Starting phenix.real_space_refine on Fri Feb 6 01:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pni_71766/02_2026/9pni_71766.map" } resolution = 3.83 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= 0.021 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 120 5.16 5 C 13178 2.51 5 N 3424 2.21 5 O 4439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 21161 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 953 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "E" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: 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: "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: 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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "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: "l" 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: "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: 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: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 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: "0" 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: "1" 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: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'MAN': 1, 'NAG': 4} 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 Time building chain proxies: 5.18, per 1000 atoms: 0.24 Number of scatterers: 21161 At special positions: 0 Unit cell: (164.63, 153.52, 160.59, 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 120 16.00 O 4439 8.00 N 3424 7.00 C 13178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN e 4 " - " MAN e 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA l 3 " - " MAN l 4 " " BMA p 3 " - " MAN p 4 " " BMA s 3 " - " MAN s 4 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 6 " " BMA p 3 " - " MAN p 5 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " 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 l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 160 " " NAG 1 1 " - " ASN I 392 " " NAG A 701 " - " ASN A 618 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 137 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 137 " " NAG I 604 " - " ASN I 339 " " NAG I 605 " - " ASN I 355 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 295 " " NAG S 1 " - " ASN C 301 " " NAG T 1 " - " ASN C 332 " " NAG U 1 " - " ASN C 363 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 448 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN G 88 " " NAG a 1 " - " ASN G 133 " " NAG b 1 " - " ASN G 156 " " NAG c 1 " - " ASN G 197 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 262 " " NAG f 1 " - " ASN G 276 " " NAG g 1 " - " ASN G 295 " " NAG h 1 " - " ASN G 301 " " NAG i 1 " - " ASN G 332 " " NAG j 1 " - " ASN G 363 " " NAG k 1 " - " ASN G 386 " " NAG l 1 " - " ASN G 448 " " NAG m 1 " - " ASN G 160 " " NAG n 1 " - " ASN G 392 " " NAG o 1 " - " ASN I 133 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 234 " " NAG s 1 " - " ASN I 262 " " NAG t 1 " - " ASN I 276 " " NAG u 1 " - " ASN I 295 " " NAG v 1 " - " ASN I 301 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 363 " " NAG y 1 " - " ASN I 386 " " NAG z 1 " - " ASN I 448 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 935.2 milliseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 43 sheets defined 19.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.853A pdb=" N ALA A 525 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.943A pdb=" N ALA A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 529 through 534' Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.318A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.165A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.766A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.738A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.858A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.692A pdb=" N CYS C 196 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.576A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.808A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.655A pdb=" N ALA B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.288A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.206A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.963A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.765A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.897A pdb=" N ASN G 197 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.104A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 474 through 481 removed outlier: 4.353A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 536 removed outlier: 3.893A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 531 through 536' Processing helix chain 'F' and resid 537 through 542 removed outlier: 3.579A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 572 Processing helix chain 'F' and resid 573 through 596 removed outlier: 3.851A pdb=" N GLN F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) removed outlier: 3.744A 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 635 Processing helix chain 'F' and resid 639 through 663 removed outlier: 4.121A pdb=" N LEU F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 removed outlier: 3.861A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 117 