc_final: 0.9013 (tt) REVERT: H 61 ASP cc_start: 0.9015 (p0) cc_final: 0.8774 (p0) REVERT: H 64 LYS cc_start: 0.9166 (tttp) cc_final: 0.8820 (tptp) REVERT: H 75 LYS cc_start: 0.9509 (mptt) cc_final: 0.9297 (mmtp) REVERT: L 47 LEU cc_start: 0.9112 (tp) cc_final: 0.8536 (mt) REVERT: L 73 LEU cc_start: 0.8808 (tp) cc_final: 0.8455 (tp) outliers start: 24 outliers final: 12 residues processed: 159 average time/residue: 0.1334 time to fit residues: 33.0185 Evaluate side-chains 131 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN C 195 ASN E 203 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.069839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050921 restraints weight = 68363.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053039 restraints weight = 35019.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054413 restraints weight = 24097.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.055312 restraints weight = 19335.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055804 restraints weight = 16847.705| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17343 Z= 0.277 Angle : 0.765 17.176 23760 Z= 0.356 Chirality : 0.047 0.386 2971 Planarity : 0.004 0.078 2795 Dihedral : 8.545 59.990 4575 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.94 % Allowed : 11.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1877 helix: 1.43 (0.29), residues: 354 sheet: -0.92 (0.23), residues: 468 loop : -0.93 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 429 TYR 0.015 0.002 TYR B 643 PHE 0.013 0.002 PHE E 383 TRP 0.024 0.002 TRP L 35 HIS 0.004 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00628 (17190) covalent geometry : angle 0.70957 (23335) SS BOND : bond 0.00330 ( 34) SS BOND : angle 1.01236 ( 68) hydrogen bonds : bond 0.04774 ( 541) hydrogen bonds : angle 5.58681 ( 1515) link_ALPHA1-3 : bond 0.00727 ( 2) link_ALPHA1-3 : angle 1.53025 ( 6) link_ALPHA1-6 : bond 0.00875 ( 2) link_ALPHA1-6 : angle 2.12067 ( 6) link_BETA1-4 : bond 0.00879 ( 59) link_BETA1-4 : angle 2.74014 ( 177) link_NAG-ASN : bond 0.00371 ( 56) link_NAG-ASN : angle 2.07068 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7585 (tpt) cc_final: 0.7326 (tpt) REVERT: A 377 ASN cc_start: 0.8485 (t0) cc_final: 0.7880 (t0) REVERT: A 475 MET cc_start: 0.8949 (tpt) cc_final: 0.8684 (tpt) REVERT: B 530 MET cc_start: 0.8699 (mmm) cc_final: 0.7854 (tpp) REVERT: B 654 GLU cc_start: 0.9363 (tp30) cc_final: 0.9004 (tp30) REVERT: C 161 MET cc_start: 0.8545 (tpt) cc_final: 0.8166 (tpt) REVERT: E 161 MET cc_start: 0.8000 (mmm) cc_final: 0.7423 (tpt) REVERT: E 473 SER cc_start: 0.8648 (m) cc_final: 0.8153 (t) REVERT: E 499 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7860 (p) REVERT: F 595 ILE cc_start: 0.9392 (tp) cc_final: 0.8915 (tp) REVERT: F 653 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8925 (tm-30) REVERT: G 575 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7855 (tm-30) REVERT: G 607 ASN cc_start: 0.9470 (t0) cc_final: 0.9252 (m-40) REVERT: G 630 GLN cc_start: 0.9093 (mt0) cc_final: 0.8687 (mp10) REVERT: G 647 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8170 (mt-10) REVERT: G 653 GLN cc_start: 0.8967 (mt0) cc_final: 0.8591 (mt0) REVERT: H 11 LEU cc_start: 0.9347 (mt) cc_final: 0.9082 (tp) REVERT: H 61 ASP cc_start: 0.8990 (p0) cc_final: 0.8672 (p0) REVERT: H 64 LYS cc_start: 0.9222 (tttp) cc_final: 0.8892 (tptp) REVERT: H 72 ASP cc_start: 0.7934 (t0) cc_final: 0.6891 (t0) REVERT: H 75 LYS cc_start: 0.9476 (mptt) cc_final: 0.8960 (mptt) REVERT: H 101 ASP cc_start: 0.9234 (t0) cc_final: 0.8812 (t0) REVERT: L 47 LEU cc_start: 0.9030 (tp) cc_final: 0.8624 (mt) outliers start: 33 outliers final: 17 residues processed: 144 average time/residue: 0.1298 time to fit residues: 29.1418 Evaluate side-chains 129 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 653 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 44 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052049 restraints weight = 69346.