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.545A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.528A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.759A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.705A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.924A pdb=" N CYS A 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.392A pdb=" N VAL C 44 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.839A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.446A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 removed outlier: 4.263A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.243A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274 removed outlier: 11.243A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.787A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 468 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.914A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 44 through 47 removed outlier: 4.323A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 84 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.830A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'G' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'G' and resid 182 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 202 through 203 removed outlier: 7.110A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.911A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.332A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.867A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.013A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.573A pdb=" N ALA G 319 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 518 through 519 removed outlier: 3.949A pdb=" N PHE F 519 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY D 31 " --> pdb=" O PHE F 519 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.026A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.731A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'I' and resid 130 through 132 Processing sheet with id=AC9, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'I' and resid 260 through 261 removed outlier: 6.891A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.666A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.665A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.621A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.661A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU L 46 " --> pdb=" O TYR L 37 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.703A pdb=" N VAL J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AE3, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.615A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU K 46 " --> pdb=" O TYR K 37 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.568A pdb=" N ASP D 58 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.147A pdb=" N LEU E 46 " --> pdb=" O TYR E 37 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 2.39 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: 6354 1.34 - 1.46: 5625 1.46 - 1.58: 9440 1.58 - 1.70: 0 1.70 - 1.83: 156 Bond restraints: 21575 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N GLN D 1 " pdb=" CA GLN D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N ASP K 1 " pdb=" CA ASP K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 ... (remaining 21570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28609 2.07 - 4.15: 577 4.15 - 6.22: 100 6.22 - 8.30: 15 8.30 - 10.37: 10 Bond angle restraints: 29311 Sorted by residual: angle pdb=" CA GLU F 647 " pdb=" CB GLU F 647 " pdb=" CG GLU F 647 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+01 angle pdb=" N VAL D 100A" pdb=" CA VAL D 100A" pdb=" C VAL D 100A" ideal model delta sigma weight residual 111.62 108.63 2.99 7.90e-01 1.60e+00 1.43e+01 angle pdb=" CB GLU I 370 " pdb=" CG GLU I 370 " pdb=" CD GLU I 370 " ideal model delta sigma weight residual 112.60 118.74 -6.14 1.70e+00 3.46e-01 1.30e+01 angle pdb=" N VAL I 371 " pdb=" CA VAL I 371 " pdb=" C VAL I 371 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" N ASP B 659 " pdb=" CA ASP B 659 " pdb=" CB ASP B 659 " ideal model delta sigma weight residual 110.28 115.43 -5.15 1.55e+00 4.16e-01 1.11e+01 ... (remaining 29306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 13929 23.34 - 46.68: 813 46.68 - 70.02: 138 70.02 - 93.36: 12 93.36 - 116.70: 6 Dihedral angle restraints: 14898 sinusoidal: 7872 harmonic: 7026 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.76 -59.76 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.56 57.56 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS I 54 " pdb=" SG CYS I 54 " pdb=" SG CYS I 74 " pdb=" CB CYS I 74 " ideal model delta sinusoidal sigma weight residual -86.00 -141.43 55.43 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 14895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2947 0.046 - 0.092: 524 0.092 - 0.137: 248 0.137 - 0.183: 20 0.183 - 0.229: 5 Chirality restraints: 3744 Sorted by residual: chirality pdb=" C3 BMA W 3 " pdb=" C2 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" O3 BMA W 3 " both_signs ideal model delta sigma weight residual False 2.41 2.18 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C4 NAG t 2 " pdb=" C3 NAG t 2 " pdb=" C5 NAG t 2 " pdb=" O4 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C4 NAG Q 2 " pdb=" C3 NAG Q 2 " pdb=" C5 NAG Q 2 " pdb=" O4 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3741 not shown) Planarity restraints: 3575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 