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054285 restraints weight = 35314.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.055750 restraints weight = 24205.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056683 restraints weight = 19315.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057181 restraints weight = 16809.679| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17343 Z= 0.125 Angle : 0.671 16.685 23760 Z= 0.306 Chirality : 0.045 0.382 2971 Planarity : 0.004 0.047 2795 Dihedral : 8.338 58.980 4575 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.76 % Allowed : 12.68 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1877 helix: 1.65 (0.29), residues: 354 sheet: -0.82 (0.23), residues: 471 loop : -0.81 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 644 TYR 0.012 0.001 TYR H 100D PHE 0.010 0.001 PHE L 98 TRP 0.012 0.001 TRP A 479 HIS 0.004 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00275 (17190) covalent geometry : angle 0.61644 (23335) SS BOND : bond 0.00238 ( 34) SS BOND : angle 0.61322 ( 68) hydrogen bonds : bond 0.03927 ( 541) hydrogen bonds : angle 5.19986 ( 1515) link_ALPHA1-3 : bond 0.00790 ( 2) link_ALPHA1-3 : angle 1.34403 ( 6) link_ALPHA1-6 : bond 0.00672 ( 2) link_ALPHA1-6 : angle 1.64390 ( 6) link_BETA1-4 : bond 0.00915 ( 59) link_BETA1-4 : angle 2.61965 ( 177) link_NAG-ASN : bond 0.00207 ( 56) link_NAG-ASN : angle 1.84451 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.643 Fit side-chains REVERT: A 161 MET cc_start: 0.7601 (tpt) cc_final: 0.7275 (tpt) REVERT: A 377 ASN cc_start: 0.8300 (t0) cc_final: 0.7698 (t0) REVERT: B 530 MET cc_start: 0.8684 (mmm) cc_final: 0.8019 (tpp) REVERT: B 539 VAL cc_start: 0.9555 (m) cc_final: 0.9311 (p) REVERT: B 654 GLU cc_start: 0.9331 (tp30) cc_final: 0.8976 (tp30) REVERT: C 320 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9086 (p) REVERT: C 434 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7596 (ttp) REVERT: E 117 LYS cc_start: 0.9282 (pptt) cc_final: 0.8940 (pttm) REVERT: E 161 MET cc_start: 0.7768 (mmm) cc_final: 0.7406 (tpt) REVERT: E 342 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8429 (tt) REVERT: F 584 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: F 595 ILE cc_start: 0.9351 (tp) cc_final: 0.8856 (tp) REVERT: G 607 ASN cc_start: 0.9451 (t0) cc_final: 0.9226 (m-40) REVERT: G 647 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8170 (mt-10) REVERT: G 653 GLN cc_start: 0.8970 (mt0) cc_final: 0.8629 (mt0) REVERT: H 11 LEU cc_start: 0.9334 (mt) cc_final: 0.8992 (tt) REVERT: H 61 ASP cc_start: 0.8978 (p0) cc_final: 0.8661 (p0) REVERT: H 75 LYS cc_start: 0.9488 (mptt) cc_final: 0.9206 (mmtm) REVERT: H 83 ARG cc_start: 0.9240 (ptp-170) cc_final: 0.8935 (ptp90) REVERT: L 47 LEU cc_start: 0.8999 (tp) cc_final: 0.8683 (mt) outliers start: 30 outliers final: 12 residues processed: 140 average time/residue: 0.1277 time to fit residues: 28.4906 Evaluate side-chains 129 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 8 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 98 optimal weight: 6.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.071808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053372 restraints weight = 66684.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.055555 restraints weight = 33686.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057026 restraints weight = 22720.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057959 restraints weight = 17913.