370 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" CD GLU I 370 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU I 370 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU I 370 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 647 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" CD GLU A 647 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU A 647 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 647 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 39 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO H 40 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 40 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 40 " -0.024 5.00e-02 4.00e+02 ... (remaining 3572 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6440 2.82 - 3.34: 19737 3.34 - 3.86: 32267 3.86 - 4.38: 33703 4.38 - 4.90: 58981 Nonbonded interactions: 151128 Sorted by model distance: nonbonded pdb=" O4 NAG y 2 " pdb=" O2 BMA y 3 " model vdw 2.300 2.432 nonbonded pdb=" O4 NAG u 2 " pdb=" O2 BMA u 3 " model vdw 2.368 2.432 nonbonded pdb=" O4 NAG Z 2 " pdb=" O2 BMA Z 3 " model vdw 2.371 2.432 nonbonded pdb=" O2 BMA V 3 " pdb=" O3 BMA V 3 " model vdw 2.409 2.432 nonbonded pdb=" O2 BMA l 3 " pdb=" O3 BMA l 3 " model vdw 2.431 2.432 ... (remaining 151123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 512 through 702) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 31 through 601 or resid 604)) selection = (chain 'G' and (resid 31 through 601 or resid 604)) selection = (chain 'I' and (resid 31 through 601 or resid 604)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'N' selection = chain 'b' selection = chain 'p' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'o' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'P' selection = chain 'e' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'l' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.360 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21771 Z= 0.193 Angle : 0.834 17.872 29858 Z= 0.382 Chirality : 0.044 0.229 3744 Planarity : 0.004 0.052 3514 Dihedral : 13.757 116.704 10251 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.61 % Allowed : 12.39 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.18 (0.17), residues: 2400 helix: 1.46 (0.29), residues: 343 sheet: -0.27 (0.19), residues: 708 loop : -1.74 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 350 TYR 0.015 0.001 TYR D 96 PHE 0.012 0.002 PHE D 34 TRP 0.009 0.001 TRP A 628 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00419 (21575) covalent geometry : angle 0.75895 (29311) SS BOND : bond 0.00317 ( 41) SS BOND : angle 1.09706 ( 82) hydrogen bonds : bond 0.14144 ( 651) hydrogen bonds : angle 5.45145 ( 1755) link_ALPHA1-2 : bond 0.00336 ( 3) link_ALPHA1-2 : angle 3.81850 ( 9) link_ALPHA1-3 : bond 0.00946 ( 11) link_ALPHA1-3 : angle 4.13028 ( 33) link_ALPHA1-6 : bond 0.00660 ( 6) link_ALPHA1-6 : angle 1.60112 ( 18) link_BETA1-4 : bond 0.01066 ( 74) link_BETA1-4 : angle 3.37077 ( 222) link_NAG-ASN : bond 0.00425 ( 61) link_NAG-ASN : angle 1.71880 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8943 (tm-30) REVERT: A 621 GLU cc_start: 0.8581 (pt0) cc_final: 0.7753 (tp30) REVERT: A 657 GLU cc_start: 0.9186 (pp20) cc_final: 0.8929 (pp20) REVERT: C 150 MET cc_start: 0.8406 (mtt) cc_final: 0.8022 (mmm) REVERT: C 475 MET cc_start: 0.8870 (mmm) cc_final: 0.7539 (tpp) REVERT: B 530 MET cc_start: 0.8481 (mmp) cc_final: 0.8036 (mmt) REVERT: B 616 ASN cc_start: 0.8791 (p0) cc_final: 0.8397 (p0) REVERT: B 655 LYS cc_start: 0.9725 (tptp) cc_final: 0.9497 (pttt) REVERT: G 271 MET cc_start: 0.7534 (tpp) cc_final: 0.7090 (ttm) REVERT: F 530 MET cc_start: 0.8920 (tpp) cc_final: 0.8269 (tpp) REVERT: F 626 MET cc_start: 0.8880 (tpp) cc_final: 0.8555 (tpt) REVERT: F 659 ASP cc_start: 0.9388 (m-30) cc_final: 0.9108 (p0) REVERT: I 416 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7713 (pp) REVERT: I 426 MET cc_start: 0.8733 (pmm) cc_final: 0.8099 (pmm) REVERT: L 75 ILE cc_start: 0.8843 (mt) cc_final: 0.8448 (tp) outliers start: 13 outliers final: 10 residues processed: 141 average time/residue: 0.1928 time to fit residues: 40.0300 Evaluate side-chains 115 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain E residue 105 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN C 203 GLN B 540 GLN B 543 ASN B 640 GLN F 640 GLN I 293 GLN H 33 HIS J 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.057853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039484 restraints weight = 134902.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.040631 restraints weight = 84897.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.041319 restraints weight = 66113.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041767 restraints weight = 57501.