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.058482 restraints weight = 15450.703| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17343 Z= 0.125 Angle : 0.655 16.814 23760 Z= 0.298 Chirality : 0.045 0.379 2971 Planarity : 0.004 0.054 2795 Dihedral : 8.274 58.118 4574 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.70 % Allowed : 12.50 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1877 helix: 1.77 (0.29), residues: 354 sheet: -0.74 (0.23), residues: 465 loop : -0.78 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 273 TYR 0.016 0.001 TYR B 643 PHE 0.009 0.001 PHE L 98 TRP 0.013 0.001 TRP G 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00279 (17190) covalent geometry : angle 0.60060 (23335) SS BOND : bond 0.00289 ( 34) SS BOND : angle 0.59165 ( 68) hydrogen bonds : bond 0.03623 ( 541) hydrogen bonds : angle 5.04059 ( 1515) link_ALPHA1-3 : bond 0.00769 ( 2) link_ALPHA1-3 : angle 1.33946 ( 6) link_ALPHA1-6 : bond 0.00677 ( 2) link_ALPHA1-6 : angle 1.61093 ( 6) link_BETA1-4 : bond 0.00931 ( 59) link_BETA1-4 : angle 2.59905 ( 177) link_NAG-ASN : bond 0.00196 ( 56) link_NAG-ASN : angle 1.77156 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.7702 (tpt) cc_final: 0.7410 (tpt) REVERT: A 377 ASN cc_start: 0.8303 (t0) cc_final: 0.7647 (t0) REVERT: B 530 MET cc_start: 0.8697 (mmm) cc_final: 0.8149 (tpp) REVERT: B 654 GLU cc_start: 0.9329 (tp30) cc_final: 0.8987 (tp30) REVERT: B 659 GLU cc_start: 0.8171 (pp20) cc_final: 0.7889 (pp20) REVERT: C 320 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9101 (p) REVERT: E 117 LYS cc_start: 0.9269 (pptt) cc_final: 0.8900 (pttt) REVERT: E 161 MET cc_start: 0.7732 (mmm) cc_final: 0.7409 (tpt) REVERT: E 342 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8456 (tt) REVERT: F 584 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: F 595 ILE cc_start: 0.9332 (tp) cc_final: 0.8845 (tp) REVERT: G 607 ASN cc_start: 0.9461 (t0) cc_final: 0.9212 (m-40) REVERT: G 633 LYS cc_start: 0.9325 (tmmt) cc_final: 0.9038 (pttm) REVERT: G 647 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8190 (mt-10) REVERT: G 653 GLN cc_start: 0.8963 (mt0) cc_final: 0.8607 (mt0) REVERT: H 11 LEU cc_start: 0.9315 (mt) cc_final: 0.8991 (tt) REVERT: H 61 ASP cc_start: 0.8977 (p0) cc_final: 0.8655 (p0) REVERT: H 75 LYS cc_start: 0.9493 (mptt) cc_final: 0.9206 (mmtm) REVERT: H 83 ARG cc_start: 0.9215 (ptp-170) cc_final: 0.8883 (ptp90) REVERT: L 47 LEU cc_start: 0.9001 (tp) cc_final: 0.8695 (mt) outliers start: 29 outliers final: 11 residues processed: 145 average time/residue: 0.1275 time to fit residues: 29.3534 Evaluate side-chains 126 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 GLN L 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.071964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053274 restraints weight = 67981.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.055424 restraints weight = 33937.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056857 restraints weight = 22777.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057788 restraints weight = 17871.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058360 restraints weight = 15343.731| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17343 Z= 0.160 Angle : 0.671 16.701 23760 Z= 0.306 Chirality : 0.045 0.375 2971 Planarity : 0.004 0.047 2795 Dihedral : 8.327 58.829 4574 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.94 % Allowed : 13.62 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1877 helix: 1.89 (0.29), residues: 351 sheet: -0.76 (0.23), residues: 465 loop : -0.76 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.015 0.001 TYR B 643 PHE 0.009 0.001 PHE E 383 TRP 0.014 0.001 TRP G 631 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00365 (17190) covalent geometry : angle 0.61855 (23335) SS BOND : bond 0.00243 ( 34) SS BOND : angle 0.67660 ( 68) hydrogen bonds : bond 0.03637 ( 541) hydrogen bonds : angle 4.99651 ( 1515) link_ALPHA1-3 : bond 0.00703 ( 2) link_ALPHA1-3 : angle 1.37126 ( 6) link_ALPHA1-6 : bond 0.00708 ( 2) link_ALPHA1-6 : angle 1.72114 ( 6) link_BETA1-4 : bond 0.00885 ( 59) link_BETA1-4 : angle 2.58191 ( 177) link_NAG-ASN : bond 0.00210 ( 56) link_NAG-ASN : angle 1.78595 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7726 (tpt) cc_final: 0.7321 (tpt) REVERT: A 377 ASN cc_start: 0.8309 (t0) cc_final: 0.7706 (t0) REVERT: B 654 GLU cc_start: 0.9298 (tp30) cc_final: 0.8976 (tp30) REVERT: B 659 GLU cc_start: 0.8224 (pp20) cc_final: 0.7972 (pp20) REVERT: C 117 LYS cc_start: 0.9270 (tttm) cc_final: 0.8998 (ttpp) REVERT: C 320 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9145 (p) REVERT: E 117 LYS cc_start: 0.9279 (pptt) cc_final: 0.8928 (pttt) REVERT: E 161 MET cc_start: 0.7818 (mmm) cc_final: 0.7515 (tpt) REVERT: E 342 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8538 (tt) REVERT: F 584 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: F 595 ILE cc_start: 0.9379 (tp) cc_final: 0.8875 (tp) REVERT: G 626 MET cc_start: 0.8070 (tpp) cc_final: 0.7853 (tpt) REVERT: G 653 GLN cc_start: 0.8942 (mt0) cc_final: 0.8526 (mt0) REVERT: G 654 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8904 (mm-30) REVERT: H 11 LEU cc_start: 0.9289 (mt) cc_final: 0.8978 (tt) REVERT: H 61 ASP cc_start: 0.9008 (p0) cc_final: 0.8680 (p0) REVERT: H 75 LYS cc_start: 0.9467 (mptt) cc_final: 0.9188 (mmtm) REVERT: H 83 ARG cc_start: 0.9218 (ptp-170) cc_final: 0.8886 (ptp90) REVERT: L 47 LEU cc_start: 0.8996 (tp) cc_final: 0.8730 (mt) outliers start: 33 outliers final: 19 residues processed: 143 average time/residue: 0.1281 time to fit residues: 28.9250 Evaluate side-chains 134 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 530 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056389 restraints weight = 68018.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058531 restraints weight = 33055.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059961 restraints weight = 21798.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060801 restraints weight = 16954.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061443 restraints weight = 14534.416| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17343 Z= 0.162 Angle : 0.674 16.578 23760 Z= 0.308 Chirality : 0.045 0.373 2971 Planarity : 0.004 0.047 2795 Dihedral : 8.350 58.876 4574 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.88 % Allowed : 14.26 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1877 helix: 2.11 (0.29), residues: 351 sheet: -0.75 (0.23), residues: 465 loop : -0.83 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.014 0.001 TYR B 643 PHE 0.009 0.001 PHE E 383 TRP 0.012 0.001 TRP G 631 HIS 0.003 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00371 (17190) covalent geometry : angle 0.62258 (23335) SS BOND : bond 0.00236 ( 34) SS BOND : angle 0.66917 ( 68) hydrogen bonds : bond 0.03614 ( 541) hydrogen bonds : angle 4.98477 ( 1515) link_ALPHA1-3 : bond 0.00675 ( 2) link_ALPHA1-3 : angle 1.37751 ( 6) link_ALPHA1-6 : bond 0.00691 ( 2) link_ALPHA1-6 : angle 1.70797 ( 6) link_BETA1-4 : bond 0.00867 ( 59) link_BETA1-4 : angle 2.56101 ( 177) link_NAG-ASN : bond 0.00207 ( 56) link_NAG-ASN : angle 1.77027 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7803 (tpt) cc_final: 0.7313 (tpt) REVERT: A 377 ASN cc_start: 0.8372 (t0) cc_final: 0.7856 (t0) REVERT: B 653 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.8886 (tm-30) REVERT: B 654 GLU cc_start: 0.9297 (tp30) cc_final: 0.8984 (tp30) REVERT: B 659 GLU cc_start: 0.8314 (pp20) cc_final: 0.8063 (pp20) REVERT: C 117 LYS cc_start: 0.9285 (tttm) cc_final: 0.9030 (ttpp) REVERT: C 320 