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042036 restraints weight = 52811.383| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21771 Z= 0.212 Angle : 0.807 18.336 29858 Z= 0.358 Chirality : 0.048 0.431 3744 Planarity : 0.004 0.055 3514 Dihedral : 8.973 74.033 5822 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.25 % Allowed : 12.63 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.07 (0.17), residues: 2400 helix: 1.54 (0.28), residues: 355 sheet: -0.14 (0.20), residues: 669 loop : -1.69 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 24 TYR 0.020 0.001 TYR D 96 PHE 0.017 0.002 PHE E 71 TRP 0.011 0.001 TRP B 571 HIS 0.004 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00474 (21575) covalent geometry : angle 0.73809 (29311) SS BOND : bond 0.00338 ( 41) SS BOND : angle 1.00105 ( 82) hydrogen bonds : bond 0.05318 ( 651) hydrogen bonds : angle 4.98483 ( 1755) link_ALPHA1-2 : bond 0.00545 ( 3) link_ALPHA1-2 : angle 4.82000 ( 9) link_ALPHA1-3 : bond 0.01461 ( 11) link_ALPHA1-3 : angle 3.82680 ( 33) link_ALPHA1-6 : bond 0.00473 ( 6) link_ALPHA1-6 : angle 1.69180 ( 18) link_BETA1-4 : bond 0.01054 ( 74) link_BETA1-4 : angle 3.06375 ( 222) link_NAG-ASN : bond 0.00476 ( 61) link_NAG-ASN : angle 1.77780 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8579 (pt0) cc_final: 0.8070 (tp30) REVERT: A 657 GLU cc_start: 0.8976 (pp20) cc_final: 0.8747 (pp20) REVERT: C 475 MET cc_start: 0.8612 (mmm) cc_final: 0.7670 (tpp) REVERT: B 530 MET cc_start: 0.8160 (mmp) cc_final: 0.7638 (mmt) REVERT: B 606 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8999 (p) REVERT: B 616 ASN cc_start: 0.8737 (p0) cc_final: 0.8349 (p0) REVERT: F 530 MET cc_start: 0.8940 (tpp) cc_final: 0.8467 (tpp) REVERT: F 659 ASP cc_start: 0.9268 (m-30) cc_final: 0.8971 (p0) REVERT: I 416 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8098 (pp) REVERT: I 434 MET cc_start: 0.8627 (mtp) cc_final: 0.8170 (tpp) REVERT: L 75 ILE cc_start: 0.8925 (mt) cc_final: 0.8430 (tp) REVERT: J 73 ARG cc_start: 0.5752 (ptp-110) cc_final: 0.5405 (mtt-85) REVERT: K 85 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7735 (p) REVERT: E 24 ARG cc_start: 0.9509 (mmt-90) cc_final: 0.9142 (mmm160) REVERT: E 70 GLU cc_start: 0.9815 (pp20) cc_final: 0.9593 (mm-30) outliers start: 48 outliers final: 24 residues processed: 152 average time/residue: 0.1559 time to fit residues: 36.5523 Evaluate side-chains 123 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN C 293 GLN G 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.057475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038737 restraints weight = 140676.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039894 restraints weight = 89759.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.040611 restraints weight = 70261.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.041049 restraints weight = 61298.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041266 restraints weight = 56681.008| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21771 Z= 0.140 Angle : 0.759 17.934 29858 Z= 0.333 Chirality : 0.047 0.432 3744 Planarity : 0.004 0.049 3514 Dihedral : 8.649 70.089 5819 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.07 % Allowed : 14.74 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.94 (0.17), residues: 2400 helix: 1.67 (0.28), residues: 355 sheet: -0.04 (0.20), residues: 672 loop : -1.62 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 66 TYR 0.019 0.001 TYR D 96 PHE 0.015 0.001 PHE E 83 TRP 0.019 0.001 TRP L 35 HIS 0.002 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00300 (21575) covalent geometry : angle 0.68918 (29311) SS BOND : bond 0.00391 ( 41) SS BOND : angle 1.44443 ( 82) hydrogen bonds : bond 0.04549 ( 651) hydrogen bonds : angle 4.74817 ( 1755) link_ALPHA1-2 : bond 0.00599 ( 3) link_ALPHA1-2 : angle 4.71064 ( 9) link_ALPHA1-3 : bond 0.01387 ( 11) link_ALPHA1-3 : angle 3.68443 ( 33) link_ALPHA1-6 : bond 0.00570 ( 6) link_ALPHA1-6 : angle 1.51434 ( 18) link_BETA1-4 : bond 0.01073 ( 74) link_BETA1-4 : angle 2.97165 ( 222) link_NAG-ASN : bond 0.00262 ( 61) link_NAG-ASN : angle 1.54668 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8585 (pt0) cc_final: 0.7991 (tp30) REVERT: C 475 MET cc_start: 0.8600 (mmm) cc_final: 0.8356 (mmm) REVERT: B 530 MET cc_start: 0.8171 (mmp) cc_final: 0.7617 (mmt) REVERT: B 616 ASN cc_start: 0.8809 (p0) cc_final: 0.8429 (p0) REVERT: F 530 MET cc_start: 0.8940 (tpp) cc_final: 0.8484 (tpp) REVERT: F 659 ASP cc_start: 0.9340 (m-30) cc_final: 0.9033 (p0) REVERT: I 416 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7985 (pp) REVERT: I 434 MET cc_start: 0.8572 (mtp) cc_final: 0.8205 (tpp) REVERT: L 75 ILE cc_start: 0.8869 (mt) cc_final: 0.8421 (tp) REVERT: J 73 ARG cc_start: 0.5868 (ptp-110) cc_final: 0.5269 (mtt-85) REVERT: K 85 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7635 (p) outliers start: 44 outliers final: 33 residues processed: 141 average time/residue: 0.1514 time to fit residues: 33.1790 Evaluate side-chains 130 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 237 optimal weight: 50.0000 chunk 135 optimal weight: 0.5980 chunk 156 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.057279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038532 restraints weight = 140381.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039664 restraints weight = 89718.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040395 restraints weight = 70420.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040765 restraints weight = 61428.