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9214 (p) REVERT: E 117 LYS cc_start: 0.9290 (pptt) cc_final: 0.8927 (pttt) REVERT: E 342 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (tt) REVERT: F 584 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: F 595 ILE cc_start: 0.9366 (tp) cc_final: 0.8867 (tp) REVERT: G 626 MET cc_start: 0.8013 (tpp) cc_final: 0.7809 (tpt) REVERT: G 647 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7623 (mt-10) REVERT: H 11 LEU cc_start: 0.9300 (mt) cc_final: 0.8989 (tt) REVERT: H 61 ASP cc_start: 0.9062 (p0) cc_final: 0.8737 (p0) REVERT: H 75 LYS cc_start: 0.9477 (mptt) cc_final: 0.9190 (mmtm) REVERT: H 83 ARG cc_start: 0.9185 (ptp-170) cc_final: 0.8833 (ptp90) REVERT: H 87 THR cc_start: 0.8675 (t) cc_final: 0.8329 (m) outliers start: 32 outliers final: 20 residues processed: 140 average time/residue: 0.1241 time to fit residues: 28.0338 Evaluate side-chains 134 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 640 GLN L 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.073276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055641 restraints weight = 67558.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057802 restraints weight = 33235.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059274 restraints weight = 22213.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060220 restraints weight = 17380.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060828 restraints weight = 14894.204| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17343 Z= 0.124 Angle : 0.667 16.552 23760 Z= 0.306 Chirality : 0.045 0.372 2971 Planarity : 0.004 0.073 2795 Dihedral : 8.281 58.753 4574 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 14.55 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1877 helix: 2.12 (0.28), residues: 351 sheet: -0.74 (0.23), residues: 468 loop : -0.79 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.014 0.001 TYR A 191 PHE 0.010 0.001 PHE L 98 TRP 0.010 0.001 TRP A 479 HIS 0.003 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00280 (17190) covalent geometry : angle 0.61718 (23335) SS BOND : bond 0.00238 ( 34) SS BOND : angle 0.82037 ( 68) hydrogen bonds : bond 0.03440 ( 541) hydrogen bonds : angle 4.87402 ( 1515) link_ALPHA1-3 : bond 0.00681 ( 2) link_ALPHA1-3 : angle 1.35147 ( 6) link_ALPHA1-6 : bond 0.00638 ( 2) link_ALPHA1-6 : angle 1.57095 ( 6) link_BETA1-4 : bond 0.00889 ( 59) link_BETA1-4 : angle 2.53646 ( 177) link_NAG-ASN : bond 0.00201 ( 56) link_NAG-ASN : angle 1.69606 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7835 (tpt) cc_final: 0.7412 (tpt) REVERT: A 377 ASN cc_start: 0.8250 (t0) cc_final: 0.7723 (t0) REVERT: B 654 GLU cc_start: 0.9286 (tp30) cc_final: 0.8970 (tp30) REVERT: B 659 GLU cc_start: 0.8317 (pp20) cc_final: 0.8097 (pp20) REVERT: C 320 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9216 (p) REVERT: E 117 LYS cc_start: 0.9266 (pptt) cc_final: 0.8955 (pttm) REVERT: E 161 MET cc_start: 0.7207 (mmm) cc_final: 0.6980 (tpt) REVERT: E 342 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8459 (tt) REVERT: F 584 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: F 595 ILE cc_start: 0.9313 (tp) cc_final: 0.8796 (tp) REVERT: F 653 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8821 (tm-30) REVERT: G 626 MET cc_start: 0.8065 (tpp) cc_final: 0.7805 (tpt) REVERT: G 648 GLU cc_start: 0.9129 (tp30) cc_final: 0.8908 (pt0) REVERT: H 11 LEU cc_start: 0.9315 (mt) cc_final: 0.9003 (tt) REVERT: H 61 ASP cc_start: 0.9084 (p0) cc_final: 0.8769 (p0) REVERT: H 75 LYS cc_start: 0.9478 (mptt) cc_final: 0.9161 (mmtm) REVERT: H 83 ARG cc_start: 0.9169 (ptp-170) cc_final: 0.8509 (ptp90) REVERT: H 87 THR cc_start: 0.8660 (t) cc_final: 0.8316 (m) REVERT: L 47 LEU cc_start: 0.8988 (tp) cc_final: 0.8719 (mt) REVERT: L 82 ASP cc_start: 0.8787 (t0) cc_final: 0.8421 (p0) outliers start: 30 outliers final: 18 residues processed: 141 average time/residue: 0.1317 time to fit residues: 29.0820 Evaluate side-chains 135 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.051806 restraints weight = 67202.