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.041054 restraints weight = 57052.095| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21771 Z= 0.147 Angle : 0.751 17.997 29858 Z= 0.329 Chirality : 0.047 0.434 3744 Planarity : 0.003 0.045 3514 Dihedral : 8.530 65.183 5817 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.49 % Allowed : 15.21 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.88 (0.17), residues: 2400 helix: 1.65 (0.28), residues: 355 sheet: 0.02 (0.20), residues: 672 loop : -1.58 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 66 TYR 0.019 0.001 TYR D 96 PHE 0.020 0.001 PHE L 71 TRP 0.013 0.001 TRP L 35 HIS 0.002 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00318 (21575) covalent geometry : angle 0.68411 (29311) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.08041 ( 82) hydrogen bonds : bond 0.04417 ( 651) hydrogen bonds : angle 4.66196 ( 1755) link_ALPHA1-2 : bond 0.00536 ( 3) link_ALPHA1-2 : angle 4.74456 ( 9) link_ALPHA1-3 : bond 0.01385 ( 11) link_ALPHA1-3 : angle 3.56889 ( 33) link_ALPHA1-6 : bond 0.00530 ( 6) link_ALPHA1-6 : angle 1.52707 ( 18) link_BETA1-4 : bond 0.01058 ( 74) link_BETA1-4 : angle 2.93975 ( 222) link_NAG-ASN : bond 0.00277 ( 61) link_NAG-ASN : angle 1.55301 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8605 (pt0) cc_final: 0.7996 (tp30) REVERT: B 530 MET cc_start: 0.8221 (mmp) cc_final: 0.7617 (mmt) REVERT: B 616 ASN cc_start: 0.8814 (p0) cc_final: 0.8419 (p0) REVERT: F 530 MET cc_start: 0.8994 (tpp) cc_final: 0.8685 (tpp) REVERT: F 659 ASP cc_start: 0.9359 (m-30) cc_final: 0.9055 (p0) REVERT: I 416 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7949 (pp) REVERT: I 434 MET cc_start: 0.8616 (mtp) cc_final: 0.8250 (tpp) REVERT: H 102 GLN cc_start: 0.8048 (mp10) cc_final: 0.7688 (mp10) REVERT: L 75 ILE cc_start: 0.8873 (mt) cc_final: 0.8370 (tp) REVERT: J 73 ARG cc_start: 0.5906 (ptp-110) cc_final: 0.5329 (mtt-85) REVERT: K 78 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8394 (mt) REVERT: K 85 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7589 (p) outliers start: 53 outliers final: 38 residues processed: 146 average time/residue: 0.1448 time to fit residues: 33.5609 Evaluate side-chains 136 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 153 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.057418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038643 restraints weight = 139232.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039831 restraints weight = 87263.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.040575 restraints weight = 68126.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040921 restraints weight = 59283.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041212 restraints weight = 55196.335| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21771 Z= 0.129 Angle : 0.737 18.027 29858 Z= 0.322 Chirality : 0.047 0.427 3744 Planarity : 0.003 0.044 3514 Dihedral : 8.391 59.941 5817 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.58 % Allowed : 15.92 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.78 (0.17), residues: 2400 helix: 1.68 (0.28), residues: 355 sheet: 0.10 (0.20), residues: 675 loop : -1.51 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 66 TYR 0.018 0.001 TYR D 96 PHE 0.017 0.001 PHE H 100C TRP 0.015 0.001 TRP L 35 HIS 0.002 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00274 (21575) covalent geometry : angle 0.67168 (29311) SS BOND : bond 0.00253 ( 41) SS BOND : angle 0.99869 ( 82) hydrogen bonds : bond 0.04094 ( 651) hydrogen bonds : angle 4.52083 ( 1755) link_ALPHA1-2 : bond 0.00537 ( 3) link_ALPHA1-2 : angle 4.73435 ( 9) link_ALPHA1-3 : bond 0.01370 ( 11) link_ALPHA1-3 : angle 3.41370 ( 33) link_ALPHA1-6 : bond 0.00546 ( 6) link_ALPHA1-6 : angle 1.48229 ( 18) link_BETA1-4 : bond 0.01056 ( 74) link_BETA1-4 : angle 2.90404 ( 222) link_NAG-ASN : bond 0.00217 ( 61) link_NAG-ASN : angle 1.48653 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 102 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8586 (pt0) cc_final: 0.8346 (pp20) REVERT: A 657 GLU cc_start: 0.9386 (tm-30) cc_final: 0.9178 (pp20) REVERT: B 530 MET cc_start: 0.8163 (mmp) cc_final: 0.7586 (mmt) REVERT: B 616 ASN cc_start: 0.8726 (p0) cc_final: 0.8325 (p0) REVERT: G 150 MET cc_start: 0.8848 (mmt) cc_final: 0.8490 (mmm) REVERT: F 530 MET cc_start: 0.9029 (tpp) cc_final: 0.8706 (tpp) REVERT: F 659 ASP cc_start: 0.9353 (m-30) cc_final: 0.9054 (m-30) REVERT: I 416 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7961 (pp) REVERT: H 102 GLN cc_start: 0.8022 (mp10) cc_final: 0.7672 (mp10) REVERT: L 75 ILE cc_start: 0.8840 (mt) cc_final: 0.8386 (tp) REVERT: K 78 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8390 (mt) REVERT: K 85 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7631 (p) outliers start: 55 outliers final: 35 residues processed: 149 average time/residue: 0.1368 time to fit residues: 32.8464 Evaluate side-chains 131 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 236 optimal weight: 40.0000 chunk 65 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 205 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** G 279 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.056243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038268 restraints weight = 139770.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040237 restraints weight = 92168.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040101 restraints weight = 59583.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.040117 restraints weight = 57582.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.040172 restraints weight = 57046.015| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21771 Z= 0.206 Angle : 0.779 18.110 29858 Z= 0.348 Chirality : 0.047 0.416 3744 Planarity : 0.004 0.080 3514 Dihedral : 8.418 59.819 5815 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.05 % Allowed : 16.29 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.84 (0.17), residues: 2400 helix: 1.58 (0.28), residues: 357 sheet: 0.02 (0.20), residues: 675 loop : -1.51 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.019 0.001 TYR D 96 PHE 0.016 0.002 PHE H 100C TRP 0.013 0.001 TRP L 35 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00461 (21575) covalent geometry : angle 0.71385 (29311) SS BOND : bond 0.00330 ( 41) SS BOND : angle 1.34384 ( 82) hydrogen bonds : bond 0.04842 ( 651) hydrogen bonds : angle 4.70020 ( 1755) link_ALPHA1-2 : bond 0.00363 ( 3) link_ALPHA1-2 : angle 4.73282 ( 9) link_ALPHA1-3 : bond 0.01367 ( 11) link_ALPHA1-3 : angle 3.32408 ( 33) link_ALPHA1-6 : bond 0.00433 ( 6) link_ALPHA1-6 : angle 1.61440 ( 18) link_BETA1-4 : bond 0.01042 ( 74) link_BETA1-4 : angle 2.92740 ( 222) link_NAG-ASN : bond 0.00437 ( 61) link_NAG-ASN : angle 1.68977 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 96 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8681 (pt0) cc_final: 0.8077 (tp30) REVERT: C 95 MET cc_start: 0.9410 (ppp) cc_final: 0.9208 (ppp) REVERT: C 122 LEU cc_start: 0.9459 (tp) cc_final: 0.9254 (tp) REVERT: B 530 MET cc_start: 0.8342 (mmp) cc_final: 0.7720 (mmt) REVERT: B 616 ASN cc_start: 0.8770 (p0) cc_final: 0.8363 (p0) REVERT: G 150 MET cc_start: 0.8935 (mmt) cc_final: 0.8569 (mmm) REVERT: F 530 MET cc_start: 0.9131 (tpp) cc_final: 0.8609 (tpp) REVERT: F 659 ASP cc_start: 0.9385 (m-30) cc_final: 0.9092 (m-30) REVERT: I 416 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8106 (pp) REVERT: L 75 ILE cc_start: 0.8743 (mt) cc_final: 0.8256 (tp) REVERT: J 97 SER cc_start: 0.7204 (OUTLIER) cc_final: 0.6771 (p) REVERT: K 18 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8421 (tpt170) REVERT: K 78 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8308 (mt) REVERT: K 85 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7451 (p) outliers start: 65 outliers final: 50 residues processed: 155 average time/residue: 0.1460 time to fit residues: 35.4645 Evaluate side-chains 146 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 91 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 450 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 236 optimal weight: 40.0000 chunk 160 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 226 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.056956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038191 restraints weight = 139343.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039355 restraints weight = 87305.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040075 restraints weight = 68154.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040514 restraints weight = 59414.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040682 restraints weight = 54897.891| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21771 Z= 0.134 Angle : 0.754 17.941 29858 Z= 0.331 Chirality : 0.046 0.411 3744 Planarity : 0.003 0.044 3514 Dihedral : 8.244 59.203 5815 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.58 % Allowed : 17.18 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.72 (0.17), residues: 2400 helix: 1.66 (0.29), residues: 357 sheet: -0.03 (0.19), residues: 711 loop : -1.38 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 71 TYR 0.018 0.001 TYR D 96 PHE 0.015 0.001 PHE H 100C TRP 0.011 0.001 TRP G 112 HIS 0.002 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00287 (21575) covalent geometry : angle 0.69110 (29311) SS BOND : bond 0.00255 ( 41) SS BOND : angle 1.28110 ( 82) hydrogen bonds : bond 0.04215 ( 651) hydrogen bonds : angle 4.51591 ( 1755) link_ALPHA1-2 : bond 0.00448 ( 3) link_ALPHA1-2 : angle 4.73500 ( 9) link_ALPHA1-3 : bond 0.01332 ( 11) link_ALPHA1-3 : angle 3.21567 ( 33) link_ALPHA1-6 : bond 0.00522 ( 6) link_ALPHA1-6 : angle 1.47818 ( 18) link_BETA1-4 : bond 0.01037 ( 74) link_BETA1-4 : angle 2.87676 ( 222) link_NAG-ASN : bond 0.00231 ( 61) link_NAG-ASN : angle 1.50736 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 99 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8617 (pt0) cc_final: 0.8039 (tp30) REVERT: A 626 MET cc_start: 0.8375 (tpt) cc_final: 0.8170 (tmm) REVERT: A 657 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9201 (pp20) REVERT: C 122 LEU cc_start: 0.9437 (tp) cc_final: 0.9222 (tp) REVERT: B 530 MET cc_start: 0.8218 (mmp) cc_final: 0.7631 (mmt) REVERT: B 616 ASN cc_start: 0.8686 (p0) cc_final: 0.8276 (p0) REVERT: G 150 MET cc_start: 0.8918 (mmt) cc_final: 0.8566 (mmm) REVERT: F 626 MET cc_start: 0.8309 (tpp) cc_final: 0.7625 (tpp) REVERT: F 659 ASP cc_start: 0.9361 (m-30) cc_final: 0.9063 (m-30) REVERT: I 416 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8051 (pp) REVERT: H 102 GLN cc_start: 0.7910 (mp10) cc_final: 0.7563 (mp10) REVERT: L 75 ILE cc_start: 0.8777 (mt) cc_final: 0.8320 (tp) REVERT: J 97 SER cc_start: 0.7188 (OUTLIER) cc_final: 0.6720 (p) REVERT: K 78 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8321 (mt) REVERT: K 85 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7601 (p) outliers start: 55 outliers final: 46 residues processed: 149 average time/residue: 0.1296 time to fit residues: 30.6009 Evaluate side-chains 142 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.056785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.038787 restraints weight = 138231.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040784 restraints weight = 92312.