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.053935 restraints weight = 34139.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055341 restraints weight = 23179.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056250 restraints weight = 18422.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.056817 restraints weight = 15952.715| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17343 Z= 0.188 Angle : 0.698 16.730 23760 Z= 0.322 Chirality : 0.045 0.374 2971 Planarity : 0.004 0.049 2795 Dihedral : 8.388 59.213 4574 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.76 % Allowed : 14.50 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1877 helix: 2.08 (0.28), residues: 351 sheet: -0.79 (0.23), residues: 468 loop : -0.83 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.015 0.001 TYR B 643 PHE 0.009 0.001 PHE E 383 TRP 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00431 (17190) covalent geometry : angle 0.64890 (23335) SS BOND : bond 0.00261 ( 34) SS BOND : angle 0.82049 ( 68) hydrogen bonds : bond 0.03646 ( 541) hydrogen bonds : angle 4.96240 ( 1515) link_ALPHA1-3 : bond 0.00624 ( 2) link_ALPHA1-3 : angle 1.40116 ( 6) link_ALPHA1-6 : bond 0.00742 ( 2) link_ALPHA1-6 : angle 1.74140 ( 6) link_BETA1-4 : bond 0.00872 ( 59) link_BETA1-4 : angle 2.54600 ( 177) link_NAG-ASN : bond 0.00245 ( 56) link_NAG-ASN : angle 1.76815 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7830 (tpt) cc_final: 0.7335 (tpt) REVERT: A 377 ASN cc_start: 0.8369 (t0) cc_final: 0.7899 (t0) REVERT: B 653 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.8894 (tm-30) REVERT: B 654 GLU cc_start: 0.9332 (tp30) cc_final: 0.9034 (tp30) REVERT: B 659 GLU cc_start: 0.8386 (pp20) cc_final: 0.8150 (pp20) REVERT: C 320 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9219 (p) REVERT: E 342 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8578 (tt) REVERT: F 584 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: F 595 ILE cc_start: 0.9380 (tp) cc_final: 0.8884 (tp) REVERT: G 626 MET cc_start: 0.8159 (tpp) cc_final: 0.7916 (tpt) REVERT: H 11 LEU cc_start: 0.9320 (mt) cc_final: 0.9013 (tt) REVERT: H 61 ASP cc_start: 0.9123 (p0) cc_final: 0.8813 (p0) REVERT: H 75 LYS cc_start: 0.9497 (mptt) cc_final: 0.9198 (mmtm) REVERT: H 83 ARG cc_start: 0.9184 (ptp-170) cc_final: 0.8855 (ptp90) REVERT: H 87 THR cc_start: 0.8656 (t) cc_final: 0.8312 (m) REVERT: L 47 LEU cc_start: 0.8980 (tp) cc_final: 0.8694 (mt) REVERT: L 82 ASP cc_start: 0.8770 (t0) cc_final: 0.8535 (p0) outliers start: 30 outliers final: 23 residues processed: 138 average time/residue: 0.1294 time to fit residues: 28.4198 Evaluate side-chains 139 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055257 restraints weight = 67257.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057492 restraints weight = 34356.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058964 restraints weight = 23389.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059861 restraints weight = 18587.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060484 restraints weight = 16166.434| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17343 Z= 0.126 Angle : 0.671 16.550 23760 Z= 0.309 Chirality : 0.045 0.370 2971 Planarity : 0.004 0.047 2795 Dihedral : 8.280 59.095 4574 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.58 % Allowed : 15.