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040688 restraints weight = 59382.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040709 restraints weight = 56801.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040711 restraints weight = 55971.006| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21771 Z= 0.144 Angle : 0.745 18.050 29858 Z= 0.329 Chirality : 0.046 0.407 3744 Planarity : 0.003 0.044 3514 Dihedral : 8.104 58.817 5815 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.82 % Allowed : 17.18 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.70 (0.17), residues: 2400 helix: 1.71 (0.29), residues: 357 sheet: 0.14 (0.20), residues: 675 loop : -1.44 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 71 TYR 0.017 0.001 TYR D 96 PHE 0.015 0.001 PHE H 100C TRP 0.013 0.001 TRP G 112 HIS 0.002 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00313 (21575) covalent geometry : angle 0.68251 (29311) SS BOND : bond 0.00287 ( 41) SS BOND : angle 1.12180 ( 82) hydrogen bonds : bond 0.04178 ( 651) hydrogen bonds : angle 4.47581 ( 1755) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 4.69997 ( 9) link_ALPHA1-3 : bond 0.01349 ( 11) link_ALPHA1-3 : angle 3.15952 ( 33) link_ALPHA1-6 : bond 0.00488 ( 6) link_ALPHA1-6 : angle 1.50233 ( 18) link_BETA1-4 : bond 0.01033 ( 74) link_BETA1-4 : angle 2.86141 ( 222) link_NAG-ASN : bond 0.00248 ( 61) link_NAG-ASN : angle 1.51528 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 98 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8676 (pt0) cc_final: 0.8039 (tp30) REVERT: C 122 LEU cc_start: 0.9456 (tp) cc_final: 0.9229 (tp) REVERT: B 530 MET cc_start: 0.8288 (mmp) cc_final: 0.7643 (mmt) REVERT: B 574 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9123 (ptpp) REVERT: B 616 ASN cc_start: 0.8778 (p0) cc_final: 0.8365 (p0) REVERT: G 150 MET cc_start: 0.8931 (mmt) cc_final: 0.8594 (mmm) REVERT: G 271 MET cc_start: 0.7814 (ttm) cc_final: 0.7484 (ttt) REVERT: F 626 MET cc_start: 0.8356 (tpp) cc_final: 0.7635 (tpp) REVERT: F 659 ASP cc_start: 0.9397 (m-30) cc_final: 0.9102 (m-30) REVERT: I 416 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7901 (pp) REVERT: I 434 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (tpp) REVERT: H 102 GLN cc_start: 0.7776 (mp10) cc_final: 0.7406 (mp10) REVERT: L 75 ILE cc_start: 0.8769 (mt) cc_final: 0.8287 (tp) REVERT: J 97 SER cc_start: 0.7184 (OUTLIER) cc_final: 0.6739 (p) REVERT: K 78 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8352 (mt) REVERT: K 85 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7304 (p) outliers start: 60 outliers final: 47 residues processed: 152 average time/residue: 0.1359 time to fit residues: 33.1645 Evaluate side-chains 145 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 236 optimal weight: 40.0000 chunk 145 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.057618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.039170 restraints weight = 137384.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040286 restraints weight = 87596.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040931 restraints weight = 68834.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041400 restraints weight = 60247.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041626 restraints weight = 55840.284| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21771 Z= 0.116 Angle : 0.740 18.082 29858 Z= 0.325 Chirality : 0.047 0.404 3744 Planarity : 0.003 0.043 3514 Dihedral : 7.889 58.327 5815 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.30 % Allowed : 17.84 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.57 (0.17), residues: 2400 helix: 1.71 (0.29), residues: 357 sheet: 0.15 (0.19), residues: 702 loop : -1.30 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 71 TYR 0.016 0.001 TYR D 96 PHE 0.016 0.001 PHE H 100C TRP 0.014 0.001 TRP L 35 HIS 0.002 0.000 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00237 (21575) covalent geometry : angle 0.68246 (29311) SS BOND : bond 0.00213 ( 41) SS BOND : angle 0.90104 ( 82) hydrogen bonds : bond 0.03533 ( 651) hydrogen bonds : angle 4.31151 ( 1755) link_ALPHA1-2 : bond 0.00558 ( 3) link_ALPHA1-2 : angle 4.68247 ( 9) link_ALPHA1-3 : bond 0.01356 ( 11) link_ALPHA1-3 : angle 3.07749 ( 33) link_ALPHA1-6 : bond 0.00561 ( 6) link_ALPHA1-6 : angle 1.41076 ( 18) link_BETA1-4 : bond 0.01063 ( 74) link_BETA1-4 : angle 2.81542 ( 222) link_NAG-ASN : bond 0.00176 ( 61) link_NAG-ASN : angle 1.37784 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8606 (pt0) cc_final: 0.7979 (tp30) REVERT: A 626 MET cc_start: 0.8190 (tpt) cc_final: 0.7492 (tmm) REVERT: A 657 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9176 (pp20) REVERT: C 122 LEU cc_start: 0.9421 (tp) cc_final: 0.9169 (tp) REVERT: B 530 MET cc_start: 0.8163 (mmp) cc_final: 0.7546 (mmt) REVERT: B 616 ASN cc_start: 0.8625 (p0) cc_final: 0.8174 (p0) REVERT: B 655 LYS cc_start: 0.9477 (ptpp) cc_final: 0.9230 (ptpp) REVERT: G 150 MET cc_start: 0.8836 (mmt) cc_final: 0.8486 (mmm) REVERT: G 434 MET cc_start: 0.8449 (mmm) cc_final: 0.8117 (tpp) REVERT: F 626 MET cc_start: 0.8188 (tpp) cc_final: 0.7475 (tpp) REVERT: F 659 ASP cc_start: 0.9342 (m-30) cc_final: 0.9072 (m-30) REVERT: I 416 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7916 (pp) REVERT: I 434 MET cc_start: 0.8564 (mmm) cc_final: 0.8251 (mpp) REVERT: H 102 GLN cc_start: 0.7841 (mp10) cc_final: 0.7485 (mp10) REVERT: L 75 ILE cc_start: 0.8829 (mt) cc_final: 0.8351 (tp) REVERT: J 97 SER cc_start: 0.7173 (OUTLIER) cc_final: 0.6687 (p) REVERT: K 78 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8403 (mt) REVERT: K 85 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7444 (p) outliers start: 49 outliers final: 39 residues processed: 153 average time/residue: 0.1282 time to fit residues: 31.2971 Evaluate side-chains 140 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 172 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 50.