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1877 helix: 2.12 (0.28), residues: 351 sheet: -0.74 (0.23), residues: 468 loop : -0.79 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 644 TYR 0.012 0.001 TYR A 191 PHE 0.009 0.001 PHE L 98 TRP 0.011 0.001 TRP G 631 HIS 0.003 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00285 (17190) covalent geometry : angle 0.62395 (23335) SS BOND : bond 0.00230 ( 34) SS BOND : angle 0.63955 ( 68) hydrogen bonds : bond 0.03376 ( 541) hydrogen bonds : angle 4.82609 ( 1515) link_ALPHA1-3 : bond 0.00633 ( 2) link_ALPHA1-3 : angle 1.36920 ( 6) link_ALPHA1-6 : bond 0.00611 ( 2) link_ALPHA1-6 : angle 1.55699 ( 6) link_BETA1-4 : bond 0.00891 ( 59) link_BETA1-4 : angle 2.50581 ( 177) link_NAG-ASN : bond 0.00195 ( 56) link_NAG-ASN : angle 1.65132 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7848 (tpt) cc_final: 0.7376 (tpt) REVERT: A 377 ASN cc_start: 0.8267 (t0) cc_final: 0.7772 (t0) REVERT: B 530 MET cc_start: 0.8214 (tpp) cc_final: 0.7691 (tpp) REVERT: B 659 GLU cc_start: 0.8360 (pp20) cc_final: 0.8114 (pp20) REVERT: E 342 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8380 (tt) REVERT: F 584 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: F 595 ILE cc_start: 0.9339 (tp) cc_final: 0.8821 (tp) REVERT: F 653 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8796 (tm-30) REVERT: G 626 MET cc_start: 0.8251 (tpp) cc_final: 0.7952 (tpp) REVERT: G 648 GLU cc_start: 0.9151 (tp30) cc_final: 0.8901 (pt0) REVERT: H 11 LEU cc_start: 0.9325 (mt) cc_final: 0.9022 (tt) REVERT: H 34 MET cc_start: 0.8977 (mmm) cc_final: 0.8748 (mmm) REVERT: H 61 ASP cc_start: 0.9126 (p0) cc_final: 0.8815 (p0) REVERT: H 75 LYS cc_start: 0.9484 (mptt) cc_final: 0.9153 (mmtm) REVERT: H 83 ARG cc_start: 0.9198 (ptp-170) cc_final: 0.8883 (ptp90) REVERT: H 87 THR cc_start: 0.8630 (t) cc_final: 0.8287 (m) REVERT: L 47 LEU cc_start: 0.8981 (tp) cc_final: 0.8697 (mt) outliers start: 27 outliers final: 22 residues processed: 142 average time/residue: 0.1304 time to fit residues: 29.0327 Evaluate side-chains 138 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 50 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 178 optimal weight: 0.0000 chunk 126 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.073590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056269 restraints weight = 66455.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058459 restraints weight = 32885.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.059917 restraints weight = 21820.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060854 restraints weight = 17022.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.061456 restraints weight = 14576.430| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17343 Z= 0.115 Angle : 0.667 16.416 23760 Z= 0.307 Chirality : 0.045 0.364 2971 Planarity : 0.003 0.047 2795 Dihedral : 8.212 59.877 4574 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.58 % Allowed : 15.08 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1877 helix: 2.12 (0.28), residues: 351 sheet: -0.68 (0.23), residues: 468 loop : -0.74 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 644 TYR 0.010 0.001 TYR A 191 PHE 0.010 0.001 PHE L 98 TRP 0.013 0.001 TRP G 631 HIS 0.003 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00259 (17190) covalent geometry : angle 0.62047 (23335) SS BOND : bond 0.00229 ( 34) SS BOND : angle 0.57270 ( 68) hydrogen bonds : bond 0.03226 ( 541) hydrogen bonds : angle 4.76233 ( 1515) link_ALPHA1-3 : bond 0.00628 ( 2) link_ALPHA1-3 : angle 1.36619 ( 6) link_ALPHA1-6 : bond 0.00597 ( 2) link_ALPHA1-6 : angle 1.53639 ( 6) link_BETA1-4 : bond 0.00867 ( 59) link_BETA1-4 : angle 2.48378 ( 177) link_NAG-ASN : bond 0.00203 ( 56) link_NAG-ASN : angle 1.60347 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2859.96 seconds wall clock time: 50 minutes 34.25 seconds (3034.25 seconds total)