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.061959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041175 restraints weight = 148240.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042352 restraints weight = 99138.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043212 restraints weight = 80010.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043406 restraints weight = 71223.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043742 restraints weight = 67751.813| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21771 Z= 0.118 Angle : 0.743 18.056 29858 Z= 0.328 Chirality : 0.046 0.402 3744 Planarity : 0.003 0.044 3514 Dihedral : 7.774 58.432 5813 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.11 % Allowed : 18.22 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.55 (0.17), residues: 2400 helix: 1.57 (0.29), residues: 360 sheet: 0.17 (0.19), residues: 702 loop : -1.25 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 24 TYR 0.016 0.001 TYR D 96 PHE 0.015 0.001 PHE H 100C TRP 0.029 0.001 TRP D 36 HIS 0.001 0.000 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00246 (21575) covalent geometry : angle 0.68565 (29311) SS BOND : bond 0.00223 ( 41) SS BOND : angle 0.90556 ( 82) hydrogen bonds : bond 0.03566 ( 651) hydrogen bonds : angle 4.31671 ( 1755) link_ALPHA1-2 : bond 0.00563 ( 3) link_ALPHA1-2 : angle 4.61949 ( 9) link_ALPHA1-3 : bond 0.01365 ( 11) link_ALPHA1-3 : angle 3.03807 ( 33) link_ALPHA1-6 : bond 0.00527 ( 6) link_ALPHA1-6 : angle 1.42497 ( 18) link_BETA1-4 : bond 0.01052 ( 74) link_BETA1-4 : angle 2.79492 ( 222) link_NAG-ASN : bond 0.00162 ( 61) link_NAG-ASN : angle 1.38980 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8644 (pt0) cc_final: 0.8028 (tp30) REVERT: A 648 GLU cc_start: 0.8899 (pp20) cc_final: 0.8555 (pp20) REVERT: A 657 GLU cc_start: 0.9527 (tm-30) cc_final: 0.9213 (pp20) REVERT: B 530 MET cc_start: 0.8204 (mmp) cc_final: 0.7536 (mmt) REVERT: B 616 ASN cc_start: 0.8685 (p0) cc_final: 0.8243 (p0) REVERT: G 150 MET cc_start: 0.8809 (mmt) cc_final: 0.8478 (mmm) REVERT: G 434 MET cc_start: 0.8515 (mmm) cc_final: 0.8123 (tpp) REVERT: F 626 MET cc_start: 0.8094 (tpp) cc_final: 0.7427 (tpp) REVERT: F 659 ASP cc_start: 0.9397 (m-30) cc_final: 0.9124 (m-30) REVERT: I 416 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7777 (pp) REVERT: I 434 MET cc_start: 0.8575 (mmm) cc_final: 0.8169 (mpp) REVERT: H 102 GLN cc_start: 0.7790 (mp10) cc_final: 0.7452 (mp10) REVERT: L 75 ILE cc_start: 0.8782 (mt) cc_final: 0.8315 (tp) REVERT: J 97 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6728 (p) REVERT: K 78 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8414 (mt) REVERT: K 85 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7300 (p) outliers start: 45 outliers final: 36 residues processed: 140 average time/residue: 0.1325 time to fit residues: 29.3200 Evaluate side-chains 130 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 415 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 0.9990 chunk 191 optimal weight: 0.0060 chunk 14 optimal weight: 8.9990 chunk 234 optimal weight: 30.0000 chunk 198 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.057638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039537 restraints weight = 143174.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040712 restraints weight = 89875.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041418 restraints weight = 69873.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041873 restraints weight = 60708.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.042114 restraints weight = 55938.360| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21771 Z= 0.118 Angle : 0.741 18.115 29858 Z= 0.326 Chirality : 0.046 0.400 3744 Planarity : 0.003 0.044 3514 Dihedral : 7.646 58.354 5810 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.07 % Allowed : 18.03 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.55 (0.17), residues: 2400 helix: 1.58 (0.29), residues: 355 sheet: 0.17 (0.19), residues: 702 loop : -1.24 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.008 0.001 TYR B 643 PHE 0.015 0.001 PHE H 100C TRP 0.018 0.001 TRP F 571 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00244 (21575) covalent geometry : angle 0.68442 (29311) SS BOND : bond 0.00222 ( 41) SS BOND : angle 0.93913 ( 82) hydrogen bonds : bond 0.03509 ( 651) hydrogen bonds : angle 4.31786 ( 1755) link_ALPHA1-2 : bond 0.00574 ( 3) link_ALPHA1-2 : angle 4.59866 ( 9) link_ALPHA1-3 : bond 0.01371 ( 11) link_ALPHA1-3 : angle 2.99524 ( 33) link_ALPHA1-6 : bond 0.00528 ( 6) link_ALPHA1-6 : angle 1.41807 ( 18) link_BETA1-4 : bond 0.01047 ( 74) link_BETA1-4 : angle 2.77096 ( 222) link_NAG-ASN : bond 0.00154 ( 61) link_NAG-ASN : angle 1.38351 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3533.56 seconds wall clock time: 62 minutes 1.44 seconds (3721.44 seconds total)